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In the name of God
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Conference Topics:
-Active Peptides and their Industrial Applications
-Protein and Enzyme Engineering and their Applications
-Protein Diseases
-Folding, Structure and Stability of Proteins
-Biophysical Chemistry of Proteins and Peptides
-Application of Proteins and Enzymes in Environmental Issues
-Proteomics
-Protein Drugs and Biomarkers
-Protein Applications in Nanotechnology
-Protein Purification
-Protein- Protein Interactions
-Protein- Ligand Interaction
-Bioinformatics in Protein Researches
Scientific Chair: Prof. Abdol-Khalegh Bordbar
Executive Chair: Dr. Asghar Taheri-Kafrani
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Protein and peptide Therapeutics – The future is here
In the two past decades protein and peptide therapeutics revolutionized the countenance of the
contemporary medicine and initiated effective therapies for numbers of refractory diseases. Since
1982, when the first therapeutic protein – recombinant human insulin – was introduced, the
global market of biotechnology drugs has been still growing. In 2008 more than 130 molecules
were approved for clinical use by FDA and at present there are almost 170 proteins and peptides
in use.
Today biopharmaceutics include: recombinant hormones, interferons, interleukins, hematopoietic
growth factors, tumor necrosis factors, blood-clotting factors, thrombolytic drugs, enzymes,
monoclonal antibodies (2nd generation) and vaccines. Today, protein and peptide drugs have
been successfully applied in treating various human illnesses including diabetes, dwarfism,
myocardial infarction, congestive heart failure, cerebral apoplexy, multiple sclerosis,
neutropenia, thrombocytopenia, anaemia, hepatitis, rheumatoid arthritis, asthma, Crohn’s disease
and cancers therapies.
The 1st generation of biopharmaceutics is dominated by structures based on the native
sequences, identical with the proteins/peptides naturally occurring in the body tissues, whereas in
the 2nd generation we find drugs with improved properties, especially PK, biodistribution,
higher specificity, efficacy and minimized side effects. To achieve these desired features, the
structures are deliberately modified by covalent attachment of the chemical compounds,
introduction of certain changes within the sequences of the protein, fusions of two or more
peptide chains or replacement of the sugar residues. The main challenge for the next, already 3rd
generation of recombinant drugs, seem to be the new route of administration, new formulations
and consequently even higher efficiency and safety.
In 2003, the global market for therapeutic proteins was worth $37 billion, more by almost 19%
than in the previous year, and achieved sales of over $90 billion in 2010. Much of this market is
dominated by erythropoietins and monoclonal antibodies, which treat common diseases such as
anaemia, arthritis and cancer. At the same time the global market for pharmaceuticals reached
approximately $650 billion in the same year. Therefore, therapeutic proteins covered
approximately 13.8% share of the global pharmaceutical market in 2010, a considerable
proportion of the total. According to the GBI research in the report “Therapeutic Proteins Market
to 2017 - High Demand for Monoclonal Antibodies will Drive the Market” the market is likely to
grow and to reach $141.5 billion in 2017. After Global Industry Analysts, Inc. in the “Protein
Drugs – Global Market Report”, nearly 400 types of protein drugs are in the process of
development and global market for protein drugs is estimated to reach $158.2 billion by 2015.
However the expiration of the patents of key protein therapeutics on the one hand and budget
limitations on the other will result in opening the market to biosimilar versions of first generation
drugs. Finally Research and Markets in “Global Protein Therapeutics Market Forecast to 2015”
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states that the global market for biopharmaceutics is still growing and is likely to reach the level
of $143.4 by 2016.
Without any doubts there is still a lot to be done in the protein and peptide recombinant drugs.
Their development always means years of efforts and high risk. Though, even if only one is
successful, the success will be outstanding.
This conference includes both lecture and poster presentation sessions, covering the latest
findings across many topics in protein and peptide sciences including: Application of Enzymes
in Medicine and Industry - Quantitative and Analytical Proteomics -Enzyme Engineering -
Protein Chemistry - Protein Folding and Dynamics - Bioactive Peptides and Their Applications -
Proteins and Metabolic Diseases - Drug Proteins and Protein Biomarkers - Advanced
Technologies in the Field of Protein Research and Development - Application of Proteins in
Nanotechnology - Protein-Drug and Protein-Protein Interactions - Innovation in Protein
Purification and Quantification –Bioinformatics - Plant Proteins and Associated Diseases.
Also four scientific workshops in the related fields will go on in parallel to the main event. We
hope that this PPS conference can create a forum for useful dialogues between Iranian
researchers committed to protein and peptide sciences.
Scientific Chair: Prof. Abdol-Khalegh Bordbar
Executive Chair: Dr. Asghar Taheri-Kafrani
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Scientific Committee of PPS Conference:
Dr. Abdolkhalegh Bordbar
Dr. Abdollah
Derakhshandeh
Dr. Abolfazl Barzegar
Dr. Abolghasem Abasi
Kajani
Dr. Abolghasem Esmaeili
Dr. Adeleh Divsalar
Dr. Ali Mohammad
Tamadon
Dr. Ali Zarrabi
Dr. Ali Akbar Moosavi-
Movahedi
Dr. Ali Akbar Saboury
Dr. Amir Razmjou
Dr. Asghar Taheri-Kafrani
Dr. Davoud Biria
Dr. Gholamhossein Riazi
Dr. Hamid Amiri
Dr. Hamidreza Karbalaei
Dr. Hasan Mohabatkar
Dr. Hedayatollah
Ghourchian
Dr. Karim Mahnam
Dr. Khosro Khaje
Dr. Mahmoud Amin lari
Dr. Mandana Behbahani
Dr. Maryam Nikkhah
Dr. Mehdi Sahihi
Dr. Mehran Habibi rezaei
Dr. Mehran Miroliaei
Dr. Mehrnaz Keyhanfar
Dr. Mohammad Rabani
Khorasgani
Dr. Mohammad Reza
Dayer
Dr. Mohammad Ali
Asadollahi
Dr. Mohammad Mahdi
Alavianmehr
Dr. Mohammad Reza
Mofid
Dr. Mojtaba Amani
Dr. Mostafa Rezaei
Tavirani
Dr. Nematollah Gheybi
Dr. Raheleh Masoudi
Dr. Rahman Emamzadeh
Dr. Reza Hasan sajedi
Dr. Reza Yousefi
Dr. Said Balalaei
Dr. Saman Hosseinkhani
Dr. Samaneh Zolghadr
Dr. Seyed Hamid Zarkesh
Esfahani
Dr. Seyed Jafar Mousavi
Dr. Seyed Mahmoud
Ghafari
Dr. Younes Ghasemi
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Executive Committee:
Dr. Asghar Taheri-Kafrani
Afrouz Khalili
Elham Shirani
Fahimeh Andarzian
Fereshteh Enami
Fereshteh Mohagheghiyan
Ghazaleh Es-haghi
Javad Abbasabad Arabi
Mahkame Amirbandeh
Masumeh Alamdaran
Nesa Rafaati
Parisa Dehghani
Parisa Rabiei
Reyhaneh Kord Sedehi
Rezvan Kazemi
Sadegh Khorrami
Shohreh Esmaeli
Yasaman Boroumand
Zahra Abdollahi
Zahra Milanian
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Table of Contents
Oral Presentation Abstracts: ................................................................................................................... 20
Modeling the DSC profile of irreversible thermal denaturation of proteins undergoing aggregation .. 20
Bioactive peptides from egg-whites of different avian species .............................................................. 21
Modified lysozymes as novel broad spectrum natural antimicrobial agents ......................................... 22
Molecular dynamics simulation for designing and predicting of bimolecular functions ....................... 23
Small substrate, big surprise. Structure and function of dihydroxyacetone kinases ............................. 24
Synthesis of therapeutic peptides and novel bioactive peptides ........................................................... 25
Cubic nanoparticles preparation to deliver protein drug (PAL36) to brain cells for possible treatment
of multiple sclerosis (MS) ........................................................................................................................ 26
The effect of the aptameric ligands’ length on the binding affinity to the analogous protein targets:
evaluation of aptamers specific to plasma coagulation factor VIIa against recombinant form of this
protein..................................................................................................................................................... 27
Antidiabetic effect of walnut peptides on blood glucose level concentration in alloxan-induced
diabetic rats ............................................................................................................................................ 28
Weak interaction at nanoparticles alter function and conformation of proteinase k ........................... 29
Evaluation of structure, stability and chaperoning function of R12C human αA-crystallin under
oxidative stress ....................................................................................................................................... 30
Application of β-casein nano-vehicles for oral drug delivery systems in cancer therapy ...................... 31
Homo-FRET in labeled proteins by steady-state fluorescence anisotropy, revising the theory,
rethinking the assumptions .................................................................................................................... 32
Effect of surface engineering at nano scale on the protein adsorption and bacterial adhesion of
polymeric and metallic substrates .......................................................................................................... 33
Spectroscopic and molecular docking studies on interaction of prodigiosin with β-Lactoglobulin ....... 34
Virtual screening of piperine analogs as survivin inhibitors and their molecular interaction analysis by
using consensus docking, MD simulation, MMPB/GBSA and alanine scanning techniques .................. 35
Heterologous expression and functional characterization of multiple isoforms of rice metallothionein
................................................................................................................................................................ 36
Assessment of antibacterial and antioxidant activity of silver nanoparticles produced by reduced
glycated casein adducts .......................................................................................................................... 37
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QM/MM spectroscopic investigation of the structure of the light-driven enzyme protochlorophyllide
oxidoreductase (LPOR) ............................................................................................................................ 38
Computer-aided design of new Typrostatin-A derivatives as simultaneous effective inhibitors of αβ-
tubulin and breast cancer resistance protein ......................................................................................... 39
Evaluation of the kappa carrageenan-chitosan nano magnetics efficiency on purification of P. indica
pectinase ................................................................................................................................................. 40
Nerve growth factor precursor and its role in alzheimer’s disease ........................................................ 41
Conformational studies of Human hemoglobin and insulin upon interaction with MTBE ..................... 42
Molecular dynamics simulations of surfactant peptides wrapping single-walled carbon nanotubes ... 43
N-methyl phenylalanine-rich peptides as potential blood -brain barrier shuttles ................................. 44
Free radical scavenging and denaturation-inhibiting effects of peptides from fish skin in vitro and in
food model system ................................................................................................................................. 45
Antibacterial evaluation of Bis (2-methyl-1H-imidazole-κN3) silver (I) dichromate (VI) by autodock vina
function ................................................................................................................................................... 46
Looking for a generic inhibitor of amyloid-like fibril formation among tri hetero cyclicsmall molecules
................................................................................................................................................................ 47
The crucial role of a Ω–loop the stability and activity of the Exo–inulinase ........................................... 48
Different strategies for designing protein inhibitors, agonists and super-agonists ............................... 49
rh-IGF-1 (mecasermin): expression, purification and formulation ......................................................... 50
Functionalized superparamagnetic nanocarriers in enzyme engineering: Highly dispersive, stable and
robust biocatalysts .................................................................................................................................. 51
Lens antioxidant defense mechanism plays an essential role against oxidative stress induced structural
damages of crystallin proteins ................................................................................................................ 52
Memory prison of protein ...................................................................................................................... 53
Isolation of α glucosidase inhibitor producers, Bacillus sp. RP073 and virgibacillus sp. RP072 from
Persian Gulf. ............................................................................................................................................ 54
Potential application of β-lactoglobulin for presence in nano scale oral drug delivery systems ........... 55
Poster Presentation Abstracts: ............................................................................................................... 56
Optimal isolation and purification of lens α-Crystalline protein ............................................................ 56
Molecular dynamics simulation of new cyclotide from viola tricolor .................................................... 57
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The impact of vitamin C on amyloid structure of treated bovine serum albumin with potassium
sorbate .................................................................................................................................................... 58
Structural intermediates of bovine serum albumin upon treatment with potassium sorbate .............. 59
Survivin gene cloning in bacterial host DH5α ......................................................................................... 60
Association of APOE and BDNF polymorphisms with alzheimer’s disease in south of Iran. .................. 61
A molecular dynamics simulation investigation into the dissociation constants (Kd) of Mn(II) binding on
the structure and stability of calprotectin using Molecular Dynamics Simulation ................................. 62
Preliminary antibacterial evaluation of the chemical compositions in mono and dinuclear cobalt(II)
complexes of 1,1,3,3-tetrakis(3,5-dimethyl-1-pyrazolyl) propane ligand .............................................. 63
A Study on Zn(II) coordination in the present of Ca(II) in human calprotectin binding sites using
molecular dynamics simulations ............................................................................................................. 64
Chaperone-like activity of new deep eutectic solvents (DESs) ............................................................... 65
Creating hierarchical nanostructures with TiO2 nanoparticle and brush polymer, a promising approach
for protein repellence behavior of biomaterial ...................................................................................... 66
Protective effect of zinc ions against protein misfolding: a dose dependent phenomenon .................. 67
Computational study of interaction between prostate-specific membrane antigen and truncated
PSMA aptamer ........................................................................................................................................ 68
Stabilization of Ca2+ regulated photoprotein aequorin by deep eutectic solvents (DESs) ..................... 69
Effect of conventional and microwave heating on glycation of bovine serum albumin through maillard
reaction ................................................................................................................................................... 70
Study of the interaction of apigenin and epigallocatechingallatewith α-Lactalbumin and their
inhibitory effect on the formation of α-Lactalbuminamyloid fibrils ....................................................... 71
A spectroscopic study on the interaction of blood carrier protein of albumin with a new designed
Palladium complex .................................................................................................................................. 72
Min impact study on catalase of Helicobacter pylori through simulation docking ................................ 73
The survey of the effect of crocin and saffranal in terms of the inhibition of the formaion beta sheets
in neurodegenerative diseases in vitro and in silico ............................................................................... 74
Prediction of triple mutation roles on the sweetness and function of brazzein according to
bioinformatical studies ........................................................................................................................... 75
Mutation at calcium binding site in cyclomaltodextrinase improve enzyme thermostability: A
bioinformatic study ................................................................................................................................. 76
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Application of albumin glycation products to increase the yield of phytase production in a
recombinant bacterial expression system .............................................................................................. 77
Analysis of the interactions between putrescine and bovine pancreatic trypsin by spectroscopic
techniques ............................................................................................................................................... 78
Fabrication and characterization of nano bio-composites scaffolds contains silk fibroin protein and
mcm-41 for tissue engineering applications ........................................................................................... 79
Theoretical study of effect of N232S, F251L and R242H mutations in myosin protein structure .......... 80
Theoretical study of the effect of mutation F117L osteoprotegerin protein on its binding to RANKL
protein by modeling methods ................................................................................................................ 81
Fabrication and charactenization of nano bio-composite scaffold for use in tissue engineering .......... 82
Investigation on the binding of metoprolol tartrate to β-lactoglobulin using spectroscopic techniques
................................................................................................................................................................ 83
Induction of point mutations in human growth hormone molecule using specific primers .................. 84
Co-immobilization of acetylcholine esterase and choline oxidase for determination of acetylcholine in
the brain of rat ........................................................................................................................................ 85
The role of glutamate oxidase in electrochemically measurement of glutamate neurotransmitter in rat
brain ........................................................................................................................................................ 86
Analysis the binding interactions of bisdemethoxycurcumin, diacetylcurcumin and
diacetylbisdemethoxycurcumin with bovine α-lactalbumin by experimental and theoretical analysis 87
An investigation into the molecular mechanisms of the bacterial for designinga competent genetic
construct for benzene biodegradation ................................................................................................... 88
The optimization of expression of recombinant denileukin diftitox in soluble form ............................. 89
Protective effect of polyphenols against mitochondrial membrane permeabilization induced by HEWL
aggregates ............................................................................................................................................... 90
Immobilization of Termomyces lanuginosus xylanase enzyme on functionalized graphen oxide and
determination of activity and thermal stability ..................................................................................... 91
Covalent binding of xylanase enzyme on functionalized superparamagnetic graphene oxide
nanoparticles and evaluation of activity and pH stability....................................................................... 92
Investigation the effects of different osmolytes on the structure of trypsin ......................................... 93
Bagging algorithm for protein thermostability prediction based on pseudo amino acid composition . 94
Efficient synthesis of novel eptifibatide analogous ................................................................................ 95
Bioactive peptides from egg-whites of different avian species .............................................................. 96
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In silico study of molecular interaction between cel-D7 (a novel drivative of celastrol) and proteasome
using the autodock software .................................................................................................................. 97
Improvement of Bacillus subtilis ZH1 biosurfactant production ............................................................ 98
Probing the interaction of chemotherapeutic drug of 5-fluorouracil and milk carrier protein of -
lactoglobulin ........................................................................................................................................... 99
Identification of RCC in structure of large envelope protein S of HBV and molecular modeling ......... 100
Antimicrobial activity of heat stable peptides in Iranian native Bacillus strains with probiotic potential
.............................................................................................................................................................. 101
Preparation and characterization of monoclonal antibody against carcinoembryonic antigen and
immunohistchemistry evaluation ......................................................................................................... 102
Construction of BSA nanogels-loaded doxorubicin and its anti-carcinoma effect on MES-SA/DX5 .... 103
Medical applications of antimicrobial peptide ..................................................................................... 104
Study of the interaction change between the cytosolic components of the NADPH oxidase in cell free
system ................................................................................................................................................... 105
Exploring of the assembly process of the NADPH oxidase complex via the structural changes of p47phox
and p67phox subunits .............................................................................................................................. 106
Effects of fermentation by cocci lactic acid bacteria isolated from Iranian dairy products on the
immunoreactivity of Cow's milk caseinate ........................................................................................... 107
A thermodynamic study on the interaction of propolis and human hemoglobin ................................ 108
Studding the solubility of EGFP upon replacing valine 12 by lysine, using bioinformatics tools .......... 109
Enhanced green fluorescent protein instability upon replacing phenylalanine 226 by alanine .......... 110
Assesment of cow’s milk β-lactoglobulin allergenicity reduction using cocci lactic acid bacteria isolated
from Iranian dairy products .................................................................................................................. 111
Computer-aided evaluation of M4 protein (a truncated version of IL-24) with Bioinformatics tools . 112
Promotion of antioxidant peptides of tomato waste seed meals by bacillus subtilis submerged
fermentation ......................................................................................................................................... 113
Comparison of radical scavenging activity of tomato and grape meal peptides by bacillus subtilis
submerged fermentation ...................................................................................................................... 114
Glutathione S-transferase protein of some cultivated wheat in Iran ................................................... 115
Studying structures and processes involved in the transfer across nuclear pore complexes using
molecular dynamics simulation ............................................................................................................ 116
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Investigating the interaction of antibacterial peptide “LLAA” with the bacterial membrane using
molecular dynamics simulation. ........................................................................................................... 117
The effects of a novel phenanthroline-imidazole derivative of platinum complex on the structure and
function of bovine liver catalase ........................................................................................................... 118
Stability of the recombinant enzyme in Lepidiumdrabaperoxidase (LDP) against heat and hydrogen
peroxide ................................................................................................................................................ 119
Effect of lysine residue acetylation on the structure of apomyoglobin ............................................... 120
Effect of spacer length of the synthetic cationic urethane gemini surfactants on the secondary
structure of insulin ................................................................................................................................ 121
Superior cytotoxicity of serum albumin on microglial cells upon hetero-seeding effect of amyloid
peptide .................................................................................................................................................. 122
Prediction and evaluation of myelin oligodendrocyte glycoprotein (MOG) antigenic epitopes .......... 123
Evaluation of MHC class I binding properties of designed peptides for DNA vaccine for induction of
multiple sclerosis tolerance in human .................................................................................................. 124
Cloning and expression of soluble extracellular domains 1-3 of human VEGF receptor-2 in Pichia
pastoris .................................................................................................................................................. 125
Study of the interaction of myricetin and Morin hydrate with bovineα-Lactalbumin ......................... 126
Protective effects of hydroalcohol extract of Zingiber Officinale on the functional disorders and
histological damages in Iron-induced renal toxicity in rats .................................................................. 127
Human asf1a c-terminal tail phosphorylation favours formation of stable secondary structures in this
intrinsically disordered peptide ............................................................................................................ 128
Bioinformatics analysis of Aspartyl/asparaginyl β-hydroxylase protein ............................................... 129
Cloning and heterologous expression of catalytic subunit of rice (Oryza Sativa) acetohydroxy acid
synthase in Escherichia coli ................................................................................................................... 130
Interaction of arachidonoyl serotonin with beta-casein nanoparticles: spectroscopy and molecular
modelin studies ..................................................................................................................................... 131
Interaction of serotonin with beta-casein nanoparticles: spectroscopy and molecular modelin studies
.............................................................................................................................................................. 132
An efficient synthesis of exenatide as an anti-diabetic drug ................................................................ 133
Preparation and biodistribution assessment of 68Ga-Bleomycin as a possible PET imaging ................ 134
The application of HER2 protein in cancer detection using graphene functionalized with specific DNA
sequences ............................................................................................................................................. 135
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Construction of BMP-2 agonists based on nanobody (VHH) ................................................................ 136
Application of bovine serum albumin- carbon nanotubes conjugated system for fabrication of highly
sensitive arsenic aptasensor ................................................................................................................. 137
Structural and functional characterization of reduced glycated adduct of bovine β-casein................ 138
Construction, expression and purification of diabody against human vascular endothelial growth
factor in bacterial system...................................................................................................................... 139
Inhibition of kanamycin-resistant bacteria by designing 10–23 deoxyribozyme targeted to kanamycin
resistance mRNA ................................................................................................................................... 140
Investigating on the synergistic inhibitory effect of aspirin and propolis on the glycation of human
hemoglobin by fructose ........................................................................................................................ 141
Comparison on the inhibitory effects of propolis on the structural changes of glycated human
hemoglobin resulted glucose and fructose ......................................................................................... 142
Subcloning, Expression, and Activity Assay of Recombinant Luciferin Regenerating Enzyme from
Lampyris Turkestanicus (T-LRE) in Yeast ........................................................................................... 143
ASA rater: A web based software for classifying surface accessibility of protein residues from the
structure ................................................................................................................................................ 144
Studying the effect of changing the wettability of polypropylene films on the protein adsorption .... 145
Molecular modeling of Zika virus NS5 and evaluating its interaction with human targets using In-silico
approach ............................................................................................................................................... 146
Extraction optimization, purification and characterization of a protease enzyme from fruits of
Withania coagulans .............................................................................................................................. 147
Designing, development and assessment a series of novel genetic constructs for aromatic
hydrocarbons bioremediation based on investigation of bacterial dioxygenases ............................... 148
Enhancing extraction efficiency of heterologously expressed recombinant prostate stem cell antigen
in Ecoli ................................................................................................................................................... 149
The properties of biosurfactant produced by Lactobacillus rhamnosus ATCC 7469 ............................ 150
Investigate the mechanism of the BAX, a pro-apoptotic protein, activation through SMBA1, an anti-
cancer treatment: a molecular modeling and molecular dynamics study .......................................... 151
Effect of mare (Equus caballus) caseins and whey proteins on breast cancer cells ............................. 152
Endolysins as new class of antimicrobial agents against pathogenic bacteria ....................... 153
Study on the interaction of novel cationic platinum complexes with human serum albumin ............ 154
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Spectroscopic and dynamic properties of arachidonoyl serotonin- β-Lactoglobulin complex: A
molecular modeling and chemometric study ....................................................................................... 155
Purified milk fractions and bioactive peptides, unknown source of health for Iranian people ........... 156
Design of ubiquitin conjugated peptide of toxoplasma gondii SAG1 antigen for presentation on MHC
class I ..................................................................................................................................................... 157
T-cell epitope prediction of different antigen for developing Toxoplasma gondii vaccines ................ 158
Kinetics of xantho-oligosaccharide production by xanthan degrading enzymes from Paenibacillus sp.
strain AS7 .............................................................................................................................................. 159
A thermodynamics study on the interaction of Allura Red AC with calf thymus DNA ......................... 160
Molecular cloning of a Bacillus licheniformis BR1390 α-amylase gene and biochemical characterization
of the recombinant enzyme .................................................................................................................. 161
Investigation on the effect of food colorant Allura Red AC on the bovine serum albumin by various
spectroscopic techniques...................................................................................................................... 162
Efficient synthesis of argirelin acetate as anti-wrinkle peptide ............................................................ 163
Thermostable alginate lyase from Pseudomonas aeruginosa strain 293 ............................................. 164
PH stability of alginate lyase from pseudomonas aeruginosa strain 293 ............................................. 165
Memory prison of protein .................................................................................................................... 166
Effects of Silver Nanoparticles on Protein Pattern and Antioxidant Enzymes Activities of Canola
(Brassica napus L.) Under In vitro Conditions ....................................................................................... 167
Spectroscopy study on interaction of amaranth with bovine serum albumin (BSA): a thermodynamic
approach ............................................................................................................................................... 168
Development a broad-spectrum immunotoxins based on in-silico ligands assay ................................ 169
Structural alterations in hemoglobin by glycation; prevention by ferulic acid and p-coumaric acid. .. 170
Protein glycation and anti-AGE agents; possible role in treatment of glycation-associated diseases. 171
A simple bioluminescence method for determination of benserazide by inhibitory effect on aequorin
in biological sample ............................................................................................................................... 172
Cognition enhancing and neuromodulatory propensity of satureiahortensis extract against lysozyme
induced cognitive impairments in rat hippocampus. ........................................................................... 173
Protective effect of 1, 3, 5 tri fluoro phenyl benzene against lysozyme oligomerization and amyloid-
mediated cell death in PC12 cells. ........................................................................................................ 174
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Structural study of wnt-pathway inhibitors, Mesd and dkk1 on LRP6, potentials for anti-cancer peptide
design .................................................................................................................................................... 175
Lactopeptides are natural antibiotics can be replace with artificial antibiotics ................................... 176
Investigation of the antifouling and protein adsorption properties of polyethersulfonemembranes by
titaniadioxide nanoparticles coating .................................................................................................... 177
Interaction of human serum albumin with the resveratrol in the presence of nanoparticles and EMF
(up to 1 MHz) ......................................................................................................................................... 178
Interaction between silver nanoparticles and human serum albumin revealed by fluorescence
spectroscopy in the presence of resveratrol ........................................................................................ 179
Comparison of phytase production in submerged and solid state fermentation of a strain of
Aspergillus niger and investigation of 3 various solid media containing wheat bran as the basic
substrate ............................................................................................................................................... 180
Hydrolysis of collagen-containing wastes as a renewable nitrogen source ......................................... 181
In silico evaluation of binding affinity of zanamivir, peramivir, and laninamivir octanoate drugs
compared with oseltamivir to the neuraminidase in influenza A (H1N1) ............................................ 182
The simulation and evaluation of fever temperature effects on the active site of neuraminidase
protein receptor in influenza A (H1N1) virus in the in silico ................................................................. 183
Investigation of binding interactions of apigenin and morin hydrate with beta-lactoglobulin............ 184
Exploring the thermal stability and activity of proteinase K in the presence of spermidin by biophysical
techniques and molecular dynamic simulations .................................................................................. 185
Investigation of the effect of spermine on the interaction between ADA and its substrate using
computational methods........................................................................................................................ 186
Study of laccase activity of Bacillus spores by zymogeraphy ............................................................... 187
Study of expression and activation of engineered coagulation factor IX with propeptid of protrombin
.............................................................................................................................................................. 188
Identification of biologically active recombinant human erythropoietin (rHuEPO) glycoforms .......... 189
Thermodynamic stability of β-lactoglobulin in the presence of cetylpyridinumbromide: UV-Vis
spectroscopy andmdocking studies ...................................................................................................... 190
Investigating Interaction of DNA and protein immobilized gold nano particles with nitrocellulose
membranes ........................................................................................................................................... 191
Prediction 3D structure of IGFBP3 using homology modeling and molecular dynamic ....................... 192
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An investigation on the interaction of antibacterial peptides "aurein 1.2" with the bacterial membrane
using molecular dynamics simulation ................................................................................................... 193
Luciferase mutation at K329 position by SDM for proteolytic stability ................................................ 194
Determination of 3-D structure of human HMGB4 protein using MODELLER software ...................... 195
Antiadhesive activity of a biosurfactant isolated by Lactobacillus acidophilus onSerratiamarcescens
strains .................................................................................................................................................... 196
Fermentative production of lysine by Corynebacterium glutamicum from different nitrogen sources
.............................................................................................................................................................. 197
Optimization of different carbon sources for production of L-lysine by Corynebacterium glutamicum
.............................................................................................................................................................. 198
In silico comparison of structural features of envelope protein of zika virus with the homologous
proteins of two close viruses ................................................................................................................ 199
Activation of EF-hand II of photoproteinaequorin by replacement of its calcium-binding loop .......... 200
Bioinformatics design of deoxyribozyme 10-23 targeted to beta-lactamase mRNA for inhibition of
ampicillin-resistant bacteria ................................................................................................................. 201
Prediction of the mode of interaction between monoterpenes and the nitroreductase from
Enterobacter cloacae by docking simulation ........................................................................................ 202
Molecular modeling, docking and molecular dynamics simulation approaches to assessment binding
of coumarin to β-casein ........................................................................................................................ 203
Exploring binding properties of coumarin with Bovine β-Casein: multispectroscopic and chemometrics
studies ................................................................................................................................................... 204
Measurement of dioxin contamination in water samples by a bioluminescence method .................. 205
Role of the pre- molten globule structure in amyloid fibril formation ................................................. 206
Nano-liposomal lipid peroxidation as a consequence of the diabetic albumin glycation .................... 207
Gold nanoparticles-capped mesoporous silica for enzyme responsive controlled release of doxorubicin
in cancer therapy .................................................................................................................................. 208
Isolation of ACE-inhibitory peptide produced by enzymatic activity of goat milk whey proteins ....... 209
The presence of JC virus VP1 capsid of genotype 2B in rheumatoid arthritis patients in Isfahan, Iran210
In Silico analysis of single nucleotide polymorphisms (SNPs) and screening of mutations affecting
protein stability and function of KRAS protein ..................................................................................... 211
Computational molecular docking studies of bioactive peptides from milk proteins as angiogenesis
converting enzyme inhibitors with antihypertensive effects ............................................................... 212
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Molecular docking and quantitative structure--activity relationships(QSAR) studies of herbal
compounds in Iris pseudopumila (Iridaceae)asacetylcholinesterase inhibitorsin alzheimer's disease
treatment .............................................................................................................................................. 213
Study of the binding of warfarin drug to β- lactoglobulin by UV- visible and isothermal titration
calorimetry techniques ......................................................................................................................... 214
Fabrication of gold nanorod assemblies on BSA amyloid fibril scaffolds ............................................. 215
The effect of modified tryptophan residues on kinetic, thermodynamic and structure of
mashroomtyrosinase ............................................................................................................................ 216
Covalent immobilization of glucoamylase on superparamagnetic graphene oxide Fe3O4
nanocomposites .................................................................................................................................... 217
Functionalized superparamagnetic chitosan nanoparticles in enzyme engineering: A highly dispersive,
stable and robust biocatalyst ................................................................................................................ 218
Investigation on physicochemical properties of [Ni (FIP) 2] (OAC)2 complex and its interaction with ct-
DNA and Its effect on ct-DNA stability .................................................................................................. 219
An in-silico investigation on the structure and function of the Phenanthrene degradative bacteria
enzymes, an introduction to development of anti-cancer probiotics .................................................. 220
The effect of time and temperature incubation on bacterial phytase activity .................................... 221
Thermal stability of lactoperoxidase stabilized on modified magnetic nanoparticle ........................... 222
Effect of over-expressing Apaf-1 on apoptosis induction ..................................................................... 223
Studying the presence of hemolysin BL and NHE subunit genes in Iranian native Bacillus strains with
probiotic potential by PCR .................................................................................................................... 224
Inhibition of angiogenesis signaling pathways by synergic administration of VEGF antibody along with
endostatin derived peptide in the human umbilical vein endothelial cells.......................................... 225
Evaluation of antioxidant activity in peptides of fermented soybean meal by Lactobacillus rhamnosus
.............................................................................................................................................................. 226
Production of antioxidant peptides from soybean meal by Bacillus subtilis ........................................ 227
Theoretical design of a new vaccine for multiple sclerosis (MS) .......................................................... 228
The effect of temperature on the formation rate of liposome of DSPC and CHOL by coarse-grained
molecular dynamics simulations studies .............................................................................................. 229
Purification of sugar beet pulp induced pectinase from P. indica by chitosan-PVA magnetic beads
.............................................................................................................................................................. 230
HTTP://UI.CNF.IR/PPS 18
Investigating the role of DADLE on 6-OHDA-induced cell toxicity in human neuroblastoma cells SH-
SY5Y as an in vitro model of Parkinson’s disease ................................................................................. 231
Interactions of β-lactoglobulin with Lovastatin .................................................................................... 232
Efficient synthesis and purification of buserelin acetate...................................................................... 233
A thermodynamic approach of the interaction between human serum albumin and a new synthesized
platinum complex ................................................................................................................................. 234
Computational analysis of miR-423 mediated drug response in breast cancer ................................... 235
Evaluation of dioxin contaminations in fish oil samples by bioluminescence method ........................ 236
Characterization of electrospun gelatin nanofibers crosslinked with tannic acid ................................ 237
Kinetics and spectrofluorimeteric the studies of catalase in presence of spermidine ......................... 238
Effect of TiO2 nanoparticle on structural stability and activity of catalase .......................................... 239
Separation and precipitation of β –lactoglobulin from commercial whey preparations by NaCl salting
out at low pH......................................................................................................................................... 240
Proteins and peptides in camel milk ..................................................................................................... 241
Efficient synthesis and purification of octreotide acetate as a somatostatin agonist analogue .......... 242
Optimization of carbon source for phytase production in submerged fermentation of a strain of
Aspergillus niger and comparison of enzyme activity between immobilized and free spores ............ 243
An investigation on the structure and function of the cell surface prostate-specific antigens for
development a new generation of immunotoxins ............................................................................... 244
A comparative study of effects of canola meal bioactive peptides, antibiotic, probiotic and prebiotic
on growth performance, some blood parameters, intestinal morphology and gut microflora in broiler
chicks ..................................................................................................................................................... 245
The investigation of stability of functionalized alkyl-peptide self-assembly innanofiber form by
molecular dynamics simulation ............................................................................................................ 246
Beta keratin solubilization: a new method for blocking sulfydryl groups ............................................ 247
Antioxidant and metal chelating ability of feather keratin................................................................... 248
Binding of carbon nanotube to carcinoembryonic antigen: A the oretical approach .......................... 249
Peroxynitrite-modified human α-Crystallin subunits indicate improved chaperone-like activity and
enhanced protection against copper-mediated ascorbic acid oxidation ............................................. 250
Investigation the use of plants as host for protein production ............................................................ 251
Immobilization of human serum albumin on modified graphene oxide nanosheets .......................... 252
HTTP://UI.CNF.IR/PPS 19
A combined spectroscopic and molecular docking approaches to probing binding of daidzein to β-
lactoglobulin ......................................................................................................................................... 253
VEGF-A epitope prediction aim to exploiting in angiogenesis stimulation in order to tissue restoration
using magnetic nanoparticles ............................................................................................................... 254
Molecular docking study of HCV proteins with phytochemical compounds from Prangos uloptera DC
.............................................................................................................................................................. 255
Investigation the antibacterial effect of peptides derived from cow's milk protein (caseinate)
hydrolysis by lactic acid bacteria .......................................................................................................... 256
Immobilization of human serum albumin protein on metal-organic framework material .................. 257
Investigation the antibacterial effect of peptides derived from cow's milk protein (Betalactaglobulin)
hydrolysis by lactic acid bacteria .......................................................................................................... 258
Prediction of post-translational glycosylation of proteins .................................................................... 259
Effectiveness of a number of natural product in improving viability of probiotic bacteria in Iranian
diary product ......................................................................................................................................... 260
Effect of Polyoxometalates (POMs) on glioblastoma cancer cells ........................................................ 261
Prediction of phosphorylation sites of proteins from their amino acid sequence ............................... 262
Functionalized superparamagnetic graphene oxide nanoparticles as a matrix for glucose oxidase
immobilization ...................................................................................................................................... 263
Immobilization of glucose oxidase on superparamagnetic/chitosan nanoparticles ............................ 264
Comparing the physiochemical properties and alpha helix percentages of different organisms’ Lactate
dehydrogenases by bioinformatics tool ............................................................................................... 265
Studying the effect of changing the micro/nano roughness and wettability of polypropylene (PP) films
on the protein adsorption ..................................................................................................................... 266
HTTP://UI.CNF.IR/PPS 20
Oral Presentation Abstracts:
Modeling the DSC profile of irreversible thermal denaturation of
proteins undergoing aggregation
Mojtaba Amani, Ali-Akbar Moosavi-Movahedi2
1Department of Biochemistry, Faculty of Medicine, Ardabil University of Medical Sciences (ArUMS), Ardabil,
Iran. 2Biophysical Chemistry lab, Institute of Biochemistry and Biophysics (IBB), Tehran University, Tehran, Iran.
Abstract
Some proteins are the cause of fatal diseases in human being and animals. These diseases arise
when a misfolded form of a protein appears and forms aggregates. Aggregates of the misfolded
form may convert the normally folded protein to its misfolded state and hence promote the
aggregation. A model has been proposed in which a misfolded protein triggers misfolding of
other proteins and aggregation. The equation describing the heat capacity on temperature has
been formulated and the theoretical DSC profiles were plotted. The effects of different variables
on theoretical profile and cases in which aggregated protein profile resembles reversible
unfolding will be discussed.
Keywords: Thermal denaturation, Aggregate, Heat capacity.
HTTP://UI.CNF.IR/PPS 21
Bioactive peptides from egg-whites of different avian species
Ladan Aminlari1, L. Hajipour2, M. Tavana3, M.M. Mohammadi3
1Department of Food Hygiene, School of Veterinary Medicine.
2 Department of Food Science and Technology School of Agriculture.
3Department of Biochemistry, Shiraz University, Shiraz, Iran.
Abstract
The aim of this study was to isolate and compare bioactive peptides from egg-white of quail,
duck and chicken and to determine their antimicrobial and antioxidant properties. The egg-white
proteins were diluted, the major proteins precipitated by trichloroacetic acid (TCA), centrifuged
to remove the precipitate and the supernatant were subjected to Sephadex G-25 gel-filtration
chromatography to isolate the peptides. The bioactive properties of the fractionated peptide were
determined. The elution pattern of peptides obtained by gel filtration chromatography of egg
white from different species of birds were different with different properties of the fractions. The
peptide fractions exhibited high antimicrobial and antioxidant properties. Most of the peptides
which were eluted at the final stage of gel-filtration chromatography showed the highest
antimicrobial properties against E. Coli and Bacillus Cereus. The results suggested that it is
possible to partially purify peptides from egg white of birds with potentially important functional
properties by a simple, one step chromatographic procedure. These peptides might substitute the
antioxidant and antimicrobial agents of chemical origin currently used in food and
pharmaceutical industries.
Keywords: Bioactive peptides, Egg whites, Quail, Duck, Chicken.
HTTP://UI.CNF.IR/PPS 22
Modified lysozymes as novel broad spectrum natural antimicrobial
agents Mahmud Aminlari, M1, 2, Ladan Aminlari3, Mohammadi Hashemi2, Armin Mirzapour2
1Departement of Biochemistry, School of Veterinary, Medicine, Shiraz University, Shiraz,
Iran.
2Departement of Food Science and Technology, College of Agriculture, Shiraz Univ., Shiraz,
Iran.
3Departement of Food Hygiene, School of Veterinary Medicine, Shiraz Univ., Shiraz, Iran.
Abstract
In recent years much attention and interest have been directed toward application of
natural antimicrobial agents in foods the objective of this study was to identify and
assess antimicrobial systems in natural sources. Some naturally occurring proteins have
received considerable attention and are being considered as potential antimicrobial
agents natural antimicrobials can be found in milk (lactoferrin, lactoperoxidase,
globulins, fatty acids), eggs (lysozyme, transferrin, globulins, avidin,ovoinhibitors),
plants (phenolics : cloves, allspice, oregano, rosemary, sage, thyme,; flavanoids : fruits,
juices ; thiosulfinates (allicin in garlic), catechins (in green tea ), glucosinolates (in
horseradish, mustard). Our laboratory is currently involved in isolation, characterization
and modification of antimicrobial proteins from milk and egg white and in their
application in foods and pharmaceutical industries. Lysozyme kills bacteria by
hydrolyzing the peptidoglycan layer of the cell wall of certain bacterial species, hence
its application as a natural antimicrobial agent has been suggested. However,
limitations in the action of lysozyme against only gram-positive bacteria have prompted
scientists to extend the antimicrobial effects of lysozyme by several types of chemical
modifications. During the last 2 decades extensive research has been directed toward
modification of lysozyme in order to improve its antimicrobial properties. This seminar
will report on the latest information available on lysozyme modifications and examine
the applicability of the modified lysozymes in controlling growth of gram-positive and
gram-negative bacteria in vitro and in vivo. The results of modifications of lysozyme
using its conjugation with different small molecule, polysaccharides, as well as
modifications using proteolytic enzymes will be reviewed. These types of modifications
have not only increased the functional properties of lysozyme (such as solubility and
heat stability) but also extended its antimicrobial activity. In conclusion this review
demonstrates that modified lysozymes are excellent natural agents which can be used in
food and pharmaceutical industries.
Keywords: Chemical-enzymatic modifications, Conjugation, glycation, Lysozyme,
Maillard reaction, Natural antimicrobial.
HTTP://UI.CNF.IR/PPS 23
Molecular dynamics simulation for designing and predicting of
bimolecular functions
Abolfazl Barzegar
Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran.
Abstract Molecular dynamics simulation (MDS) is computer simulation with atoms and/or molecules
interacting using particular rules of physics. MDS can provide the critical detail regarding
specific particle motions as a function of time. It is important tool for understanding the physical
basis of the structure and function of biological macromolecules. Current MDS of biomolecules
typically allow using a very large number of atoms that are involved over timescales of many
nanoseconds. Herein, the MD simulation process was applied for the aim of designing peptides
to functionalize carbon nanotubes based on the aromatic residue numbers and also designing new
fullerene derivatives as anti-HIV drugs. Data indicated that stacking interaction between the
aromatic residue and π electrons of nanotube is important for dispersing carbon nanotubes. Also,
we found that the fulleropyrrolidine derivatives with one and two acetoxy-hydroxyl groups, as
new carbon naostructures of fullerene-based compounds which possibly have potential use as
effective HIV-1 protease inhibitors. The usage of MDS provides new insight into biomolecular
design strategies for future nano-biomedical applications.
Keywords: Molecular dynamic; AIDS, Fullerene, Carbon nanotube; Aromaticity.
HTTP://UI.CNF.IR/PPS 24
Small substrate, big surprise. Structure and function of
dihydroxyacetone kinases
Bernhard Erni
Departement of Chemistry and Biochemistry, University of Bern, Switzerland.
Abstract
Dihydroxyacetone (Dha) kinases are a sequence-conserved family of enzymes which utilize
either ATP (in animals, plants, bacteria) or phosphoenolpyruvate (PEP, in bacteria) as source of
high-energy phosphate. The PEP-dependent kinase of E. coli consists of three subunits: DhaK is
a stable homodimer that binds Dha covalently by a hemiaminal linkage between an imidazole-
nitrogen of a histidine and the carbonyl carbon of Dha. DhaL contains a tightly bound ADP,
which - in contrast to the nucleotide of the ATP-dependent kinases - does not exchange but is
rephosphorylated in situ by DhaM. DhaM transfers phosphoryl groups from the general
phosphorylcarrier proteins HPr and enzyme I of the bacterial phosphotransferase system (PTS).
PEP→EI (His)→HPr(His)→DhaM(His)→DhaL(ADP)→DhaK(Dha) DhaR is the transcription
activator of the dhaKLM operon. It is a member of the AAA+ family of enhancer binding
proteins. The kinase subunits DhaL and DhaK act antagonistically as coactivator and corepressor
by mutually exclusive binding to the sensing domain of DhaR. In the presence of Dha, DhaL is
dephosphorylated, DhaL::ADP displaces DhaK and stimulates DhaR activity. In the absence of
Dha, DhaL::ATP accumulates. DhaL::ATP does not bind to DhaR. DhaR::DhaKinactive +
DhaL(ATP) + Dha → DhaR::DhaL(ADP)active + DhaK::DhaP
Keywords: Dihydroxyacetone, Substrate, Enzymes, Phosphoryl groups.
HTTP://UI.CNF.IR/PPS 25
Synthesis of therapeutic peptides and novel bioactive peptides
Saeed Balalaie1, 2
1Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416
Tehran, Iran. 2Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
Abstract
Peptides have a huge potential as drugs. They can be considered as “Natural Pharmaceuticals”.
The importance of peptides as pharmaceutical compounds has increased significantly and
peptide drugs have an essential role in pharmaceutical market. Meanwhile, today, following the
sequencing of the human genome, peptides have become a focus of biotechnological research.
Techniques have been developed for an easier, faster and cost effective synthesis of peptides.
Throughout the course of its story, the synthesis of pharmaceutical peptides and synthesis of
bioactive peptides has served as a principal driving force for discovering new chemical
reactivity, testing the power of existing synthetic methods, and enabling biology and medicine.
This talk will highlight elements of our efforts for: a) Synthesis of pharmaceutical peptides, Such
as GnRH analogues, Triptoreline, Leuprolide, Desloreline, Fertireline, Buserelin, Onclogy
peptides, Octrotide, Octrotate. b) Combining of solid and solution phase peptide synthesis with
new approaches such as multicomponent reactions for the synthesis of pseudo peptides and
investigation of their biological activities. c) Synthesis of novel cyclopeptides through Ugi
ligation/click reaction to construct the cyclopeptides which have a triazole moiety and also
lipophilic moieties. d) Combination of bioactive heterocyclic skeletons with active peptides.
Keywords: Therapeutic peptides, Bioactive peptides, Multicomponent reactions, Protected amino
acids, Cyclopeptides, Disulphide bridges.
HTTP://UI.CNF.IR/PPS 26
Cubic nanoparticles preparation to deliver protein drug (PAL36) to
brain cells for possible treatment of multiple sclerosis (MS)
Behjat Nafari1 and Abbasali Palizban2
1Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.
2Department of Clinical Biochemistry, Isfahan University of Medical Sciences, Isfahan, Iran.
Abstract
Many peptides and proteins are being used because of potential therapeutics. Delivery of these
peptide/protein drugs is one of the biggest difficulties for clinical application. Taking advantage
of nanoparticles encapsulated protein to target specific cells and prevent degradation, we
investigated how to deliver nanoparticles containing protein drugs to brain cells by crossing
blood brain barrier. Poly (lactic acid-co-glycolic acid) (PLGA) and Poly (L-lactic acid) (PLA),
first used for structures. PLGA and PLA are degradable and then metabolized by the Krebs
cycle. Avidin were conjugated with fatty acids in sodium deoxycholate (2%). Avidin-
stearatolyated /palmitolyated -PLGA (50/50) nanoparticles were prepared with encapsulated
PAL36 protein (Trade Mark). The Nanoparticles were characterization using FT-IR for chemical
binding, SEM for morphology, zeta potential for nanoparticle size, UV-Vis spectrometer for
PAL36 protein drug release behavior and entrapment efficiency (% EE). The FT-IR results show
that NHS-fatty acids were properly conjugated to Avidin. The scanning electron microscopy
experiment revealed cubic morphology for nanoparticle with size of 100-400 nm. The % EE and
drug loading were calculated to be 59% and approximately 1, respectively. Avidin on the surface
of nanoparticles which encapsulated protein of PAL36 enables potentially add biotinylated
ligand to the formulation of nanoparticles to improve specific targeting brain cells. Currently we
are looking to establish a method to understand how to deliver these particles containing PAL36
to human brain cells for treatment of Multiple Sclerosis (MS) patients.
Keywords: PLGA, Cubic Nanoparticle, Avidin-fatty acid conjugated, Multiple Sclerosis (MS).
HTTP://UI.CNF.IR/PPS 27
The effect of the aptameric ligands’ length on the binding affinity to
the analogous protein targets: evaluation of aptamers specific to
plasma coagulation factor VIIa against recombinant form of this
protein
Maryam Tabarzad1, Marzieh Jafari2, Nastaran Nafissi-varcheh3
1 Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
2 Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ahvaz Jundishpur University of Medical
Sciences, Ahvaz, Iran.
3 Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical
Sciences, Tehran, Iran.
Abstract
Aptamers are single stranded oligonucleotides comparable in selectivity and affinity to the
monoclonal antibodies, in addition to several strategic properties in design, development and
applications. Ease of design and development, simple chemical modification and the attachment
of functional groups, easily handling and more adaptability with analytical methods, small size
and adaptation with nanostructures are valuable characteristics of aptamers in comparison to
large protein based ligands. Among a broad range of aptamers’ targets, proteins and peptides
have significant position. Aptamers, especially DNA aptamers, as nucleic acid based affinity
ligands are more stable than monoclonal antibodies for protein purification or analysis.
Coagulation factor vii (FVII) is a plasma serine protease that has a significant role in coagulation
process and natural human hemostasis. Activated FVII (FVIIa) specific RNA aptamers were
developed previously with the aim of therapeutic applications. FVIIa specific DNA aptamers
were also presented in a patent considering plasma protein purification. In this study, two of the
aptameric DNA oligonucleotides that showed acceptable affinities for coagulation factor VIIa
purification from plasma, were selected to evaluate their affinity against a recombinant form of
FVIIa. Results showed the binding affinity of the 40 nucleotides aptamer was more than 81
nucleotides aptamer sequence. This might be the results of more probability of conformational
adaption in aptamer 3D structure when encounter minor differences in target molecule.
Therefore, this aptamer could be optimized in order to develop aptamer based affinity
chromatography process for this form of recombinant coagulation factor VIIa.
Keywords: Aptamer, Coagulation factor VIIa, Plasma, Recombinant, Conformational adaption.
HTTP://UI.CNF.IR/PPS 28
Antidiabetic effect of walnut peptides on blood glucose level
concentration in alloxan-induced diabetic rats
Raheleh Jahanbani1, Mahmood Ghaffari1, Kourosh Vahdati2, Maryam Salami3, Ameneh
Rezayof 4, Zahra Ghasemzadeh4, Ali Akbar Moosavi-Movahedi1,5
1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
2 Department of Horticulture, University of Tehran, College of Aburaihan, Pakdasht, Tehran, Iran.
3Department of Food Science and Engineering, University College of Agriculture & Natural Resources, University
of Tehran, Karaj, Iran.
4Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
5Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.
Abstract
In view of the fact that synthetic drugs for control of diabetes has some side effects and cannot
be use in the period of pregnancy, researchers have shown an increased interest in the use of
natural products to induced hypoglycemic effect. The present study was carried out to evaluate if
walnut peptides exert any effects on pancreatic ß cells in alloxan-induced diabetic rats and to
observe and determine the morphology of islets of animals from different treatment groups.
Twenty eight male Wistar rats (weighting 220-240 g at the start of experiments) were divided
into four groups. The first group was served as control and received no treatment. The second
group was served as diabetic control which they received 120 mg/kg of alloxan. The other two
groups were diabetic rats which were injected with 0.5 mg/kg of glibenclamide or 200 mg/kg of
walnut peptide for 21 days. Blood glucose readings and body weight were monitored during the
treatment period. Histological analysis was carried out on the pancreas and the kidneys of
animals in the treated and control groups. Our results showed that walnut peptides reduced
hyperglycemia in the diabetic animals. Histological analysis also indicated that walnut peptides
may be able to regenerate the damaged islets in the diabetic rats. Walnut peptides as a
nutraceutical agent may have potential regenerative effects towards the diabetic rats and can be
considered in different industries.
Keywords: Hyperglycemia, Alloxan, Walnut peptide, Rats.
HTTP://UI.CNF.IR/PPS 29
Weak interaction at nanoparticles alter function and conformation
of proteinase k
Mansoore Hosseini Koupaei1, Behzad Shareghi1, Ali Akbar Saboury2, 3, Fateme Davar4, Aboulfazl
Semnani5
1Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O. Box.115, Iran.
2 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
3Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.
4 Department of Chemistry, Isfahan University of Technology, Isfahan, Iran.
5Department of Chemistry, Faculty of Science, University of Shahrekord, Shahrekord, Iran.
Abstract
Weak protein- nanoparticle (Np) interactions are studied in a low binding regime as a model for the soft
protein corona around nanoparticles in complex biological fluids. No covalent interaction between
proteinase K (a serin protease) and zinc oxide nanoparticles (around 30nm) shows significant alteration in
conformation and enzymatic activity. Enzyme inhibition is accompanied by changes in the proteinase K
conformation. Changes in the stern- Volmer quenching constant and the fluorescence quenching of the
proteinase K suggesting a more polar location of Trp residues. Far-UV circular dichroism (CD) studies
showed that zinc oxide nanoparticles could change the secondary structure of proteinase K via increasing
in the content of α-helix structure. The thermodynamic parameters also indicated that the binding of
proteinase K on nanoparticles was spontaneous and the hydrogen bonds played a major role in interaction
of enzyme (proteinase K) with nanoparticles (zinc oxide).
Keywords: Proteinase K- nanoparticle, Weak interaction, CD- enzyme inhibition.
HTTP://UI.CNF.IR/PPS 30
Evaluation of structure, stability and chaperoning function of R12C
human αA-crystallin under oxidative stress
Kazem Khoshaman and Reza Yousefi
Protein Chemistry Laboratory (PCL), Department of Biology, Shiraz University, Shiraz, Iran.
Abstract
The oxidative stress in eyeball which occurs under chronic hyperglycemia and during
inflammation has been already indicated in the pathogenesis of cataract disorders. As the main
fraction of soluble lens proteins, α-crystallin has been indicated to play a vital role in the
maintenance of eye lens transparency. In the current study, the cataractogenic R12C mutant αA-
crystallin and its wild-type protein counterpart were incubated under oxidative stress for various
times. Then, several spectroscopic techniques and gel mobility shift analyses were applied to
investigate stability and structural/functional properties of these recombinant proteins. Upon
incubation with hydrogen peroxide, extensive disulfide covalent cross-linking was induced in
R12C mutant protein. Also, hydrogen peroxide-induced cross-linking was accompanied with an
important reduction in stability and significant loss of chaperone activity of this mutant protein.
The obtained results suggest that individuals carrying the R12C mutation are at an increased risk
to develop early-onset cataract under medical conditions such as diabetes mellitus and
inflammation which are associated with oxidative stress.
Keywords: αA-crystallin, Hydrogen peroxide, Disulfide cross-linking, Chaperone, Cataract.
HTTP://UI.CNF.IR/PPS 31
Application of β-casein nano-vehicles for oral drug delivery systems
in cancer therapy
Adeleh Divsalar1 and Ali Akbar Saboury2
1Department of Biological Sciences, Kharazmi University, Tehran, Iran.
2Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
Abstract
The clinical applications of platinum drugs are limited due to poor water solubility, low
stability, interactions with healthy tissues, and severe side effects. Then, in the present study, we
have explored a novel protective nano-platform based on the self-assembly of β-Casein (β-CN)
copolymers for the oral delivery of a platinum drug. Initially, affinity and stoichiometry of
association of Pt (II) complex to β-CN was characterized by fluorescence spectroscopy. Then,
the influences of pH and protein concentration on the formation of a colloidally-stable
nanocarrier system composed of drug-loaded β-CN in the absence and presence of chitosan
were investigated using dynamic light scattering (DLS)/zeta potential analysis and scanning
electron microscopy (SEM). Finally, the bioefficacy and cytotoxicity of Platinum drug loaded
in β-CN nanoparticles were evaluated on colorectal carcinoma HCT116 cells and compared with
the free drug. The results obtained from the DLS and SEM analyses are proof for the formation
of the β-CN -Platinum drug nanoparticles with very good colloidal stability and average particle
sizes of 200-250 nm. Treatment of colorectal carcinoma HCT116 cells with free and
encapsulated platinum drug indicated that the cytotoxicity and cellular uptake of the drug
was enhanced when entrapped in β-CN nanoparticles. Finally, it can be concluded that the β-
CN nanoparticles containing platinum drug can be a very promising candidate for the use in oral
drug delivery for cancer treatment.
Keyword: β-CN, Pt (II) complex, Bioavalibility, Nanocarrier, Oral drug delivery.
HTTP://UI.CNF.IR/PPS 32
Homo-FRET in labeled proteins by steady-state fluorescence
anisotropy, revising the theory, rethinking the assumptions
Zahra Zolmajd-Haghighi1, Quentin Hanley2, Aliakbar Saboury1
1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 2School of Science and Technology, Nottingham Trent University, Nottingham, UK.
Abstract
Oligomerization of proteins are involved in many biological functions and mal-functions. Model
systems that simulate such phenomena can be used to monitor oligomerization of proteins. Techniques based on Resonance Energy Transfer between identical fluorophores (homo-FRET)
can uncover the oligomerization state of proteins. Homo-FRET causes the fluorescence
anisotropy of the system to decrease when the number of identical fluorophores within energy
transfer distance increases. Theories that describe these systems applied an assumption of equal
fluorescence efficiency for all sites that means emission intensity of fluorophores do not change
when in close proximity with each other in a cluster. However, most fluorophores in close
proximity show either self-quenching or emission enhancement. Bovine serum albumin (BSA)
solutions that were fractionally labelled with FITC was chosen to mimic aggregation of
fluorescently labeled proteins. Previous theories were then applied to analyze the data and to fit
the results. The analysis showed that the model system did not follow the assumption of equal
fluorescence efficiency and by applying the assumption the cluster sizes were under-estimated. It
was also shown that applying the assumption of equal fluorescence efficiency would over-
estimate the cluster size in systems that show enhancement of emission upon proximity of
fluorophores. Modified analytical expressions were then presented for fully labeled and
fractionally labeled systems that show a range of quenching or enhancement behavior and the
experimental results of BSA were analyzed.
Keywords: Oligomerization, Bovine serum albumin (BSA).
HTTP://UI.CNF.IR/PPS 33
Effect of surface engineering at nano scale on the protein adsorption
and bacterial adhesion of polymeric and metallic substrates
Amir Razmjou, Parisa Moazzam, Fatemeh Noorisafa
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, P.O. Box
73441-81746, Isfahan, Iran.
Abstract
Protein adsorption is the first of a complex series of events that regulates many phenomena at the
nano-bio interface, e.g. cell adhesion, biofilm formation, in vivo inflammatory responses and
protein crystallization. Understanding of how nanoscale morphology and hierarchical structure
influences protein adsorption and cell adhesion is strategic for providing insight into all of these
processes. The tendency of proteins attachment to the surface depends on the material properties
such as surface energy, structure, texture, and relative charge distribution. Here a systematic
superhydrophobic and superhydrophilic surface modification were done to find out the rule of
surface morphology and chemistry on the biomaterial- cells interactions. In this study surface
modification via grafting technique in the surface of polymer and metal alloys were done to
investigate the effect of modification on the biomaterials biocompatibility. A systematic
characterization was conducted to elucidate the role of each parameters on the protein adsorption
and bacterial adhesion. The aluminum surfaces were characterized by SEM, EDAX, XPS, AFM,
FTIR, contact angel (CA) goniometry, surface free energy (SFE) measurement, MTT, Bradford,
Lowry and microtiter plate assays and also flow cytometry and potentiostat analyses.
Engineering the surface wettability towards superhydrophilicity/superhydrophobicity has been
found an impressive technique to enhance biocompatibility and reduction in protein-material
interactions.
Keywords: Protein adsorption, Super hydrophobicity, Super hydrophilicity, Hierarchical
nanostructured surfaces.
HTTP://UI.CNF.IR/PPS 34
Spectroscopic and molecular docking studies on interaction of
prodigiosin with β-Lactoglobulin
Banafsheh Rastegari and Hamid Reza Karbalaei-Heidari
Molecular Biotechnology Laboratory, Department of Biology, Faculty of Science, Shiraz University, Shiraz 71454,
Iran.
Abstract
β-Lactoglobulin (β-Lg), the major whey protein in bovine milk, has a high affinity for
encapsulating poor souble drugs in oral drug delivery. Prodigiosin is a family member of
tripyrrole red pigments called prodiginines which shows attracting increasing interest because of
their antimicrobial, antimalarial, immunosuppressive and remarkable selective anticancer
activities. In this study, the interaction of prodigiosin with β-Lg was investigated through far-UV
circular dichroism (CD) spectroscopy, fluorescence spectroscopy and molecular docking studies.
Prodigiosin interacts with the central calyx of β-Lg with association constant of 1.99 × 104 M-1
to form 3:2 complexes at 300 K. The results indicated that binding of prodigiosin to β-Lg caused
strong fluorescence quenching of protein through static quenching mechanism. Hydrophobic
interactions are the major forces in the stability of Prodigiosin–β-Lg complex with entropy-
driving mode. CD spectra showed slight conformational changes in β-Lg due to the binding of
prodigiosin. Moreover, pH-dependent interaction survey confirmed that the prodigiosin binds to
residues located in the central calyx of β-Lg with association constant of 1.99 × 104 , 1548 and
184 M-1 in pH 7.4, 5.5 and 3.0, respectively.
Keywords: Prodigiosin, β-Lactoglobulin, Fluorescence, CD, Molecular docking.
HTTP://UI.CNF.IR/PPS 35
Virtual screening of piperine analogs as survivin inhibitors and
their molecular interaction analysis by using consensus docking,
MD simulation, MMPB/GBSA and alanine scanning techniques
Elham Sattarinezhad, Abdol-Khalegh Bordbar, Najmeh Fani
Department of Chemistry, University of Isfahan, Isfahan, 81746-73441, Iran.
Abstract
Survivin, as a potential target for cancer therapeutics, is essential for tumor cell proliferation and
viability. In this study, consensus docking of AutoDock and AutoDock Vina was carried out in
order to improve the reliability of docking in a virtual screening of a library of 2497 Piperine
derivatives as a novel group of survivin inhibitors. The initial docking of these compounds into
the binding site of survivin, using AutoDock Vina program, resulted in the selection of the
top100 derivatives with the highest binding affinities. A subsequent screening was done on these
100 compounds by recalculation of the binding energies using the Auto Dock program.
Considering the obtained binding energies, the top two highest ranked compounds, as well as
piperine, were selected and subjected to three independent10 ns molecular dynamics (MD)
simulations in order to further validate the proposed binding modes and interactions.
Subsequently, the contributions of van der waals interactions, electrostatic forces, and the polar
and non-polar solvation in the total binding free energies were calculated using the
MMPB/GBSA methods and the entropy component as a further refinement of the total free
energy was calculated by the nabnmode module of AMBER. In addition to MMBP/GBSA
methods, the contribution of each active site residue to the total binding free energy was assessed
using alanine scanning. The results represent a key role by the hydrophobic forces in the
molecular interactions and elucidate the binding modes of Piperine analogs for further
experimental studies.
Keywords: Survivin, piperine, Consensus docking, MD simulation; MMPB/GBSA; Alanine
scanning.
HTTP://UI.CNF.IR/PPS 36
Heterologous expression and functional characterization of multiple
isoforms of rice metallothionein
Azar Shahpiri, Mohsen Zarei, Rezvan Mohammadi Nezhad, Iman Soleimanifard, Soheil Piezadeh
Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111,
Iran.
Abstract
Metallothioneins (MTs) are a superfamily of low-molecular-weight, cysteine (Cys)-rich proteins
that are believed to play important roles in protection against metal toxicity and oxidative stress.
Plants have several MT isoforms, which are classified into four types based on the arrangement
of Cys residues. In this study, four rice (Oryza sativa) MT isoforms OsMTI-1b, OsMTI-2a,
OsMTI-3a and OsMTII-1a that belong to type 1, type 2, type 3 and type 4, respectively, were
heterologously expressed in Escherichia coli as carboxy-terminal extensions of glutathione-S-
transferase (GST). The tolerance of E. coli cells expressing GST–OsMTI-1b, GST-OsMTI-2b
and GST-OsMTI-3a considerably increased to Ni2+, Cd2+ and Zn2+ through the accumulation of
more metal ions compared with cells expressing GST alone. However, the tolerance of cells
expressing GST-OsMTII-1a protein increased slightly only to Ni2+. The recombinant MTs were
extracted from E. coli cells and purified using affinity chromatography. The apo forms of these
MTs were provided by acidification and then were exposed to Cd2+ , Ni2+ and Zn2+. The UV
absorption spectra and competitive reactions of in vitro Cd2+/Ni2+-incubated proteins with 5-5_-
dithiobis(2-nitrobenzoic) acid revealed that GST–OsMTI-1b, GST-OsMTI-2b and GST-OsMTI-
3a are able to form Cd/Ni/Zn-thiolate clusters. However these different rice MT isoforms has
different ability in binding to different metals. The recombinant form of GST-OsMTII-1a was
not able to bind metals. In addition none of new strains were not able to bind Cu2+.
Keywords: Metallothionein, Rice, Metal-binding characterization.
HTTP://UI.CNF.IR/PPS 37
Assessment of antibacterial and antioxidant activity of silver
nanoparticles produced by reduced glycated casein adducts
Zohreh Tavaf1,3, Mohammad Tabatabaei1, Farhad Panahi2, Tanaz Sadeghian3, Ali Khalafi-Nezhad2
1Department of Pathobiology, Schools of Veterinary Medicine, Shiraz University, Shiraz, Iran.
2Department of Chemistry, Shiraz University, Shiraz, Iran.
3Protein Chemistry Laboratory (PCL), Department of Biology, Shiraz University, Shiraz, Iran.
Abstract
The inappropriate antibiotic prescribing and use have been identified as major factors in the
emergence of antibiotic resistance. The cariogenic bacterium Streptococcus mutans (S.mutans) is
the major cause of dental caries worldwide. Due to their effective antibacterial and antiviral
properties and lower propensity to develop resistance, silver nanoparticles (AgNPs) have
recently gained much attention. In the current study, we report an economically green route for
the synthesis of biocompatible AgNPs, employing reduced glycated adducts of whole casein
fraction (gWCF) from bovine milk as the reducing/capping agents. We applied different
spectroscopic techniques and microscopic assessment for characterization of AgNPs. moreover,
the antimicrobial properties of AgNPs against S. mutans were evaluated, using zone of inhibition
method. According to the results of our study, gWCF demonstrates significant ability for the
efficient synthesis of stable AgNPs which indicated reasonable size ranges. Additionally, the
AgNPs produced in the presence of gWCF exhibited promising antibacterial properties against
cariogenic bacterium S.mutans. Overall, this study recommends the application of reduced
glycated casein adducts (gWCF) as a novel and important source of biomaterials for the
economic and efficient production of relatively stable AgNPs with reasonable antibacterial
properties against cariogenic bacteria S. mutans.
Keywords: Silver nanoparticles (AgNPs), Antimicrobial properties, Streptococcus mutans,
Whole casein fraction (WCF), Glycation.
HTTP://UI.CNF.IR/PPS 38
QM/MM spectroscopic investigation of the structure of the light-
driven enzyme protochlorophyllide oxidoreductase (LPOR)
Samira Gholami1, AbdolKhalegh Bordbar1 , Marco Garavelli2, Ivan Ravilta2, Artur Nenove3, Mehdi
Davari4, Marco Bocola4, Ulrich Schwaneberg5
1 Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
2 Laboratoire de Chimie, Ens de Lyon, Site Jacques Monod - 46 allée d'Italie, 69364 Lyon cedex 07, France.
3 Dipartimento di chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy. 4 Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany.
5 DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany.
Abstract
POR, catalyzes one of the latter steps in the chlorophyll biosynthesis pathway, the trans addition
of hydrogen from NADPH (as cofactor) across the C17–C18 double bond of the D-ring of
Pchlide (protochlorophyllide) to produce Chlide (chlorophyllide). Regarding to the lack of the
crystal structure of LPOR a full identification of the reaction pathway at room temperature, the
identification of the initial intermediate state(s) involved, and the nature of structural changes
that lie at the origin of the activation process, still is unclear in this enzyme. In this paper, we
first present a refined homology model of the ternary POR enzyme of T.elongatus based on the
previous ssPOR model. In this model, missing parts and the orientation of the active site residues
was refined and the binding mode of the substrate and cofactor was corrected. Molecular
dynamics simulations suggested that coordination number of central magnesium is 6 in both free
and bound Pchlide, as previously also proposed in FLN spectra. QM/MM spectroscopic
investigations revealed that there is no any characteristics shift in the first band of the absorption
spectra (Qy) from solvent to protein, and the Qy is not influenced by the environment and the
magnesium coordination number, therefore linear absorption cannot undoubtedly be used to
justify the reported experimental shift in Qy solvent to protein. However, computational transient
IR spectra of the enzyme-substrate complex was in agreement with the experimental one which
led to re-assigning of the important peaks involved in the catalytic reaction and validating the
accuracy of our model.
Keywords: Light-driven protochlorophyllide oxidoreductase (LPOR), Protochlorophyllide,
homology modeling, QM/MM calculations, Computational spectroscopy.
HTTP://UI.CNF.IR/PPS 39
Computer-aided design of new Typrostatin-A derivatives as
simultaneous effective inhibitors of αβ-tubulin and breast cancer
resistance protein
Najmeh Fani, Abdol- Khalegh Bordbar, Elham Sattarinezhad
Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Abstract1
In the first part of this paper, docking method was employed in order to study the
structure−activity relationships (SAR) for a group of previously synthesized and designed
Tryprostatin-A (TPS-A) derivatives (which considered in our previous study as potent inhibitors
of αβ-tubulin) in the binding site of breast cancer resistance proteins (BCRP). The results
represent that these compounds bind to the binding site of BCRP with relatively suitable binding
energies and therefore could be potential inhibitors of both αβ-tubulin and BCRP proteins. In the
second part, virtual molecular docking method was utilized with the aim of design novel
analogues of TPS-A with significant inhibitory effect on both αβ-tubulin and BCRP proteins. For
this purpose binding energies and binding poses of a library of TPS-A derivatives in the binding
sites of αβ- tubulin and BCRP have been investigated using molecular docking calculations.
Molecular docking results revealed that a group of 37 compounds among them exhibit strong
anti-tubulin and anti-BCRP activity.
Keywords: Tryprostatin-A, Breast cancer resistance Protein, αβ-tubulin, Molecular docking,
Structure−activity relationships.
HTTP://UI.CNF.IR/PPS 40
Evaluation of the kappa carrageenan-chitosan nano magnetics
efficiency on purification of P. indica pectinase
Parisa Fathi Rezaei1, Shahab Ghanbari1, Saleh Shahaabivand1, Gholamreza Mahdavinia2
1Department of Biology, Faculty of Science, University of Maragheh, Maragheh, Iran.
2Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh, Iran.
Abstract
Pectinases are one of the most important industrial enzymes and hydrolyze pectin to galacturonic
acid. Pectin is one of the main polysaccharides in plant cell wall. Pectinases have a large number
of applications in food industries and biomass conversion. Various methods are used for
pectinase purification from microbial sources including precipitation and chromatography.
Nowadays many studies focused on purification and immobilization of enzymes on magnetic
beads. In this investigation purification of Piriformospora indica pectinase on kappa
carrageenan-chitosan nano magnetics was investigated. P. indica was cultured on YPG medium
supplemented with pectin. The slurry was filtered by centrifugation at 10,000 rpm at 4 ºC for 15
min. Later the supernatant was incubated with kappa carrageenan-chitosan nano magnetics at 4
ºC overnight with continues shaking. The enzyme was desorbed from nano magnetics by
phosphate buffer. The protein content of samples was determined by Bradford assay. Based on
the results, the protein content of the solutions treated with kappa carrageenan-chitosan nano
magnetics was elevated significantly in comparison to untreated solutions. In conclusion, kappa
carrageenan-chitosan nano magnetics could open new insights for purification of pectinase and
the optimization of its immobilization on magnetic beads is running in our group.
Keywords: P. indica, Pectinase, Pectin, Carrageenan-chitosan, Nano magnetics.
HTTP://UI.CNF.IR/PPS 41
Nerve growth factor precursor and its role in alzheimer’s disease
Raheleh Masoudi
Shiraz University, Biology Department, Shiraz, Iran.
Abstract
Nerve growth factor (NGF) is one of the key factors in neuronal survival and function. In
Alzheimer’s disease (AD), there is increase in the level of NGF precursor, proNGF.
Interestingly, no change in the level of NGF mRNA has been detected. There is controversy
regarding the biological activity of proNGF. While some researches show the neurotrophic
activity of this protein, others believe that this protein is apoptotic. NGF binds to TrkA receptor
with high affinity while proNGF has more affinity for p75NTR receptor which could lead to
neuronal death. We have already shown that the ratio of TrkA to p75NTR may determine the
apoptotic or neurotrophic activity of proNGF. In this review, we focus on the role of this
precursor in Alzheimer disease considering that the level of its receptors alter in AD. Moreover,
its relation with amyloid beta and tau will be discussed.
Keywords: Alzheimer’s disease, Pro nerve growth factor, Apoptotic, Neurotrophic.
HTTP://UI.CNF.IR/PPS 42
Conformational studies of Human hemoglobin and insulin upon
interaction with MTBE
Parvaneh Maghami1, 3 , Masoumeh Valipour1,4, Mostafa Sadeghpour5, Mohamad Ali Khademian6,
Khadijeh Mosavi6 , Ali Akbar Moosavi-Movahedi1,2
1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
2Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.
3Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
4Department of Cellular and Molecular biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz,
Iran.
5Office of Health, Safety and Environment (HSE) Oil Ministry, Tehran, Iran.
6Office of Health, Safety and Environment (HSE) Oil Ministry, Bandar Mahshahr, Iran.
Abstract
Methyl tertiary butyl ether (MTBE) is the most widely used motor vehicle fuel oxygenate since it
reduces harmful emissions due to gasoline combustion. The emission of MTBE into the
environment occurs mainly during the production, distribution, storage, and use of gasoline.
There is evidence that MTBE is a toxic substance in higher dose that may have adverse effects
on both animals and humans. Due to MTBE is well absorbed after inhalation, oral, or dermal
exposure it is necessary to clear the molecular mechanism of it. Hemoglobin (Hb) and insulin are
most functional proteins in blood and play critical role in oxygen transport and regulation of
glucose in body respectively. The aim of this study was to analyze and compare structural
changes of Hb and insulin in the presence of different concentrations of MTBE. Our result shows
that different structural changes in hemoglobin and insulin in the presence of MTBE by
spectroscopic methods. According to fluorescence and circular dichroism spectroscopy, insulin
formed a molten globule (MG)-like structure in the presence of MTBE under physiological pH
while heme degradation was observed in hemoglobin structure. To delineate the mechanisms
involved in MTBE-protein interactions, the formation of reactive oxygen specious (ROS) was
measured by chemiluminesence technique. As a result, the interaction of MTBE with cited
proteins which possess different conformational states in order to carry their biological functions
would be different.
Keywords: Methyl tertiary butyl ether, Molten-globule, ROS, Insulin, Heamoglubin.
HTTP://UI.CNF.IR/PPS 43
Molecular dynamics simulations of surfactant peptides wrapping
single-walled carbon nanotubes
Karim Mahnam2 , Alireza Mansouri2,3 , Abolfazl Barzegar2
1 Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran.
2Department of Biophysics, Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran.
3Department of Young Elites scientific Site, Iran.
Abstract
The non-covalent interaction of single-walled carbon nanotube (SWCNT) with surfactant
peptides makes them soluble in biological media for application in nanomedicine, drug delivery
and gene therapy. In this study, ten surfactant peptides with the length of 8 residues were
designed using Lys, Trp, Tyr, Phe and Val amino acid residues. 300 ns MD simulation was
performed for free surfactant peptides in water and surfactant peptides near to a (6 6) carbon
nanotube. Our results indicate that the binding affinity of peptides to SWCNT increase with the
increase aromatic residue content. Among of aromatic residues, the peptides containing Trp
residues have higher binding affinity to SWCNT than the peptides with Phe or Tyr residue. The
results of binding affinity showed aromaticity parameter is more important than the
hydrophobicity in binding peptides to SWCNT. In addition, steric hindrance between aromatic
residues and the distance between them is important for binding free energy of peptides to
SWCNT.
Keywords: Single-walled carbon nanotubes, Surfactant Peptide, Molecular dynamics simulation,
Binding free energy.
HTTP://UI.CNF.IR/PPS 44
N-methyl phenylalanine-rich peptides as potential blood -brain
barrier shuttles
Morteza Malakoutikhah1, † Meritxell Teixidó, Ernest Giralt2
Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10, E-08028
Barcelona, Spain.
Abstract
The blood-brain barrier (BBB) protects the brain from harmful substances in circulating blood
and regulates the entry of particular molecules from blood into the central nervous system
(CNS). This physical and enzymatic barrier is the major bottleneck for the delivery of
therapeutic agents to the brain. The BBB is formed by endothelial cells that are sealed through
tight junctions, which significantly block paracellular transport. To bypass the BBB and deliver
drugs to the brain, several strategies have been used: temporarily opening the BBB,
administration of very high doses of a drug, and direct injection of a drug into the spinal cord.
However, these approaches imply risks of infection and toxicity and, in addition, require
qualified personnel.1, 2 here several peptide families containing N-methylated amino acids were
designed and synthesized using solid phase peptide synthesis (SPPS). The permeability and
lipophilicity of these compounds were studied by parallel artificial membrane permeability assay
(PAMPA) and immobilized artificial membrane chromatography (IAMC) to select the best
peptides in terms of length, terminal groups, and amino acid replacement to be used as carriers
that pass through a model of the blood-brain barrier (BBB) by passive diffusion. Furthermore,
the enzymatic stability of these peptides in human serum and their cell viability by MTT assay
were tested. These peptide families showed great stability and nontoxicity. The three peptides
that showed the greatest permeability were coupled to levodopa, GABA, Nip, and ALA to
examine their passive BBB permeation by means of PAMPA and their lipophilicity by IAMC.
Unaided, these nonpermeating drugs alone did not cross the PAMPA barrier and the BBB
passively; however, the peptides tested as potential BBB shuttles transferred them by passive
transfer through the PAMPA phospholipid. The permeability of peptides that showed the highest
permeability in PAMPA was also examined in bovine brain microvessel endothelial cells
(BBMECs).3,4 These peptide-based BBB shuttles can open up the possibility to overcome the
formidable obstacle of the BBB, thereby achieving drug delivery to the brain.
Keywords: Blood-brain barrier, N-methyl phenylalanine, Parallel artificial membrane
permeability assay (PAMPA), Immobilized artificial membrane chromatography (IAMC).
HTTP://UI.CNF.IR/PPS 45
Free radical scavenging and denaturation-inhibiting effects of
peptides from fish skin in vitro and in food model system
Mehdi Nikoo1
1Department of Fisheries, Faculty of Natural Resources, Urmia University, Urmia, West Azerbaijan 5756151818,
Iran.
Abstract
From the skin of fish the peptide with amino acid sequence of proline-alanine-glycine-tyrosine
and molecular weight of ~406 Da was isolated from using RP-HPLC and antioxidant activity and
cryoprotective effect of the peptide and skin gelatin hydrolysates in vitro and in fish mince
model system was investigated. Peptide showed scavenging activity against free radicals (DPPH,
ABTS and hydroxyl). Addition of peptide into model system lowered the peroxide and
thiobarbituric acid-reactive substances when compared to the control, most probably due to their
free radical scavenging potency. Based on low-field proton nuclear magnetic resonance analysis,
peptides in hydrolysates prevented the displacement of water molecules between the different
muscles compartments, thus stabilizing the water associated with myofibrils (as reflected by T21)
induced by freeze–thawing. Peptides were able to retard protein oxidation as indicated by the
retarded protein carbonyl formation and lower loss in sulfhydryl content. As determined by
differential scanning calorimetry, at freeze-thaw cycle 0, enthalpy (ΔH) of myosin ranged from
1.49 to 1.84 mJ mg-1 and control mince had significantly lower ΔH than those with added 25 and
50 ppm of peptide. After 6 freeze-thaw cycles, ΔH of myosin in minces with added peptide was
higher than that of the control. Enthalpy of the second peak (actin) at freeze-thaw cycle 0 ranged
from 0.29 to 0.46 mJ mg-1 and higher ΔH was found for minces with added 25 ppm peptide.
Furthermore, when gelatin hydrolysates were added, higher transition temperature (Tmax) of
myosin and higher enthalpy of myosin and actin was observed.
Keywords: Free radicals, Peptides, Fish skin protein, Denaturation-inhibiting effect, Food model
system.
HTTP://UI.CNF.IR/PPS 46
Antibacterial evaluation of Bis (2-methyl-1H-imidazole-κN3) silver
(I) dichromate (VI) by autodock vina function
Faeze Hashemi*1, Azizolla Beheshti1, Hossein Motamedi2
1Department of Chemistry, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran. 2Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran.
Abstract
A novel silver complex [Ag(C4H6N2)2]2Cr2O7(1) has been synthesized and fully characterized by
single crystal X-ray diffraction ,UV–Vis, elemental analysis and FT-IR techniques. The
antibacterial tests of free 2-methylimidazole ligand, Ag2[CrO4] and its complex 1 were studied
by using molecular docking technology and antibacterial test in vitro. The 3 three-dimensional
(3D) structures of the 5 compared compositions an 2-methylimidazole ligand and
[Ag(C4H6N2)2]2Cr2O7 were established by Autodock vina function The antibacterial activity
studies of the free 2-methylimidazole ligand, Ag2[CrO4] and its complex 1 show that, the ability
of these compounds to inhibit growth of the tested bacteria. Molecular-docking investigations
between the five standard antibiotic, free 2-methylimidazole ligand, complex 1 and fragment of
bacterial DNA and five biological macromolecule enzymes (receptors) were carried out. The
results of docking studies confirm that the antibacterial activities of these compounds.
Keywords: Molecular-docking, scoring function, Antibiotic experiment in vitro, Bacterial DNA.
HTTP://UI.CNF.IR/PPS 47
Looking for a generic inhibitor of amyloid-like fibril formation
among tri hetero cyclicsmall molecules
Hassan Ramshini and Najmeh Annabestani
Biology Department, Payam Noor University, 19395-4697 Tehran, I.R. of Iran.
Abstract
A range of diseases is associated with amyloid fibril formation. Despite different proteins being
responsible for each disease, all of them share similar features including beta-sheet-rich
secondary structure and fibril-like protein aggregates. A number of proteins can form amyloid-
like fibrils in vitro, resembling structural features of disease-related amyloids. Given these
generic structural properties of amyloid and amyloid-like fibrils, generic inhibitors of fibril
formation would be of interest for treatment of amyloid diseases. Several natural and synthetic
flavone derivatives have been reported to inhibit formation of amyloid fibrils or to remodel
existing fibrils. These studies suggest that heterocyclic aromatic small molecules are effective as
amyloid inhibitors. At the present study, we have evaluated 7Tri Aryl Benzene derivatives to
reduce amyloid fibril formation by hen egg white lysozyme (HEWL) and its associated
cytotoxicity. The inhibitory effect of the compounds was investigated against hen egg white
lysozyme (HEWL) fibrillation. The molecules were tested using ThT, AFM and MTT assay. We
found all 7 compounds able to inhibit HEWL aggregation in a dose-dependent manner. Our
study showed that these compounds also inhibit the cytotoxic activity of aggregated HEWL
toward cell culture. In conclusion, we found the core structure of the compounds plays the
primary inhibitory role and the side chain groups of the compounds modulate their effects.
Keywords: Lysozyme, Amyloid aggregation, Tri ArylBenzene, Cytotoxicity.
HTTP://UI.CNF.IR/PPS 48
The crucial role of a Ω–loop the stability and activity of the Exo–
inulinase
Maryam Rezaei Arjomand1, Mehran Habibi–Rezaei1, 2, Gholamreza Ahmadian3
1School of Biology, College of Science, University of Tehran, Tehran, Iran. 2Nano–Biomedicine Center of Excellence, Nanoscience and Nanotechnology Research Center, University of
Tehran, Tehran, Iran. 3Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and
Biotechnology, Tehran, Iran.
Abstract
Inulinases are considered in the food and medical industries. They especially have industrial
potential for production of high–fructose syrup (HFS), inulooligosaccharides, and bioethanol.
Inulinases are members of family 32 (GH32), (CAZy) (http://www.cazy.org/) and are divided
into endo– and exo–inulinases. Endo–inulinases (EC 3.2.1.7) hydrolyse internal (2→1) β–D–
fructosidic linkages in inulin and produce inulooligosaccharides while exo–inulinases (EC
3.2.1.80) hydrolyse (2→1) β–D–fructofuranose linkages from the non–reducing end of the inulin
to release D–fructose and a D–glucose. Here, we report the deletion of a juxta active site loop
fragment (74YGSDVT79 sequence) from third Ω–loop of the exo–inulinase (PDB ID: 1Y4W) from
Aspergillus niger to study its structural and functional importance. To investigate the flexibility
of this region, molecular dynamics simulations for 80 ns were performed in two parts of the
native and mutant (Δ6SL) enzymes. MD simulation data were shown that deleted region has a
role in increasing the rigidity of the enzyme. Moreover, molecular docking was performed to
compare the interactions in the active sites of native and Δ6SL enzymes with fructose. The
functional thermostability, kinetic parameters and activation energy (Ea) of the catalysis of both
enzymes indicate on the importance of the deleted sequence on the catalytic performance of the
enzyme. In conclusion, juxta active site loop fragment not only plays an important role in the
stability of the enzyme, it involves in the enzyme catalysis through lowering the activation
energy of the catalysis and effective improving the catalytic performance.
Kewword: inulinase, molecular dynamic, enzyme catalysis.
HTTP://UI.CNF.IR/PPS 49
Different strategies for designing protein inhibitors, agonists and
super-agonists
Sayyed Hamid Zarkesh Esfahani1, Zeinab Monajjemi Rarani2
1Sayyed Hamid Zarkesh Esfahani, PhD, Immunology, Department of Biology, Faculty of Sciences, University of
Isfahan, Isfahan, Iran.
1Zeinab Monajjemi Rarani, MSc student, Microbiology, Department of Biology, Faculty of Sciences, University of
Isfahan, Isfahan, Iran.
Abstract
Proteins do not function in isolation; it is their interactions with one another and also with other
molecules (e.g. DNA, RNA) that mediate metabolic and signaling pathways, cellular processes,
and organismal systems. Protein–protein interactions are central to most biological processes.
Many human diseases can be traced to aberrant protein–protein interactions, either through the loss
of an essential interaction or through the formation of a protein complex at an inappropriate time
or location. The inhibition of these aberrant associations is of obvious clinical significance. In
some cases, the nonfunctional proteins due to mutations may cause diseases in human. Growth
hormone deficiency in children that leads to dwarfism is an example of such diseases that can be
successfully cured using recombinant human growth hormone.
A range of approaches are being developed to generate inhibitors, agonists and super-agonists of
protein–protein interactions that may form useful therapeutics for human disease. These
therapeutic proteins proved to be very efficient and have improved the management of many
diseases that were incurable for centuries. Protein agonists and antagonists have raised the hope for
treatment of many other diseases and are one of the biggest market in pharmaceutical industries.
Multiple approaches have been developed to prevent or mimic the effects of proteins including:
recombinant protein production, anti-receptor antibodies, soluble receptors, mutant proteins,
siRNAs, small molecule inhibitors, etc.
Keywords: protein, agonist, antagonist, super-agonist
HTTP://UI.CNF.IR/PPS 50
rh-IGF-1 (mecasermin): expression, purification and formulation
Mohammad Reza Mofid
Department of Biochemistry, School of Pharmacy and Bioinformatics Research Center, Isfahan University of
medical sciences, Isfahan, Iran.
Abstract
Insulin-like growth factor-1 (IGF-1) is a single chain polypeptide made up of 70 amino acids
with three helix and three disulfide bonds. IGF-1 is mainly secreted by the liver as a result of
stimulation by growth hormone (GH). More than 99% of IGF-1 in blood is in complex with IGF
binding proteins (IGFBPs). IGFBP-3 is the major IGF binding moiety in plasma. Mecasermin
(rh-IGF-1 with point mutation T4I) is a pharmaceutically noticed recombinant protein.
Mecasermin has a 20 times longer half-life than IGF-1 in plasma. The object of present research
is over- production of Mecasermin by employing effective factors in order to achieve more
native protein and reduce extensive losses of product during purification.
After production of Mecasermin in E. coli, purification of the protein was performed by
extraction of Inclusion body, solubilization in 6M Gdn-HCl, refolding, purification by gel
filtration column and further formulation of them. The analyses of mecasermin were
accomplished by SDS-PAGE, Western-blot, ESI-MS, ELISA of IGF-1, Endotoxin assay, SEC
chromatography and biological assay.
Here we set up an over- production method with novel and efficient downstream purification to
achieve both high quantity and quality of mecasermin.
Keyword: Mecasermin, Purification, SEC chromatography, Recombinant protein.
HTTP://UI.CNF.IR/PPS 51
Functionalized superparamagnetic nanocarriers in enzyme
engineering: Highly dispersive, stable and robust biocatalysts
Asghar Taheri-Kafrani, Asieh Soozanipour and Maryam Royvaran
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan,
Isfahan, 81746-73441, Iran.
Abstract
Immobilized enzymes are used as biocatalysts for analytical purposes in diagnostics and for
preparative purposes in large scale industrial processes. Immobilization can increase the half-life,
improve the stability, and increase the catalytic activity of an enzyme. It facilitates the separation
and recovery of the catalyst from the reaction products, and allows for multiple use of the
biocatalysts. Herein, we demonstrated synthesis of silica-coated modified magnetite
nanoparticles via cyanuric chloride activation, magnetic nanoparticles supported hyperbranched
polyglycerol (MNP/HPG) and graphene oxide nanosheets decorated with superparamagnetic iron
oxid nanoparticles (SPGO) as convenient nano platforms for immobilization of enzymes. Then,
an important industrial enzyme, xylanase, was immobilized on the nanocarriers to produce robust
biocatalysts. A variety of analytical tools was used to study the morphological, structural and
chemical properties of the biocatalysts. Additionally, the results of biocatalyst systems exhibited
the substantial improvement of reactivity, reusability and stability of xylanase due to this
strategy, which might confer them a wider range of applications.
Keywords: Functionalized magnetite nanoparticles, Immobilization, Xylanase, Enzyme activity.
HTTP://UI.CNF.IR/PPS 52
Lens antioxidant defense mechanism plays an essential role against
oxidative stress induced structural damages of crystallin proteins
Reza Yousefi
Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
Abstract
α, β, and γ-crystallins are present at extremely high concentration (>300 mg/ml), accounting for
more than 90% of the total soluble proteins in the lenticular tissues. Due to their remarkable
longevity, lens crystallins accumulate a substantial amount of post-synthetic modifications on their
structures which ultimately culminate in development of cataract disorders. The generation of
reactive oxygen species in the lenticular tissues occurs from a variety of sources which may
subsequently induce protein structural damages, accelerates the rate of ascorbic acid oxidation and
catalyzes non-enzymatic glycation of lens crystallins. Using different spectroscopic methods, gel
mobility shift assay, and lens culture assessment, we indicated important capacity of antioxidant
defense mechanism of eye lens against various structural and functional damages of lens
crystallins which induced under oxidative sates. We believe that under normal conditions lens
antioxidant defense mechanism effectively prevent these structural and functional insults. However
mass production of oxidative agents in the lenticular tissues, under a variety of conditions such as
diabetes, aging, senile cataract, infection and exposure to sunlight may overcome the capacity of
the antioxidant defense mechanism leading to lens opacification.
Keywords: Lens crystallins, Oxidative stress, Antioxidant, Structural damages, Dehydroascorbate.
HTTP://UI.CNF.IR/PPS 53
Memory prison of protein
Gholamhossein Riazi1, Shahryar Pooyan, Nima Allahyari
Neuroorganic Lab, Department of Biochemistry, Institute of Biochemistry and Biophysics (I.B.B),
University of Tehran, Tehran, Iran.
Abstract
The mechanism of information custody in biological specious in perhaps the most
complex subject among life’s processes to study such mechanism has been tested since
several centuries ago. Based on fractal theory, the human memory of mimics small
molecules such of proteins, complex globular structure of proteins in protect candidate for
keeping information so called memory. Primary sequence and geometry of third and
fourth structure would be involved in memory of biological organisms. Naturally more
complexity drives the protein to more ability for prisoning information inside.
Microtubules proteins which in a polymer of thousands of tubulin monomer, with
hydrophobic pocket changing hydrophobic pocket structure has been shown to the very
stable while microtubule protein, as to as vesicle transporter at the time.
Keywords: Memory, Microtubules, Complexity, Fractal theory.
HTTP://UI.CNF.IR/PPS 54
Isolation of α glucosidase inhibitor producers, Bacillus sp. RP073
and virgibacillus sp. RP072 from Persian Gulf.
Roya pournejati, Samira Rezaei, Hamid Reza Karbalaei-Heidari
Molecular Biotechnology Laboratory, Department of Biology, Faculty of Science, Shiraz University, Shiraz 71454,
Iran.
Abstract
Diabetes mellitus is an advanced metabolic disorder which shows increase of blood glucose level
followed by serious damages in several organs such as kidney, nerves and retina. Alpha-
glucosidase is a key enzyme which produces by epithelial cells of duodenum and helps to digest
of foods by hydrolyzes of starch and disaccharides. Inhibitors of this enzyme have suitable
potential for using indiabetes mellitus type 2 treatment as a drug. These compounds can delay the
absorption of carbohydrates through the intestine and consequently reduces the blood sugar and
insulin level immediately after feeding. Secondary metabolites are organic molecules that are not
involved in the normal growth and development of an organism, but have great importance for
human health due to their bioactive properties such as antibacterial, antitumor, anti-
inflammatory, immunosuppressant, and etc. In the present investigation, 39 bacterial marine
isolates from coastal area of Persian Gulf were selected and screened for production of secondary
metabolites with the ability to inhibit rat α-glucosidase. The results showed that the two isolates
which were characterized by 16S rDNA sequencing as Bacillus sp. strain RP073 and
Virgibacillussp. strain RP072 capable of producing secondary metabolites in TSB medium
during incubation at 30 oC after 5 days which have inhibitory effects on rat alpha-glucosidase.
Methanolic extract of the isolates biomass show 88% and 66% inhibition on the enzyme activity,
respectively.
Keywords: Alpha glucosidase inhibitors, Secondary metabolite, Bacillus, Persian gulf.
HTTP://UI.CNF.IR/PPS 55
Potential application of β-lactoglobulin for presence in nano scale
oral drug delivery systems
Behafarid Ghalandari1, 2, Adeleh Divsalar3, Ali Akbar Saboury4, 5
1Department of Medical Nanotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
2Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran.
3Department of Cell & Molecular Biology‚ Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
4Institute of Biochemistry and Biophysics‚ University of Tehran, Tehran, Iran.
5Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.
Abstract
The possibility of biopolymers presence in nano scale oral drug delivery system is one of the
most interest topics in nanobiotechnology. β-lactoglobulin (β-LG) as a globular milk whey
carrier protein can be candidate for this aim due to its unique structure and physicochemical
properties. In this study, we investigated the design and production of β-LG nanoparticles as
nanocarrier for anticancer metal based drugs. First, β-LG interaction with oxalipalladium was
examined using fluorescence spectroscopy. Results showed that drug was bind to β-LG with
molar ratio of 1:1 by driving force of hydrophobic and predominant contribution of static
quenching mechanism. Then, β-LG nanoparticles were prepared and characterized using
dynamic light scattering (DLS) and scanning electron microscopy (SEM) and equilibrium
dialysis methods. The results show that the lowest size of nanoparticles were formed close to
isoelectric point of β-LG in the presence of low methoxyl pectin (LMP) with colloidal stability
and spherical shape. On the other hand, the equilibrium dialysis results show that the rate of drug
release in the simulated gastrointestinal tract from β-LG nanoparticles in the presence of LMP is
very low so that it can be concluded β-LG nanoparticles are resistant to acidic medium. In
addition, the highest rate of in vitro drug release is occur in the simulated terminal ileum fluid
and simulated colon fluid during simulated release time. Consequently, based on our findings β-
LG is potential biopolymer and promising candidate for presence in nano scale oral drug delivery
system.
Keywords: β -LG, Oral drug delivery, Nanoparticle, Fluorescence spectroscopy, Release.
HTTP://UI.CNF.IR/PPS 56
Poster Presentation Abstracts:
Optimal isolation and purification of lens α-Crystalline protein
Shohreh Yazdani1,2, Reza Khodarahmi1, Khosrow Khajeh2
1Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
2Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Abstract
Alpha Crystalline as measure of structural protein of eye lens contains two subunits αA and αB
Crystalline. Due to its chaperon-like activity, this protein plays a preventive role in a number of
disorders such as neurodegenerative disease and cataract. For research studies, it is necessary to
develop simple and efficient strategy for isolation of the target protein of interest. Here we
designed an appropriate procedure that yields a proportion of purified α-Crystalline through a
combination of extraction of crude protein from bovine eye lenses followed by several steps of
centrifugation and sequential dialysis by the same buffer at different molarities. The efficacy of
the purification step was evaluated using electrophoretic resolution at each stage and non-
specific peroxidase activity.
Keywords: α-Crystalline, Isolation, Purification.
HTTP://UI.CNF.IR/PPS 57
Molecular dynamics simulation of new cyclotide from viola tricolor
Rayeheh Vafaee and Mahboobeh Zarrabi
Biotechnology Department, Biological Sciences Faculty, Alzahra University, Tehran, Iran.
Abstract A current trend in pharmaceutical industry is to produce medications by using peptide. They tend
to develop stable drugs with new functionality as an oral administration. Accordingly, with
respect to their properties, cyclotides are the best choice. The cyclotides are antimicrobial
circular peptides that have a variety of biological activities such as anti-HIV, anti-tumor,
cytotoxic, hemolytic activity and etc. They keep their functionality in the presence of
denaturation circumstances as proteolysis, GndHC16M and such like. On the other hand, a new
cyclotide is obtained from a local species of Viola Tricolor in the north part of Iran. They
motivate us to study the stability of this kind of cyclotide in the water solvent via considering
different parameters including potential energy, RMSD, Gyradius and solvent accessible surface.
In the beginning, the cyclotide tertiary structure model has been built by Modeller software.
Hence, we run several simulations based on Molecular Dynamics by means of GROMACS
software. Corresponding results are presented and discussed in detail in this paper.
Keywords: Cyclotide, Molecular dynamics, Antimicrobial, Gromacs, Modeller.
HTTP://UI.CNF.IR/PPS 58
The impact of vitamin C on amyloid structure of treated bovine
serum albumin with potassium sorbate
Elham Vahdatahar, Fereshteh Taghavi, Ali Akbar Moosavi-Movahedi
Institute of Biochemistry and Biophysics (IBB), the University of Tehran, Tehran, Iran.
Abstract
Vitamin C (ascorbate) is a powerful antioxidant that through scavengering reactive oxygen and
nitrogen species performs its antioxidant activities. Evidence is suggested that vitamin C can
interact with radicals and oxidant substances and by this way the reaction of these substances
with protein and other soluble components is prevented strongly. The potassium sorbate is a food
preservative and previous researches refer to its role in protein structural changes through
creation of glycotoxins(Maillard products and reactive radicals).The formation of amyloid
structures is initial result of these structural changes which lead to amyloid aggregate and
amyloid -like fibril. In order to investigate the effect of vitamin C on amyloid structural changes
in treated bovine serum albumin with potassium sorbate, ThT and circular dichroism techniques
were used. Incubation of protein with potassium sorbate at 55 ° C caused distinc changes in the
secondary structure of protein and creation of amyloid structure which were in associasion with
ThT intensity increament. But the presence of vitamin C in the studied time interval (24,72,120
hours) considerably reduced the intensity of ThT. This result can be considered as the deterrent
effect of vitamin C on formation of amyloid structure of bovine serum albumin and importance
of this vitamin for designing of anti-amyloid drugs.
Keywords: Bovine serum albumin, Potassium sorbate, Vitamin C, Amyloid aggregates, Amyloid
-like fibril.
HTTP://UI.CNF.IR/PPS 59
Structural intermediates of bovine serum albumin upon treatment
with potassium sorbate
Elham Vahdatahar, Fereshteh Taghavi, Ali Akbar Moosavi-Movahedi
Institute of Biochemistry and Biophysics (IBB), the University of Tehran, Tehran, Iran.
Abstract: Today with the growing population, the need for food preservative is highly felt. Potassium
sorbate is a food preservative which is vastly used in the production of Dairy products, baked
foods, juices, frozen fruit, bread, cakes, food products, including fish, processed vegetables,
spices, jams, vegetables and gelatin products, fast food, and drinks. The toxicity of this substance
on the cells was confirmed by previous experiments. The aim of present study is to investigate
structural changes of bovine serum albumin (BSA) due to use of potassium sorbate. To evaluate
structural changes of BSA, intrinsic fluorescence and to investigate the changes in
hydrophobicity, ANS assay have been used. The results of intrinsic fluorescent study showed
reduction in intensity according to treatment of BSA with Potassium sorbate. It is worth
mentioning that the results of ANS study represents increase of intensity according to increase in
hydrophobic patches in protein surface, partially unfolding and creation of intermediate structure
of protein. Then in the next step decrease of intensity at wavelength 390nm, represents reduction
of available hydrophobic patches as a result of creation of intermediates and after that protein
aggregation to achieve greater stability. It is obvious that, understanding of protein intermediate
formation and restructure process can play a crucial role in designing of inhibitory mechanisms
for these structures.
Keywords: Bovine serum albumin, Potassium sorbate, Intermediate structure, Hydrophobic
patches.
HTTP://UI.CNF.IR/PPS 60
Survivin gene cloning in bacterial host DH5α
Rashid Hooshdarpoor1, Maryam Moradi1, Mohsen Alipoor2, Farangis Ataei 1*, Saman Hosseinkhani1
1 Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
2 Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
Abstract
Survivin (BIRC5), is the smallest family member of the family of inhibitors of apoptosis proteins
(IAPs). Survivin is a 142-amino acid, 16.5 kDa protein encoded by a single gene located on the
human 17q25 chromosome. Survivin is a multifunctional protein that inhibits apoptosis,
regulates cell division and enhances angiogenesis. Survivin is preferentially and highly expressed
in cancer cells, with low expression in the most normal non-dividing adult tissues. The integral
role of survivin in cancer cell, division and survival makes it an attractive therapeutic target to
inhibit cancer cell growth and drug screening. In this study, wild type of survivin gene was
cloned in pDB2 eukaryotic vector for future investigation. In order to molecular cloning of
survivin gene, total RNA was extracted from breast cancer cells, MCF-7, and then survivin
cDNA was synthesized by reverse transcriptional (RT)-PCR. Thereafter, survivin gene was
amplified by PCR with PrimeSTAR®HS Taq DNA Polymerase (Takara). Then PCR product
and pDB2 vector were restricted by Hind III and Nhe I at 37 °C for 8 h and ligated at 22 °C for 4
h and then 4 °C overnight. The ligation mixture was transformed into E.coli DH5α and screened
by antibiotic (50 μg/ml ampicillin) selection. Plasmid DNA was isolated from positive colonies
(selected by colony PCR) and sequenced (Macrogen, Korea) to check inserted DNA for future
cell survival investigation.
Keywords: Survivin, MCF-7, PDB2, Cloning, Cancer.
HTTP://UI.CNF.IR/PPS 61
Association of APOE and BDNF polymorphisms with alzheimer’s
disease in south of Iran.
2, Ali Javadpour1, Raheleh Masoudi1Zohreh Harati
1 Department of Biology, College of Science, Shiraz University, Shiraz, Iran.
2 Research Center for Psychiatry and Behavior Sciences, Shiraz university of Medical Science, Shiraz, Iran.
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder and, in elderly people, is the most
common cause of dementia. Accumulation of beta-amyloid plaques and neurofibrillary tangles in
brain are two major pathological hallmarks of AD. Apolipoprotein E, the most important
cholesterol carrier in the brain, plays a role in clearance of amyloid plaques. APOE has three
major alleles E2, E3 and E4. E4 allele is an important risk factor for AD. Brain-derived
neurotrophic factor (BDNF) promotes neuronal survival and synaptic plasticity and is
downregulated in AD. BDNF Val66Met polymorphism (rs6265) decrease secretion of BDNF and
subsequently memory impairments and loss of hippocampal volume. The aim of this study was
to investigate the association of these three polymorphisms with risk of AD in a population of
South of Iran. 67 patients and 62 healthy controls were included in this case-control study. Two
groups were genotyped for this polymorphisms using Allele specific PCR or amplification-
refractory mutation system (ARMS). The difference in allelic and genotype frequency between
case and control groups was assessed using chi-square and regression logistic statistical analysis.
There was a significant association between E4 allele of APOE gene and risk of AD (OR= 2/9,
95% CI= 1/18- 7/16, P= 0/02). However, no association was found between BDNF
polymorphism and risk of AD in this population. This study was the first in Iran which
investigate the association between rs6265 BDNF polymorphism and risk of AD. Combination
of this polymorphisms and their association with AD was also investigated.
Keywords: Alzheimer’s disease (AD), APOE, BDNF, Allele specific PCR, South of Iran.
HTTP://UI.CNF.IR/PPS 62
A molecular dynamics simulation investigation into the dissociation
constants (Kd) of Mn(II) binding on the structure and stability of
calprotectin using Molecular Dynamics Simulation
Faezeh Hashemi*, Mohammad Reza Dayer, Azizolla Beheshti
Department of Chemistry, Faculty of Science, Shahid Chamran University, Ahvaz, Iran.
Abstract
Human Calprotectin (CP) is an antimicrobial protein that competes with pathogens for transition-
metal binding belongs to Ca(II)-binding proteins of the S100 family. Crystallographic
characterization of CP heterotetramer () indicate the presence of two His4 and two His3Asp
binding sites at subunits interface. The dissociation constants for calcium-insensitive binding
Mn(II) for His4 and His3Asp binding sites were reported as 194 ± 203 nM (for Kd1) and 21 ± 5
μM (Kd2) respectively. In order to understand the role of Ca(II) in dynamic properties of protein
and its effect on dissociation constants (Kd) of metal ions, we decided to simulate calcium and
manganese bound and free structures of CP's structures in native like conditions of 310K
temperature, 1 atm of pressure and in a rectangular box of water with 6.163x6.721x6.268 nm of
dimensions for up to 10ns period. Our results indicate that the presence of Ca(II) stabilize CP-
Mn(II) complex via conferring more negative potential energy probably through their
interactions as electrolyte with negatively charged groups when contrasted to free CP. Our
findings also analysis indicate that in calcium-bound form of CP His4 binding site exhibits
higher affinity for Mn(II) in contrast to at His3Asp binding site. Based on Irving williams and
hofmeister series for calcium and manganese are expected to be of destabilizing nature for
proteins but our data show that in case of CP these two elements provide essential flexibility and
stability CP those are absolutely necessary for native function of the protein.
Keywords: Molecular dynamics simulation, Calprotectin, Dissociation constants.
HTTP://UI.CNF.IR/PPS 63
Preliminary antibacterial evaluation of the chemical compositions in
mono and dinuclear cobalt(II) complexes of 1,1,3,3-tetrakis(3,5-
dimethyl-1-pyrazolyl) propane ligand
Faeze Hashemi1 , Azizolla Beheshti*2, Mohammad Reza Daye 2, Hossein Motamedi2
1Department of Chemistry, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran. 2Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran.
Abstract
Two new mono- and dinuclear Co(II) complexes namely [Co(tdmpp)Cl2]2.H2O (1) and
[Co2(tdmpp)Cl4] (2) were prepared by one- pot reaction in methanol as a solvent. These
compounds have been characterized by single crystal X-ray diffraction, elemental analysis,
infrared spectroscopy, antibacterial activity and computational studies. The in vitro antibacterial
activity studies of the free tdmpp ligand, compounds 1 and 2 show that, the ability of these
compounds to inhibit growth of the tested bacteria increase progressively from tdmpp to the
dinuclear complex 2. Molecular-docking investigations between the five standard antibiotic, free
tdmpp ligand, complexes 1, 2 and five biological macromolecule enzymes (receptors) were
carried out by using Autodock vina function. The results of docking studies confirm that the
metal complexes are more active than the free ligand. This is consistent with the results obtained
by the antibacterial activities of these compounds.
Keywords: Mono and dinuclear Co (II) complexes, Gromacs, Molecular-docking investigation,
In vitro antibacterial activity.
HTTP://UI.CNF.IR/PPS 64
A Study on Zn(II) coordination in the present of Ca(II) in human
calprotectin binding sites using molecular dynamics simulations
Faezeh Hashemi*, Mohammad Reza Dayer, Azizolla Beheshti
Department of Chemistry, Faculty of Science, Shahid Chamran University, Ahvaz, Iran.
Abstract
Calprotectin (CP) is an antimicrobial protein produced and released by neutrophils that inhibits
the growth of pathogenic microorganisms by sequestering essential metal nutrients in the
extracellular space. CP is a tetramer made up of two heterodimer of S100A8 and S100A9. The
two proteins belong to Ca(II)-binding proteins of the S100 family. In this work, for a better
understanding of the role of Ca(II) and Zn(II) on the dynamics of CP, were studied using
Molecular dynamics simulations. The simulations were carried out on Ca(II)-free and Ca(II)-
bound, Zn(II)-free, Zn(II)-bound, Ca(II)- CP-Zn(II) models, using crystal structures obtained
from the Protein Data Bank, and trajectories at 37 ºC and 1 atmosphere pressure for 10ns period.
Our molecular dynamic analysis confirmed that Ca(II) binds to both seven-coordinate,
“canonical” sites and five-coordinate, “non-canonical” sites. Also, the simulations demonstrated
that Ca(II) and Zn(II) ions can stabilize the conformation of their binding site. During simulation,
due to CP structure alteration, the RMSD of Ca(II)-CP-Zn(II) is slightly lower than its free state.
Although the Zn(II) and Ca(II)-binding to CP leads to decreased activity of the protein, the
RMSF curve illustrated that Ca(II)-CP-Zn(II) complex has lower flexibility and mobility than
CP-Zn(II). Taken together, these data provide a working model whereby CP responds to
physiological Ca(II) gradients to become a potent Zn(II) chelator in the extracellular space. The
results of this study indicated that although Zn (II) in Irving-Williams series of proteins known to
be stable, its natural presence to create flexibility in the protein structure CP is absolutely
necessary.
Keywords: Molecular dynamics simulation, Calprotectin, Zn (II), Ca (II).
HTTP://UI.CNF.IR/PPS 65
Chaperone-like activity of new deep eutectic solvents (DESs)
Foruzan Niknaddaf1, Reza Hasan. Sajedi1, Akbar Heydari2
1Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
2Department of organic Chemistry, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Iran.
Abstract
Green solvents such as natural deep eutectic solvents (DESs) have recently been shown to
prepare liquid media like intracellular water space of the cells. For this reason, and because of
the solvents are biodegradable, inexpensive andnon-toxic, DESs have gained much attention in
many fields. DESs are mixtures of a salt and a hydrogen bond donor which have lower melting
point in comparison with the individual components. In this study, some artificial chaperones
have been utilized as one of the components of the solvents. Artificial chaperones are small
molecules with chaperone-like activity against forms of protein aggregation. In the present work,
the synthesis of three kinds of DES is reported, including choline chloride (ChCl): lacticacid,
lactic acid: L-glutamine andlactic acid: L-arginine. Chaperone-like activity of these solvents has
been studied by DTT-induced and dilution-induced aggregation of hen’s egg white lysozyme in
400 nm. Single factor experiments have been done to investigate the effects of chaperone-like
activity, including the amount of DES, the concentration of protein and the incubation time.
DTT-induced aggregation carried out indifferent concentrations of DESs (1, 2.5, 5 and 10
%(v/v)). All concentrations showed full inhibition of protein aggregation and enhancement in the
yield of refolding. Our findings suggested that the use of molecular chaperones increases the
efficiency of chaperone-like activity deep eutectic solvents.
Keywords: Deep eutectic solvents, Artificial chaperone, Protein aggregation, DTT-induced
aggregation, Refolding.
HTTP://UI.CNF.IR/PPS 66
Creating hierarchical nanostructures with TiO2 nanoparticle and
brush polymer, a promising approach for protein repellence
behavior of biomaterial
Fatemeh Noorisafa and Amir Razmjou
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, P.O. Box
73441-81746, Isfahan Iran.
Abstract
Advanced surface modification approaches of biomaterials alongside the advent of sophisticated
analytical techniques have provided a great opportunity to understand how the physicochemical
characteristics of materials determine cell–surface dynamics at molecular and atomic scale.
Appropriate molecular and cellular response to biomaterial surfaces is essential for implants and
biomedical devices. The tendency of proteins attachment to the surface depends on the material
properties such as surface energy, structure, texture, and relative charge distribution. Engineering
the surface wettability towards superhydrophilicity has been found an impressive technique to
enhance biocompatibility and reduction in protein-material interactions. In this study surface
modification of polyurethane plates by poly ethylene glycol thin layer via grafting technique and
TiO2 nanoparticle entrapment in the brush polymer was investigated with respect to the surface
chemistry and surface structure to increase the biocompatibility. A systematic characterization
was conducted to elucidate the role of each parameter on the biocompatibility and biofilm
formation. The surface protein absorption capacity reduced by 8.7 times and based on MTT
assay the modification has no toxic effect on HeLa cells. The modified samples have also the
ability to reduce the biofilm formation by 71%. In general, when a micron-nano scale roughness
appeared on PU surface, the impact of morphological changes on the biocompatibility, protein
adsorption and biofilm formation becomes significantly higher than that of the surface chemistry
alteration.
Keywords: Protein adsorption, Biocompatibility, Superhydrophilicity, Hierarchical surfaces.
HTTP://UI.CNF.IR/PPS 67
Protective effect of zinc ions against protein misfolding: a dose
dependent phenomenon
Sepideh Noorzadeh1 and Mohammad Reza Dayer2
1Nourdanesh institute of higher education of Meymeh, Esfahan, Iran.
2Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
Abstract
Protein misfolding is an inherited character of certain small proteins that expressed in life
threatening diseases such as Alzheimer’s disease, cystic fibrosis and prion-associated spongiform
encephalopathies (bovine spongiform encephalopathy and Creutzfeldt-Jacob’s disease). The
precise mechanism and factors facilitate amyloidogenic process are not well understood. Here an
aliphatic alcohol of ethanol was used to induce amyloid fibrils and to simulate misfolding
process in human insulin as a model protein. Using different techniques of UV-Vis, fluorescence,
CD, FTIR spectroscopy we measured protein turbidity at 398nm, melting temperature at 280nm,
Thioflavin T (ThT) fluorescence quenching, protein secondary structure determination at Far-UV
CD and FTIR to study insulin misfolding at different concentrations of ethanol at the presence
and absence of Zinc ions concentrations. Our findings indicate that I-ethanol at optimum
concentration of 20%(v/v) accelerates insulin misfolding and reduces ThT fluorescence by 38%.
II-Zinc ions at high concentrations of ≥25mM prevent insulin misfolding induced by ethanol
while lower concentrations of Zinc ions accelerates insulin misfolding even at the absence of
ethanol. III-Our data also show that 25mM concentration of Zinc ions increase insulin melting
temperature by 5 degree centigrade. IV-Far-UV CD and FTIR experiments reveal that 20%
ethanol increases beta structure content of insulin by 10% while it is abolished at the presence of
25mM concentration of Zinc ions. Based on our findings and previous reports we can conclude
and hypothesize that zinc ions at high enough concentrations by stabilizing hexamer associations
with native conformation, prevent their dissociation to monomer forms and subsequently to
protofibriles, the structures that facilitate protein misfolding.
Keywords: Misfolding, Zinc ions, Amyloidogenic disease, Ethanol.
HTTP://UI.CNF.IR/PPS 68
Computational study of interaction between prostate-specific
membrane antigen and truncated PSMA aptamer
Farzaneh Namazifar1, Masoud Ayatollahi-Mehrgardi1, Mehdi Sahihi2
1Analytical Chemistry Group, Department of Chemistry, Isfahan University, Isfahan, Iran.
2 Physical Chemistry Group, Department of Chemistry, Isfahan University, Isfahan, Iran.
Abstract
Cancer is a class of diseases characterized by out-of-control cell growth. There are over 100
different types of cancer, and each is classified by the type of cell that is initially affected.
Prostate cancer is the most common cancer types with increasing PSMA protein on the surface
of prostate cancer cells as a biomarker for detect of this cancer. Aptamers are
oligonucleotide or peptide molecules that bind to a specific target molecule. Here, we used RNA
structural prediction and protein/RNA docking algorithms that enabled us to predict the
interaction between A9g, a truncated RNA aptamer to prostate-specific membrane antigen
(PSMA), with great potential for targeted therapeutics. In addition, the modeled RNA tertiary
structure and protein/RNA docking predictions revealed key nucleotides within the aptamer
critical for binding to PSMA and inhibiting its enzymatic activity. Finally, this work highlights
the utility of existing RNA structural prediction and protein docking techniques that may be
generally applicable to developing RNA aptamers for therapeutic use.
Keywords: Cancer, Truncated aptamer, Prostate specific membrane antigen (PSMA), Molecular
docking.
HTTP://UI.CNF.IR/PPS 69
Stabilization of Ca2+ regulated photoprotein aequorin by deep
eutectic solvents (DESs)
Negin Nazari Moghadam1, Reza Hasan Sajedi1, Akbar Heydari2, Bijan Ranjbar3
1Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
2Department of organic Chemistry, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Iran.
3Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Abstract Deep eutectic solvent (DES) is a fluid generally composed of two or three cheap and safe
components that are capable of self-association, often through hydrogen bond interactions, to
form a eutectic mixture with a melting point lower than that of each individual component. DESs
exhibit similar physico-chemical properties to the traditionally used ionic liquids, while being
much cheaper, non-toxicity and environmentally friendlier. Generally, proteins are best stored at
about 4°C in clean, autoclaved glassware or polypropylene tubes. Storage at room temperature
often leads to protein degradation and/or inactivity, commonly as a result of microbial growth.
Several kinds of photoproteins, including aequorin, isolated from hydrozoan jellyfishes and
hydroids. Aequorin is a photoprotein that emits light upon binding calcium. When Ca2+ binds to
the photoprotein, the 2-hydroperoxycoelenterazine decomposes into coelenteramide and CO2,
accompanied by the emission of light.The purpose of this study is to investigate the protein
stability in the presence of some DESs at room temperature and increase its thermostability. In
this work, the stability of aequorin has been studied in choline chloride: urea and choline
chloride: glycerol (choline chloride (ChCl) as the salt and urea (U) and glycerol (G) as the
hydrogen bond donor). The results showed that after incubation of apoaequorin by 20% ChG and
2.5% ChU at room temperature, aequorin activity was increased to 1.5 and 3 times, respectively.
Also, interestingly aequorin thermostability was increased at 70 ºC and 80 ºC in the presence of
10% ChG, wherease ChU had no effect on the protein thermostability.
Keywords: Deep eutectic solvents, Aequorin, Protein stability.
HTTP://UI.CNF.IR/PPS 70
Effect of conventional and microwave heating on glycation of bovine
serum albumin through maillard reaction
Farzaneh Nasrollahzadeh1, Mehdi Varidi2, Arash Koocheki3, Farzin Hadizadeh4
1, 2, 3 Department of Food Science and Technology, Ferdowsi University of Mashhad, Mashhad, Iran.
4 Medicinal Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
Abstract The aim of present study was to evaluate the effect of Microwave (MH) and conventional
heating on the glycation progress of a model protein, bovine serum albumin (BSA) via Maillard
reaction. For this purpose, three different weight ratios (1:1, 1:3 and 1:5) of BSA and
maltodexrin (MD) were chosen and thermal treatments were done at 90 ºC. Conjugation was
confirmed by o-phthaldialdehyde (OPA), absorbance at 420, UV absorbance and CIE lab
parameters. Statistical analysis showed significant differences between MH and water bath
heating (WH) in reduction of free amino groups and increase in Abs 420 and UV absorbance.
The value of L*and a* were increased in the time of heating. However, dramatic difference
between MH and WH was not seen (p>0.05). The least and the greatest glycation percent were
observed about 9% in both WH and MH during 15 min, and 66.65% by MH in 120 min,
respectively. It showed that graft reactions under MH were much faster than those by WH and
microwave can accelerate the rate of Maillard reaction.
Keywords: Bovine serum albumin, Maillard reaction, Microwave heating, Conventional heating.
HTTP://UI.CNF.IR/PPS 71
Study of the interaction of apigenin and epigallocatechingallatewith
α-Lactalbumin and their inhibitory effect on the formation of α-
Lactalbuminamyloid fibrils
Zahra Nadermohammadi and Fakhrosadat Mohammadi
Department of Chemistry, Institute for Advanced Studies in Basic Science, Gavazang, Zanjan, Iran.
Abstract:
Amyloid fibrillogenesis of almost twenty different proteins followed by deposition of amyloid
fibrils in organs results in several neurodegenerative disorders such as Alzheimer's, Parkinson's,
Huntington's diseases and type II diabetes. Bovine α-Lactalbumin (BLA) is an acidic Ca2+-
binding protein that forms amyloid fibrils at low pH. At present there is no effective treatment
for these diseases and all drugs have failed in different stages of clinical trials. However
identification and development of small molecules that can inhibit fibrillation is an interesting
subject of research. Flavonoids are small natural polyphenols found in many grapes, fruits,
berries, vegetables and herbs as well as other plants. These small polyphenols act as fibrillation
inhibitors. Natural polyphenolic compounds are introduced as appropriate candidates for
inhibition of amyloid formation. In the present study, the inhibitory activities of apigenin and
epigallocatechingallate as two bioactive flavonoids on the amyloid fibrillation of bovine alpha-
lactalbumin as an appropriate model protein for in vitro fibrillation were investigated using
thioflavin T (ThT) fluorescence and atomic force microscopy (AFM). Also, the binding
interaction evaluations were carried out using fluorescence quenching, fluorescence resonance
energy transfer (FRET), synchronous fluorescence and molecular docking approaches.The
binding parameters including binding constant and number of binding sites, thermodynamic
parameters, and distance between the bound ligands and tryptophan residues of alpha-
lactalbumin were determined from the fluorescence experiments. The amyloid fibrillation assays
showed that both apigenin and epigallocatechingallate have considerable capability to inhibit
amyloid fibrillation of alpha-lactalbumin.
Keywords: Amyloid fibrils, Flavonoids, α-Lactalbumin.
HTTP://UI.CNF.IR/PPS 72
A spectroscopic study on the interaction of blood carrier protein of
albumin with a new designed Palladium complex
Akram Najaran1, Adeleh divsalar2, Ali Akbar Saboury3, Nasim Hayati Rudbari1
1Department of Science and Research Branch, Islamic Azad University, Tehran, Iran.
2 Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
3 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
Abstract
Human serum albumin (HAS) is the major protein component of human plasma and has very
important roles in transporting of various drugs, smaller organic compounds and inorganic ions.
In the present study, the interaction of human serum albumin (HSA) and a new designed
Plladium complex was studied by using different spectroscopic techniques of fluorescence and
circular dichroism (CD) at two temperatures of 25 and 37 C. By the analysis of fluorescence
spectra, it was observed that the palladium complex has an ability to quench the intrinsic
fluorescence of protein through a static quenching procedure. The number of binding sites and
the association binding constant as well as thermodynamic parameters of palladium complex
were calculated at both temperatures according the quenching methods. Also, far-UV-CD spectra
of the protein in the absence and presence of various concentrations of complex represented that
the regular secondary structure of protein did not show any significant alterations. From above
results, it can be concluded that the new design palladium complex can bind to blood carrier of
HSA without any alteration in secondary structure of protein which can be considered in
designing of new anticancer drugs with low cytotoxicity in future.
Keywords: Palladium complex, HSA, Fluorescence, Quenching.
HTTP://UI.CNF.IR/PPS 73
Min impact study on catalase of Helicobacter pylori through
simulation docking
Pardis Naderi -Dehkordi and Fatemeh Raiesi
Islamic Azad University, Shahrekord Branch, Shahrekord Iran.
Abstract
The purpose of this article is to study the effect of mint on catalase of Helicobacter pylori using
simulation docking. The effect of mint on Helicobacter pylori catalase docking procedure was
carried out in this way on catalase compounds were mint. Docking with the software Autodock 4
were done. Mint extract contains: (Chrysophanol, Mentol, Terpinolene) results showed
chrysophanol that the binding energy (-6/33 kj/mol) are the best and can be used as medicine.
Helicobacter pylori is a gram-negative, curved s-shaped bacterium, which also has a non-cultural
cocoid form with rounded ends The species name stems from: helico, meaning helical or spiral
shape, bacter, meaning bacteria, and pylori, refering to pylorus region of the stomach. This
pathogen possesses five to seven distinct flagella and grows best when cultured at 37°C.
Interestingly, in resting individuals, 37°C is the stomach's temperature - the targeted organ;
however, the bacteria is able to withstand temperatures as low as 25°C. The purpose of this
article is to study the effect of mint on catalase of helicobacter pylori using simulation docking.
The effect of mint on helicobacter pylori catalase docking procedure was carried out in this way
on catalase compounds were mint. Docking with the software Autodock 4 were done. Mint
extract contains: (Chrysophanol, Mentol, Terpinolene) results showed chrysophanol that the
binding energy (-6/33 kj/mol) are the best and can be used as medicine.
Keywords: Helicobacter pylori, Mentha longifolia, Docking, Catalase.
HTTP://UI.CNF.IR/PPS 74
The survey of the effect of crocin and saffranal in terms of the
inhibition of the formaion beta sheets in neurodegenerative diseases
in vitro and in silico
Tahereh Naderi Jelodar1, Marzihe Dehghan1 , Ali Akbar Saboury1, Mohamad Ali Ebrahimi2
, Atiyeh
Ghasemi1
1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 2Department of Agriculture Biotechnology, Payame Noor University, Tehran, Iran.
Abstract
Aggregation of proteins is a major feature of the pathogenesis of many neurodegenerative
diseases such as Alzheimer's, Parkinson and Prion. Lysosyme plays an important role in creation
systemic amyloid diseases. Lysosyme aggregation was observed under laboratory conditions,
high temperature and highly acidic pH. In this study, structural properties and kinetics of protein
in the presence of effective material of Saffron namely safranal and crocin were investigated
individually using fluorescence method, circular dichroism, SEM and docking. In the
fluorescence of ThT, the emission intensity decreased after adding the protein that had been
incubated with safranal and crocin separately with increasing concentration of treatments and
increasing incubation time. The results showed beta-amyloid sheets were separated from each
other and they lead to inhibit protein aggregation. The binding of ANS marker to hydrophobic
surface protein caused to increase emission intensity and subsequently to decrease the surface
hydrophobicity. To determine the probable impact of safranal and crocin on the secondary
structure of lysozyme, CD spectrophotometer was used in the long-wavelength ultraviolet. The
study showed that the formation of amyloid fibrils decreased in the various concentrations of
crocin and safranal. To prove the exact mechanism of the mentioned effect, the incubated
samples were surveyed by SEM. Docking method were performed to demonstrate the results of
inhibitory activity of compounds on the process of protein aggregation and to determine the
interaction region of compounds with crocin and safranal. Docking analysis revealed crocin and
safranal interact to the central hydrophobic region of lysozyme through Van der Waals
interaction. Hydroxyl group in crocin through hydrogen bonds connected to the hydrophilic
amino acids of lysosyme such as aspartic acid, lysine, serine and threonine while there is just one
hydroxyl group in safranal that through hydrogen bonds connected to aspartic acid in lysozyme.
As a consequence, crocin and safranal prevent the formation of aggregation in the beta sheets
which induce neurodegenerative diseases. Crocin have more potent than safranal .
Keywords: Safranal, Crocin, Fluorescence, Circular dichroism, Docking.
HTTP://UI.CNF.IR/PPS 75
Prediction of triple mutation roles on the sweetness and function of
brazzein according to bioinformatical studies
Ziba Mirzaei, Soraya Pirmohammadi, Vahab Jafarian
Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
Abstract
Recently, Brazzein due to of convenient features such as sweetness potential, high solubility,
tolerate a wide temperature range and pH to reduce the risk of diseases such as diabetes and
obesity sugar consumption is taken into consideration. Our and another previous theoretical and
experimental studies had shown that replacing the glutamic acid9, alanine19 and glutamic acid41
residue with lysine, a single mutation, increased power sweets Brazzein. Therefore, in this study
to examined the role of triplemutation in structure and function of possible designed protein.
Following theoretical and bioinformatics studies with using the Moderller9v7 software, single
(E9K, A19K, E41K) and triplemutation (E9K/A19K/E41K) done and three-dimensional
structure of the mutants were modeled using chimera software. The best model according to the
ModEval program, Spdbviewer Software and SAVES server selected on the basis of structural
parameters, biochemical and physical properties of wild protein and mutated were examined
findings. Experimental results from single mutations showed that the brazzein double mutant has
been stable and is expected to have more power sweets than single mutation. Check results and
match it with single mutations experimental results indicate that the triplemutant Brazzein has
been stable and is expected to power more sweets than to have a single mutation.
Keywords: Brazzein, Triplemutation, Sweetness, Bioinformatic studies.
.
HTTP://UI.CNF.IR/PPS 76
Mutation at calcium binding site in cyclomaltodextrinase improve
enzyme thermostability: A bioinformatic study
Ziba Mirzaee and Vahab Jafarian
Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
Abstract
Cyclomaltodextrinases are multidomain and often dimeric proteins from glycoside hydrolase
family 13 (GH13), and catalyzes the degradation of cyclomaltodextrins or cyclodextrins to
maltose and glucose, Analysis of the native cyclomaltodextrinase sequence with GenBank code
KT633577, has predicted the presence of two Ca2+ binding sites. The aim of this study was to
evaluate and select appropriate mutation in first Ca2+ binding sites to improve thermostability of
the enzyme. For this purpose, the mutations were designed using structural and sequence
analysis tools such as ProtParam, ProtScale. Then, Rosetta Bachrub server and MODELLER
program were used for construction of the three-dimensional structure of WT and mutant and the
best model were selected for further studies with programs under the SAVES server as well as
ModEval program. Upon selection of the best model based on the structural features, the status
of interactions and physico-chemical properties of wild-type and mutant were evaluated. Based
on our study, it was revealed that replacement of Asparagine149 by Aspartic acid, the possibility
of binding to Ca2+ increased through the aspartate carbonyl oxygen and enzyme's thermostability
was significantly improved by increasing in ionic interactions and salt bridges.
Keywords: Cyclomaltodextrinase, Modeling, Mutation, Thermostability, Calcium binding site.
HTTP://UI.CNF.IR/PPS 77
Application of albumin glycation products to increase the yield of
phytase production in a recombinant bacterial expression system
2, Bijan Bambaei1Rezaei-Mehran Habibi ,1Naeini-Sadat Mirtavousi-Fateme
1School of Biology, College of Science, University of Tehran, Tehran, Iran.
2National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.
Abstract
Phytases (EC 3.1.3.8, EC 3.1.3.26, EC 3.1.3.72) are enzymes that hydrolyze stepwise release of
phosphate from phytate (myo-inositol (1, 2, 3, 4, 5, 6) hexakisphosphate) therefore are proposed
as an animal feed additive to enhance the value of plant material in animal feed by liberating
phosphate. Phytate has a negative impact on the availability of the phosphate and valuable trace
elements; about 80 percent of the phosphorous exist in the bound form as phytate in plant-based
feed and due to its high negative charge under physiological condition, renders the absorption of
minerals and trace elements. In this study, the detergency effect of morph aggregated form of the
serum albumin prepared upon a time dependent protein glycation, then fibrillation are explored
to increase the periplasm to medium secretion of the phytase in an engineered phytase
heterologous expression system. Experiments were designed using response surface
methodology (RSM) approach in which various parameters were optimized including aggregate
concentration and state of fibrillation. The products of albumin fibrillation were added to the
recombinant bacterial culture before and after growth of bacteria that are assigned as pre-
treatment or post-treatment modes, respectively. As a result, the product of albumin glaycation
represented the highest efficiency at 20 days of albumin fructation products, determined through
phytase activity assay in the supernatant of culture centrifugation product in pre- treatment mode.
In conclusion, the serum albumin glycation products are effectively used to enhance the yield of
phytase production most probably upon detergency effect on the bacterial outer membrane.
Keywords: Glycation, Phytase, Detergency effect, Response surface methodology, Serum
albumin.
HTTP://UI.CNF.IR/PPS 78
Analysis of the interactions between putrescine and bovine
pancreatic trypsin by spectroscopic techniques
Lida Momeni1, Behzad Shareghi 2, Ali Akbar Saboury 3
1 Department of Biology, Faculty of Science, University of Payam Noor, Tehran, Iran. 2 Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O.
Box.115, Iran. 3 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
Abstract
Information on protein stability is essential to study protein structure, activity, and interactions
with ligands. The interaction of putrescine with trypsin was investigated by using different types
of spectroscopic techniques in an aqueous medium at two temperatures of 25 and 35°C. The
enzyme activity of Trypsin showed that putrescine increased the activity of the enzyme and its
thermal stability was increased by enhancing the concentration of putrescine. Far- UV circular
dichroism (CD) studies showed that putrescine could change the secondary structure of trypsin
via increasing the content of the α- helix structure and decreasing the β-sheet. The fluorescence
spectroscopic experiments revealed that putrescine had the ability to quench the intrinsic
fluorescence of trypsin through a static quenching procedure. The intrinsic fluorescence of
trypsin was decreased in the presence of putrescine due to the excited-state proton transfer. The
binding constant was determined using the Stern-Volmer equation. The thermodynamic
parameters also indicated that the binding process was spontaneous and that hydrogen bonds and
van der Waals forces played a major role in the interaction of putrescine with trypsin. Moreover,
the increased thermal stability of trypsin might be due to the lower surface hydrophobicity and
the higher hydrogen bond formation after putrescine enhancing, which was reflected in the
increase of UV absorbance, the quenching, as well as the increase of α-Helix content.
Keywords: Trypsin, Putrescine, Thermal stability, Fluorescence, Circular dichroism.
HTTP://UI.CNF.IR/PPS 79
Fabrication and characterization of nano bio-composites scaffolds
contains silk fibroin protein and mcm-41 for tissue engineering
applications
and Abbas Teimouri Nafiseh mobadi
3697, Tehran, I. R. of Iran.-Department, Payame Noor University, 19395Chemistry
Abstract
A scaffold possessing certain desired features such as biodegradation, biocompatibility, and
porous structure could serve as a template for tissue engineering. In this regard, exploration of
new and suitable biomaterials is needed. Silk is a strong and lustrous natural fiber which mainly
contains protein polymer. Silk protein obtained from different silkworm species consists of two
totally different families of proteins, namely fibroin and sericin. Silk fibroin (SF) is used as one
of the most preferable biomaterials for fabrication of scaffolds and several new techniques are
being adopted to fabricate silk scaffolds with greater ease, efficiency and perfection. Mesoporous
MCM-41 is a bioactive material which is comprised of siloxane and silanol groups and offers
opportunities for modification of its surface via bonding organosilanes of desirable structure and
functionalities. In continuation of our recent study on the construction of composite scaffolds, in
this study nano bio-composite sponges were successfully prepared with an interconnected
porous structure and proper mechanical properties.The composite scaffold was characterized by
SEM, XRD, BET and FT-IR studies. In addition, the water uptake capacity, degradability and
biomineralization capability of the composite scaffolds were assessed.Cytocompatibility of the
scaffolds was also assessed by an MTT assay and cell attachment studies using Human Gingival
Fibroblast cells.The results showed the cells were found to attach to the pore walls within the
scaffolds and no signs of toxicity. Thus, we suggest that this nano bio-composite scaffold is a
potential candidate to be used for tissue engineering.
Keywords: Silk fibroin protein, Biomaterials, Tissue engineering, Scaffolds.
HTTP://UI.CNF.IR/PPS 80
Theoretical study of effect of N232S, F251L and R242H mutations in
myosin protein structure
Karim Mahnam1 and Tayebeh Rabani2
1. Biology Department, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.
2. Department of Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran.
Abstract
Mutations in muscle proteins are directly responsible for a class of human disease, such as
familial hypertrophic cardiomyopathy (HCM). Over than 75% of mutations accrue within the
myosin motor domain in four distinct functional regions: the ATP binding site, the actin binding
interface, the reactive sulfhydryl or converter region and the light chain binding domain. In this
study we decide to investigate the affect of there important mutation, i.e. N232S, F251L and
R242H mutations on structure of myosin. These mutations accrue in exon 8 and 9 MYH7 gene
and are near to region of binding myosin to actin and related to HCM disease. At fist 3D
structure of myosin was made by multiple template modeling (PDB codes : 4DB1 and 4P7H )
via modeler 10 and the best model was selected based on DOPE energy. Then this model was
used as starting structure for 10 ns MD simulation via Gromacs 5 package and final structure
(wild type structure) was obtained. Then N232S, F251L and R242H mutations created in wild
type and the mutated structures were used for MD simulation with the same condition of wild
type. Three loop of myosin are important for function and binding myosin to actin that contain
loop 1: Pro401-Lys412, loop2: Lys564-His575 and loop3: Ala621-Val646. Then the accessible
surface area of these loops in wild type and mutated structures were calculated. Our results
indicated that accessible surface area of loop 2 and 3 increase after mutation N232S and F251L.
Also the surface of all loops increase after mutation R242H. Then we can concluded that these
mutation lead to more tight binding of myosin to actin and cause to functional impairment of the
cardiac muscle.
Keywords: Myosin, Molecular dynamics simulation, N232S, F251L and R242H mutation,
Hypertrophic cardiomyopathy.
HTTP://UI.CNF.IR/PPS 81
Theoretical study of the effect of mutation F117L osteoprotegerin
protein on its binding to RANKL protein by modeling methods
Karim Mahnam 1, Zahra Mousavi2, Razye Pourahmad2
1 Biology Department, Faculty of Sciences, Shehrekord University, Shahrekord, Iran.
2 Faculty of Science, Department of Genetics, Shahrekord University, Shahrekord, Iran.
Abstract
Osteoporosis is a multifactorial skeletal disease that characterized by low bone mineral density,
which leads to increase of bone fragility and fracture risk. Osteoprotegerin protein (OPG)
secreted by osteoblasts cells is a negative regulator of osteoclastogenesis that prevent activation
of osteoclast precursors. Polymorphism of the phenylalanine 117 to Leucine was seen in some
patient with osteoporosis in china people. Then it suggested that this mutation probably alters the
structure of OPG and leads to osteoporosis. The model of native and mutated OPG dimer protein
were built by modeler 10 and used for molecular dynamic simulation by Gromacs 4 for 10
nanoseconds in NPT ensemble in presence of water molecules and ions. Then the obtained
structure was docked to RANKL protein by HADDOCK web server. According to docking
results, both native and mutated OPG protein can bind to RANKL protein and have negative
binding energy. Then this mutation or polymorphism probably has no effect on osteoporosis
diseases.
Keywords: Osteoprotegrin (OPG), Docking, Mutations, Molecular dynamics simulations,
Modeling.
HTTP://UI.CNF.IR/PPS 82
Fabrication and charactenization of nano bio-composite scaffold for
use in tissue engineering
Ghasem Mehranzadeh1, Abbas Teimouri1, Hossein Salehi2
1 Department of Chemistry, Payame Noor University, P. O. Box 19395-3697, Tehran, Iran.
2Department of Anatomical Sciences, Medical School, Isfahan University of Medical Sciences, Isfahan, Iran.
Abstract
The urge to repair and regenerate natural tissues can now be satisfactorily fulfilled by various
tissue engineering approaches. Tissue engineering through the integrated use of cells, scaffolds
and regulatory molecules represents a promising approach towards functional tissue
replacements in regenerative medicine. Silk protein fibroin can be effectively used as a
scaffolding material in these treatments. Silk fibers are obtained from diverse sources, among
them, silk of silkworms is a good source for the development of biomedical device. Nano
diopside powders have been shown to be bioactive biomaterial for bone repair. Diopside was
synthesized through a novel sol-gel synthesis. In continuation of our recent study on the
construction of composite scaffolds, in this work, a bio-composite scaffold containing organic
materials and nano materials was prepared by freeze drying method. The silk fibroin (SF)/nano
diopside composite scaffold was characterized by SEM, XRD and FT-IR studies.The biological
response of MG-63 cells on nanocomposite scaffolds was very good in terms of cell attachment
and cell proliferation was analysed by MTT assay.This nano composite has suitable properties
for bio-applications such as bone tissue engineering application in the future.
Keywords: Tissue engineering, Silk fibroin, Nano diopside, Bone tissue.
HTTP://UI.CNF.IR/PPS 83
Investigation on the binding of metoprolol tartrate to β-
lactoglobulin using spectroscopic techniques
Nayereh Mahdieh-Najafabadi, Asghar Zeini-Esfahani, Ali Asghar Rastegari
Department of Molecular and Cell Biochemistry, Islamic Azad University, Falavarjan, Esfahan, Iran.
Abstract
β-Lactoglobulin (β-Lg) is the major whey protein of bovine milk present at a concentration of 2–
3 g L–1. Its biological role is still not well-known. However, many studies have suggested that β-
Lg may play either nutritional or specific transporter role. Metoprolol tartrate (MPT), 1-[4-(2
methoxyethyl)phenoxy]-3-[(1-methylethyl)amino]-2-propanol tartrate, is a selective β-blocker
drug. In the present work, binding of MPT drug to β-Lg at pH 6.7, has been studied by UV-
Visible and circular dichroism (CD) spectroscopy methods. The binding constant for MPT/β-Lg
interaction has been found to be 103 M. The binding processes between protein and drug
molecules were endothermic and spontaneous owing to positive ∆H and negative ∆G values,
respectively. According to far- and near-UV CD results, these ligands have no apparent influence
on β-Lg secondary structure, however they partially destabilize its tertiary structure.
Keywords: β-Lactoglobulin, Metoprolol tartrate, UV-Visible spectroscopy, Circular dichroism
spectroscopy.
HTTP://UI.CNF.IR/PPS 84
Induction of point mutations in human growth hormone molecule
using specific primers
Zeinab Monajjemi Rarani, Seyed Hamid Zarkesh Esfahani, Rahman Emamzadeh, Mohammad Rabbani
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
Abstract
Human growth hormone (hGH) or somatotropin is a protein consists of 191 amino acid and
22kDa molecular mass which is synthesized by the somatotropic cells of the pituitary gland and
is secreted into the blood. GH synthesis and secretion are controlled by at least two hypothalamic
hormones; growth hormone releasing hormone (GHRH) and somatostatin (SMS). Some
biological activities of GH include its ability to regulate protein synthesis, cell proliferation,
differentiation of pre adipocytes to adipocytes and development of the immune system. The most
significant bioactivities of GH are protein anabolism, nitrogen and phosphate retention. GH plays
these roles by binding to specific cell surface receptors that belong to the class I cytokine
receptor superfamily. GH deficiency results in dwarfism in children and metabolic changes in
adults (e.g. acromegaly and gigantism). GH antagonist is needed in conditions such as
acromegaly and pituitary tumors. There are different approaches for making antagonists for GH.
One method is introduction of different mutations in the molecule to inhibit its biological
activity. To this aim, it's necessary to determine important parts of hGH which have main role in
interaction with receptors. These parts then could be replaced by primer design and PCR. So, the
resulted molecule may have antagonist properties and could be used in clinical trials for
therapeutic aims. In this study, we designed primers by using Oligo7 and Gene runner softwares
to replace important residues in GH molecule.
Keywords: Human growth hormone, Somatotropin, Point mutation, Oligo7, Gene runner.
HTTP://UI.CNF.IR/PPS 85
Co-immobilization of acetylcholine esterase and choline oxidase for
determination of acetylcholine in the brain of rat
Alireza Montazeri1, Hosna Tavakoli2, Gholamreza Herfehdost2, Hassan Tavakoli2
1Department of Biophysics, Islamic Azad University Science and Research Branch of Tehran, Iran.
2Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
Abstract
Because of the essential role of acetylcholine (Ach) in several neurodegenerative diseases such
as Alzheimer and dementia, precise determination of ACh is very important for clinical
diagnosis. In this investigation an electrochemical biosensor is developed for measuring ACh in
the brain of rat. For construction of biosensor, acetylcholinesterase (AChE; E.C 3.1.1.7) and
choline oxidase (ChOx; 1.1.3.17) co-immobilized by nafion on the surface of glassy carbon
electrode. The nafion increased the stability and improves the constructed biosensor responses.
For brain sample preparation, five rats were sacrificed, their brains was extracted, homogenized
in buffer phosphate solution and centrifuged. The supernatant was utilized for ACh
measurement. The biosensor was located into the samples, the cathodic and anodic peak currents
as the responses of the biosensor were obtained through cyclic voltammetry. The known
concentration of the pure solution of ACh was used for drawing the calibration curve. The
biosensor responses were linear up to 1mM. The cathodic and anodic peak currents obtained
8.626µA, -1.523µA respectively and the concentration of ACh was estimated 51.84 µM. AChE
hydrolyzed acetylcholine to choline and acetate and in turn, ChOx, catalyzed the oxidation of
choline to betaine and H2O2. The H2O2 which formed in this reaction iselectrochemically
detectable by the biosensor. It is important to note that the amount of produced H2O2 during
enzymatic reactions was indirectly proportional to the concentration of ACh. Consequently, the
biosensor could measure the ACh concentration in the biological samples such as the brain of rat.
Keywords: Acetylcholine Neurotransmitter, Electrochemical biosensor, Choline oxidase,
Acetylcholine esterase, Co-immobilization.
HTTP://UI.CNF.IR/PPS 86
The role of glutamate oxidase in electrochemically measurement of
glutamate neurotransmitter in rat brain
Alireza Montazeri1, Hosna Tavakoli2, Asgar Imamgholi2, Hassan Tavakoli2
1Department of Biophysics, Islamic Azad University Science and Research Branch of Tehran.
2Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
Abstract Glutamate oxidase (GOx; EC 1.4.3.11) belongs to the oxidoreductases family that catalyzes the
oxidative deamination of L-glutamate (Glu) to ketoglutarate, ammonia and hydrogen peroxide,
H2O2. During this enzymatic reaction, the amount of H2O2, in which detectable by
electrochemical biosensor is proportional to Glu concentration. In this research, electrochemical
method was utilized for measuring Glu neurotransmitter in rat’s brain. In order to prepare the
brain sample, five adult rats were deeply anaesthetized by ether and their brain was dissected by
a transcardially perfusion. The brain was homogenized in phosphate buffer solution and
centrifuged. After that, the clear supernatant was picked up for measurement of Glu level. For
electrochemically determinationof Glu, GOx–based biosensor was fabricated by immobilization
of GOx at the surface of platinum electrode. To assess the biosensor performance, the cyclic
voltammetry experiment was performed and cyclic voltammograms was considered as biosensor
response. The calibration curve was sketched using different concentrations of pure Glu solution.
For Glu measurement, the biosensor was dipped in the brain sample. The concentration of H2O2
in which produced in presence of Glu and GOx, was electrochemically measured by GOx –
based biosensor. The peak currents of brain samples obtained 0.812 µA by cyclic voltammetry
experiments and considered as the responses of GOx – based biosensor. the calibration curve
was linear up to 1mM and the concentration of Glu in rat’s brain obtained 36.5 µM. The results
showed that the GOx had a crucial role in electrochemical measurement of Glu and GOx
biosensor can be applicable for analytical and clinical determination of Glutamate.
Keywords: L-Glutamate oxidase, Enzymatic biosensors, Electrochemical biosensor,
Neurotransmitter.
HTTP://UI.CNF.IR/PPS 87
Analysis the binding interactions of bisdemethoxycurcumin,
diacetylcurcumin and diacetylbisdemethoxycurcumin with bovine
α-lactalbumin by experimental and theoretical analysis
and Fakhrossadat Mohammadi Marzieh Moeeni
Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang, Zanjan 45137-
66731, Iran.
Abstract
Milk proteins are one of the natural delivery systems for transporting drugs and bioactive
compounds. Biodistribution of drugs and minerals are affected by the extent and molecular
details of the binding of these proteins to the bioactive compounds. Bovine α-lactalbumin (BLA)
is an important whey protein which can be utilized as valuable vehicle for essential minerals. In
the present study the interaction of BLA with bisdemethoxycurcumin (BDMC),
diacetylcurcumin (DAC) and diacetylbisdemethoxycurcumin (DABC) as three bioactive
compounds was investigated by fluorescence quenching measurements and docking studies. The
stern-volmer equation was utilized to obtain the binding constants and the binding stoichiometry.
The extent of resonance energy transfer (FRET) and Forster’s distance between donor and
acceptor was estimated. Thermodynamic parameters confirmed that the final BDMC-BLA
complex was stabilized by hydrogen bonds, whereas the final DABC-BLA and DAC-BLA
complexes were stabilized by hydrophobic bonds which are in accordance with their chemical
structures. Theoretical and experimental studies verified that theTrp-26 has the most contribution
in the binding process. This considerable binding interaction between these curcuminoids and
BLA may be useful in enriching milk products by binding these anti-oxidant and anti-cancer
compounds to the proteins of the milk such as BLA. The considerable enhancement in the
nutritional value of milk can be obtained by these types of bindings.
Keywords: Alpha-lactalbumin, Disdemethoxycurcumin, Diacetylcurcumin,
Diacetylbisdemethoxycurcumin, Fluorescence quenching
HTTP://UI.CNF.IR/PPS 88
An investigation into the molecular mechanisms of the bacterial for
designinga competent genetic construct for benzene biodegradation
Marzie Mozafari1 and Aliakbar Haddad-Mashadrizeh2, 3
1Department of Biology, Science and Research branch, Islamic Azad University, Khorasan Razavi, Neyshabur, Iran. 2Cell and Molecular Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad,
Iran. 3Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
Abstract
Benzene is one of the aromatic hydrocarbons and the most stable one that can enter to the human
body through various ways such as smoking, processed food products and contaminated drinks.
This compound could be accumulate into the various organs such as gastrointestinal and/or
metabolize at corresponding organs. This element and its derivatives recognized as carcinogenic
in the body and reported as carcinogenesis risks factor at higher concentration. In this regard,
destructive effects of this compound on stem cells, pronormoblasts, normoblasts and stomas have
been demonstrated. On the other hand, this element has key role in leukemia induction so that
called as leukemiagene. Considering, provide the solutions for decrease the resource of this type
of components, and or strategies for metabolisms without creation carcinogenic intermediates in
the body, could be provided promising vision for reducing negative effects of compulsory
attendance of it in communities, which are considered in this study via application of the
bioremediation potency of the bacteria and non-bacteria microorganisms for probiotic
development. Bearing in mind, investigations into the molecular mechanisms of the bacterial
were performance for designing a competent genetic construct for benzene degradation. In this
regard, a comprehensive profile of the bacterial microorganisms with the ability of metabolizing
aromatic hydrocarbons especially benzene were gathered and then molecular mechanisms and
key and effective enzymes in the process were determined. Sequences of the selected enzymes
were retrieved from data banks such as NCBI and UniProt. Molecular survey of them have been
taken via CD search, Motif Scan, InterProScan, Blast, MEGA6, Hex and ClusPro2.0programs.
Subsequently, new genetic constructs with capacity to benzene degradation have been designed
based on detection of the functional domains of selected enzymes, and the structural modelling
of them was done with Modeller program. Assessments the qualities of the minimized structures
were done via MOE and RAMPAGE programs. Moreover, binding affinity of designed enzymes
to benzene was performance by using of the PatchDock web server. The results of this study
while introducing some strains of Pseudomonas and Mycobacterium with the ability to digest
aromatic hydrocarbons, especially benzene, led to presented the structural and functional
domains of corresponding enzymes such as deoxygenates and monooxygenates. Moreover,
provide a series of optimized genetic construct with capacity to transforming probiotic strains
that ought to be examined in experimental condition.
Keywords: Benzene, Carcinogen, Cancer, Bioremediation, Probiotic.
HTTP://UI.CNF.IR/PPS 89
The optimization of expression of recombinant denileukin diftitox in
soluble form
Bahareh Mortezagholi1, Reza Hasan Sajedi1*, Mehdi Zeinoddini2 , Khosro Khajeh3
1*Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
2Department of Bioscience and Biotechnology, Mallek Ashtar University of Technology, Tehran, Iran.
3Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Abstract
Denileukin diftitox (trade name Ontak®) was constructed using recombinant DNA technology
(1999) to target malignant cells expressing the IL-2 receptor, after confirmation America Food
and Drug Administration (FDA) by Eisai Company became available. Recombinant Denileukin
diftitox is made by combining a part of the amino acid sequences for IL-2 followed by the
sequences for diphtheria toxin. In order to produce the recombinant protein, design of an
expression system is essential that E. coli is the most famous and widely used expression system
that has fast-growing production in mass volumes however high level expression of recombinant
Denileukin diftitox in E. coli leads to the formation of insoluble aggregation as inclusion body.
In this project, to provide optimal condition for expression of the Soluble form of the protein in
E. coli strain BL21 (DE3). For this purpose, with different temperatures, various concentrations
of IPTG and different times, expression performed and finally, protein in soluble form was
obtained. The protein solution was passed from the Ni-NTA affinity chromatography and soluble
proteins were isolated from the sedimentat. The SDS-PAGE was indicated the maximum
expression and high purity of the soluble protein.
Keywords: Denileukin diftitox, Aggregation, Soluble protein, High purity.
HTTP://UI.CNF.IR/PPS 90
Protective effect of polyphenols against mitochondrial membrane
permeabilization induced by HEWL aggregates
Bijan Akbari1, Ali Akbar Meratan2, Mahshid Shafizadeh1, Shahin Ahmadian1
1 Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, 1417614411 Tehran, Iran.
2 Department of Biological Sciences, Institute in Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran.
Abstract
A growing body of evidence demonstrates that mitochondrial dysfunction is the earlier and the
most common character of a wide range of protein-deposition disorders, including
neurodegenerative diseases and peripheral disorders such as systemic amyloidosis and type II
diabetes. In regard to the mechanism of mitochondrial dysfunction, it has been proposed that
interaction of prefibrillar intermediates with mitochondrial membrane is a major determinant of
cytotoxicity. In line with this concept, compounds that interfere with the aggregate species to
bind lipid membranes may serve as therapeutic agents for the treatment of amyloid-associated
disorders. In the present study, the ability of two naturally occurring polyphenols including
resveratrol and curcumin in preventing the HEWL oligomer-induced membrane permeabilization
of mitochondria isolated from brain, liver and heart was investigated. Mitochondrial membrane
permeabilization was investigated following an approach involving the release of malate
dehydrogenase located in the mitochondrial matrix. Our results demonstrated that both
polyphenols effectively inhibit HEWL oligomer-induced membrane permeabilization in a
concentration-dependent manner. Polyphenol-induced protection was found to be more effective
in liver and heart compared to brain mitochondria. In conclusion, we suggest that resveratrol and
curcumin can effectively hinder mitochondrial membrane damage by HEWL oligomers and may
serve as important drug leads to alleviate mitochondrial dysfunction in neurodegenerative
diseases.
Keywords: Hen egg white lysozyme, Mitochondria, Membrane permeabilization, Oligomer,
Polyphenol.
HTTP://UI.CNF.IR/PPS 91
Immobilization of Termomyces lanuginosus xylanase enzyme on
functionalized graphen oxide and determination of activity and
thermal stability
Vajihe Mehnati-Najafabadi1, Abdol-khalegh Bordbar2, Asghar Taheri- Kafrani3
1Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
2Department of Chemistry, University of Isfahan, Isfahan, Iran.
3Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University
of Isfahan, Isfahan, Iran.
Abstract
The covalent binding of xylanase enzyme on functionalized Graphen Oxide
was investigated. The structure, size, and magnetic properties of the
support and immobilized xylanase were characterized by transmission
electron microscopy (TEM), Fourier-transform infrared spectra (FTIR) and
thermo-gravimetric analysis (TGA). The TEM images showed that the
Enzyme was immobilized on support succesful. The FTIR results
demonstrated the successfully immobilization of xylanase on functionalized
magnetic nano particles Graphen Oxide (MNPsGO). Results from Bradford protein
assay and TGA indicated that xylanase was covalently attached to the
surface of magnetic support. Enzymatic activity, reusability, thermo-
stability, and storage stability of the immobilized xylanase were found
significantly superior to those of the free one. The Immobilized enzyme
exhibited maximal catalytic activity at 60 0 C and were found to keep high
more than 80% of the activity of free ones. Notably, xylanase-MNPsGO
showed quite impressive stability, even after 10 reaction cycles, it could
still retain more than 65% of the initial activity. Results indicated that the
MNPsGO could be a suitable support for Xylanase in food, chemical and
biofuel product industries.
Keywords: Xylanase, Immobilization, Graphen oxide, Enzyme stability, Enzymatic Activity.
HTTP://UI.CNF.IR/PPS 92
Covalent binding of xylanase enzyme on functionalized
superparamagnetic graphene oxide nanoparticles and evaluation of
activity and pH stability
Vajihe Mehnati-Najafabadi1, Abdol-khalegh Bordbar2, Asghar Taheri- Kafrani3
1Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran. 2Department of Chemistry, University of Isfahan, Isfahan, Iran. 3Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University
of Isfahan, Isfahan, Iran.
Abstract
The covalent immobilizayion of xylanase enzyme on functionalized
Graphen Oxide was investigated. The structure, size, and magnetic
properties of the support and immobilized xylanase were characterized by
transmission electron microscopy (TEM), Fourier-transform infrared spectra
(FTIR). The results from TEM and FTIR demonstrated that xylanase was
covalently attached to the surface of magnetic support. Enzymatic activity,
reusability, pH-stability, and storage stability of the immobilized xylanase
were found significantly superior to those of the free xylanase. The
Immobilized enzyme exhibited maximal catalytic activity at pH 6.5 and
were found to keep high more than 80% of the activity of free xylanase.
Notably, immobilized enzyme showed quite high stability, even after 10
reaction cycles, it could still retain more than 50% of its initial activity.
Results reflected that the immobilized xylanase could be an appropriate
matrix for xylanase in food, chemical and bevarage industries.
Keywords: Xylanase, Immobilization, Graphen oxide, Enzyme stability, Enzymatic Activity.
HTTP://UI.CNF.IR/PPS 93
Investigation the effects of different osmolytes on the structure of
trypsin
Sheyda Mahmoodian, Behzad Shareghi, Elham Dadaie
Department of Biochemistry, College of Sciences, Shahrekord University, Iran.
Abstract
Trypsin EC (3.4, 21, 4) is a serine proteases that contains a water-soluble globular protein,
hydrolizing peptide binding.In this study the effects of different Osmolytes (i.e., sucrose,
erythrose, and tyrosine) on Trypsin enzyme structure was investigated .For all fluorimetry
experiments Spectrofluorophotometer device Shimadzu model RF-5103PC was used at 2
different temperatures (25 and 35 °C), pH 8, using an excitation wavelength of 280 nm and
emission wavelength of 340-290 nm. The Flourescence Spectrometry indicated that all
Osmolytes could quench the intrinsic Flourescence of Trypsin throuh static quenchin.
Furthermore, thermodynamic analysis indicated that the hydrogen bonds and Van der Waals
force are the dominant forces in interaction trypsin with the osmolytes.
Keywords: Trypsin, Osmolytes, The structure of the enzyme, Fluorescence.
HTTP://UI.CNF.IR/PPS 94
Bagging algorithm for protein thermostability prediction based on
pseudo amino acid composition
Maryam Mahmoudi, Seyed Shahriar Arab, Javad Zahiri, Mozhgan Mozaffari Legha
Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IRAN.
Abstract
Proteins in terms of thermal stability are divided into several categories at different temperatures.
Thermophile and hyperthermophile proteins have high thermal stability and are able to maintain
the structure and function at higher temperatures near or above the boiling point of water. The
mesophilic proteins are stable at lower temperatures. The role of thermal stable protein in design
of enzymes, protein engineering, drug design, medical and industrial processes cause them one
of interesting research fields in the recent years. Stability in the different temperature is
associated with the structural and sequence features of proteins. Identifying these features to
build an efficient computational model for termal stability prediction is of critical importance
due to the costs of in vitro studies. In this study, we exploited bagging algorithm using pseudo
amino acid composition feature to predict the protein thermostability. The results show that
pseudo amino acid composition is one of the most important feature in discrimination of
thermophilic and mesophilic proteins. Proposed model achieved accuracy of 96.9%.
Keywords: Protein thermostability, Thermophilic proteins, Mesophilic proteins, Structure and
sequence features, Machine learning methods, Bagging.
HTTP://UI.CNF.IR/PPS 95
Efficient synthesis of novel eptifibatide analogous
Kazem Mahmoudzadeh1, Azam Monfared1, Saeed Balalaie2, 3
1University of Payame Nour, Tehran Branch
2Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416.
3Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
Abstract
Eptifibatide is an antiplatelet drug of the glycoprotein IIb/IIIa inhibitor class. It is
a cyclic heptapeptide. It belongs to the class of the arginin-glycin-aspartat-mimetics and
reversibly binds to platelets. Eptifibatide has a short half-life. In continuation of our program for
the synthesis of some pharmaceutical active ingredients peptides which have disulfide bridge,
herein we report the synthesis of eptifibatide and their novel analogues using a combination of
solid phase peptide synthesis and solution phase. The novel analogues contain the ethylamide,
semicarbizide, and thiosemicarbazide which has been added at the C-terminal. The structure of
the synthesized compounds was confirmed based on HR-MS(ESI). The antiplatelet investigation
of the synthesized compounds compared to eptifibatide is in progress.
Keywords: Analogous, Eptifibatide, Antiplatelet.
HTTP://UI.CNF.IR/PPS 96
Bioactive peptides from egg-whites of different avian species
Ladan Aminlari1, Leila Hajipour2, Maryam Tavana3, Mohamad Mohsen Mohammadi3
1Department of Food Hygiene, School of Veterinary Medicine, Shiraz University, Shiraz, Iran.
2Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran.
3Department of Biochemistry, School of Veterinary Medicine, Shiraz University, Shiraz, Iran.
Abstract
The aim of this study was to isolate and compare bioactive peptides from egg-white of quail,
duck and chicken and to determine their antimicrobial and antioxidant properties. The egg-white
proteins were diluted, the major proteins precipitated by trichloroacetic acid, centrifuged to
remove the precipitate and the supernatant subjected to G-25 Sephadex gel-filtration
chromatography to isolate the peptides. The bioactive properties of the fractionated peptide were
determined. The elution pattern of peptides obtained by gel filtration chromatography of egg
white from different species of birds were different with different properties of the fractions,
indicating that endogenous proteases had significantly different effects on the proteins of egg
whites of different species. The peptide fractions exhibited high antimicrobial and antioxidant
properties. Most of the peptides which were eluted at the final stage of gel-filtration
chromatography showed the highest antimicrobial properties against E. Coli and Bacillus Cerus.
The results suggested that it is possible substitute the antioxidant and antimicrobial agents of
chemical origin with peptides naturally present in egg-whites of duck, chicken and quail.
Keywords: Bioactive peptides, Egg white, Gel filtration chromatography, Antioxidant,
Antimicrobial properties.
HTTP://UI.CNF.IR/PPS 97
In silico study of molecular interaction between cel-D7 (a novel
drivative of celastrol) and proteasome using the autodock software
Elmira Mohammadi1, Mohammadreza Mofid2 , Neda Fayyazi3, Sana Pirmardvand Chegini4, Ali Jahanian
Najafabadi1
1 Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Pharmaceutical Sciences, Univercity of
Medical Sciences. Isfahan, Iran.
2 Department of Biochemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Univercity of Medical Sciences.
Isfahan, Iran.
3 Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Univercity of
Medical Sciences. Isfahan, Iran.
4 Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, Univercity of Medical Sciences.
Isfahan, Iran.
Abstract
The proteasome is a multicatalytic enzyme complex with a molecular weight of 2.5 MDa.
Usually, the cellular proteasome is referred to as the 26S proteasome in accordance with its
sedimentation coefficient. The 20S proteasome is the catalytic core of the 26S proteasome
complex, which contains of four stacked rings that form a barrel with a central cavity. These
stacked rings include two non-catalytic α rings (each with seven nonidentical subunits) outside of
two catalytic β. The catalytic activity of the β rings are found within the β1(caspase or
peptidylglutamyl peptide-hydrolyzing-like (PGPH) activity), β2(trypsin-like activity), and
β5(chmotrypsin-like proteolytic activity) subunits. In all the three β-subunits, a threonine residue
at the amino terminal (Thr1) is considered to be the catalytically active amino acid. Inhibition of
proteasome have some biological effects especially in cancer inhibition; consist of: cell cycle
arrest and apoptosis. In various studies several natural compounds with proteasome inhibitory
activity were assessed such as celastrol. Cel-D7 is a novel derivative of celastrol with low cell
toxicity. In this study in silico intraction of cel-D7 with subunit β5, S1 pocket, of proteasom was
assessed with auotodock soft ware. Result from docking study revealed that this compound
intracted with minimum H bonding energy with Thr1 and also has intraction with Met45.
Keywords: Cel-D7, Celastrol derivative, Proteasome, Molecular docking.
HTTP://UI.CNF.IR/PPS 98
Improvement of Bacillus subtilis ZH1 biosurfactant production
Atieh Motaghi Golshan, Jamshid Fooladi, Parichehr Hanach
Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
Abstract
Biosurfactants are surface active agents produced by microorganisms. They have many
applications in food, pharmaceutical industries as natural emulsans and some of them have
biocidal, insecticidal activities. Bacillus subtilis biosurfactants are among the most powerful ones
as they reduce the surface tension of distilled water from 72 to 28 mN m-1 and are suitable for
bioremedation of oil-contaminated lands. We try to improve the biosurfactant production of
Bacillus subtilis ZH1 by adding both organic nitrogen source and inorganic nitrogen source in
the growth medium. Different concentration of ammonium dihyrogen phosphate, 1%, 1.5% and
2%, was added to the medium as the inorganic nitrogen source. Oil spreading test, using ODA
(Oil Displacement Area) as an index, is an indirect method for measuring the amount of
produced biosurfactant. These tests showed that 2% ammonium dihyrogen phosphate has larger
ODA and thus, improves the biosurfactant production.
Keywords: Biosurfactant, Bacillus subtilis, Improvement, Oil spreading test, Ammonium
dihydrogen phosphate.
HTTP://UI.CNF.IR/PPS 99
Probing the interaction of chemotherapeutic drug of 5-fluorouracil
and milk carrier protein of -lactoglobulin
Amineh Leilabadi-Asl1, Adeleh Divsalar2, Ali Akbar Saboury3, Kazem Parivar1
1Department of Science and Research Branch, Islamic Azad University, Tehran, Iran.
2 Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
3 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
Abstract
In the present study, the interaction and side effects of a chemotherapeutic anti-cancer drug of5-
Fluorouracil with milk carrier protein of β-lactoglobulin (BLG) was investigated using various
spectroscopic methods of fluorescence and circular dichroism at two temperatures of 25 and 37
°C. The analysis of fluorescence spectra showed that the addition of the 5-Fluorouracil to BLG
solution led to a significant reduction in the intrinsic fluorescence spectra of protein and then
quenched it. Values of the number of binding sites and the binding constants of 5-Fluorouracil on
protein were calculated at different temperatures according quenching method. Analysis of
Stern-Volmer curve of protein showed that the dynamic mechanism has a major role in
fluorescence quenching of BLG. Also, binding results have represented that there is 2 binding
sites on BLG for binding of 5-Fluorouracil at two temperatures of 25 and 37 °C, respectively.
Finally, according above results, it can be concluded that the anticancer drug of 5-Fluorouracil
can bind to carrier protein of BLG and changed the tertiary structure of it.
Keywords: β-Lactoglobulin, 5-Fluorouracil, Fluorescence, Binding site.
HTTP://UI.CNF.IR/PPS 100
Identification of RCC in structure of large envelope protein S of
HBV and molecular modeling
Mojtaba mortazavi1, Safa Lotfi1, Masoud Torkzadeh1, Mehdi Rahimi1, Abdorrasoul Malekpou2, Mohsen
ModaresKia1
1Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate
University of Advanced Technology, Kerman, Iran. 2Gastroenterohepathology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
Abstract HBV causes the death of over one million persons per year by liver failure or hepatocellular
carcinoma. The virus particle (virion) consists of an outer lipid envelope and an icosahedral
nucleocapsid core composed of protein. Recent studies suggest that rare codon clusters are
functionally important for protein activity. Here, for the first time we analyzed and reported rare
codon clusters in HBV genome and their protein structure. This analysis was performed using
the Sherlocc program that detects statistically relevant conserved rare codon clusters. By this
program, the rare codon cluster was identified in large envelope protein S (PF00695). For further
understanding of the role of these rare codon clusters, we studied location of these rare codon
cluster in structure of large envelope protein S. We identified some of critical residues near or
within rare codon cluster. It should be mentioned that characteristics of these critical residues
such as location and situation of side chains are important in assurance of the HBV life cycle.
The results of this study provide new and deep perspectives about structure of HBV proteins for
further researches and designing new drugs for treatment of HBV.
Keywords: HBV genome and proteins, Rare codon cluster, Sherlocc program, Ribosomal pauses.
HTTP://UI.CNF.IR/PPS 101
Antimicrobial activity of heat stable peptides in Iranian native
Bacillus strains with probiotic potential
Mohsen Golnari Maranni1, Nastaran Bahrami2, Mohammad Rabbani3, Mohammad Ali Asadollahi1
1Biotechnology Department, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
2Microbiology group, Nour Danesh non-profit higher education institute of Meymeh, Isfahan, Iran.
3Biology Department, Faculty of Science, University of Isfahan, Isfahan, Iran.
Abstract
Probiotics are beneficial microbes with healthy effects on their hosts and consumers. Recently
the use of Bacillus strains as probiotics has received a great deal of attention because of their
sporulation and resistance to stress conditions like low pH of the gastric fluid. Bacillus bacteria
could play a significant role in the gastrointestinal tract because of the high resistance of their
spores, immune-stimulatory and antimicrobial activities. Most of the antimicrobial substances
produced by Bacilli have peptide structures but some strains produce antibiotics belonging to
other chemical classes. In this study, the antimicrobial activity of heat stable peptides of Bacillus
isolates was investigated. Thirty-nine Bacillus strains were isolated from a variety of dairy
products, soil samples, vinegar, livestock excreta and poultry excreta samples. Isolates were
identified by biochemical and molecular methods. These Bacillus strains were screened for
probiotic characteristics and 14 strains were selected and investigated for antimicrobial activities
against potential bacterial pathogens such as S. aureus, S. enterica, Shigellea sonei, Listerai
monocytogenes, E. coli and S. pyogenes. These strains were identified as B. subtilis, B.
licheniformis, B. toyonensis, B. pumilus, B. coagulans, B. amiloliquifaciens, B. endophitycus and
B. siamensis. Three different experimental approaches (Spotting, Well Diffusion and Mixed
Culture) were used to detect antibacterial activities and results revealed that these activities could
be because of the presence of heat stable peptides.
Keywords: Bacillus, Probiotics, Antimicrobial activity, Heat-stable peptides.
HTTP://UI.CNF.IR/PPS 102
Preparation and characterization of monoclonal antibody against
carcinoembryonic antigen and immunohistchemistry evaluation Mohammad Keyvanloo Shahrestanaki 1, Bratali Mashkani 1, Mahboobeh Alamdari 2, Mohammad Nadri 1,
Mohsen Sisakhti 3, Taiebe Kianosh 1, Seyed Isaac Hashemy1,5, Amir Hossein Jafarian Mohammad
Soukhtanloo 1,4,
1Department of Clinical Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad,
Iran.
2Department of Biochemistry, School of Science, Payame Noor University, Mashhad, Iran.
3Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
4Cancer Molecular Pathology Research Center, Ghaem Hospital, School of Medicine, Mashhad University of
Medical Sciences, Mashhad, Iran.
5Surgical Oncology Research Center, Imam Reza hospital, Faculty of Medicine, Mashhad University of Medical
Sciences, Mashhad, Iran.
Abstract
Carcinoembryonic antigen (CEA) considered as a tumor- associated antigen. It is a highly
glycosylated protein, which overexpressed in many different cancers, mainly in colorectal
cancer. Specific monoclonal antibodies (mAb) against this antigen provide helpful strategies for
detection of this antigen in serum and tissue, which in turn can be used for diagnostic and
therapeutic purposes. our goal was production of anti- CEA mAb. This mAb can detect CEA in
sera of patient with colon carcinoma and also can be used for immunohistochemical assays.
Briefly two male mice 6-old-week immunized with CEA. Anti-CEA levels of mAbs in sera
evaluated with designing indirect ELISA. Hybridoma cells produced by fusion of SP2/0
myeloma cells and spleen cells of immunized animals. After screening of fused cells in RPMI-
HAT, HT media, mAb secretion of each colon evaluated by indirect ELISA. Best clone (RM1)
selected and used for isotyping and immunohistochemistry analysis. Efficiency of fusion was
65%, which implicated fairly good immunization of animals. Isotype of RM1 determined IgG2b,
and kappa light chain. The affinity of this antibody estimated 5×10-6 M. According to
immunohistochemical analysis, predominant staining of gland lumina performs very well with
RM1. RM1 can be considered as a valuable tool for detecting CEA in the sera of patient with
colon carcinoma. RM1 shows very good immunohistochemical results in comparison to Dako
antibody and can be used for determining of this antigen in tissue and other related fluids.
Keywords: Carcinoembryonic antigen, Monoclonal antibody, Hybridoma.
HTTP://UI.CNF.IR/PPS 103
Construction of BSA nanogels-loaded doxorubicin and its anti-
carcinoma effect on MES-SA/DX5
Zahra Kayani1, Abdol-khalegh Bordba1, 2, Omidreza Firuzi1, 3
1Biotechnology Department, University of Isfahan, Isfahan, Iran.
2Chemistry Department, University of Isfahan, Isfahan, Iran.
3Medicinal and natural products chemistry research center, Shiraz University of Medical Sciences, Shiraz, Iran.
Abstract
BSA nanogels (BSA ng) for the treatment of cancers were prepared successfully. These nanogels
were synthesized and used for loading doxorubicin as a nano-system for enhancing intracellular
uptake via endocytosis by cancer cells. The results indicated that BSA nanogels loaded with
doxorubicin (DBSA ng) can effect on drug-resistant MES-SA/DX5 cells compared with
doxorubicin. Increased therapeutic efficiency of doxorubicin loaded BSA nanogels were also
tested in MES-SA/DX5 cells and compared with doxorubicin. In addition, the cell accumulation
levels of DBSA ng in MES-SA/DX5 was time dependent for these nanoparticles. DBSA ng
(effective diameter: 109 ± 1.1 nm; polydispersity index: 0.193) could significantly boost cellular
accumulation of doxorubicin and overcome the drug efflux mechanism of MDR in resistant cell
lines. In conclusion, DBSA ng can be used as a potentially effective drug delivery system.
Keywords: BSA nanogel, Doxorubicin, MDR mechanism, drug delivery.
Keywords: BSA nanogels, doxorubicin, drug delivery, anti-carcinoma effect.
HTTP://UI.CNF.IR/PPS 104
Medical applications of antimicrobial peptide
Sahar Kashkouli 1, Nasrin Molavi 1, Hossein Mazarei 1, Hadi Zare-Zardini 2, Azam Hashemi 2
1 Student of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran.
2 Hematology and Onccology Research Center, Shahid Sadoughi University of Medical Sciences and Health
Services, Yazd, Iran.
Abstract
Increasing use of antibiotics for treating infectious diseases has provided fields for creating
resistant strains, so that nowadays some bacterial strains are not under the influence of any of
today's common antibiotics. So today we should be looking for a suitable alternative to these
compounds so that we can be able to deal with this problem. Through this it has been determined
that antimicrobial peptides (AMPs) that produced by all organisms and play important role in
innate immunity, have significant effects against various microbes. These peptides are suitable
candidates for treatment and prevention of microbial infections. In this review, the properties,
mechanism and application of AMPs as potent antimicrobial drugs was discussed. Methods that
used in this study is a literature review of important research on AMPs. According to this review,
natural and modified AMPs have potent properties for application as antimicrobial drugs. These
peptides can be modified for reduction of side effects and then, obtained Food & Drug
Administration approval for any topical or systemic medical indications. AMPs are useful for
treatment of infectious diseases. However, their usefulness as a new class of antimicrobial drugs
still remains to be proven.
Keywords: Antibiotics, Antimicrobial peptides, Antimicrobial drugs, Infectious diseases.
HTTP://UI.CNF.IR/PPS 105
Study of the interaction change between the cytosolic components of
the NADPH oxidase in cell free system
Gilda Karimi1 and Tania Bizouarn2
1 Department of Biological Sciences, Kharazmi University, Tehran, Iran.
2Laboratoire de Chimie physique, UMR8000, CNRS-Université Paris Sud-Orsay, Franc.
Abstract
The NADPH oxidase (NOX) is the major source of superoxide radicals in phagocyte cells. The
system is made of several cytosolic (p47phox, p67phox, rac) and membrane (gp91phox, p22phox)
proteins. We have constructed a cell-free Nox system in order to explore some aspects of the
functioning of this enzyme. Using various methods such as surface plasmon resonance (Biacore),
fluorescence measurements and kinetics measurements in cell free system, we are studying the
assembly process of NADPH oxydase of phagocyte. Our results confirm that p47phox subunit
helps the binding of p67phox on the complex but with less extend than found in the literature
secondly it increases the rate of superoxide production suggesting a true adaptor role of p47phox.
In addition, our experiments show that in our system, p47phox is not a competitor for the dimer
p67phox-p47phox which means that p47phox alone would not tightly bind to the flavocytochrome.
Finally we will present a comparison of EC50 obtained with various mutants of p47phox that
gives information on the domains that are involved in this assembly process.
Keywords: NADPH oxidase, Cell free system, Assembly process.
HTTP://UI.CNF.IR/PPS 106
Exploring of the assembly process of the NADPH oxidase complex
via the structural changes of p47phox and p67phox subunits
Gilda Karimi
Department of Biological Sciences, Kharazmi University, Tehran, Iran.
Abstract
The NADPH oxidase (NOX) is the major source of superoxide radicals in phagocyte cells. The
system is made of several cytosolic (p47phox, p67phox, rac) and membrane (gp91phox, p22phox)
proteins. We have constructed a cell-free Nox system in order to explore some aspects of the
functioning of this enzyme. Our aim is to get new insights into the assembly process of the
NADPH oxidase complex and to investigate the structural modifications induced by the
assembly of its different partners. Using SRCD spectroscopy, we investigated the conformational
changes associated with the assembly process, the role of arachidonic acid in the process and the
conformation changes induced by post-translational modifications.
Keywords: NADPH oxidase, Assembly process, Structural changes.
.
HTTP://UI.CNF.IR/PPS 107
Effects of fermentation by cocci lactic acid bacteria isolated from
Iranian dairy products on the immunoreactivity of Cow's milk
caseinate
Reihane Kordesedehi1, Mohammad Rabbani-khurasgani2, Asghar Taheri-Kafrani1, Rezvan Kazemi1
1Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.
2Departement of biology, Faculty of sciences, University of Isfahan, Isfahan, Iran.
Abstract
Bovine milk is the best substitution for infant's diet when breast feeding is not possible. Cow’s
milk contains 30–35 g of different proteins per litre. The coagulum of milk can be obtained
through the acidification of raw skim milk or action of renin which consists of four proteins
(αS1-, αS2-, β and к-casein). Caseins form ordered aggregates that termed micelles. Cow's milk
caseins play a basic role in persistent of cow’s milk allergy (CMA), so the feeding of an infant
allergic to cow’s milk casein may create serious allergenic reactions. Probiotic Lactic acid
bacteria (LAB) have long been used by consumers in fermented dairy products. It should be
highlighted that the proteolytic enzymes of LAB can reduce the allergenicity of hydrolyzed
proteins such as caseins. The aim of this study was to screen out cocci LAB from cow and camel
milk samples and evaluate their proteolytic activity on caseinate digestion and their ability to
degrade the main allergenic sequences. The ability of LAB supernatant to hydrolyze caseinate
was tested after growing the bacterial cells in milk citrate agar media (MCA) for 48 h at 37°C.
The effects of proteolytic activity of these bacteria on milk proteins were investigated using
SDS-PAGE and RP-HPLC techniques. The most effective bacteria for the hydrolysis of
caseinate were isolated. Residual antigenicity of these proteins was determined by competitive
ELISA test, using a pool of sera from cow’s milk allergy patients. The study findings show that
caseinate hydrolysates are less able to bind to IgE from serum of patients with allergy to cow's
milk. The results indicated that lactic acid fermentation can attenuate caseinate antigenity in
cow's milk. These bacteria can be used to reduce allergy in Iranian dairy products.
Keywords: Caseinate, Lactic acid bacteria, Cow’s milk allergy, Competitive ELISA.
HTTP://UI.CNF.IR/PPS 108
A thermodynamic study on the interaction of propolis and human
hemoglobin
Fatemeh Kazemi1, Adeleh Divsalar2, Ali Akbar Saboury1
1 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
2Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
Abstract
Propolis or bee glue is a resinous hive product collected by honey bees from buds and leaves
secretions of trees and has several biological properties such as antimicrobial, antifungal, anti-
aging, anticancer, anti-inflammatory, and antioxidant properties. In the present study, we have
investigated the structural changes in purified human hemoglobin (Hb) upon interaction with
propolis using various spectroscopic techniques at two temperatures of 25 and 37 C.
Fluorescence results have shown that adding of propolis extract to Hb solution lead to significant
reduction in intrinsic fluorescence of protein and can quench it. Also, the number of binding sites
and binding constants of this interaction calculated according quenching method at two
temperatures of 25 and 37 C. Binding analysis represented that there is one binding site for
propolis on the human at both of the temperatures of 25 and 37 C. Since during heme
degradation in Hb, two fluorescent compounds produces. Then, the induction of heme
degradation in Hb in the presence of various concentrations of Propolis was checked and results
showed that low concentrations of propolis did not induce any significant heme degradation in
Hb.From above results, it can be concluded that propolis can bind and interact with human Hb
without any significant structural changes which might be considered as an herbal drug with low
side effect.
Keywords: Hemoglobin, Propolis, Quenching, Hem degradation, Fluorescence.
HTTP://UI.CNF.IR/PPS 109
Studding the solubility of EGFP upon replacing valine 12 by lysine,
using bioinformatics tools
Sheida Kazemi 1, Rahman Emamzadeh 2, Behnaz Safar 3
1Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran 2Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran. 3Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran.
Abstract
Enhanced green fluorescent protein (EGFP) has a β-barrel structure and a low molecular weight
of about 27 kDa. This fluorescent protein after excitation in 395 nm, emits a green beam of light
in 508 nm with no extra chemical ingredient or substrate. These features make it an appropriate
tag for detection of proteins expression, protein-protein expression and transformation or
transfection analysis. In spite of these application, its approximately low stability faced its usage
with difficulty. Thus altering EGFP to more soluble mutants is an attractive field of protein
engineering. In this study the protein 3D structure was built using SWISS-MODEL server and
based on homology modeling. Then the structure analyzed with SPDBV software and accessible
residues determined. Valine 12 as a non-polar and exposed residue was chosen. Finally valine 12
replaced with lysine and its solubility was studied using ESPRSSO (mbs.cbrc.jp/ ESPRSSO).
The result expressed that upon this mutagenesis, replacing valine 12 by lysine, protein solubility
might increase slightly. Regarding to the lysine feature as a polar and ionic residue this result has
been expected.
Keywords: EGFP, Mutagenesis, Solubility, Valine 12.
HTTP://UI.CNF.IR/PPS 110
Enhanced green fluorescent protein instability upon replacing
phenylalanine 226 by alanine
Sheida Kazemi 1, Rahman Emamzadeh 2, Behnaz Safar 1
1 Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran.
2 Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran.
Abstract
Enhanced green fluorescent protein (EGFP) is a fluorescent protein that is widely used as a
protein reporter in conjugation with other proteins. This protein tag used for monitoring in time
of several biological phenomena in living cells. Although protein instability is a general
limitation in protein utilization assays. Thus protein engineering to achieve more stable protein is
an active field of search. In this study protein stability upon mutagenesis was predicted. PDB
file of EGFP was made using SWISS-MODEL server based on homology modeling. Then PDB
file was uploaded in HotSpot Wizard 1.7 server, and high mutability residues were evaluated.
Finally phenylalanine 226 was chosen and its stability was predicted upon replacing by alanine
using DUET server (http://bleoberis.bioc.cam.ac.uk/duet/stability). The mutation caused a
negative value of DDG (-2.265 Kcal/mol) which means manipulation of F226 has an unstable
effect on EGFP structure. This result represents that phenylalanine 226 may participate in
hydrophobic interaction with other residues in the β-barrel structure of EGFP, and thus replacing
of that by alanine caused a destabilizing effects.
Keywords: EGFP, Protein stability, DUET server, Hydrophobic interaction.
HTTP://UI.CNF.IR/PPS 111
Assesment of cow’s milk β-lactoglobulin allergenicity reduction
using cocci lactic acid bacteria isolated from Iranian dairy products
Rezvan Kazemi, Asghar Taheri-Kafrani, Reihane Kordesedehi
Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.
Abstract
The prevalence of food allergies has increased around the world, so the World Health
Organization (WHO) has declared it as a sixth human health problem. Nearly few foods are
responsible for the majority of considerable food-induced allergic reactions. Cow's milk proteins
(CMA) are the most important food allergens have been reported. Today, 4-8 % of children
under 3 years old suffer from allergy to cow's milk (CMA). The milk protein β-lactoglobulin (β-
lg) caused about 80% of all main cases of milk allergies for children and infants. Some studies
showed that the enzymatic activity of probiotic bacteria can reduce the potential allergenicity of
milk proteins. Therefore, in the present work, 20 kinds of traditional milk have been collected
from different regions of Iran, and 13 types of Lactic acid cocci bacteria have been isolated in
M17 broth and agar medium. The effects of proteolytic activity of these bacteria on milk proteins
were investigated using SDS-PAGE and RP-HPLC techniques. The most effective bacteria for
the hydrolysis of β-lg were isolated. Residual antigenicity of these proteins was determined by
competitive ELISA test, using a pool of sera from cow’s milk allergy patients. The study
findings show that β-lg hydrolysates are less able to bind to IgE from serum of patients with
allergy to cow's milk. The results indicated that lactic acid fermentation can attenuate β-lg
antigenity in cow's milk. These bacteria can be used to reduce allergy in Iranian dairy products.
Keywords: β-Lactoglobulin, Lactic acid bacteria, Cow’s milk allergy, Competitive ELISA.
HTTP://UI.CNF.IR/PPS 112
Computer-aided evaluation of M4 protein (a truncated version of
IL-24) with Bioinformatics tools
Reza Ghavimi1, Mohammadreza Mofid2, Ali Jahanian Najafabadi1, Mohammad Keyvanloo2, Neda
Fayyazi3
1 Department of Pharmaceutical Biotechnology, Faculty ofPharmacy and Pharmaceutical Sciences, University of
Medical Sciences.Isfahan, Iran.
2 Department of Biochemistry, Faculty ofPharmacy and Pharmaceutical Sciences, University of Medical Sciences.
Isfahan, Iran.
3Department of PharmaceuticalChemistry, Faculty ofPharmacy and Pharmaceutical Sciences, University of Medical
Sciences. Isfahan, Iran.
Abstract
Fusion proteins (FPs) are chimeric proteins constructed by genetically fusing two or more
protein domains together by a linker molecule. In most cases a cell penetrating or apoptosis
inducing peptide along with another protein domain as a targeting moiety are participated in
structure of FPs. FPs have wide applications in biological and pharmaceutical research such as
protein purification, drug delivery, tumor targeting and designing of anticancer drugs. IL-24 is a
cytokine with 206 aa that could selectively induce apoptosis in cancer cells without harming
normal cells. An N-terminal truncated molecule, M4 having amino acid residues 104–206 of IL-
24, contains essential domains required for cancer-specific apoptotic activity of this molecule, so
by connecting of M4and targeting moiety with a suitable linker, itcan be applied in the structure
of FPs.According to growing importance of FPs, bioinformatics evaluation of M4 can reveal
some new avenues for structure manipulating to increase itsapplication value. Thus, the aim of
this study was evaluation of M4 using bioinformatics tools. In this study, virtual cloning of M4
in pET32a+ vector performed step by step by Vector NTI® Software (Thermo Fisher Scientific)
and some of M4 features evaluated by bioinformatics tools. Finally, interaction of M4 evaluated
by docking online tools. Result from current study revealed that M4 has sufficient potential for
using into FPs.
Keywords: Fusion protein, IL-24, M4, Bioinformatics.
HTTP://UI.CNF.IR/PPS 113
Promotion of antioxidant peptides of tomato waste seed meals by
bacillus subtilis submerged fermentation
Elham Ghanbari, Fakhri sadat Hoseini, Zahra Moosavinejad.
Microbial National Laboratory, Alzahra University, Tehran, Iran.
Abstract
The vast uses of tomato in culinary preparations and processes it into products such as juices,
sauce, ketchup, and powder cause to remain seed waste of it with high nutritive value to reach
bioactive peptides owing to they are economic, acceptable, and safe type of protein sources
among the different plants and animals proposed. In this study, we used tomato meal as by-
product of oil industry have good biological value and with a minimum processing we can reach
to peptides that are useful and healthful component with higher antioxidant activity. Ground
deoiled tomato seed meal was used for bacillus subtilis submerged fermentation in the 100 ml
cultivate medium in 250 ml flask for 72 hr incubation. Every 24 hr sampling and antioxidant
activity measured by radical scavenging activity in DPPH test and iron chelating activity in
ferrozine test on the peptides precipitated in ammonium sulfate were conducted. Data are
presented as mean ± SEM and they were analyzed by unpaired t test. Increasing radical
scavenging activity and iron chelating activity were respectively from 13.44±0.83 to 20.07±0.54
and 8.72±2.93 to 26.32±3.60 after 48 hr incubation. (p<0.05) Submerged fermentation of the
tomato seed meal by bacillus subtilis can increase antioxidant activity. Further studies are needed
to peptide sequences and structure analysis.
Keywords: Radical scavenging, DPPH test, Tomato seed meal, Submerged fermentation.
HTTP://UI.CNF.IR/PPS 114
Comparison of radical scavenging activity of tomato and grape meal
peptides by bacillus subtilis submerged fermentation
Elham Ghanbari, Fakhri sadat Hoseini, Zahra Moosavinejad
Microbial National Laboratory, Alzahra University, Tehran, Iran.
Abstract:
Tomato and grape seed flours as by-product of juice and food industry represent an available,
economic, and excellent source of protein due to own biological value to reach peptides that are
bioactive, natural, and relatively free from anti nutritional factors. The seed meals of tomato and
grape after oil elimination were used for submerged fermentation in the 100 ml cultivate medium
supplementation with K2HPO4 and MgSO4 in 250 ml flask by bacillus subtilis. Peptides were
precipitated in 90% saturated ammonium sulfate and to evaluate the antioxidant activity DPPH
test was used on samples after 0 and 48 hr incubation. Data are presented as mean ± SEM and
they were analyzed by unpaired t test. Radical scavenging activity increased from
5777.44±123.57 to 7440.51±302.47 in grape peptides and 13.44±0.83 to 20.07±0.54 in tomato
peptides after 48 hr incubation. (p<0.05). Note that grape seed meal in compared with tomato
seed meal have considerable antioxidant activity and both of them antioxidant activity after
bacillus subtilis submerged fermentation can increased. Further studies are needed to structure
analysis and peptide sequences.
Keywords: Radical scavenging, Grape seed meal, DPPH test, Tomato seed meal, Submerged
fermentation.
HTTP://UI.CNF.IR/PPS 115
Glutathione S-transferase protein of some cultivated wheat in Iran
and Sasan Mohsenzadeh *GhanbarzadehZohreh
Department of Biology, Faculty of Sciences, Shiraz University, Shiraz, Iran.
Abstract
Glutathione s-transferase is a family of multifunctional detoxification enzymes which are mainly
cytosolic that detoxify natural and exogenous toxic compounds by conjugation with glutathione
tripeptide. In this study, the sequence of 11 wheat cultivars of the protein gene for this enzyme
was investigated and phylogenetic analysis was drowning. These cultivars are Bosostaya,
Chamran, Roushan, Shahi, Sardari, Omid, Mahouti, Bayat, Darab, Zarrin and Alvand. The
sequences were isolated and submitted in NCBI GeneBank. Nucleotides analaysis, alignment
and draw a phylogenetic tree was performed by CAIcal Server, Multalin and CLC sequence
viewer software, respectively. The results showed that alignment between the wheat cultivars is
about 65% to 90%. The highest percentages of nucleotides in cultivars were: Sardari (T,
18.64%), Chamran (A, 20.45%), Omid (C, 28.55%), Shahi (G, 38.48%), Omid (GC, 63.72) and
Bosostaya (AT, 38.48%). GC rich proteins have more resistant to high temperature, so probably
glutathione s-transferase of Omid wheat is more resistant to high temperatures than other
cultivars. It is noteworthy that other bioinformatics data derived from these cultivars.
Keywords: Alignment, Glutathione S-transferases, Nucleotides, Phylogenetic analysis.
HTTP://UI.CNF.IR/PPS 116
Studying structures and processes involved in the transfer across
nuclear pore complexes using molecular dynamics simulation
Zeinab Ghesmati1 and Sarah Mohammadinejad2
1 Department of Biological sciences, Institute for Advanced Studies in Basic Sciences (IASBS), GavaZang, Zanjan,
Iran.
2 Department of Biological sciences, Institute for Advanced Studies in Basic Sciences (IASBS), GavaZang, Zanjan,
Iran.
Abstract
Nuclear pore complexes (NPCs) are selectively gated pathways between nucleoplasm and
cytoplasm. Whereas small molecules can diffuse freely through NPCs, large molecules (>40
KDa) can pass only when bound to transport receptors. The NPC central channel is filled with
disordered proteins, rich in phenylalanine-glycine (FG) repeats, referred to as FG-nups. Previous
experimental studies prove that FG-nups are the main agents responsible for the selective
function of NPC. In this research, we use molecular dynamics simulation to study the mechanism
behind this selective function.We use a coarse-grained model for the FG-nups, in which each
amino acid is modeled with four spheres. Our results, show that individual FG-nups form
globular structures, whereas arrays of FG-nups tethered to a planar surface, at an FG-repeat
density found in the NPC, form brush-like structures of multi-protein bundles. More than half of
the FG-repeats are found on the surface of the bundles, offering a favorable environment for the
transmission oftransport receptors. Our results confirm the virtual-gate model for the mechanism
of selective function observed for NPCs. Also our simulations with NTF2, as a transport
receptor, show that NTF2 can pass through the NPC central channel by hydrophobic interactions
with FG-repeats, when added into the brush-like structure.
Keywords: Nuclear pore complexes, Coarse-grained model, Brush-like structure,
Transportreceptors, Virtual-gate model.
HTTP://UI.CNF.IR/PPS 117
Investigating the interaction of antibacterial peptide “LLAA” with
the bacterial membrane using molecular dynamics simulation.
Goli Ghobadi1 and Sarah Mohammadinezhad 2
1 Institute for Advanced Studies in Basic Sciences (IASBS), Department of Biological Sciences, Gava Zang,
Zanjan, Iran.
2 Institute for Advanced Studies in Basic Sciences (IASBS), Department of Biological Sciences, Gava Zang,
Zanjan, Iran.
Abstract Antimicrobial peptides (AMPs) are important components of the innate immune systems of the
most organisms. AMPs are generally amphipathic and cationic and have a tendency to interact
with lipid bilayers. LLAA is a 13 residue peptide with antibacterial and anticancer properties and
this peptide is a modified analog of Aurein 1.2 peptide that has more positive charge than Aurein
and its antibacterial effect is about 3 times stronger than Aurein 1.2 peptide. In this work,
molecular dynamics simulation and GROMACS package have been used for investigation of
interaction of LLAA with modeled bacterial membranes that consist of phospholipids with the
ratio 3:1 of POPE/POPG. We have also studied of phospholipid acyl chain which show that
increasing the peptide concentration, causes of significant perturbation bacterial membrane and
decreased the stability of membrane and increases the permeability of the bacterial membrane.
Also calculating the extent of thining of membrane peptide due to interaction with the peptide
shows that increasing the in number of peptides causes more thinning of the membrane. All these
observations together show that the LLAA peptides have better antibacterial performance in the
group relative to a single peptide. Our results show that despite the high affinity of peptides
LLAA to the bacterial membrane, but over 400 ns of our simulation time, no considerable
penetration of the peptide into the membrane of bacteria is observed. This difficulty for the
penetration could be related to the small hydrophobic part of the LLAA peptide in comparison
with its polar part.
Keywords: Antibacterial peptides, Lipid bilayer, LLAA peptide, Molecular dynamics simulation,
GROMACS package.
HTTP://UI.CNF.IR/PPS 118
The effects of a novel phenanthroline-imidazole derivative of
platinum complex on the structure and function of bovine liver
catalase
Rohollah Ghobadi1, Adeleh Divsalar2, Alireza Harifi Mood1, Ali Akbar Saboury3, Mahboube Eslami
Moghadam4
1 Department of Chemistry, Kharazmi University, Tehran, Iran.
2Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
3 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
4Chemistry & Chemical Engineering Research Center of Iran, Tehran, Iran.
Abstract:
Catalase is ahighly active, ubiquitous enzyme which occurs in almost allaerobically respiring
organisms and protectsthe cells from the toxic effects of hydrogen peroxide. In the present study,
the effects of a new synthesized phenanthroline-imidazole derivative of platinum complex were
investigated on the structure and function of bovine liver Catalase (BLC)using. Different
spectroscopic methods of UV–visible, fluorescence, and circular dichroism (CD) at various
temperatures of 25 and 37 °C.UV-visible spectroscopy results declared that the enzymatic
activity decreases slightly with increasing platinum compound’s concentration. Meanwhile,
raising the concentration of platinum complex lead to a significant quenching of intrinsic
fluorescence of catalase resulted changes in three-dimensional environment around the
chromophores of the enzyme structure. Analysis of fluorescence quenching data showed that
there are two binding sites on BLC for this complex and the binding constant values were
calculated 427 × 107 and 3.25 × 107 M−1, respectively at temperatures of 25 and 37 °C. Also,
circular dichroism (CD) data represented a significant decreasing in α-helix content of enzyme at
high concentrations of platinum compound. Consequently, it can be concluded that this novel
platinum complex can interact with catalase and induce minor changes in the function and major
alterations in the structure of catalase.
Keywords: Catalase, Fuorescence, Circular dichroism, Platinum complex, Quenching.
HTTP://UI.CNF.IR/PPS 119
Stability of the recombinant enzyme in Lepidiumdrabaperoxidase
(LDP) against heat and hydrogen peroxide
Alireza Ghaseminasab1, Ali Riahi-Madvar2, Yaser Fattahian2
1Department of Biotechnology, Faculty of Science and Modern Technology, Graduate University of Advanced
Technology, Kerman, Iran.
2Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate
University of Advanced Technology, Kerman, Iran.
Abstract
Peroxidases, a class of enzymes in animal, plant and microorganism tissues, catalyze
oxidoreduction between H2O2 and various reductants. Peroxidases have been divided into
different superfamilies: plant peroxidases, animal peroxidases and catalases. The plant
peroxidases superfamily, which contains peroxidases from both prokaryotic and eukaryotic
origin, can be divided into three classes, based on structural similarities and certainly in a
suspected common evolutionary origin.The main purpose of this research,was investigated the
stability of the recombinant Lepidiumdraba peroxidase(LDP) against hydrogen peroxide and
heat.Therefore, after purification and refolding of the enzyme, its stability was examined against
heat in the temperature range of 35-90 °C and hydrogen peroxide in the range of 0-
14mMH2O2.The results showed that the LDP loses 50% of its activity at 67 °C (T1/2) after 10
min.whilst, the enzyme activity decreased by 40 percent at 60 °C after one hour(t1/2). The results
also showed that treatment enzyme with H2O2, lead to decrease about 50 percent of enzyme
activity in the presence of 11 Mm H2O2. Accordingto the results it may be purposed that the
enzyme has stability comparable to HRP.
Keywords: Lepidiumdrabaperoxidase, Recombinant protein, Stability.
HTTP://UI.CNF.IR/PPS 120
Effect of lysine residue acetylation on the structure of apomyoglobin
Mehrnaz Azami-Movahed1, Ali Akbar Meratan2, Atiyeh Ghasemi1, Azadeh Ebrahim-Habibi3, Ali Akbar
Saboury1, Mohsen Nemat-Gorgani4
1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
2Department of Biological Sciences, Institute in Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran.
3Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran, Iran.
4Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.
Abstract
It is well known that various chemical modifications, by bringing about significant changes in
the net charge and/or surface hydrophobicity, play important role in the structure of proteins. In
this study, effect of lysine residue acetylation, as one of the most common reversible post-
translational modifications targeting a wide range of proteins, on the structure of apomyoglobin
(apoMb) was investigated. Given that acetylation neutralizes the positive charges of basic lysine
residues, it expects that this modification would correspondingly affect the structure of the
apoMb. The extent of acetylation was verified by the fluorescamine assay and a range of
techniques including far- and near-UV CD spectroscopies, ANS and intrinsic fluorescence assays
were employed to explore structural changes of apoMb upon acetylation. Our results clearly
indicate that acetylation of lysine residues strongly destabilize the native conformation of apoMb
by altering both secondary structure and folding properties of the protein. Moreover, results
obtained by ANS fluorescence assay, demonstrated a considerable decrease in surface
hydrophobicity of the acetylated apomyoglobin compare to native form, suggesting disruption of
heme pocket upon acetylation. Our results suggest that variation in the charge distribution at the
protein surface may play a key role in the conformation stability of apoMb.
Keywords: Apomyoglobin, Lysine modification, Acetylation, Surface charge, Structural stability.
HTTP://UI.CNF.IR/PPS 121
Effect of spacer length of the synthetic cationic urethane gemini
surfactants on the secondary structure of insulin
Rezvaneh Ghasemi Tabesh1, Pouneh Sadat Pourhosseini1, Ali Akbar Saboury2, and Farhood Najafi3
1 Faculty of Biological Sciences, Alzahra University, Tehran, Islamic Republic of Iran.
2 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Islamic Republic of Iran.
3 Department of Resin and Additives, Institute for Color Science and Technology, Tehran, Islamic Republic of Iran.
Abstract
Gemini surfactants are new classes of surfactants finding their way into surfactant-based
formulations. Recently they have attracted considerable interest in the academic and industrial
communities working on surfactants. The interaction of gemini surfactants with bio-
macromolecules (proteins, genes, lipids, …) have been the subject of extensive studies because
of their applications in food and pharmaceutical industries, analytical biochemistry studies,
cosmetics, and drug delivery. In this research two kinds of cationic urethane gemini surfactants
differing in their spacer length (C2 and C4) were used and their interaction with insulin at pH 7.4
was investigated by circular dichroism spectroscopy. Far-UV CD data revealed changes in the
secondary structure of insulin as changes in the helical content as well as the β-structure of the
protein. It showed the longer the spacer, the lower the helical content. The trend of beta structure
changes was in reverse direction, however. Besides, for both surfactants the maximum helical
content was occurred at the surfactant to protein molar ratio of 3.
Keywords: Cationic gemini surfactant, Urethane, Circular dichroism spectroscopy, Insulin,
Interaction.
HTTP://UI.CNF.IR/PPS 122
Superior cytotoxicity of serum albumin on microglial cells upon
hetero-seeding effect of amyloid peptide
Maryam Ferdousi1, Mehran Habibi-Rezaei1,2,Saeed Balalaie3, Sorour Ramezanpour3, Farzaneh Sabouni4,
Najmeh Poursasan5, Manijheh Sabokdast1, Ali Akbar Moosavi-Movahedi5,6
1School of Biology, College of Science, University of Tehran, Tehran, Iran. 2Nano-Biomedicine Center of Excellence, Nanoscience and Nanotechnology Research Center, University of Tehran,
Tehran, Iran. 3 Peptide Chemistry Research Center, K. N. Toosi University of Technology, Tehran, Iran. 4Department of Basic Sciences of Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran,
Iran. 5Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 6Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.
Abstract
We demonstrate in vitro cross-seeding of bovine serum albumin (BSA) in the presence of Aβ25-35 and
their cytotoxic effects on microglial cells. To investigate the cross-seeding of BSA in the presence of
Aβ25-35 fibrils, we examined how Aβ25-35 fibrils can function as seeds to trigger and accelerate BSA
fibrillogenesis using ThT, intrinsic fluorescence, ANS fluorescence, and transmission electron
microscopy (TEM). Moreover, the effects of these fibrils on microglial viability were measured using
MTT and Annexin V/propidium iodide (PI) staining. Although Aβ25-35 is toxic against microglia, it
acted as seed and affected the aggregation pathway and accelerated the fibrillogenesis of BSA in
vitro, resulted in an enhanced cytotoxic effect in comparison with Aβ25-35 or BSA alone. These
observations thought to be helpful to understand the molecular mechanism of enhanced toxicity due
to the coexistence and cross-seeding of proteins and their effects on microglial cells that may involve
in neurodegenerative diseases such as Alzheimer’s disease (AD).
Keywords: Aβ25-35, Alzheimer’s disease, BSA, Cross-seeding, Microglia.
HTTP://UI.CNF.IR/PPS 123
Prediction and evaluation of myelin oligodendrocyte glycoprotein
(MOG) antigenic epitopes
Narjes Farajzadeh-dehkordi, Mostafa Shakhsi-Niaei, Behnaz Saffar
Department of Genetics, Faculty of Sciences, Shahrekord University, Sharekord, Iran.
Abstract
Multiple sclerosis (MS) is the most common autoimmune disease involving the nervous system.
T cells reactive to the major constituents of the myelin sheath, myelin oligodendrocyte
glycoprotein (MOG). The major histocompatibility complex (MHC) class I is expressed on the
cell surface of all nucleated cells, and plays an important role in antigen presentation to
autoreactive T-cells. A neuroantigen DNA vaccine can be used for induction of tolerance of in
human. In this study, some prediction softwares such as Paproc, Netchop3.1 and Mappp were
used for prediction of proteasome cleavage sites of MOG. Generally each softwares produced
different 8-11cleaved aminoacid peptides despite some overlapping results. Therefore, to find the
best epitope, amino acid residues of 105-112, 104-111, and 243-252 which subsequently
produced by Paproc, Netchop3.1, and Mappp Softwares were checked for antigenisity by using
Predicted Antigenic Peptides web server. Results showed that antigenic amino acid residue of
243-252 which was predicted by Mappp showed the best matchable epitope with antigenisity
criteria among all predicted peptides. Altogether, prediction tools may help select more antigenic
peptides for design of DNA vaccines.
Keywords: Cleavage prediction tools, protein, DNA vaccine, MOG, MS.
HTTP://UI.CNF.IR/PPS 124
Evaluation of MHC class I binding properties of designed peptides
for DNA vaccine for induction of multiple sclerosis tolerance in
human
Narjes Farajzadeh-dehkordi, Mostafa Shakhsi-Niaei, Behnaz Saffar
Department of Genetics, Faculty of Sciences, ShahrekordUniversity, Sharekord, Iran.
Abstract
One of biological functions of the immune system is the prevention of autoreactive T and B cells
activation whichare potential threatsfor autoimmune diseases like Multiple sclerosis (MS). The
major histocompatibility complex (MHC) class I is expressed on the cell surface of all nucleated
cells and plays an important role in antigen presentation to autoreactiveTcells. A neuroantigen
DNA vaccine can be used for induction of tolerance in human. In our previous study, some
prediction softwares were used for finding immunogenic epitopes by prediction of proteasomal
cleavage sites of Myelin Oligodendrocyte Glycoprotein (MOG), a related MS antigen. Therefore,
obtained antigenic amino acid residues of, 105-112,104-111 and 243-252, were analyzed for
evaluation of binding affinity of human MHC class I by using the IEDB web server. The best
results were related to MHC class I alleles of HLA-A*31:01 and HLA-A*33:01 which interact
more efficiently with epitope of KFSSLCYKQ (243-252) predicted by MAPPP software.
Altogether, prediction tools may help select better epitopes with better interaction with MHC
alleles for design of DNA vaccine.
Keywords: DNA vaccine, MHC class I, Multiple sclerosis, MOG, Tolerance.
HTTP://UI.CNF.IR/PPS 125
Cloning and expression of soluble extracellular domains 1-3 of
human VEGF receptor-2 in Pichia pastoris
Zahra Fathi1, Reza Hassan Sajedi2, M. Mashhadi, Akbar Boojar1, Ehsan Dehnavi3
1Department of Cellular and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran. 2Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran. 3Gene Transfer Pioneers research group, Shahid Beheshti University, Tehran, Iran.
Abstract
Vascular endothelial growth factor (VEGF) is a key regulator of pathological angiogenesis,
vascular permeability and overexpressed by most solid tumors. VEGF receptor-2 (VEGFR-2 or
KDR as it is called in human) is a specific receptor of VEGF with a high binding affinity. In this
study, a solube recombinant extracellular domain 1-3 of human VEGFR-2 (rKDR1-3) was
expressed in Pichia pastoris to inhibit the VEGF-induced angiogenesis. The 975 bp DNA
fragment, containing 948 bp extracellular domains 1-3 kdr, was designed according to the
nucleotide sequence at GenBank and protein sequence at SwissProt. The recombinant Pichia
Pink secretory expression vector (pPinkαHC/KDR1-3) was constructed and transferred into
Pichia pastoris (Pichia Pink strain 4) by electroporation. The high expression transformants were
identified through complementation of adenine auxotrophy and methanol induction. The
recombinant KDR1-3 was successfully expressed and confirmed by using SDS-PAGE and
western blot techniques. VEGF-A/KDR1-3 interaction was proved by ELISA receptor binding
assay using recombinant VEGF and bevacizumab (avastin), a anti-VEGF monoclonal antibody,
for cancer therapy. Pichia pastoris expresses soluble and highly efficient recombinant protein.
Also, it has many advantages such as protein processing, protein folding and the availability of
post-translational modifications. In conclusion, we developed a soluble extracellular domain of
KDR with high-affinity against VEGF, which could be of therapeutic value for a variety of
pathological angiogenesis. The rKDR1-3 could also be used to develop a novel monoclonal
antibody, and a fusion protein composed of the antibody and rKDR1-3 to block the
VEGF/VEGFR interaction more effectively.
Keywords: Angiogenesis, VEGF-A, VEGFR-2, Pichia pastoris.
HTTP://UI.CNF.IR/PPS 126
Study of the interaction of myricetin and Morin hydrate with
bovineα-Lactalbumin
Yasir FatehiBabi and Fakhrosadat Mohammadi
Department of Chemistry, Institute for Advanced Studies in Basic Science, Gavazang, Zanjan, Iran.
Abstract
Bovine α-Lactalbumin (BLA) is an acidic Ca2+-binding protein found in milk. One of the major
roles of milk proteins is the transport of the drugs/bioactive compounds and facilitating their
functionality in delivery system. To better understanding the transport and metabolic process of
the bioactive compounds/drugs, it is essential to explore the mechanism of interactions between
these compounds and carrier proteins. Flavonoids are small natural polyphenols found in many
grapes, fruits, berries, vegetables and herbs as well as other plants. In this study fluorescence
assayshave been used to investigate the binding characteristics of Morin hydrate and Myricetin
as two bioactive flavonoids with α-Lactalbumin. The binding parameters of Myricetin and Morin
hydrate with BLA such as binding constants and the number of substantive binding sites have
been estimated from the analysis of fluorescence quenching measurements. The differences in
affinities of Myricetin and Morin hydrate for BLA were discussed based on the chemical
structure of these flavonoids and involved molecular interactions with BLA. The short Förster's
distance between donor (BLA) and acceptor (Morin hydrate and Myricetin) and also the binding
constant values demonstrated the strong interaction between these two flavonoids and BLA. The
thermodynamic parameters were obtained from the fluorescence quenching measurements in
different temperatures. It can be concluded from the sign and magnitude of ΔH and ΔS that the
final ligand–protein complexes were stabilized by hydrogenbonds. The considerable change in
microregion of the Trp residues in BLA is observed upon the binding of theMyricetin and Morin
hydrate to BLA by synchronous fluorescence.Molecular docking studies indicated that these two
compounds bind to BLA by hydrogen bonds.
Keywords: Flavonoids, α-Lactalbumin, Fluorescence quenching.
HTTP://UI.CNF.IR/PPS 127
Protective effects of hydroalcohol extract of Zingiber Officinale on
the functional disorders and histological damages in Iron-induced
renal toxicity in rats
Firoozeh Gholampour1, Fatemeh Behzadii, 1 and seyed mohamad Owji2
, Shiraz University, Shiraz, Iran.of SciencesDepartment of Biology, Faculty 1
, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.of PathologyDepartment 2
Abstract
Iron overload in the body is associated with toxic effects and endanger health. Evidences have
suggested that various forms of kidney injuries may be caused by free radical formation and
subsequent oxidative stress. The roots of Zingiber officinale contain polyphenol compounds
which have a high antioxidant activity. The aim of this study was to evaluate the protective role
of hydroalcohol extract of Zingiber officinale against ferrous sulfate-induced renal toxicity in
rats. Renal damage was induced by i.p. injection of ferrous sulfate (30 mg/Kg/day) for 14 day in
male wistar rats (220-260g). In final blood samples collected for determination of the serum
creatinine, urea nitrogen and sodium (Na) concentration. Then kidney samples were removed
and preserved for histological studies and estimation of lipid peroxidation. Hydroalcohol extract
of Zingiber Officinale (400 mg/kg/day in 1 ml distilled water) was administered by gavage for 14
days. Ferrous sulfate caused deterioration of renal function, renal morphology and a significant
renal oxidative stress. Administration of hydroalcohol extract of Z. officinale significantly (p <
0.01) reversed the levels of renal functional markers and lipid peroxidation marker. All these
changes were corroborating by histological observations of kidney. This study demonstrated the
protective role of hydroalcohol extract of Z. officinale in reducing toxic effects of ferrous sulfate
in experimental male rats.
Keywords: Creatinine, Ferrous sulfate, Lipid peroxidation, Kidney, Zingiber officinale.
HTTP://UI.CNF.IR/PPS 128
Human asf1a c-terminal tail phosphorylation favours formation of
stable secondary structures in this intrinsically disordered peptide
Sayed Shahryar Alavi Hejazi1
1Genomics Department, Agricultural Biotechnology Research Institute of Iran (ABRII), Isfahan, Iran.
Abstract
When replication machinery reaches a nucleosome, the histone core must be evicted temporarily
and then be deposited onto the newly synthesised daughter strands just behind the replication
fork. In addition, as the DNA being duplicated during replication, cells need to double the
number of core histones to restore their chromatin organisation properly. The histone chaperon
Asf1a binds newly synthesised heterodimer of H3-H4 histones to provide an active histone pool
for DNA replication. In response to histone depletion for nucleosome assembly, protein kinase
TLK1 phosphorylates human Asf1a (hAsf1a) C-terminal tail, which increases the hAsf1a affinity
for H3-H4. This segment is responsible for regulation of hAsf1a activity, however the hAsf1a
tail is highly flexible and disorder analysis has showed it is unstructured. So using Amber
molecular dynamics simulation programme, the effects of phosphorylation upon hAsf1a tail
conformation have investigated. Two stretched form of hAsf1a tail, native and phosphorylated,
was constructed for 10 ns MD simulations in implicit solvent. When phosphorylated on serines
166 and 175, the flexibility of the hAsf1a tail was reduced and tended to fold and form a more
stable structure. These results suggest that phosphorylation pattern of the C-terminal tail of
hAsf1a regulates the activity of this histone chaperone by favouring formation of stable
secondary structures.
Keywords: hAsf1a, Phosphorylation, Molecular dynamics, Histone chaperone, Chromatin
replication.
HTTP://UI.CNF.IR/PPS 129
Bioinformatics analysis of Aspartyl/asparaginyl β-hydroxylase
protein
Reza Azizi1, Mohammad Reza Mofid2, Ali Jahanian-Najafabadi3, Hadi Bakhtiari2, Amir Ansari2
1 Students’ Research Committee, School of Pharmacy, Isfahan University of Medical sciences, Isfahan, Iran.
2 Department of Biochemistry, School of Pharmacy, Esfahan University of Medical Sciences, Isfahan, Iran.
3 Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences,
Isfahan, Iran.
Abstract
Membrane Protein human Aspartyl/Asparaginyl beta-hydroxylase (HAAH) play an
important role in calcium homeostasis. The gene is expressed from two promoters and undergoes
extensive alternative splicing. The encoded set of proteins share varying amounts of overlap near
their N-terminal but have substantial variations in their C-terminal domains resulting in distinct
functional properties. The longest isoforms (a and f) include a C-terminal HAAH domain that
hydroxylates aspartic acid or asparagine residues in the epidermal growth factor (EGF)-like
domains of some proteins. In human tumorous cells expression of this enzyme can be elevated,
which is associated with progression of tumor. Serum level of HAAH served as indicator for
different carcinomas. In this article we study the structure and some aspects of bioinformatics in
HAAH using different bioinformatics methods and sites. The amino acid sequence of the enzyme
was taken from the NCBI site. One part of the study was carried out with bioinformatics tools
that are available on the NCBI and Expasy and was done online. Another part was performed by
Pdb Viewer-Swiss. There are several isoforms of this enzyme in different organisms, so we draw
its phylogenetic trees using the blast review software on NCBI.In addition to drawing
phylogenetic tree, we determined the amino acid sequence. Also we identified the main physico-
chemical properties of a protein, predicted primary, secondary, tertiary structure analysis, looked
for transmembrane segments and coiled-coil regions, of HAAH. Finally we used the
hydrophobicity to identify the groups with hydrophobic characterization of HAAH.
Keywords: HAAH, Tumor, Bioinformatics, Structure.
HTTP://UI.CNF.IR/PPS 130
Cloning and heterologous expression of catalytic subunit of rice
(Oryza Sativa) acetohydroxy acid synthase in Escherichia coli
Ghazaleh Arabzadeh and Azar Shahpiri
Faculty of Agriculture, Isfahan University of technology, Isfahan, Iran.
Abstract
Acetohydroxyacid synthase (AHAS) EC 2.2.16, is the first enzyme that catalyses the
condensation of two molecules of pyruvate to form acetolactate in the biosynthesis of leucine,
and valine, or the condensation of pyruvate and 2-oxobutyrate to form acetohydroxybutyrate in
the biosynthesis of Isoleucin. AHAS is the target enzyme for several classes of herbicides
including sulfonylureas, imidazolinones and triazolopyrimidines that inhibit the activity of this
enzyme. AHAS holoenzymes are assembled from large catalytic subunits and small regulatory
subunits. In the absence of the small subunits, the large catalytic subunits of AHAS enzymes are
insensitive to product feedback inhibition. Higher plants have one or more AHAS isozyme
localized in the chloroplasts. The AHAS gene from Oryza Sativa, including the chloroplast
transit peptide, was purchased from NIAS cDNA library and was amplified by polymerase chain
reaction with the oligonucleotid primers containing EcoRI and HinDIII site in forward and
reverse primers respectively, and after cleavage by appropriate restriction enzyme, the PCR
product was cloned into the bacterial expression plasmid pET41a. The resulting plasmid was
used to transform an expression host Escherichia coli strain Rosetta (DE3) and Oryza Sativa
AHAS (OsAHAS) was expressed in these bacteria as a protein fused with glutathione S-
transferase (GST). The considerable amount of recombinant form of GST, GST-OsAHAS
proteins were produced from cell harboring pET41a (control) and pET41a-osAHAS plasmid
respectively after induction with Isopropyl-β-D-thiogalactoside (IPTG). The fusion product
GST-os AHAS was purified using affinity chromatography. The AHAS protein was estimated to
a molecular mass of 72 kD.
Keywords: Acetohydroxy acid synthase, Oryza sativa.
HTTP://UI.CNF.IR/PPS 131
Interaction of arachidonoyl serotonin with beta-casein
nanoparticles: spectroscopy and molecular modelin studies
Maryam Atrian, AbdolKhaleg Bordbar, Mehdi Sahihi
Department of Chemistry, University of Isfahan, Isfahan, 81746-73441, Iran.
Abstract
β-casein micelles of milk can carry hydrophobic drugs like natural nanostructures. Arachidonoyl
serotonin (AA-5-HT) which derives from tryptophan have different physical and psychological
actions. However, due to its low solubility in water, it needs biocompatible vectors for transport
in the body. In this study, β-casein’s potential in carrying ligand has been analyzed using
experimental (fluorescence spectroscopy) and computational methods. Temperature is an
important factor in analyzing β-casein’s structural stability and its complexes with other
compounds. The present study investigates the interaction of β-casein and in Arachidonoyl
serotonin different temperatures through spectroscopic methods, molecular dynamics simulations
and molecular docking. Based on fluorescence titration results and fluorescence enhancement
equations, the binding constant and the number of active binding sites of this ligand to β-casein
were calculated. Moreover, the nature of the forces involved in the interactions of this ligand and
the protein was analyzed through Van 't Hoff equation and Russ - Subramanian theory. These
analyses showed that arachidonoyl–serotonin is involved in the interactions with hydrophobic
forces and that it has one binding site. Arachidonoyl serotonin is located on the surface of this
protein. The binding constant of of arachidonoyl β-casein is proof to the higher stability of this
complex. Furthermore, results of experimental calculations (fluorescence spectroscopy)
confirming the molecular docking results. Through molecular dynamics simulation of β-casein
and its complexes arachidonoyl serotonin, RMSD, Rg, RMSF and solvent accessible surface area
were measured. Increase in RMSD, Rg, and solvent accessible surface area at the end of the
simulation for β-casein arachidonoyl serotonin complex compared to the free protein, shows an
increase in the degrees of freedom and a lack of compactness in this complex. Moreover, RMSF
in β-casein and the aforementioned complex showed less local mobility in this complex which is
a sign of its stability. These results were very much in line with experimental and molecular
docking results.
Keywords: β-casein, Arachidonoyl Serotonin, Fluorescence Spectroscopy, Docking, Molecular
Dynamics Simulation, Molecular Modelling
HTTP://UI.CNF.IR/PPS 132
Interaction of serotonin with beta-casein nanoparticles:
spectroscopy and molecular modelin studies
Maryam Atrian, AbdolKhaleg Bordbar, Mehdi Sahihi
Department of Chemistry, University of Isfahan, Isfahan, 81746-73441, Iran.
Abstract
β-casein micelles of milk can carry hydrophobic drugs like natural nanostructures. Serotonin (5-
HT) which derives from Tryptophan has different physical and psychological actions. However,
due to its low solubility in water, it needs biocompatible vectors for transport in the body. In this
study, β-casein’s potential in carrying ligand has been analyzed using experimental (fluorescence
spectroscopy) and computational methods. Temperature is an important factor in analyzing β-
casein’s structural stability and its complexes with other compounds. The present study
investigates the interaction of β-casein and serotonin in different temperatures through
spectroscopic methods, molecular dynamics simulations and molecular docking. Based on
fluorescence titration results and fluorescence enhancement equations, the binding constant and
the number of active binding sites of its ligand to β-casein were calculated. Moreover, the nature
of the forces involved in the interactions of this ligand and the protein was analyzed through
van't Hoff equation and russ subramanian theory. These analyses showed that serotonin is
involved in the interactions with hydrophobic forces and that it has one binding site. Molecular
docking results showed binding sites for this ligand. Serotonin is in one of β-casein’s pores.
Furthermore, results of experimental calculations (fluorescence spectroscopy) confirming the
molecular docking results. Through molecular dynamics simulation of β-casein and its complex
serotonin, RMSD, Rg, RMSF and solvent accessible surface area were measured. Decrease of
these quantities for β-casein serotonin shows the higher compactness and stability of this
complex. Moreover, RMSF in β-casein and the aforementioned complex showed less local
mobility in this complex which is a sign of its stability. These results were very much in line
with experimental and molecular docking results.
Keywords: β-casein, Serotonin, Fluorescence spectroscopy, Docking, Molecular dynamics
simulation, Molecular modelling.
HTTP://UI.CNF.IR/PPS 133
An efficient synthesis of exenatide as an anti-diabetic drug
1, 2, Saeed Balalaie1Ramezanpour, Sorour 1, Somayeh Ahadi1Maryam Alizad
4416, Tehran, Iran.-Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 158751
Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.2
Abstract
There are so many drug as hypoglycemic drug recently. The use of peptides as natural drug is an
interesting subject in treatment of diabetes. Exenatide (marketed as Byetta, Bydureon) is a
glucagon-like peptide-1 agonist (GLP-1 agonist) medication. It could categorized based on the
group of incretin mimetics and for treatment of diabetes mellitus type 2. Exenatide has an
distinguished point as an anti-diabetic drug and it uses for the patients who the oral drug doesn't
affect the blood sugar. Exenatide is a 39-amino-acid peptide, was synthesized through Solid
Phase Peptide Synthesis (SPPS) approach and then was purified using preparative HPLC. The
structure of the product was approved using HR-MS (ESI) data. The details about the synthesis
and purification will be further discussed in the conference. The amino acid sequence for
exenatide is shown below.
Keywords: Exenatide acetate, GLP-1 agonist, Anti-diabetic peptide, Incretin.
HTTP://UI.CNF.IR/PPS 134
Preparation and biodistribution assessment of 68Ga-Bleomycin as a
possible PET imaging
Saeed Kakaei1, Hamid reza Tayeri2, Elham Sattarzadeh khameneh1, Dariush Sardari2
1NSTRI, Nuclear Fuel Cycle Research Institute, P.O. Box 11365/8486, Tehran, Iran. 2Department of Nuclear Engineering, Tehran, Iran Research Branch, Islamic Azad University, Tehran, Iran.
Abstract
Bleomycin is an anti-cancer ("antineoplastic" or "cytotoxic") chemotherapy drug which is
classified as an "antitumor antibiotic. Several radiolabeled Bleomycin derivatives have been
developed for imaging and/or therapy of neoplastic tissues. The most important imaging
compounds contain indium-111,1 cobalt-57,2 technetium-99m,3 radioferric salts4 and rhodium-
105.5 The positron-emitting Ga(III) radioisotopes, 66Ga3+and 68Ga3+, have been proposed for
applications in positron emission tomography (PET) imaging. In this study, by applying a
produced 68Ge/68Ga generator, a simple technique for the synthesis and quality control of 68Ga-
Bleomycin was introduced; followed by preliminary animal studies. 68GaCl3 eluted from the
generator was studied in terms of quality control factors including radiochemical purity (assessed
by RTLC), chemical purity and radionuclide purity. This study reports the preparation and bio
distribution assessment of Gallium-Bleomycin (68Ga-BLM) complex as a radiopharmaceutical
and optimization of its labeling conditions; pH, reaction time, temperature, concentration of
Bleomycin and its bio distribution in normal mice. The bio distribution of the complex was
compared with 68Ga-Cl3 in 11 selected organs including blood, liver, lung, spleen, muscle, skin,
heart, kidney, colon, colon content, and bladder at 4 selected times of 1, 2, 4, 24 hours after
injection. The optimized pH condition was found 2 at temperature of 90ºC for reaction
temperature of 30 minutes when 1 mg of bleomycin was mixed of about 2 mCi of 68Ga-Cl3.
Radio thin layer chromatography showed an overall radiochemical purity of 90-94% at the
optimized conditions with a specific activity of about 1.5mCi/m mole and radiochemical purity
greater than 93% in 15 min.
Keywords: Bleomycin, Gallium-68, Tomography, Radiochemical, Radionuclide.
HTTP://UI.CNF.IR/PPS 135
The application of HER2 protein in cancer detection using graphene
functionalized with specific DNA sequences
Abdollah Noorbakhash1 and Arezou Tabasi1
1 Department of Nanotechnology Engineering, Faculty of Advanced Science and Technology, University of Isfahan,
Isfahan, 81746-73441, Iran.
Abstract
Human epidermal growth factor receptor 2 (HER2) protein also known as ErbB2 (avian
erythroblastosis oncogene B) is a cancer marker. HER2 overexpression on the surface of breast
cancer cells is about 20-30%. Recent studies have shown that measurement of the amount of
HER2 protein in serum is a useful noninvasive method for the early detection of breast cancer.
The extracellular domain of the HER2 is often cleaved and released into the bloodstream.
Normal individuals have a HER2 concentration between 2 and 15 ng/ml in their blood but it’s
amount in breast cancer patient’s blood is between 15 and 75 ng/ml. So it is essential to develop
a rapid, sensitive, specific, label-free, and cost-effective diagnostic test for detection of HER2
serum level. For detecting HER2, it is possible to use electrochemical biosensors.
Electrochemical detections have some advantages including simplicity, quick response, low cost,
high reproducibility, simple of instrumentation, and sensitivity. Aptamers can be used as sensing
elements in biosensors and their properties make them play a crucial role in the development of
biosensors. In the present work, a sensitive electrochemical aptasensor was fabricated for the
determination of HER2 antigen. For this purpose, HER2 specific aptamer was immobilized on
the surface of reduced graphene oxide-chitosan nanocomposite modified-glassy carbon electrode
and is used for HER2 detection. Detection limit of the fabricated aptasensor for HER2 was
evaluated to be 0.225 ng/ml with two linear response ranges of 0.5 to 2 ng/ml and 2 to 75 ng/ml.
Keywords: HER2 antigen, Aptamer, Breast cancer, Electrochemical aptasensor, Reduced
graphene oxide.
HTTP://UI.CNF.IR/PPS 136
Construction of BMP-2 agonists based on nanobody (VHH)
and Sadegh Hasannia Zahra Sahraee
Biochemistry Laboratory, Department of Biology, College of sciences, Tarbiat Modares University, Tehran, Iran.
Abstract
In all the cases that bone regeneration is not completed and the progress cannot be done
perfectly, tissue engineering can be the best option for repairing, when the rebuilding of the bone
has been failed and has not been mended. There are three important and essential factors in the
bony and collagen tissue engineering. They include of 1- scaffold 2- biomolecules and 3- stem
cells. Biomolecules and the derived peptides are able to repair the bone and induced it, that it can
improve VHH by putting the active residual in CDR3 area. For generating of an effective
nanobody, at the first, the bioinformatic must be consideration BMP-2/ BMPR-II protein
complex with 2GOO PDB code and the related residual were determined in the interaction.
These residual in BMP-2 structure determine the sequence in the CDR3 part of nanobody. Then
the two generated VHH were linked together by a linker which includes of fibronectin. In the
other step, the said sequence "VHH" was modelled protein was simulated by the GROMACS
software in the said condition. Then the said protein was docked with BMPR-II in order to
examine the way of the said nanobody has been modelled successfully and the conclusion, come
from the dock, has predicted the good and efficient interaction whit BMPR-II.
Keywords: VHH, BMP-2, Bioinformatic, Biomolecules, Agonists.
HTTP://UI.CNF.IR/PPS 137
Application of bovine serum albumin- carbon nanotubes conjugated
system for fabrication of highly sensitive arsenic aptasensor
Soroor Salehi and Abdollah Noorbakhsh
Department of Nanotechnology Engineering, Faculty of Advanced Science and Technology, University of Isfahan,
Isfahan, 81746-73441, Iran.
Abstract
Bovine serum albumin (BSA) is a carbohydrate-free, single-chain, highly soluble, 66.4 kDa
globular protein with a 30–35 reactive primary amino groups and contains 583 amino acids in a
single polypeptide chain. BSA is used in many biochemical applications due to its stability and
lack of interference within biochemical reactions. In addition, compared with other high
molecular weight proteins, BSA is relatively cheap and readily available and also it can be
employed for biosensor and bioreactor systems. In this work, BSA-carbon nanotube (BSA-CNT)
hybrid system was employed for fabrication of very sensitive arsenic (As (III)) impidimetric
aptasensor and signal amplification. As (III) is one of the most toxic heavy metals that is
dangerous for human health even in low concentrations. BSA was bioconjugated with the
abundant amount amino groups onto the carboxylic acid functionalized CNTs. Atomic force
microscopy (AFM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy
(EIS) was used to characterization of fabricated aptasensor. BSA-CNTs nano-bioconjugated
system shows very good ability for signal amplification.
Keywords: Bovine serum albumin- Carbon nanotube, Aptasensor, Arsenic (III), Signal
amplification, Electrochemical impedance spectroscopy.
HTTP://UI.CNF.IR/PPS 138
Structural and functional characterization of reduced glycated
adduct of bovine β-casein
Tanaz Sadeghian, Zohreh Tavaf, Reza Yousefi
Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
Abstract
As a member of intrinsically disordered protein family, the amphiphilic chaperone β-casein
prevents aggregation of whey proteins in milk. Also, β-casein is an important component of
casein micelle. In order to mimic the potent reducing environment of milk, β-casein was glycated
under reducing condition. The reduced glycated β-casein adduct was applied to both structural
and functional analyses, using different techniques. Our results suggest significant structural
alteration of β-casein upon non-enzymatic glycation. While micellization and chaperoning action
of the glucose modified protein were significantly altered, its allerginicity profile remained
largely unchanged. In addition, antioxidant activity was improved after non-enzymatic glycation
of this protein. Normally, glucose levels in breast milk are approximately one-fourth of the
mother's blood glucose level. Therefore, the effective reducing environment of human milk may
provide a suitable environment for the reduced glycation of β-casein particularly in diabetic
mothers with chronic hyperglycemia.
Keywords: β-casein, Glycation, Chaperone, Structure, Allerginicity.
HTTP://UI.CNF.IR/PPS 139
Construction, expression and purification of diabody against human
vascular endothelial growth factor in bacterial system
Seyed Amir Sadeghi1, 2, Mahdi Behdani1, Fatemeh Kazemi-Lomedasht1
1 Biotechnology Research Center, Venom & Biotherapeutics Molecules Lab., Pasteur Institute of Iran, Tehran, Iran.
2 Department of science, College of biology, Tehran Science and Research branch, Islamic Azad University, Tehran, Iran.
Abstract
Antibodies and their derivative fragments have long been used as tools in a variety of
applications, in fundamental research work, biotechnology, diagnosis, and therapy. Camels
produce single heavy-chain antibodies (VHH) in addition to usual antibodies. These minimal-
sized binders are very robust and bind the antigen with high affinity in a monomeric state.
Vascular endothelial growth factor (VEGF) is one of the most important key regulators of
angiogenesis during embryogenesis, reproductive functions and skeletal growth. VEGF has also
been implicated in pathological angiogenesis associated with tumor, intraocular neovascular
disorders and other. In this study, we expressed and purified anti-VEGF Diabody. Two variable
fragments of a same camel anti-VEGF antibody were linked together by a linker to make a
diabody. Constructed diabody transferred into BL-21 E. coli cells and expression of recombinant
protein was induced by IPTG. Anti-VEGF diabody purified using nickel affinity chromatography
and confirmed by SDS-PAGE and western blot analysis. Diabodies can be produced in the low-
cost and high-yeild prokaryotic expression system, so they are suitable molecules for diagnosis
and therapeutic issues.
Keywords: Diabody, Nanobody, Vascular endothelial growth factor.
HTTP://UI.CNF.IR/PPS 140
Inhibition of kanamycin-resistant bacteria by designing 10–23
deoxyribozyme targeted to kanamycin resistance mRNA
Sanaz Sadeghi, Abolghasem Esmaeili, Fateme Javadi Zarnaghi
Department of Biology, University of Isfahan, Isfahan, Iran.
Abstract
Deoxyribozymes are oligodeoxyribonucleotides that catalyze reactions such as cleaving
ribonucleotide (RNA). Deoxyribozymes have different diagnostic and therapeutic applications.
Due to DNA stability and fast and cheap synthesis, it is a good option for therapeutic
applications. 10-23 deoxyribozyme includes a cation-dependent catalytic domain of 15
nucleotides and two variable binding arms. Deoxyribozymes are used as therapeutic agents by
cutting mRNAs that lead to antibiotic resistance, cancer, neurological and cardiovascular
diseases. Fluorogenic deoxyribozyme have the ability to detect cancer cells.Materials and
Methods: Gene map of pEGFP-N1 plasmid was obtained from addgene server and the
kanamycin resistance gene sequence was determined. Then, the correct reading frame was
chosen by comparison of protein sequences of different reading frames using expasy server. The
mRNA sequence is obtained by reverse the sequence complementary. Secondary structure with
the lowest free energy was selected from the server mfold and a region without spatial exclusion
was found. Considering that 10-23 deoxyribozyme has the ability to cleave any RNA substrate
between an unpaired purine (A, G) and a paired pyrimidine (U, C), we selected a AC in the
ribosome binding site in the untranslated region with 9 bases on both sides. The absence of
similar sequences in host bacteria was checked by the NCBI server. Finally, activity and binding
of deoxyribozyme were predicted by the mfold server. Deoxyribozyme prevents the ribosome
binding and could inhibit translation of mRNA to protein. Therefore it could be used as a novel
therapeutic reagent.
Keywords: Deoxyribozyme, Ribosome binding site, Antibiotic resistance, Translation.
HTTP://UI.CNF.IR/PPS 141
Investigating on the synergistic inhibitory effect of aspirin and
propolis on the glycation of human hemoglobin by fructose
Uones Sahebi1, Adele Divsalar1, Ali Akbar Saboury2
1Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
2Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.
Abstract
In the presence of sugar such as fructose, structural and functional properties of proteins are
induced by glycation. It is the main cause of damages to cellular and extracellular proteins in
diabetics. A high percent of flavonoid exist in the propolis which gifts to it lots of biological
properties such as antioxidant activity. Thus we assessed the effect of co-existence of aspirin and
propolis on the fructose induced-protein changes. Fructose was added to the purified human
hemoglobin in the presence and absence both of aspirin and ethanolic extract of propolis (EEP)
for 5 week. Then, samples were gathered and the extents of hemoglobin structural changes were
measured by destruction rate of heme group extent and fluorescamine test, both via fluorimetry.
Results from this study showed that in the presence of aspirin and propolis, heme destruction and
therefore generation of heme products, which arises from fructose binding to the hemoglobin,
was prevented. Extrinsic fluorescence study showed a significant reduction in fluorescence
emission of fluorescamine, which reflected reduction of free amine content in the glycated
hemoglobin that is resulted from fructose binding to the free amine groups, while it is inhibited
in the samples containing both of aspirin and propolis. It can be concluded that aspirin, as a
known anti-glycating drug, and propolis, as a novel anti-glycating substance, could prevented
synergically the structural changes of hemoglobin which induced in the presence of fructose.
Hence, synergistic inhibitory effect of these agents potentially is useful for decreasing
complication and destructive effects of high dosage of sugars in diabetics.
Keywords: Synergistic, Aspirin, Structure, Hemoglobin, Propolis.
HTTP://UI.CNF.IR/PPS 142
Comparison on the inhibitory effects of propolis on the structural
changes of glycated human hemoglobin resulted glucose and
fructose
Unes Sahebi1, A. Divsalar1, Ali Akbar Saboury2
1 Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
2 Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.
Abstract
The non-enzymatic glycation was originally considered as a specialized case of the reaction of
glucose with hemoglobin. The glycation of proteins alters both their structure and function which
have been linked to diabetic disorders. Ethanolic extract of propolis (EEP) has high percent of
flavonoids which is attributed to its biological activities. Thus, we compared the glycation of
hemoglobin in the presence of glucose and fructose in the absence and presence of and propolis
extract. The purified hemoglobin samples were incubated with glucose and fructose, separately,
in the presence and absence of EEP for 5 weeks. The extent of glycation was determined by the
means of uv-visible spectroscopy and Thioflavin T (ThT) test. Results demonstrate that
incubation of hemoglobin with glucose decreases the absorption of hemoglobin significantly in
soret band region due to destruction of heme group. The increace in flouresence emission of
ThT, which binds to amyloid fibrils was also observed, in the sample containing sugar, which
occur as a result of glycation.These changes have higher rates in the presence of fructose. In the
other hand, our results have shown that EEP can inhibit all of these alterations.In conclusion, the
higher glycating effect of fructose in comparison with glucose may be due to more potent
reducing effect of fructose. In addition, the inhibitory effect of propolis on the glycation of
hemoglobin can be resulted from its antioxidant property and decrease in oxidative stress.
Keywords: Propolis, Glycation, Glucose, Fructose, Inhibition.
HTTP://UI.CNF.IR/PPS 143
Subcloning, Expression, and Activity Assay of Recombinant
Luciferin Regenerating Enzyme from Lampyris Turkestanicus
(T-LRE) in Yeast
, Saman Hosseinkhani , Farangis Ataei Fateme sahebazzamani
Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Abstract
Bioluminescence, the production of light by living organisms, have been as a powerful
technology for numerous applications in biotechnology and it is dependent on two principal
components, an enzyme luciferase and the substrate luciferin. The Luciferin-regenerating
enzyme from Iranian species of Lampyris turkestanicus (T-LRE) with theoretical weight of
33.57 kD may have role in the recycling of D-luciferin from oxyluciferin; and leads to increase
of intensity and duration of luciferase light emission. The active purification of such an enzyme
would provide great development in most of luciferase application fields. Before studies on the
T-LRE expression in E.coli revealed that expressed proteins were often as inclusion bodies.
Therefore, in this study the yeast Pichia pastoris expression system was used as a eukaryotic
cell, which possesses many capabilities of a higher eukaryotic expression system, concerning
protein folding and processing. So, suitable primers were designed according to Kex2 cleavage
site and frame of the secretion signal of vector; then, T-LRE gene resulted from PCR was sub-
cloned into the pPinkα-HC plasmids. The confirmed vectors were linearized by Sac1
endonuclease in order to integrate the expressive cassette into the genome AOX1 locus of P.
pastoris (Pichiapink); and transformation was successfully completed by electroporation and
then the target protein expressed in the transformed cells. Although, no protein was detected in
the supernatant, SDS-PAGE analysis of the soluble cell extract revealed that T-LRE protein has
remained inside the cell. This protein was purified using affinity chromatography and confirmed
by western blotting. Finally, the T-LRE activity was investigated.
Keywords: Bioluminescence, Luciferin-regenerating enzyme, Luciferase, Yeast.
HTTP://UI.CNF.IR/PPS 144
ASA rater: A web based software for classifying surface accessibility
of protein residues from the structure
Niloofar Shirvanizadeh1and Seyed Shahriar Arab1
1 Department of Biophysics, Faculty of Biological Sciences, TarbiatModares University, Tehran, IRAN.
Abstract Protein engineering have proven revolutionary to improve protein properties. For protein
manipulation many parameters needed to be consider. Surface accessibility of each residue is one
of the important parameter to consider and a proper guide for many manipulations. Mostly
hydrophilic residues are placed at the exposed parts and hydrophobic at the internal parts yet it
does not happen for all, although these parts are not favorable according to energy, but they have
some application such as protein binding or dimerization. One of the common application of
surface accessibility parameters is in thermal stabilization by the replacement of these exceptions
with appropriate amino acids of course after consideration of the other effective parameters.
ASA rater is a web based software for determining the surface accessibility. It has a user friendly
interface. User can either upload pdb file or enter the pdb ID. the threshold can be specified by
the user. At the output page the number, chain, surface accessibility, secondary structure, ACC
and ASA of each residue is specified. These characteristics help users better understanding of
their protein. Here, surface accessibility is classified in to three categories of exposed, buried and
intermediate The output table can be downloaded. ASA rater is publicly available at
http://bioinf.modares.ac.ir/software/asa_rater.
Keywords: Bioinformatics tool, Protein engineering, Accessible surface area.
HTTP://UI.CNF.IR/PPS 145
Studying the effect of changing the wettability of polypropylene
films on the protein adsorption
Elham Shirani and Amir Razmjou
Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.
Abstract
Polymeric materials have an important role in human health and life. Biofilm formation is a
common feature of exposing these materials to body fluids, which causes chronic infection. In
order to prevent biofilm formation, the substratum should have protein resistance property,
whereas considering the fact that protein adsorption is known the first stage of biofilm formation.
An efficient way to prevent protein adsorption and infection is the surface modification of
materials. Hence, in this work, we desired to achieve a biomaterial that protein adsorption and
subsequent cell adhesion are minimized. Polypropylene was chemically oxidized and then was
coated with titanium dioxide nanoparticles (NPs) to obtain a hydrophilic polypropylene (PP)
surface. Superhydrophobic modification was also practiced on the PP film by incorporating of H,
1H, 2H, 2H-perfluor-ododecyltrichlorosilane (FTCS) polymer molecules. Fluoro branches of the
FTCS polymer molecules, which were attached on the 𝑇𝑖𝑂2 NPs, could inhibit intimate contact
of the surface with any biofluid including protein. The results show that the contact angle for
hydrophilic and superhydrophobic surface was 60° and 154°, respectively. For assessment of
protein adsorption on the surface, bradford assay has been employed. Bovine serum albumin
(BSA) was used as a model protein in this method. Minimized protein attachment was achieved
after surface modification of polypropylene. Finally, employing PP polymeric materials is a
promising alternative which can be used in medicine for future.
Keywords: Protein adsorption, Biofilm formation, Hydrophilicity, Superhydrophobicity,
Bradford assay.
HTTP://UI.CNF.IR/PPS 146
Molecular modeling of Zika virus NS5 and evaluating its interaction
with human targets using In-silico approach
Ghazaleh Sheikhi1 and Hassan Mohabatkar1
1Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan,
Iran.
Abstract
The goal of this study was to generate a three dimensional structure of Zika Virus NS5, an
emerging arbovirus of flavivirus genus, using homology and Ab-Initio modeling methods and to
predict its interactions with human proteins. 3-D structures were generated using I-Tasser web
server for homology modeling and Robetta web server for Ab-Initio modeling. Structural
analysis was performed by ERRAT and PROCHECK programs. To predict protein-protein
interactions in a sequence-based manner web servers LR_PPI and iPPI-Esml were used. The
model built by Robetta was more accurate than the other model generated by I-Tasser due to
Ramachandran plots provided by PROCHECK and overall quality factor of 98.075% given by
ERRAT programs. Interacting pairs between Zika Virus NS5 and human proteins were
determined by the high interaction score from both servers. The generated model and predicted
interacting pairs can be used in drug design and vaccine development to facilitate experimental
procedures.
Keywords: Zika Virus, NS5, 3-D structure, Modeling, Protein-protein interaction.
HTTP://UI.CNF.IR/PPS 147
Extraction optimization, purification and characterization of a
protease enzyme from fruits of Withania coagulans
Saeideh shavandi1, Mehdi varidi2, Ahmad Asoodeh3
1The Ferdowsi University of Mashhad, Mashhad, Iran.
2Department of Food Science and Technology, Ferdowsi University of Mashhad, Mashhad, Iran.
3Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran.
Abstract
Enzyme proteases are one of the most important enzymatic groups in the industry. In recent
years, extracted proteolytic enzymes from plant resources have attracted much attention because
of high activity, stability in a wide range of pH and temperature, resistance to various metal ions,
inhibitors and organic solvents. Withania coagulans is a subtropical plant with important
medicinal properties. The plant fruit is used as a milk coagulant in the east Mediterranean and
south Asia traditionally for cheese production. Withania coagulans have been investigated as a
possible source of an aspartic protease enzyme. Response surface methodology (RSM) using a
central composite design (CCD) was employed to optimize the conditions for extraction of serine
protease from fruits of Withania coagulans. The effect of independent variables, namely
temperature (30-70) sample to buffer content ratio (1/4-1/10) and buffer pH (3–8) on protease
activity, specific activity and protein content of aspartic protease from fruits of Withania
coagulans was investigated. This study showed that the optimum conditions for extracting
protease enzyme from Withania coagulans fruit are, temperature 44.5 ° C, pH 3 and sample to
buffer content ratio 1/6. Protease activity, protein concentration and specific activity in optimum
conditions were 0.609 U/ml, 0.764 mg/ml and 79.8 U/mg respectively. Then in the optimal point,
purification was performed with the method of precipitation with ammonium sulfate 0/85 % and
with the ion exchange chromatographic method (column Q-Sepharose) in following, and
components molecular weight was determined using SDS-PAGE. Electrophoresis image analysis
showed 7 bond with molecular weights between 20-70 kDa.
Keywords: Optimization, Extraction, Protease enzyme.
HTTP://UI.CNF.IR/PPS 148
Designing, development and assessment a series of novel genetic
constructs for aromatic hydrocarbons bioremediation based on
investigation of bacterial dioxygenases 1, Jafar Saeedi*2, 3Mashadrizeh-, Aliakbar Haddad1Mojahed-Safoora Shahreki
1. Department of Biology, Science and Research branch, Islamic Azad University, Khorasan Razavi
Neyshabur, Iran.
2. Cell and Molecular Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad,
Mashhad, Iran.
3. Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
Abstract
Deformation, behavior and cancerous features of the cells could be as old as human history;
however, industrialization of the societies and emergence of numerous carcinogenic compounds
such as aromatic hydrocarbons led to increase these diseases and challenged the human public
health. This type of compounds that could be through consumption of contaminated food,
drinking, smoking, occupational exposure and so on through the lungs, skin and gastrointestinal
tract can enter to the body, due toxic and mutagenic properties could induce canceric features in
a range of cells as direct or indirect. Clearing this type of pollution in the environment due to
characteristics such as solubility, non-polar and hydrophobic has always been difficult. Today,
bioremediation techniques based on the use of bacterial and non-bacterial microorganisms
greatly developed, which can provide promising solutions based on probiotics development via
genetic engineering. Bearing in mind, molecular investigation of the bacterial dioxygenases were
performed in this study for designing a series of competent genetic constructs with aromatic
capacity to hydrocarbons degradation and probiotics transforming. In this regard, the profile of
the bacterial microorganisms with the ability to digest aromatic hydrocarbons as well as
corresponding molecular mechanisms and related key enzymes were determined. Subsequently,
required sequences were retrieved from databanks such as NCBI and UniProt. Molecular
investigation of them in structures, functions and binding affinity have been taken via CD search,
Motif Scan, Blast, MEGA6, Hex and ClusPro2.0 programs. New genetic constructs have been
designed based on provision of the functional domains, and after modeling with Modeller
program, assessed and minimized via MOE. Moreover, binding affinity of the designed
constructs on aromatic compounds that are retrieved from PubChem and Colby database was
performed by using of the PatchDock web server. The results of this study while demonstrated
the various strains of the bacteria with high capacity in aromatic hydrocarbons degradation,
provided the structural and functional features of the bacteria dioxygenases as well as
dioxygenases like proteins. Moreover, provide a series of optimized genetic construct with
capacity to transforming probiotic strains that ought to examine in experimental condition.
Keywords: Cancer, Aromatic hydrocarbons, Bioremediation, Probiotics.
HTTP://UI.CNF.IR/PPS 149
Enhancing extraction efficiency of heterologously expressed
recombinant prostate stem cell antigen in Ecoli
Mahboube Shahrabi-Farahani1, Mohammad M Farajollahi1, Neda Saraygord-Afshari1
1Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences,
Tehran, Iran.
Abstract
Prostate stem-cell antigen (PSCA), a cell-membrane glycoprotein, has shown to be
overexpressed in several major cancers, including prostate, bladder and pancreatic neoplasms.
Highly specific expression pattern of PSCA in the most prevalent cancers leads to drastic
medical applications of this biomarker. In order to apply PSCA in medical and biological
investigations, many researchers have tried to produce this valuable biomarker via recombinant-
protein technology. Considering the hydrophobic nature of PSCA, extraction yield of this
membrane protein by heterologous expression is a subject matter. Therefore, in the present study
PSCA gene was cloned in pET-28a(+) vector, which was expressed in BL21(DE3) Ecoli strain
as a His-taged protein. Yields of recombinant-PSCA exaction were then evaluated for different
ultrasound exposure time (30s, 5 and 10) in different lysis buffer solutions. All the solutions
were composed of 0.05% 2-mercaptoethanol, 1 mM PMSF and 50 mM Tris but varied in
detergent type and/or concentration. TritonX-100 and SDS were the two detergents which were
examined here. After extraction, total protein content was subjected to electrophoretic separation
followed by a blotting procedure using anti-His-HRP-conjugates. Comparison of the blotting
patterns confirmed that the PSCA extraction yield was obviously increased in the presences of
high concentration of SDS (5%) in the lysis solution. Likewise, prolonged ultrasound exposure
(10) yielded a higher-level of PSCA in each extraction procedure. In conclusion we approved
that the nature of PSCA as a glycosylphosphatidylinositol-anchored membrane glycoprotein
demands more rigorous extraction conditions to extract it from the cell membrane and keep it in
the soluble phase.
Keywords: Prostate stem cell antigen, Extraction, Sonication, Detergent.
HTTP://UI.CNF.IR/PPS 150
The properties of biosurfactant produced by Lactobacillus
rhamnosus ATCC 7469
Maliheh Shokouhfard1, Rouha Kasra-Kermanshahi1, Mohammad Mehdi Feizabadi 2, Shahram
Teimourian 3
1 Department of Microbiology, Faculty of Biological sciences, Alzahra University, Tehran, Iran.
2 Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
3 Department of Medical Genetics, Iran University of Medical Sciences, Tehran, Iran.
Abstract
lactobacilli, which constitute an important part of natural microbiota, are recognized as potential
interfering bacteria by producing various antimicrobial agents such as organic acids, hydrogen
peroxide, bacteriocins, and adhesion inhibitors, such as biosurfactants. Biosurfactants, a group of
surface active molecules synthesized by microorganisms, have recently become an important
product of biotechnology for medical applications. The Lactobacillus rhamnosus ATCC 7469
was selected as a probiotic strain to produce biosurfactant. In this study, the Drop-collapse
method and FTIR assay was used for the determination of biosurfactant. In Drop-collapse
method, biosurfactant was able to decrease the surface tension between water and hydrophobic
surfaces. The FTIR analysis showed biosurfactant appears to have more protein than
polysaccharide and phosphate. Anti-adhesive activities was determined using co- incubation
method on the Serratia marcescens strains. This biosurfactant in 2.5 mg/ml concentration
showed antiadhesive activity. The results obtained suggest the possible use of this biosurfactant
as an anti-adhesive agent in the medical field for applications against micro-organisms
responsible for the infections.
Keywords: Lactobacilli, Biosurfactant, FTIR, Anti-adhesive.
HTTP://UI.CNF.IR/PPS 151
Investigate the mechanism of the BAX, a pro-apoptotic protein,
activation through SMBA1, an anti-cancer treatment: a molecular
modeling and molecular dynamics study
Yaser Shabanpour, Parviz Abdolmaleki, Esmaeil Behmard
Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran.
Abstract
Bax is a central death regulator that lead the cell toward apoptosis. Serine 184 (S184) of Bax is a
momentous functional switch controlling for its pro-apoptotic activity. Experimental methodes
had shown that SMBA1, a small molecule from NCI library and Bax agonist, induces
conformational changes in Bax by blocking S184 phosphorylation, facilitating Bax insertion into
mitochondrial membranes and forming Bax oligomers. The latter leads to cytochrome c release
and apoptosis in human lung cancer cells. At first was used AutoDock 4.2 to find the best
conformation of protein- ligand complex, from docking was obtained 30 results with different
energy binding score and different conformation that was selected the best one for molecular
dynamic simulation study, one that had minimum energy binding score, for this docking we
considered 8 residues as flexible residues around the serine 184 pocket Such as Asp 98, Asp 102,
ASn 106, Arg 109, Phe 176, Val 180, Ala 183, Ile 187and serine 184 itself. Molecular dynamic
simulation during the simulation time, 110 nanosecond, shown that SMBA1 creates
conformational change in BAX protein, was obtained rmsd graph, rmsf Graphs, distance Graphs
between residues, hydrogen bond charts and Salt bridge charts for BAX protein in water box and
then for BAX-ligand complex in water box. This result was compared and was found out
conformatinal changes that occurred.
Keywords: BAX, Pro-apoptotic protein, SMBA1, Molecular modeling, Anti-cancer treatment.
HTTP://UI.CNF.IR/PPS 152
Effect of mare (Equus caballus) caseins and whey proteins on breast
cancer cells
Malihe Shariatikia and Mandana Behbahani
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Abstract
Breast cancer is the most common cancer in women and the leading cause of cancer death in
middle-aged women. There are many therapeutic ways for breast cancer, including surgery,
radiation therapy and hormone therapy. Anticancer drugs often cause severe side effects so
further investigations is required to search for potential drugs. In the present study anti-tumor
effects of mare caseins and whey proteins on MCF7 cell line (human breast cancer cell) were
investigated in vitro. Mare milk samples were collected and caseins and whey proteins were
obtained after precipitation of caseins at pH 4.6 with 1 N HCl and centrifugation. The anticancer
activity of caseins and whey proteins was evaluated, using MTT assay. Breast cancer cells
(MCF-7) were cultured in RPMI-1640 medium containing 10% fetal calf serums. Results
showed that mare caseins have 75% cytotoxicity and whey proteins had no effect on cancer cells.
In conclusion, all the data indicated that mare milk is potential drug candidates for inducing
apoptosis in human breast cancer cells.
Keywords: Mare milk, Caseins, Whey proteins, Anticancer, MTT assay.
HTTP://UI.CNF.IR/PPS 153
Endolysins as new class of antimicrobial agents against
pathogenic bacteria
Khashayar Shahin, Majid Bouzari
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
Abstract
Bacteriophage endolysins (peptidoglycan hydrolases) are enzymes coded and used by
bacteriophages at the end of their replication cycle(specially lytic cycle) to degrade the murine
structure of the bacterial host from within, resulting in cell lysis and release of progeny
virions. The absence of an outer membrane (Lipopolysaccharide) in the gram-positive
bacterial cell wall make it possible for endolysins to access the peptidoglycan and destroy them
when applied externally as well as internally. This potential making endolysins interesting as
novel antimicrobial candidates, particularly in light of increasing in antibiotic resistance in
pathogenic bacteria in recent decades. It is now widely recognized that alternative bactericidal
agents for the prevention and treatment of bacterial infections are urgently required. Besides the
use of native and engineered endolysins for controlling of pathogen bacteria in medical manner,
this also can be used as biocontrol agent to prevent of food spoilage in different stage of food
production procedures. This review summarizes the basic structure and functions of different
groups of endolysins and presents the most recent application of native and engineered ones to
treat multi drug resistance gram-positive bacterial species and also their new application in food
safety.
Keywords: Endolysin, Bacteriophage, Antibiotic resistance bacteria.
HTTP://UI.CNF.IR/PPS 154
Study on the interaction of novel cationic platinum complexes with
human serum albumin
1, Reza Yousefi2Masoud Nabavizadeh, Seyed 1, Mehrnaz Jamshidi1Mohammad Bagher Shahsavani
1Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
2Department of Chemistry, College of Sciences, Shiraz University, Shiraz, Iran.
Abstract
Human serum albumin (HSA) predominantly functions as a transport carrier for a vast variety of
natural ligands and pharmaceutical drugs. In the present study, three structurally related cationic
Pt (II) complexes ([Pt(ppy)(dppe)]CF3CO2: 1, Pt(bhq)(dppe)]CF3CO2: 2, and
[Pt(bhq)(dppf)]CF3CO2: 3) were used to assess their interaction with HSA using different
biophysical methods. The spectroscopic results suggest that upon binding to HSA, the Pt(II)
complexes could efficiently induce structural alteration of this protein. The complexes can bind
to HSA with the binding affinities of the following order: 3 > 2 > 1. Also, thermodynamic
parameters of binding between these complexes and HSA indicated the existence of entropy-
driven spontaneous interaction which mostly dominated with the hydrophobic forces. In
addition, molecular docking revealed the involvement of π–π stacking and hydrophobic
interaction between these complexes and HSA. Moreover, CD results exhibited that 1 & 2 could
induce the secondary structural alteration of this protein to larger extent than 3. Complex 3 with
the highest binding affinity for HSA indicates lowest denaturing effect on this protein. The low
denaturation properties of 3 appear important in the terms of lower susceptibility of this platinum
complex for possible development of harmful side effects.
Keywords: Cationic Pt(II) complexes, Human serum albumin, Structural alteration,
Fluorescence, Docking simulation.
HTTP://UI.CNF.IR/PPS 155
Spectroscopic and dynamic properties of arachidonoyl serotonin- β-
Lactoglobulin complex: A molecular modeling and chemometric
study
Samira Gholami, AbdolKhalegh Bordbar, Nadia Akvan
Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Abstract
UV– -lactoglobulin (BLG) and arachidonoyl serotonin (AA-5HT) in
BLG complex were examined and analyzed using chemometrics method. Analysis of the spectral
data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS)
algorithm resulted to the pure concentration calculation and spectral profiles resolution of the
, 1-, (4.532±0.007)×104 M1-chemical constituents and the values of (6.433±0.019)×104 M
as estimated equilibrium constants at 288, 1-and (2.977±0.013)×104 M 1-(3.364±0.010)×104 M
293, 298 and 303 K, respectively. The number of chemical constituents involved in the
interaction, was extracted by PCA method were free and bound BLG. The spontaneity of the
binding process and critical role of hydrogen bonding and Van der Waals interactions as main
driving forces in stabilizing protein-ligand complex have been designated by negative values of
Gibbs free energy, entropy and enthalpy changes of AA-5HT binding. Molecular docking study
showed that AA-5HT binds to Val(41), Leu(39), Leu(54), Ile (71), Phe (82), Asn(90), Val(92),
Phe(105), Met(107), Glu(108) with the free binding energy of –37.478 kJ/mol. Computational
studies predicted that, in spite of serotonin (5HT) which anchors to the outer surface of the BLG
by hydrogen bonds, AA-5HT is situated in the calyx pose and stayed there during the entire time
of simulation with no any major secondary and tertiary protein structural changes which pointed
that BLG could be considered as a suitable carrier for AA-5H.
Keywords: Arachidonoyl Serotonine (AA-5HT), Binding modes, UV–Vis absorption,
Multivariate curve resolution-alternating least squares (MCR-ALS), Molecular docking,
Molecular dynamics simulation.
HTTP://UI.CNF.IR/PPS 156
Purified milk fractions and bioactive peptides, unknown source of
health for Iranian people
Delfan-, Abbas SoleimaniMohammad Rabbani Khorasgani
Department of Biology, Faculty of Science, University of Isfahan, Hezar Jerib Street , Isfahan Islamic Republic of
IRAN.
Abstract
Milk is the first source of food for infant mammals before they are able to eat other types of
food. Use of food supplements, milk derivatives and amino acid and peptides supplements are
increasing rapidly in many countries .Furthermore milk and some fermented products of milk
like yogurt consist of various amino acids and peptides molecules such as alpha-lactalbumin that
could be use in relaxation products, lactoferrin in blends, ß-lactoglobulin in products for high
blood pressure, cGMP in appetite regulation and IgG supplement to fight pathogenic bacteria or
infections resistant to antibiotics. In other hands some pure amino acids like Arginine is essential
for growth of muscles and these supplements can be use directly in some sport groups diets. Also
the main structural proteins in milk, Whey and Caseines, can be use in raw material as a food
supplement. Unfortunately, only some raw material like Caseines and Whey proteins is
remarkable to Iranian markets and the potential of these bioactive peptides of milk are unknown
yet. However and in conclusion, in this short study we argued about the potential of these
derivatives and amino acids for marketing in Iran.
Keywords: Milk, Bioactive peptides, Health, Marketing, Iran.
HTTP://UI.CNF.IR/PPS 157
Design of ubiquitin conjugated peptide of toxoplasma gondii SAG1
antigen for presentation on MHC class I
Soudabeh Soltani1, Behnaz Saffar1, Mostafa Shakhsi Niaii1, Karim Mahnam2
1Department of Genetic, College of Sciences, Shahrekord University, Shahrekord, Iran.
2Department of Biochemistry, College of Sciences, Shahrekord University, Sharekord, Iran.
Abstract
Toxoplasmosis, a zoonotic transmitable disease among different host species, can infect all warm
blooded mammals as well as birds worldwide. An acute infection with this parasite in the early
stage of pregnancy can cause prenatal malformations and abortion in hosts. The major
histocompatibility (MHC) class I antigen presentation pathway plays an important role in
alerting the immune system responses to intracellulary infected cells. MHC class I molecules are
expressed on the cell surface of all nucleated cells and present peptide fragments derived from
intracellular proteins. Ubiquitin, a 76-amino-acid peptide is used to enhance DNA vaccine
responses to antigens in the adjuvant setting. Conjugating ubiquitin to a DNA construct was
intended to enhance the proteasome dependent degradation of endogenously synthesized
antigens, which would also result in an increased cell-mediated response against the conjugated
antigens in vivo. In the present study, some prediction softwares such as Vaxijen, PropredI,
Paproc, Syfpeithi, Netctl, Netmhc were used to prediction of proteasome cleavage sites, and
antigenicity of SAG1 antigen. Comparing results of Paproc, Netctl and PropredI softwares
(detection proteosome digestion site)with results of Vaxijen, Syfpeithi, Netmhc softwares(
prediction immunogenicity )led to identification of different epitopes (amino acid residues of: 8-
15, 65-72, 169-185, 101-109, 199-206, 270-278). Bioinformatics analysis showed that this
region has proper epitope characterization therefore this analysis can be useful for producing
recombinant DNA vaccine design.
Keywords: Toxoplasmosis, Epitope prediction, Ubiquitin.
HTTP://UI.CNF.IR/PPS 158
T-cell epitope prediction of different antigen for developing
Toxoplasma gondii vaccines
, Mohammad Reza 2Karim Mahnam, 1, Mostafa Shakhsi Niaii1, Behnaz Saffar1Soudabeh Soltani3Mahzunie
1 Department of Genetic, College of Sciences, University of Shahrekord, Sharekord, Iran.
2 Department of Biochemistry, College of Sciences, University of Shahrekord, Sharekord, Iran.
3 Department of Immunology, College of Veterinary Medicine, University of Shahrekord, Sharekord, Iran.
Abstract
Toxoplasma gondiiis is an obligate intracellular protozoan parasite responsible for toxoplasmosis
in warm-blooded animals, including man. Although it is generally clinically asymptomatic in
healthy individuals, toxoplasmosis may cause severe complications in pregnant women and
immunocompromised patients. The development of subunit vaccines thus constitutes an
alternative way to achieve effective protection of humans against congenital infection and to
prevent infection of immunosuppressed individuals. In immunocompetent hosts, a robust T cell
response controls parasite growth via the protective cytokine gamma interferon, although
parasites can persist within cysts in the brain and muscle for the lifetime of the infected host. The
crucial role of T cells in controlling T. gondiiinfection is highlighted by the susceptibility of
patients with T cell deficiencies to toxoplasmosis. In the present study, a wide range of on-line
prediction software (such as Vaxijen, Epijen, Ctlpred, Tappred, Iedb) was used to predict T-cells
epitopes, secondary structure and antigenicity SAG1, ROP2, MIC4, GRA7 antigens. The
bioinformatics approach used in the present study was validated by comparing its results with
eight available experimental epitope predictions. Bioinformatics analysis identified T-cell
epitopes at AA residues SAG1 (288-297,155-163), ROP2 (457-465,424-432), MIC4 (467-
475,279-287), GRA7 (208-217,189-197). Finally, all of T-cell predicted epitopes, showed
antigenicity ability except 424-432 (ROP2) and 189-197 (GRA7) residuals. Bioinformatics
analysis showed that this region has proper epitope characterization and so may be useful for
producing recombinant DNA vaccine for Toxoplasma gondii.
Keywords: Toxoplasmosis, Epitope prediction, T-cell epitope.
HTTP://UI.CNF.IR/PPS 159
Kinetics of xantho-oligosaccharide production by xanthan
degrading enzymes from Paenibacillus sp. strain AS7
Maede Sarvi, Mohammad Reza Soudi, Seyed Zahra Mousavi-nejad, Simin Ashraf
Departments of Microbiology and Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.
Abstract
Xantho-oligosaccharides are products of enzymatic reactions by xanthan degrading bacteria.
Much like as many other oligosaccharides, they have a good potential to be used in many
applications such as prebiotic, antimicrobial and antiviral developments. In this study, the
bacterium was cultivated in liquid medium in presence of xanthan. The supernatant of the culture
was sampled at intervals and mixed with 0.5% (w/v) xanthan in 0.03 molar phosphate buffer (pH
6) and incubated for 4h. Thin layer chromatography showed the production of all of the
monosaccharide residues in addition to two different oligosaccharides. The results revealed the
release of the metabolites 12 hours after inoculation. The oligosaccharides were mainly produced
within 24 hours. DNS assay showed that the culture produced the greatest concentration of
reducing sugars at 18h (0.54 mg/ml). According to the results, the related enzymatic activity of
the strain increased to the maximum value in 18-24h while the maximum cell growth was
observed much later, during the time 36h to 48h.
Keywords: Oligosaccharide, Paenibacillus, Xanthan, Xanthan dingrading enzymes.
HTTP://UI.CNF.IR/PPS 160
A thermodynamics study on the interaction of Allura Red AC with
calf thymus DNA
Nasrin Sohrabi1, Nahid Rasouli2, Sahar Alamatsaz3
1,2 Department of Chemistry, Payame Noor University, PO. Box 19395-3697, Tehran, Iran.
3 Department of Chemistry, Payame Noor University, Isfahan, Iran.
Abstract In the present study, the aggregation behavior of a food colorant such as Allura Red AC is
investigated in 5 mM aqueous phosphate buffer of pH 7.0 at 25.0 °C at various concentrations
and ionic strengths using optical absorption spectroscopy. The results suggest that Allura Red
AC do not aggregate in the experimental concentration range. Also, the interaction of Allura Red
AC with ct-DNA is studied by optical absorption, fluorescence spectroscopy, thermal
Denaturation and viscosity measurements. The Allura Red AC bind to ct-DNA via van der
Waals mode as illustrated by hypochromism in the UV-vis absorption band of Allura Red AC
with addition of ct-DNA.The binding constants are determined by analysis of the optical
absorption spectra of the Allura Red AC at various temperatures. The fluorescence intensity ofct-
DNA-ethidium bromide complex decrease withincreasing of concentration of Allura Red
AC.The viscosity studies showed no considerable changes in the viscosity of ct-DNA with the
increasing of the concentration of Allura Red AC. The thermodynamic parameters are also
calculated by van't Hoff equation. The enthalpy and entropy values of the reaction are both
negative and showed that the reaction is enthalpy-favored and entropy-disfavored.
Keyword: Calf thymus DNA, Allura Red AC, UV-vis spectroscopy, Thermal denaturation,
Fluorescence spectroscopy.
HTTP://UI.CNF.IR/PPS 161
Molecular cloning of a Bacillus licheniformis BR1390 α-amylase
gene and biochemical characterization of the recombinant enzyme
Fatemeh Sabzalizadeh and Hamid Reza Karbalaei-Heidari
Molecular Biology Laboratory (MBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
Abstract
Bacillus licheniformis α-amylase (BLA) is an important industrial enzyme which is used to make
corn syrup from starch. In this study, an α-amylase gene fragment with 1536 bp was amplified
using strain BR1390 genome as template by PCR and then cloned into pET 24b (+) expression
vector. Sequencing of the construct, pET24-Amy, showed that the new amylase gene has a
mutation at the position of 33th amino acid in compare to BLA Uniprot P06278. Which actually
is the 4th aa in the mature form of enzyme. Optimum extracellular expression of the recombinant
amylase in Escherichia coli BL21 (DE3) cells using the native signal peptide was obtained after
induction by 0.1 mM IPTG as inducer and 24 h incubation at 30 oC and 220 rpm. The enzyme
was purified by using DEAE-sepharose anion exchange and Ni-NTA affinity column. The
recombinant amylase showed optimum activity in the pH range of 4.0-8.0 and temperature of 90
°C. Study on the effect of 5 mM EDTA on the recombinant amylase activity revealed that the
optimum temperature was decreased to 55 oC. Positive effect of calcium in thermal stability of
the enzyme had the similar behavior of previous reported amylase from Bacillus licheniformis.
Keywords: Amylase, Calcium effect, Overexpression, Thermal stability.
HTTP://UI.CNF.IR/PPS 162
Investigation on the effect of food colorant Allura Red AC on the
bovine serum albumin by various spectroscopic techniques
3Zahra Arabpour, 2, Nahid Rasouli1Nasrin Sohrabi
, Iran., Tehran3697-Department of Chemistry, Payame Noor University, PO. Box 19395 1,2
, Iran.Department of Chemistry, Payame Noor University, Isfahan 3
Abstract
In the present study, the aggregation behavior of a food colorant such as Allura Red AC is
investigated at various concentrations and ionic strengths in 5 mM aqueous phosphate buffer of
pH 7.0 at 25.0 °C by optical absorption spectroscopy. The results showed that Allura Red AC do
not aggregate in the experimental concentration range. Then, the interaction of Allura Red AC
with Bovine Serum Albumin (BSA) is studied by optical absorption, fluorescence spectroscopy
and viscosity measurements. The Allura Red AC bind to Bovine Serum Albumin (BSA) via
hydrophobic mode as illustrated by hypochromism in the UV-vis absorption band of Allura Red
AC with addition of Bovine Serum Albumin (BSA) and also the decreasing of fluorescence in
the presence of different concentrations of Allura Red AC. The binding constants are determined
by analysis of the optical absorption spectra of the Allura Red AC at various temperatures. The
viscosity studies showed no considerable changes in the viscosity of Bovine Serum Albumin
with the increasing of Allura Red AC concentration. The thermodynamic parameters are also
calculated by van't Hoff equation and the results indicate that the process is entropy-driven and
suggest that the main driving forces are hydrophobic interactions.
Keywords: Bovine serum albumin, Allura Red AC, UV-vis spectroscopy, Viscosity.
HTTP://UI.CNF.IR/PPS 163
Efficient synthesis of argirelin acetate as anti-wrinkle peptide
Ali Nikbakht1,2, Hossein Zahedian1, Sorour Ramezanpour1, Saeed Balalaie1,2
1 Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416, Tehran, Iran.
2 Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
Abstract
Peptides are among the most powerful and interesting skin care ingredients being used in
successful anti-aging and anti-wrinkle products to date. Peptides are frequently created by the
digestion of proteins in the body and are readily and rapidly absorbed by the bloodstream. For
this reason, peptides that are synthesized from plants are non-toxic, safe and particularly
effective ingredients for skin care products. Argirelin acetate is an acetyl hexapeptide that works
to relax certain types of facial wrinkles. Acetyl Hexapepitde-3 Argireline and Acetyl Glutamyl
Heptapeptide-1, Snap 8, when topically applied, treat the same type of wrinkles as Botox,
botulinum toxin injections. Argireline decreases wrinkles on the face initiated by the contraction
of muscles of facial expression, especially in the forehead and round the eyes. Argireline is a
safer, lower, and milder alternate to Botulinum Toxin, topically aiming at the identical wrinkle
formation mechanism in a very distinct way. Ac-Glu-Glu-Met-Gln-Arg-Arg-NH2. We report
herein the synthesis of API argirelin acetate through the solid phase peptide strategy and using
the fmoc-protected amino acids. The safe used resin was 2-chlorotrityl chloride and TBTU was
used as coupling reagent.The crude product was purified using preparative HPLC and finally the
structure was confirmed using HRMS (ESI) data. The details about the synthesis approach and
other details will discuss in the conference.
Keywords: Solid phase peptide strategy, Argiriline, Anti-aging, Anti-wrinkle.
HTTP://UI.CNF.IR/PPS 164
Thermostable alginate lyase from Pseudomonas aeruginosa strain
293
Maryam Zali1, Parinaz Ghadam1*, Ahya Abdi Ali2 and Sara Gharavi1
1- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
2- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
Abstract
Mucoid strains of Pseudomonas aeruginosa produce alginate which is a viscous
exopolysaccharide and express alginata lyase activity which can degrade this polymer. These
bacteria are important pathogens in cystic fibrosis (CF) patients commonly colonizing the
respiratory tract and the persistence of these bacteria to treatment by antibiotics, make this
pathogen the major cause of mortality in these patients. One attempt to alleviate the infection is
the destruction of the bacterial biofilm by alginate lyase enzyme. This enzyme is a member of
the polysaccharide lyases that have been isolated from various sources including marine algae,
molluscs and a wide range of microorganisms. Alginate lyases , poly(β-D-1 ,4-mannuronide)
lyase (EC 4.2.2.3) and poly(α-L-I,4-guluronide) lyase (EC 4.2.2.11), cleave the 1-4 glycosidic
linkage in alginate by β-elimination reaction. Alginate is a linear polymer of α-L-guluronate
and β-D-mannuronate arranged in homo- and hetero- polymeric blocks. In this study, alginate
lyase produced by Pseudomonas aeruginosa strain 293(from Rajai hospital in Tehran) was
partially purified and the thermal stability was determined. For this purpose, bacteria were
cultured in the liquid medium YTG (yeast extract, tryptone, glucose) and alginate lyase was
extracted by heat shock method. Enzyme activity was assayed by the thiobarbituric acid (TBA)
method. The enzyme lost just 20% of its activity after 5 hours incubation at 80 ° C. This
indicates that the enzyme has a high thermal stability and it may have many applications in
industry and medicine.
Keywords: Pseudomonas aeruginosa, Alginate lyase, Thermal stability, Thiobarbituric acid.
HTTP://UI.CNF.IR/PPS 165
PH stability of alginate lyase from pseudomonas aeruginosa strain
293
Maryam Zali1, Parinaz Ghadam1, Ahya Abdi Ali2, Sara Gharavi1
1 Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
2 Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic bacterial pathogen that secretes a
capsule-like polysaccharide called alginate that is a linear, acetylated polymer consisting of β (1-
4)-linked D-mannuronate and L-guluronate residues and a key component of mucoid biofilm
matrix. This biofilm is important for the evasion of host defenses and antibacterial therapies,
especially during chronic pulmonary disease of patients with cystic fibrosis. Most proteins for
alginate biosynthesis are encoded by the 12-gene algD operon. Interestingly, this operon also
encodes AlgL, a lyase that degrades alginate and in particular, it enhances phagocytosis and
killing of P. aeruginosa by human immune cells. Alginate lyases (also called alginases) have a
preference for either L-guluronic or D-mannuronic acid residues and have been characterized in
a variety of bacteria including marine organisms, Bacillus circulans, and Pseudomonas species,
including P. aeruginosa. Alginases cleave the 4-0-linked glycosidic bonds between uronate
residues by an eliminative mechanism, resulting in a molecule containing an unsaturated uronic
acid residue at the non-reducing end. In this research, alginate lyase produced by Pseudomonas
aeruginosa strain 293 (from Rajai Hospital in Tehran) was partially purified and the pH stability
characterized. Bacteria were cultured in YTG (yeast extract, tryptone, glucose) liquid medium
and alginate lyase was extracted by heat shock method. The enzyme was then placed in different
pH (2, 4.5, 7.5, 12) of wide range buffer for a 6 hour period and enzyme activity was assayed by
the thiobarbituric acid (TBA) method. This demonstrated that enzyme lost just 50% of its
activity after incubation in alkaline and acidic pH and can therefore be used at extreme pH.
Keywords: Pseudomonas aeruginosa, Alginate lyase, PH stability, Thiobarbituric acid.
HTTP://UI.CNF.IR/PPS 166
Memory prison of protein
Gholamhossein Riazi1, Shahryar Pooyan, Nima Allahyari
Neuroorganic Lab, Department of Biochemistry, Institute of Biochemistry and Biophysics (I.B.B),
University of Tehran, Tehran, Iran.
Abstract
The mechanism of information custody in biological specious in perhaps the most
complex subject among life’s processes to study such mechanism has been tested since
several centuries ago. Based on fractal theory, the human memory of mimics small
molecules such of proteins, complex globular structure of proteins in protect candidate for
keeping information so called memory. Primary sequence and geometry of third and
fourth structure would be involved in memory of biological organisms. Naturally more
complexity drives the protein to more ability for prisoning information inside.
Microtubules proteins which in a polymer of thousands of tubulin monomer, with
hydrophobic pocket changing hydrophobic pocket structure has been shown to the very
stable while microtubule protein, as to as vesicle transporter at the time.
Keywords: Memory, Microtubules, Complexity, Fractal theory.
HTTP://UI.CNF.IR/PPS 167
Effects of Silver Nanoparticles on Protein Pattern and Antioxidant
Enzymes Activities of Canola (Brassica napus L.) Under In vitro
Conditions Roya Razavizadeh
Department of Biology, Payame Noor University, PO BOX 19395 Tehran, Iran
Abstract
The effect of Silver Nanoparticles was investigated on protein pattern changes, silver
accumulation and alterations in antioxidant capacity in canola (Brassica napus L.) cultivar
Ocapy under in vitro conditions. The grown seedlings on MS medium were subjected to MS
medium containing 0, 0.5, 1, 1.5 and 2 ppm concentrations of silver nanoparticles for four
weeks. Application of different concentrations of nanosilver had no significant effect on the total
soluble protein in shoot but had decreased protein content in 1.5 ppm concentration in root. The
study of shoot and root protein patterns using one dimension gel electrophoresis (SDS-PAGE)
and consequence analysis of bands by ImageJ program showed some remarkable changes.
Relative expression of three proteins in shoot and five proteins in root were changed in response
to nanosilver treatment. Silver accumulation was only detected in shoot tissue. There were some
changes in antioxidant enzymes activities. The reduced sugars were increased in 1.5 ppm of
nanosilver comparing with the control plants in shoot. It seems that the nanosilver at 1.5 ppm
concentration is the best treatment of nanosilver as an ethylene action inhibitor under in vitro
condition for B. napus L. cultivar Ocapy in this study.
Keywords: antioxidant enzymes, Brassica napus, nanosilver, protein pattern
HTTP://UI.CNF.IR/PPS 168
Spectroscopy study on interaction of amaranth with bovine serum
albumin (BSA): a thermodynamic approach
3Nafiseh Rezvani, 2, Nahid Rasouli1Nasrin Sohrabi
3697, Tehran, Iran.-Department of Chemistry, Payame Noor University, PO. Box 19395 1, 2
Department of Chemistry, Payame Noor University, Isfahan, Iran. 3
Abstract
In the present study, at first aggregation behavior of a food colorant such as amaranth is
investigated in 5 mM aqueous phosphate buffer of pH 7.0 at 25.0 °C at various concentrations
and ionic strengths using optical absorption spectroscopy. The results suggest that amaranth do
not aggregate in the experimental concentration range. Also, the interaction of amaranth with
bovine serum albumin (BSA) is studied in 5 mM aqueous phosphate buffer of pH 7.0 by optical
absorption, fluorescence spectroscopy and viscosity measurements. The amaranth bind to (BSA
via hydrophobic mode as illustrated by hypochromism in the UV-vis absorption band of
amaranth with addition of BSA and also the decreasing of fluorescence in the presence of
different concentrations of amaranth. The binding constants are determined by analysis of the
optical absorption spectra of the amaranth. The viscosity studies showed no considerable
changes in the viscosity of BSA with the increasing of the concentration of amaranth. The
thermodynamic parameters are also calculated by van't Hoff equation. The results indicate that
the process is entropy-driven and suggest that the main driving forces are hydrophobic
interactions.
Keywords: Amaranth dye, Bovine serum albumin (BSA), UV-vis Spectroscopy, Fluorescence,
Viscosity.
HTTP://UI.CNF.IR/PPS 169
Development a broad-spectrum immunotoxins based on in-silico
ligands assay
Mohammad Rastegar Moghadam Baghestani 1, Aliakbar Haddad-Mashadrizeh2, Javad Baharara 3
1 Department of Biology, Science and Research branch, Islamic Azad University, Khorasan Razavi, Neyshabur,
Iran.
2 Cell and Molecular Biotechnology Research Group, Institute of Biotechnology and Department of Biology, Faculty
of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
3 Department of Biology, Mashhad branch, Islamic Azad University.
Abstract
Prostate cancer, after the cardiovascular disease and lung malignancies is the third major cause of
death in the men of society. Therefore, wide strategies for diagnostic and treatment of this
disease such as immunotoxin therapy have been developed. Accordingly, development a series
of broad-spectrum immunotoxins could be valuable for targeting several cancerous tissues and or
metastatic cells, which in turn is required to detecting broad-spectrum antigens. In this regard,
cell surface specific antigens were gathered; in-silico expression assays of them were then
performed by proteinatlas into the breast, cervix, colon, skin, brain, head and neck, liver, lymph
nodes, lung, uterus, ovary, pancreatic, prostate, kidney, gallbladder, stomach, testicular, thyroid,
and urinary tract cancerous tissues. Subsequently, common antigens have been selected, and then
corresponding nucleotide and protein sequences retrieved from related databank. Moreover, 3D
structures of these antigens have been determined. On the other hand, ligands assays performed
via string program and validated by cluspro based on scoring and binding affinity. The results of
this study led to reveal 15 cell surface prostate-specific antigens. Among these antigens, PAGE3
and KDM5D showed the highest expression on the cancerous cell surface of prostate and other
tissues which are surveyed in this study. Interestingly, the expression of these antigens on the
surface of normal cells was negative. Moreover, HPA062248, HPA049086 with high binding
affinity, short in length and limited in post-translational modification candidate as the best
ligands for broad-spectrum immunotoxins development, with 20 targets of cancer cells.
Keywords: Cancer, Prostate, Immunotoxins, Antigen, Ligand.
HTTP://UI.CNF.IR/PPS 170
Structural alterations in hemoglobin by glycation; prevention by
ferulic acid and p-coumaric acid.
Esmat Rahmanifar1 and Mehran Miroliaei2
1Department of Biology, College of Sciences, Institute of Nourdanesh, Isfahan, Iran. 2Cell, Developmental and Molecular Biology Division, Department of Biology, College of Sciences, Isfahan
University, Isfahan, Iran.
Abstract
Protein glycation is a non-enzymatic reaction between reducing sugars and free amino groups of
proteins. This reaction finally produces advanced glycation end-products (AGEs). The
accumulation of AGEs in body leads to structural and functional modifications of tissue proteins.
Since oxidative reactions participate in the process of AGEs formation, so antioxidants may
prevent this event. Therefore, we studied effects of ferulic acid and p-Coumaric acid in human
hemoglobin/fructose system. The formation of AGEs, level of glycation and conformational
alterations were assessed by various spectroscopic techniques including uv-vis, circular
dichroism and fluorescence spectroscopy. Alterations in the secondary structure of hemoglobin
was observed upon glycation, which was mitigated by applying the ferulic acid and p-Coumaric
acid. Accordingly, these compounds may have potential of block the refolding of hemoglobin.
Our results showed that ferulic acid and p-Coumaric acid may have beneficial roles in the
prevention of glycation-associated diseases.
Keywords: Protein glycation, Hemoglobin, Fructose, Antioxidants.
HTTP://UI.CNF.IR/PPS 171
Protein glycation and anti-AGE agents; possible role in treatment of
glycation-associated diseases.
Esmat Rahmanifar1and Mehran Miroliaei2
1Department of Biology, College of Sciences, Institute of Nourdanesh, Isfahan, Iran. 2Cell, Developmental and Molecular Biology Division, Department of Biology, College of Sciences, Isfahan
University, Isfahan, Iran.
Abstract
Protein glycation is a non-enzymatic browning reaction between reducing sugars and free amino
groups of proteins. This reaction finally produces advanced glycation end-products (AGEs). The accumulation of AGEs in body leads to structural and functional modifications of tissue
proteins. There is emerging evidence that protein glycation is implicated in the aging process,
pathogenesis of the complications of diabetes (retinopathy, neuropathy, nephropathy and
atherosclerosis) and Alzheimer’s disease. It has been proposed that discovery of inhibitors of
glycation cascade should offer a promising therapeutic approach for the prevention of diabetic or
other pathogenic complications. There have been many reports on the inhibitory activities of
some phenolic compounds in plant against glycation of proteins. Therefore, we studied
therapeutic potential of curcumin and chlorogenic acid in human hemoglobin/fructose system.
The formation of AGEs, level of glycation and conformational alterations were assessed by
various spectroscopic techniques including uv-vis, circular dichroism and fluorescence
spectroscopy. Alteration in the secondary structure of hemoglobin was observed upon glycation,
which was mitigated by applying the curcumin and chlorogenic acid. Higher amount of α-helix
in the presence of these compounds could be ascribe to their anti-glycation effects. Our results
showed that curcumin and chlorogenic acid may have therapeutic potential in treatment of
glycation-associated diseases.
Keywords: Protein glycation, Hemoglobin, Anti-AGE agents.
HTTP://UI.CNF.IR/PPS 172
A simple bioluminescence method for determination of benserazide
by inhibitory effect on aequorin in biological sample
Hossein Rahmani and Reza H. Sajedi
Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Abstract
The increasing development of diagnostic systems in drug monitoring require to design new
approach to create. Aequorin as a bioluminescence protein due to ease of use, non-toxic and high
capability of detecting has long been interest of researchers. Bioluminescence properties of
photoproteins are strongly dependent on conformation and stability of their substrate, namely
coelentrazine, in the binding pocket. Slight change in the binding pocket and microenvironment
of coelentrazine leads to alteration of protein-substrate interactions and strongly influence the
bioluminescence properties. This method has been considered recently to measure the analytes is
the assessment of the inhibitory effect of analyte on phtoprotein. Therefore, it can be used to
detect and measure compounds with structural similarity to coelentrazine. Benserazide (BA) is a
drug used indirectly for clinical treatment of Parkinson’s disease. This analyte can significantly
reduce bioluminescence of aequorin in a concentration-dependent mode. Linear calibration curve
were obtained in a range of about 0.1 to 10 μM with a detection limit down to 10 nM.
Furthermore, we demonstrate the application of the approach in human serum samples, which
suggests its great potential for diagnostic purposes.
Keywords: Aequorin, Benserazide, Biolumencence inhibition assay, Drug monitoring.
HTTP://UI.CNF.IR/PPS 173
Cognition enhancing and neuromodulatory propensity of
satureiahortensis extract against lysozyme induced cognitive
impairments in rat hippocampus.
Hassan Ramshini1 and Nayyereh Kovsari2
1Biology Department, Payam Noor University, 19395-4697 Tehran, I.R. of Iran.
2Mobinihospital, Sabzevar University of Medical Sciences, Sabzevar, Iran.
Abstract
Alzheimer's disease is the most common form of dementia among the elderly and is
characterized by massive neuronal loss and progressive cognitive impairment. Beta amyloid
hypothesis is the main theoretical research frame work for Alzheimer's disease which states that
extracellular aggregation of beta amyloid results in synaptic loss and cell apoptosis. Although
intensive research was done for its diagnostics and/or treatment, a drug that inhibits amyloid β
aggregation and ameliorates the disorder has not been approved to date. One important approach
in the development of therapeutics is the use of herbal extracts which are rich in aromatic
molecules. At the present study, we induce amyloid aggregation in hen egg white lysozyme
(HEWL), and the therapeutic efficacy of Satureiahortensis extract on amyloid aggregation
inhibition, spatial learning and memory of rats was investigated. 24 male wistar rates (250-280
gr) were divided into 4 groups (n=4): control, received scopolamine, received lysozyme amyloid
aggregates and received lysozyme aggregates formed in presence of Satureiahortensis extract.
The Morris Water maze was used for studying the spatial learning memory. The results showed
that the hippocampal injection of HEWL aggregates damaged the spatial memory rates but
amyloid aggregates formed in presence of Satureiahortensis, there was no significant effect on
spatial memory in rat. These observations suggest that aromatic molecules of Satureiahortensis
extract are capable directly insert into amyloidogenic core of early aggregates and inhibit
amyloid fibril formation. Second, showed the importance of using model proteins as a valid tool
to investigate the pathogenesis of Alzheimer’s disease.
Keywords: Hen egg white lysozyme, Amyloid aggregation, Satureiahortensis extract, Alzheimer,
Spatial memory.
HTTP://UI.CNF.IR/PPS 174
Protective effect of 1, 3, 5 tri fluoro phenyl benzene against lysozyme
oligomerization and amyloid-mediated cell death in PC12 cells.
Hassan Ramshini and Najmeh Annabestani
Biology Department, Payam Noor University, 19395-4697 Tehran, I.R of Iran.
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative brain disorder that affects millions
among the aging population.The progressive production and subsequent accumulation of the
βamyloid peptides (Aβ) in the brain play a central role and thus Methods to prevent Aβ
aggregation have been proposed for treatment of AD. Recent studies have suggested that
interactions between aromatic small molecules may play an important role in amyloid
aggregation inhibition. At the present study, we have evaluated a tri phenyl benzene as a
aromatic small molecule to reduce hen egg white lysozyme (HEWL) aggregation.HEWL was
chosen for induction amyloid aggregation and effect of the compound was assayed via various
techniques including: Thioflavin T (ThT) and Congo red absorption and atomic force
microscopy. Our studies showed that the compound dose-dependently inhibit HEWL lysozyme
aggregation processes. This compound, not only inhibited the formation of aggregated structures
by HEWL but also the cytotoxic activity of HEWL aggregates toward cultured cells. The results
of this study provide further experimental support for the paradigm of amyloid inhibition by
heteroaromatic interaction and point to tri indole derivatives as a simple molecular platform for
the development of novel fibrillization inhibitors.
Keywords: lysozyme, Amyloid aggregation, Drug design.
HTTP://UI.CNF.IR/PPS 175
Structural study of wnt-pathway inhibitors, Mesd and dkk1 on
LRP6, potentials for anti-cancer peptide design
Najme Dehghan–Bonadaki and Majid Taghdir
Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Abstract
Signaling pathways are the most overriding part of cellular communications and life
development is coupled to increment of these pathways. The significance of their role in
embryonic events and adult tissues homeostasis is exhaustively obvious and in human diseases,
particularly cancers, some of these pathways are aberrantly active. Interestingly, in triple
negative breast cancer (TNBC), a highly aggressive subtype of breast carcinoma, Wnt/β catenin
signaling is aberrantly activated because of overexpression of crucial co-receptor of the
pathway”LRP6”. The pathway is conserved and highly regulated with lots of mechanisms.
DKK1, sFrp and Wif1 are the most structurally known inhibitor of the path. On the other hand,
Mesd, an essential chaperon for proper folding of BP domains of LRP6, is a universal inhibitor
and shows anti-cancer effect. Mesd and DKK1 bind to lrp6 and inhibit the pathway. But the
mechanism of their inhibition is not fully understood. Here, we used a series blind and site-
directed docking and long term molecular dynamic simulation to create some of Mesd and
DKK1 complexes with LRP6 to get a clearer picture about their interaction mode and binding
sites on LRP6. The results show that some binding regions on LRP6 are overlapping and
common for Mesd and DKK1. Additionally, the pattern of interaction and mechanism of action
seems similar from RMSD, RMSF and gyration plots, extracted from MD trajectory. Free Gibbs
energy calculation give meaningful results about mechanism of action of these inhibitors. This
finding is matched to some experimental assays. Interestingly affinity of Mesd to domain 12 of
LRP6 is more than domain 34 and this is vice versa for DKK1. These results proposed new
insight to design of novel anti-cancer proteins or peptides based on Mesd and DKK1.
Keywords: Breast cancer, Anti-cancer, Docking simulation.
HTTP://UI.CNF.IR/PPS 176
Lactopeptides are natural antibiotics can be replace with artificial
antibiotics
Saleeme khajepour and Ali Niazi
Departement of Biotechnology, Shiraz University, Shiraz, Iran.
Abstract Animal milks have good nutritive value, in addition to their antigenotoxic and anticytotoxic
effects. milk also offers several unique health benefits attributed to the presence of high
concentration of insulin/insulin like protein, immunoglobulin, lactoferrin, lactoperoxidase and
peptidoglycan recognition protein. The disease spectrum is broad and includes acute disease,
such as erysipelas, sepsis, pneumonia, and numerous other infections, having a direct association
to a given pathogen, as well as chronic diseases, where microbes often cause a long-standing
inflammatory state. In many respects, we have reached a point for certain infections where no
therapeutic agents are longer available. As a result of these accelerating problems with multidrug
resistance, there is a large current interest in antimicrobial peptides (AMPs). AMPs are key
components of the innate immune system, where they constitute a first line of defense against
invading pathogens. Although AMPs affect bacteria in many different ways, including inhibition
of cell wall, DNA, RNA, and protein synthesis, and inhibition of enzymatic activity, the main
mode of action of AMPs is the disruption of bacterial membranes. Some of the important milks
AMPs are lactoferrin, lactoferampin, lactoferricin,… each of them besides work as antibiotics do
some other important reaction in different situations and we can replace them with these
dangerous and artificial antibiotics, todays are common.
Keywords: Lactopeptide, Antimicrobial peptides, Antibiotics.
HTTP://UI.CNF.IR/PPS 177
Investigation of the antifouling and protein adsorption properties of
polyethersulfonemembranes by titaniadioxide nanoparticles coating
Mahsa Khalili1, Parisa Moazzam2, Amir Razmjou1, Rasoul Shafiei3
1Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, P.O. Box
73441-81746, Isfahan Iran.
2Department of Nanotechnology, Faculty of Advanced Science and Technology, University of Isfahan, Isfahan, Iran.
3Department of Biology, Faculty of Sciences, University of Isfahan, Iran.
Abstract
Although polymeric membrane has superior properties, its applications in biomedical and
industrial fields are very limited. Biofouling is a major concern in membrane which is created
from particular interactions between membrane and untreated water content. Here, for the first
time we showed that a carful superhydrophilic modification of polyethersulfone (PES)
membrane can address those drawbacks which have hindered their utility. Development of
nanocomposite membrane is a suitable strategy to reduce protein adsorption and biofouling
formation. The PES membrane surfaces were characterized by SEM, EDAX, AFM, contact
angel (CA) goniometry, surface free energy (SFE) measurement, Bradford and microtiter plate
assays and also flow cytometry analyses. Results showed that CA and SFE changed
from57°and30° to 0°in 25 seconds and 43 to 44mN/m, respectively. The stable and durable
modification led to a substantial reduction in static BSA protein absorption. The effect of such a
treatment on the biofilm formation was analyzed by using two different bacteria. The microtiter
plate assay and flow cytometry analysis showed that the superhydrophilic modification could
substantially reduce the bacterial adhesion and then biofouling formation. Hence, combination of
chemical and mechanical modification due to a significant effect on surface pore size, bacterial
attachment and protein adsorption resistance as well as hydrophilicity.
Keywords: Polymeric membrane, Polyethersulfone, Biofouling, Biofilm formation.
HTTP://UI.CNF.IR/PPS 178
Interaction of human serum albumin with the resveratrol in the
presence of nanoparticles and EMF (up to 1 MHz)
Nooshin Khaghani1
, Azar Fani2, Jamshidkhan Chamani1
1 Department of Biochemistry and Biophysics, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
2 Assistant Professor of Radiation Oncology, Cancer Research Center Mashhad University of Medical Sciences,
Mashhad, Iran.
Abstract
Human serum albumin (HSA) as a kind of main carrier protein is the most abundant in human
blood plasma and provide about 80% of osmotic compression of blood. HSA has a high affinity
to an extraordinarily divers range of materials such as drugs, fatty acids. Metabolites and metal
ions, so it is transporter for the materials. Resveratrol (RES) is a dietary polyphenolic, non-
flavonoid antioxidant derived from grapes, peanuts, barriers, and other plant sources. Resveratrol
has various health benefits, such as cardiovascular and cancer prevetive properties, and it induces
apoptosis by up- regulating pro-apoptotic genes while simultaneously down- regulating anti-
apoptotic genes. Possibility that RF (Radio Frequency) radiation may cause changes in protein
conformation and hence in biological properties has been revealed. In our work, the binding of
resveratrol to plasma protein, human serum albumin (HSA) in the presence of EMF and
nanoparticles, have been investigated systematically by fluorescence quenching technique, UV-
Vis absorption spectroscopy, circular dichroism (CD) spectroscopy and FRET. The fluorescence
data showed that the binding of resveratrol to HSA is a static quenching procedure. The CD
spectroscopy indicates that the secondary structures of the protein is changed in the presence of
resveratrol with nanoparticles and EMF. The result of fluorescence spectra UV-Vis absorption
spectra and FT-IR spectra showed that the conformation of human serum albumin has been
changed in the presence of resveratrol and EMF. The Stern-Volmer curve of the fluorescence
quenching of HSA by resveratrol indicated that the quenching mechanism between resveratrol
and HSA was mainly static quenching.
Keywords: Human serum albumin, Resveratrol, Electro magnetic field, FTIR, UV-Vis, Circular
dichroism.
HTTP://UI.CNF.IR/PPS 179
Interaction between silver nanoparticles and human serum albumin
revealed by fluorescence spectroscopy in the presence of resveratrol
Nooshin Khaghani1, Azar Fani2
, Jamshidkhan Chamani1
1 Department of Biochemistry and Biophysics, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
2 Assistant Professor of Radiation Oncology, Cancer Research Center Mashhad University of Medical Sciences,
Mashhad Iran.
Abstract
The interaction between silver nanoparticles (SNPs) with three different sizes and human serum
albumin (HSA) was studied by fluorescence spectroscopy in this work. Human serum albumin
(HSA) is a principal carrier protein in serum known to bind an extensive variety of endogenous
compounds with dissociation binding constants (KD) in the range of 10-3 to 10-8 mol 1-1.
Resveratrol (3, 5, 4-trihydroxystilbene) is a natural polyphenolic compound produced in plants
(e.g., grapes, mulberries, peanuts) in response to damage and fungal attack. Resveratrol exists as
trans and cis isomers. Most of its biological activities are attributed to the trans isomer.
Nanoparticles are used in a large variety of scientific and industrial applications and their
chemical behavior has begun to be well studied on the nanoscale. The interaction between
nanoparticles and human serum albumin was investigated at physiological pH in an aqueous
solution using fluorescence spectroscopy. The analysis of fluorescence spectrum and
fluorescence intensity indicates that SNPs have a strong ability to quench the intrinsic
fluorescence of HSA by static quenching mechanisms. Resonance light scattering (RLS) spectra
showed the formation of a complex between HSA and SNP in presence of resveratrol. The
analysis results suggested that the electrostatic interactions played key roles in the reaction
process. The CD spectra proved secondary structure alteration of HSA in the presence of
resveratrol.
Keywords: Silver nanoparticles, HSA, Resveratrol, Fluorescence spectroscopy.
HTTP://UI.CNF.IR/PPS 180
Comparison of phytase production in submerged and solid state
fermentation of a strain of Aspergillus niger and investigation of 3
various solid media containing wheat bran as the basic substrate
Atefeh Hamzeh1 Jamshid Fooladi 1, Fakhri Sadat Hosseini 2
1 Laboratory of Industrial Microbiology, Faculty of Biology, Alzahra University, Tehran, Iran.
2 Faculty of Biology, Alzahra University, Tehran, Iran.
Abstract
Phytases are enzymes that catalyze hydrolysis of inorganic phosphate from phytic acid. Simple
stomached animal have any or little amount of this enzyme. So phosphate will be added to their
feed dietary; but additional phosphate and undigested phytate will excrete to environment and
lead to phosphate pollution and eutrophication. Therefore using phytase in simple stomached
dietary can improve their growth and reduce environmental pollution (Broz et al.1994; Cromwll
et al.1995). Solid state fermentation can use agricultural wastes as substrate; hence enzyme
production with this method is more cost–effective. In this study, solid state fermentation of
Aspergillus niger for phytase production was carried out with 3 different media in 250 ml
Erlenmeyer flasks: 1-wheat bran + glucose +dextrin (Bhavsar et al.2010) 2-wheat bran, 3-wheat
bran + malt extract 1 %. Flasks were incubated in 30 OC for 96 hours. Enzyme assay was carried
out with Phosphomolybdenum blue method (Engelen et al. 1994). Furthermore we compared
enzyme production of submerged and solid state fermentation. Among different solid media, the
maximum and minimum enzyme activity was observed in the second and the first media
respectively. In the first media, glucose has inhibitory effect on phytase production, because of
its influence on gene level. Batal and Karem reported similar results in 2002. It seems that due to
the presence of malt extract in the third media, phytate concentration increases and eliminates
phytase production. But obviously the solid state fermentation had higher enzyme activity than
submerged fermentation.
Keywords: Phytase, Aspergillus niger, Solid state fermentation, Wheat bran.
HTTP://UI.CNF.IR/PPS 181
Hydrolysis of collagen-containing wastes as a renewable nitrogen
source
2, Mohammadhadi Jazini1Mojtaba Hasiri
Iran. Department of Chemical Engineering, Isfahan University of Technology, Isfahan,1
Department of Chemical Engineering, Isfahan University of Technology, Isfahan, Iran.2
Abstract
According to the rapid population growth in recent years, the demand for livestock meat
consumption increased.Massive production of meat has been resulted in huge amount of animal
tissue wastes. These wastes cannot be disposed in the environment because of extremely bad
smell and high organic carbon content. Hence, they must be somehow treated to be ready to
release to the environment. Tissues from intestine of cows are one of the main solid wastes
produced by slaughterhouses. This tissue consists of different kinds of proteins, lipids and
carbohydrates which are arranged in a multi-layer structure. One of the layers is used as natural
skid in sausage industry. The others are wasted. This kind of waste consists of protein, mainly
collagen. Hydrolysis of this protein could provide a renewable source of nitrogen. This organic
nitrogen source could be used in microbiology for formulation of media. Besides, it can be used
in the production of chelated minerals in animal nutrition. The hydrolysis of collagen is difficult
because of its recalcitrant structure. Hence, in this study different methods for hydrolysisof
collagen were presented and theiradvantages and disadvantages were discussed. These methods
include acidic, basic, thermal, microbial and enzymatic hydrolysis. The hydrolysis methods then
were compared in terms of their potential to be implemented in relevant industries.
Keywords: Hydrolysis, Protein, Collagen, Animal tissue, Collagen-containing waste.
HTTP://UI.CNF.IR/PPS 182
In silico evaluation of binding affinity of zanamivir, peramivir, and
laninamivir octanoate drugs compared with oseltamivir to the
neuraminidase in influenza A (H1N1)
Seyed Ali Hosseinian1 and Seyedeh Samira Hosseinzadeh2
1Department of Biology, Science and Research Branch, Islamic Azad University, Khorasan Razavi, Neyshabur, Iran.
2Department of biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
Abstract
The 2009 pandemic swine origin influenza A H1N1 virus (pH1N1) has reminded the world of
the threat of pandemic influenza, and resulted in 140 confirmed deaths in Iranian population in
this year. The influenza neuraminidase (NA) enzyme is the most successful drug target against
the seasonal and pandemic flu. Treatment of influenza with the neuraminidase inhibitors (NAIs)
oseltamivir phosphate (Tamiflu®), zanamivir (Relenza®), laninamivir octanoate (Inavir®), and
peramivir (Rapiacta®) has become common among Japanese primary care providers. In this
study, first the structures of receptor and ligands from PDB were received. The neuraminidase
(NA) selection and determination of ligand binding site through Discovery Studio3.0 Client,
docking and data analyzing by AutoDock Tools 4.2.6 (AutoDock Vina), the study of
conformations and bindings through Pymol and the comparison and valuation of the data using
SPSS, were accomplished. The data from the calculations in 27 conformations for each of
ligands in 3 repeat, for following values: binding energy, RMSD, hydrogen bonds, and VDW
and electrostatic interactions; demonstrates more binding affinity of Zanamivir, Peramivir, and
Laninamivir Octanoate drugs, respectively, compared with Oseltamivir. Due to the increasing
resistance to Oseltamivir in influenza A (H1N1) virus and considering the results of the
calculation of the interaction of receptor-ligand, it seems that these novel neuraminidase
inhibitors, especially Zanamivir, can be good alternatives to Oseltamivir in the treatment of
influenza A (H1N1).
Keywords: H1N1, Novel NAIs, Oseltamivir, AutoDock Vina.
HTTP://UI.CNF.IR/PPS 183
The simulation and evaluation of fever temperature effects on the
active site of neuraminidase protein receptor in influenza A (H1N1)
virus in the in silico
Mohammad Fatehi Abdolabadi, Vahid Mirzabayati, Seyed Ali Hosseinian
Department of Biology, Science and Research Branch, Islamic Azad University, Neyshabur, Khorasan Razavi, Iran.
Abstract
Influenza is an important cause of morbidity and mortality. The treatment of influenza with
neuraminidase (NA) inhibitors has been very common. Fever is listed as a predominant symptom
for influenza on the centers for disease control and prevention (CDC) website. First, the
structure of chain A of protein NA with ID: 3ti6 was received from PDB. Then the identification
of the active site amino acids (AAs) including: ARG118, GLU119, ASP151, ARG152, ARG292,
and ARG371 was accomplished through DiscoveryStudio3.0Client. The simulation of protein
modes were performed using GROMACS5.07, containing gromos96 43a1 force field. That was
done for two different modes: 1- Normal body temperature, 37°C (310°K), in 1000ps of time,
and 2- Fever temperature, 39°C (312°K), in 1000ps of time. The mentioned data was fed in
NVT→NPT→MD simulation steps, respectively. The alignment and analysis of protein modes
was done by Pymol.
The analyzed results in pymol showed: 1- the change of the direction of AAs conformations of
ARG118, ARG152, ARG292, and ARG371 moving toward the inside of the active site and 2-
the deletion of intra-AAs hydrogen bonds of ARG118, GLU119, ASP151, and ARG152. Our
results suggest that in fever temperature, the AAs conformation of active site causes the decrease
of protein's cave space, so it is expected that it results in the decrease of drug's penetration into
the active site. Due to the deletion of hydrogen bonds in this temperature and regarding the little
simulation time it is expected that the protein conformation cannot be stable in the active site. As
a general conclusion, this study can explain that fever temperature may result in the destruction
of the structure and the function of virus NA protein.
Keywords: H1N1, Fever, Neuraminidase, Binding site,
GROMACS5.07.
HTTP://UI.CNF.IR/PPS 184
Investigation of binding interactions of apigenin and morin hydrate
with beta-lactoglobulin
MohammadiFakhrosadat andMasoomeh Hoseini
Department of Chemistry, Institute for Advanced Studies in Basic Science, Gavazang, Zanjan, Iran.
Abstract
β -Lactoglobulin is the major whey protein of cow and sheeps milk, and is also present in many
other mammalian species; a notable exception being humans. This protein can bind many
hydrophobic molecules, suggesting a role in their transport. β -Lactoglobulin is a small protein,
soluble in dilute salt solution as befits a globulin, with 162 amino acid residues. In this study, we
investigated the binding interactions of apigenin and morin hydrate with the milk protein β-
Lactoglobulin. Apigenin (4′, 5, 7-trihydroxyflavone), found in many plants, is a natural product
belonging to the flavone class that is the aglycone of several naturally occurring glycosides. It is
a yellow crystalline solid that has been used to dye wool. Morin Hydrate (3, 5, 7, 2′, 4′-
pentahydroxyflavone) is a yellow chemical compound that can be isolated from osage orange,
old fustic and from leaves of common guava. In a preclinical in vitro study. In this study,
spectroscopic techniques such as UV–Vis absorption, steady-state fluorescence and synchronous
fluorescence have been used. The fluorescence titration experiments showed that these two
compounds have quenching effect on the fluorescence intensity of β-Lactoglobulin. The binding
parameters including number of binding sites and binding constant have been calculated based
on the fluorescence quenching data. The short Förster's distance between donor (BLG) and
acceptor (Apigenin and Morin Hydrate) and also the binding constant values demonstrated the
strong interaction between these two flavonoids and BLG. The synchronous fluorescence results
indicated that binding of these two compounds may not cause considerable alterations in the
conformation of β-Lactoglobulin.
Keywords: β-Lactoglobulin, Apigenin, Morin hydrate, Fluorescence quenching, Synchronous
fluorescence.
HTTP://UI.CNF.IR/PPS 185
Exploring the thermal stability and activity of proteinase K in the
presence of spermidin by biophysical techniques and molecular
dynamic simulations
Mansoore Hosseini Koupaei1, Behzad Shareg 2 , Ali Akbar Saboury2,3, Aboulfazl Semnani4 , Fateme
Davar5 , Fateme Reisi1
1Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O. Box.115, Iran.
2 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
3 Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.
4 Department of Chemistry, Faculty of Science, University of Shahrekord, Shahrekord, Iran.
5 Department of Chemistry, Isfahan University of Technology, Isfahan, Iran.
Abstract
Polyamines such as spermidine are ubiquitous to all living organisms, can have interactions with proteins.
The aim of the present study was to investigate how spermidine could influence the thermal stability and
activity of proteinase K as a model enzyme. Here UV Visible spectroscopy, fluorescence spectroscopy
and molecular dynamic (MD) simulation techniques have been employed to understand the stability and
activity changes of proteinase K. The thermal stability results showed that by increasing the
concentrations of polyamine, the thermal stability of enzyme increased. We report that polyamine
enhance the enzyme activity of proteinase K using para nitrophenyl acetate (pNA) as a synthetic substrate
of proteinase K in 50 mM Tris-HCl with pH8. The intrinsic fluorescence of proteinase K was decreased in
the presence of polyamine due to excited- state proton transfer. Molecular docking also indicated that the
hydrogen bonds and hydrophobic interactions dominated in the binding site of polyamine on proteinase
K.
Keywords: Poly amine, Activity, Molecular dynamic, Proteinase K
HTTP://UI.CNF.IR/PPS 186
Investigation of the effect of spermine on the interaction between
ADA and its substrate using computational methods
Seyedeh zohreh Hosseini1, Marzieh Dehghan-Shasaltaneh2, Seyedeh Zahra Moosavi-Nejad1
1Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.
2Institute of Biochemistry and Biophysics (IBB), the University of Tehran, Tehran, Iran.
Abstract
Adenosine deaminase (ADA) is an aminohydrolase which shares in the purine metabolism. It
degrades either adenosine or 2’-deoxyadenosine producing inosine or 2’-deoxyinosine,
respectively. ADA plays important roles in proliferation, maturation, function and development
of the immune system. Its activity may be changed by variety of components including synthetic
or natural products. Spermine is a natural metabolite and a member of polyamines family which
exists in all cells and tissues. This compound affects the cell proliferation and enzyme regulation.
To regulate the function and stabilize its structure, it interacts with negative charge of the
macromolecules such as DNA, proteins and enzymes. In this study, the effect of spermine on the
interaction between ADA and its substrate has been investigated using docking studies. So first
of all, adenosine as a substrate was docked with adenosine deaminase. Then, the enzyme was
docked with adenosine in the presence and absence of spermine. All processes were performed
using autodock vina. Ligplot and VMD were used to evaluate hydrogen and vdw bonds between
all components. The results showed adding spermine to enzyme leads to occur three hydrogen
and 27 vdw bonds, while adenosine did not perform any hydrogen bonds with ADA. We can
conclude polyamine makes to stabilize enzyme structure and it held positive effect on the
interaction between substrate and enzyme, because polyamine and substrate were interacted to
the different sites of adenosine deaminase. As a consequence, effector role of spermine plays an
important role in the interaction between substrate and enzyme.
Keywords: Adenosine deaminase, Spermine, Vina, Hydrogen bond.
HTTP://UI.CNF.IR/PPS 187
Study of laccase activity of Bacillus spores by zymogeraphy
Afrouzossadat Hosseini-Abari, Giti Emtiazi, Maryam Fanaei
Department of Biology, University of Isfahan, Isfahan, Iran.
Abstract
Bacillus spores are resistance to lethal extreme conditions so they are suitable particles for use in
industry and elimination of hazardous material from environment. They have several enzymatic
activities that the most of them are because of the crystalline CotA protein. Since spores help
bacteria to survive at high temperatures or extreme pH values, spore-associated enzymes might
also resist in such conditions which it would be advantageous for industrial applications. In the
present study, laccase activity in the spores of new marine bacillus isolated from Persian Gulf
was confirmed by SDS-PAGE and Native- PAGE. Native-PAGE analysis was performed by
using a 10% gradient gel (Bio-Rad) under nondenaturing conditions )i.e., SDS and 2-
mercaptoethanol were omitted in the sample buffer and the samples were not boiled). The
Native- PAGE gels containing the same samples were stained with catechol as a substrate. The
catechol staining was performed by incubating the gel in a solution containing 75mM catechol in
pH 5 at 40˚C. Zymogram analysis and comparison of Native-PAGE and SDS-PAGE indicated
that the molecular weight of the spore coat laccase is 65 KDa. By using this novel zymogram
staining technique, it was possible to identify and distinguish laccase from other proteins.
Keywords: Laccase, Bacillus spores, Zymogeraphy.
HTTP://UI.CNF.IR/PPS 188
Study of expression and activation of engineered coagulation factor
IX with propeptid of protrombin
Motahareh Hassankhani1, Jafar Vatandoost2, Ali Akbar Jannatabadi3
1 Msc student, Deparment of biotechnology Azad University, Sabzevar, Iran.
2 Assistant professor, Department of Biology. Hakim Sabzevari University, Sabzevar Iran.
3 Assistant professor, Deparment of biotechnology, Azad University, Sabzevar Iran.
Abstract:
Factor IX and other vitamin K-dependent blood coagulation factors require gamma
carboxylation of Gla domin for its biological function that catalyzed by gamma carboxylase
enzyme. Propeptide of vitamin K-dependent proteins is first recognition site of gamma
carboxylase and a reduced affinity allowing greater substrate turnover and result in high gamma
carboxylation. Since the gamma carboxylase enzyme has least affinity for prothrombin, it was
hypothesized that exchanging the propeptide of factor IX with prothrombin would enhance
gamma carboxylation. A chimeric cDNA consisting of the human prothrombin pre-propeptide
followed by mature human factor IX was generated and transfected into S2 cells. The expression
and activity of the normal and chimeric recombinant factor IX were investigated by ELISA and
APTT after various times of transfection. The results showed that the concentrations and activity
of factor IX and so gamma carboxylation in chimeric factor IX more than normal factor IX.
Keywords: Coagulation factor IX, Gamma carboxylase, Propeptid, Prothrombin.
HTTP://UI.CNF.IR/PPS 189
Identification of biologically active recombinant human
erythropoietin (rHuEPO) glycoforms
Somaye Chayani1, Hooman Kaghzian2, Mansure Ghezlue3, Farzad Mokhtari4
1Department of Biotechnology, Faculty of Advanced sciences & Technology, Pharmacutical Siences Branch,
Islamic Azad University, Tehran-Iran (IAUPS). 2Research and Production Complex of Pasteur Institute of Iran. 3Group of biophysics, faculties of science, Science and Research Branch of Islamic Azad University. 4Tehran university institute for biochemistry and biophysics research, Tehran, Iran.
Abstract
The human Erythropoietin (EPO) is a glycoprotein growth factor (30 kD) which originally
secreted from kidney due to hypoxia conditions. EPO has an important role on red blood cells
population and had a positive effect on erythropoiesis. Nowadays recombinant EPO (rHuEPO)
considered as therapeutic biological drugs for severe anemia. Oligosaccharide moiety of rHuEPO
made more than 40 percent of its molecular mass. rHuEPO could be glycosylated at three N-
linked glycosylation sites (asparagine 24, 38 or 83) and one C-linked site (serine 126). Many
evidences has been elucidated the role of glycosylation containing sialic acid at the end of
antennaon rHuEPO biological activity. Therefore, specific isoforms with determined sialic acid
selected as a proper drug with high biopotency. In this study, we identified the glycosylated
isoform of rHuEPO with most biological activity. rHuEPO provided from Pasteur institute of
Iran. The rHuEPO had been expressed in CHO cell line and purified by various chromatography
techniques. The erythropoiesis assay in rabbit showed the biological activity of samples. Due to,
capillary zone electrophoresis (CZE), we identified that only one percent increasing in
concentration of 13 sialylated glycan branch forms could promote rHuEPO biological activity
more than two-fold. In conclusion we can propose that any modification in production process
which causes increasing in 13 sialylated glycan-branchwould have favorable responses to
rHuEPO biological activity.
Keyword: Erythropoietin, Glycoforms, Biologically active molecue.
HTTP://UI.CNF.IR/PPS 190
Thermodynamic stability of β-lactoglobulin in the presence of
cetylpyridinumbromide: UV-Vis spectroscopy andmdocking studies
and Mehdi Sahihi Zahra ChavoshpourNatanzi
Department of chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Abstract
In this work, the stability of β-lactoglobulin (BLG), variant A in the presence of cationic
surfactant cetylpyridinum bromide (CPB) in a temperature range from 298-338 K was studied
using UV-Vis spectroscopy. The results of UV-Vis show that denaturation process of BLG at
difference concentrations of CPB is cooperative. All of denaturation curves, assumes a linear
concentration dependence of the pre-and-post transition base lines and gave the most realistic
values for ∆GD (H2O). The results show that the minimum value of ∆GD (H2O) occurs at 328 K
(16.740 kJ.mol-1). Also, cooperative structure changes of protein due to its interaction with
surfactant was confirmed by fluorescence spectroscopy. Thermodynamic analysis by Gibbs-
Helmholtz equation found ∆HD (H2O) and ∆SD (H2O) were 86.025 kJ.mol-1 and 212.24 J.mol-1. k-
1,respectively. Molecular docking results suggest that, CPB binds on the surface of BLG with the
binding energy of -5.52 kcal.mol-1. Analysis of the molecular docking results represents that
Tyr(102) interacts with CPB by one hydrogen bond interaction.
Keywords:β-lactoglobulin, Cetylpyridinum bromide,Denaturation, UV-Vis spectroscopy,
Molecular docking.
HTTP://UI.CNF.IR/PPS 191
Investigating Interaction of DNA and protein immobilized gold
nano particles with nitrocellulose membranes
Atefeh Javani and Fatemeh Javadi-Zarnaghi
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
Abstract
In recent years the use of nanoparticles, particularly gold nanoparticles by having the
physicochemical properties has improved for diagnostic and therapeutic applications. Among
these are noted the use of nanoparticles functionalized with proteins and nucleic acids. The
conjugates based on their applications, are fixed on different membrane. One of the surfaces is
nitrocellulose membranes, the binding biomolecules such as nucleic acids or proteins on
nitrocellulose membranes is of particular importance, since the nitrocellulose membranes are
hydrophobic property, thereby to improve the interaction of biomolecule-nanoparticle with
nitrocellulose membranes must be optimized with a variety of test conditions. Including
conditions that must be examined include: the conditions of buffer and its pH, temperature,
concentration of biomolecule-nanoparticle to attach to the substrate, the humidity, the time
required for better connectivity and more. In this study we try to do multiple tests to optimize
conditions for better connection biomolecule-nanoparticle access.
Keyword: Nanoparticles functionalized with biomolecules (DNA-Protein), Nitrocellulose
membrane, Interaction.
HTTP://UI.CNF.IR/PPS 192
Prediction 3D structure of IGFBP3 using homology modeling and
molecular dynamic
3, Karim Mahnam2, Mohammad reza Mofid 1iElham Jafar
1 Department of Medicinal Chemistry and Bioinformatics Research Center, School of Pharmacy and Pharmaceutical
Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.
2 Department of Clinical Biochemistry and Bioinformatics Research Center, School of Pharmacy and
Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, Iran
3 Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, I.R. Iran.
Abstract
Three helix bundle small polypeptide hormone, Insulin growth factor (IGF1) is one of key
regulator in cell proliferation, differentiation and death. In normal and neoplastic cells, growth
and differentiation effects of IGF1 are performed through interaction with the insulin-like growth
factor 1 receptor (IGF1R). Around 99% of IGF1 bound to IGF binding proteins (IGFBPs), with
most bound to IGF binding protein 3 (IGFBP3). IGFBP3 regulate its availability for receptor and
increase the half-lives of circulating of IGF1. IGFBPs families are six soluble proteins with 219–
292 residues. IGFBP3 (291 aa) applied therapeutically in a complex with IGF1 as iPlex. IGFBP3
plays a role in cancer reduction, by both IGF1 dependent and independent mechanisms.
According to multifaceted role of IGFBP3 in body, as well as, the lack of 3D-Structure of this
protein, structure of this protein was predicted using of homology modeling (modeler, phyre 2
and Gromaxs softwares) in this study. IGFBP3 considered 3 domains (N-terminal with high
affinity to IGF1, linker-domain with protease, glycosylation, phosphorylation site and C-terminal
domain with thyroglobulin motive has affinity to acid labile subunit (ALS). Protein-Protein-
Interaction of key residue of the best designed model with IGF1 was performed by haddock
software. Results showed that final obtained 3D model of phyre 2 was satisfactory after MD.
HADDOCK clustered 159 structures in 15 clusters. Obtained results of haddock revealed that
helix 1 of IGF1 including; GLu3 and (Gly7–Cys18 residues) are important region for binding to
Ser 121 and (38-44 residues) of N-domain of designed IGFBP3.
Keywords: Homology modeling, Molecular dynamics, IGFBP3, Protein-protein-interaction.
HTTP://UI.CNF.IR/PPS 193
An investigation on the interaction of antibacterial peptides "aurein
1.2" with the bacterial membrane using molecular dynamics
simulation
Marziye Jazini and Sarah Mohammadi nejad
Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.
Abstract
Short cationic antimicrobial peptides (AMPs) are produced by almost all living organisms in a
defense strategy against invading pathogens. These peptides stop bacteria activity by disturbing
their membrane and rapidly kill pathogens. Aurein 1.2 is a short peptide (13 residues) shows a
broad spectrum of antibacterial activity. In this study, some of the structural and functional
properties of Aurein 1.2 in solution as well as in interaction with membrane are studied using
molecular dynamics simulations. For modeling membrane of bacteria, lipid compositions of
POPE/POPG (3:1 ratio) have been used. Our results show that, Aurein 1.2 tends to penetrate into
the membrane in an inclined orientation and by their C-terminal face to the membrane.
Calculating the distance between the center of mass of peptide with the center of mass of the
membrane and the distance between both peptide terminals with membrane center of mass
confirms these results. Also the number of water molecules penetrated into the membrane show
that Aureins 1.2 penetrates easier into the membrane of bacteria than a single Aurein 1.2. The
thinning of the membrane is examined because of penetration of peptides and pore formation. It
is observed that phosphates also penetrate to the membrane besides peptide. In the other hand,
hydrophilic side of Aurein faces to the inside of membrane. These observations lead to the
conclusion that toroidal pore mechanism can for the action of this peptide.
Keywords: Aurein1.2, Atomic-scale molecular dynamics, Antibacterial activity mechanism,
Bacterial membrane.
HTTP://UI.CNF.IR/PPS 194
Luciferase mutation at K329 position by SDM for proteolytic
stability
Samane Jarchi, Roghaye Hamidi, Farangis Ataei, Saman Hosseinkhani
Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
Abstract
Firefly luciferase from Photinus pyralis is a single polypeptide chain (62 kDa), responsible for
emission of yellow-green light; known to be most efficient bioluminescence system that make it
an excellent tool for reporter in nano-system biology and medicine. However, it is very sensitive
to proteolytic degradation, which reduces its intracellular half-life, leads to loss in sensitivity and
precision in analytic applications. In order to generate more stable luciferase against protease
digestion, we substituted a tryptic site, Lysine 329, with other amino acid, Isoleucine; K329I. The
aim if this study is the expression and purification of this mutant and comparison of its stability
against trypsin serine protease digestion with wild type luciferase. The quik-change site-directed
mutagenesis method is performed. After confirmed by sequencing, this mutant enzyme, K329I,
under different conditions such as temperature, time and concentration of lactose was
successfully expressed and then by Ni-NTA sepharose column chromatography purified.
Proteolysis conditions of this mutant and native enzymes are being investigated.
Keywords: Luciferase, Mutation, K329 I, Proteolysis, Trypsin.
HTTP://UI.CNF.IR/PPS 195
Determination of 3-D structure of human HMGB4 protein using
MODELLER software
Safa Lotfi and Mojtaba Mortazavi
Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate
University of Advanced Technology, Kerman, Iran.
Abstract
HMGB proteins are the most abundant group of non-histone HMG proteins. This family consists
of four members including HMGB1, HMGB2, HMGB3 and recently discovered HMGB4.
HMGB1-3 proteins are transcriptional activators which possess two DNA-binding domains
named HMG-box A and B respectively. In contrast to the other members of HMGB family,
HMGB4 functions as a potent transcriptional repressor. This protein is strongly and
preferentially expressed in the testis. HMGB proteins are known to reinforce the cytotoxic
properties of platinum-based anticancer drugs like cisplatin. It seems the hypersensitivity of
testicular germ cell tumors to cisplatin stems from high expression of HMGB4 in these cells. To
date, the 3-D structure of HMGB4 protein was not determined in any mammalian species. In this
study, 3-D structure of human HMGB4 was determined using MODELLER software (version
9.15). Prediction of 3-D structure of proteins by MODELLER software consists of several steps
including finding the PDB structures related to the target protein, selecting the best template,
aligning target and template sequences, building and evaluating the models. 2yrq which is
corresponding to human HMGB1 PDB structure was selected as a template for HMGB4
modelling. In overall, five models were built by MODELLER software and the best model was
selected according to DOPE score. The results demonstrate although HMGB4 like HMGB1 has
two HMG-box domains for DNA-binding, the overall structure of two proteins shows distinct
differences. The results obtained from the project will be helpful to understand the structure-
function relationship of the protein and to design new anticancer drugs.
Keywords: HMGB proteins, HMGB4, HMG-box domain, MODELLER software, Protein 3-D
structure.
HTTP://UI.CNF.IR/PPS 196
Antiadhesive activity of a biosurfactant isolated by Lactobacillus
acidophilus onSerratiamarcescens strains
Maliheh Shokouhfard1, Rouha Kasra-Kermanshahi1, Mohammad Mehdi Feizabadi2,
ShahramTeimourian3
1 Department of Microbiology, Faculty of Biological sciences, Alzahra University, Tehran, Iran.
2 Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
3 Department of Medical Genetics, Iran University of Medical Sciences, Tehran, Iran.
Abstract
Serratiamarcescens usually cause secondary infections like urinary, respiratory, wound, septic
arthritis. The ability to adhere to medical devices and host epithelial surfaces to form biofilm is
an important feature in the pathogenesis of S. marcescens. Lactobacillus acidophilus ATCC
4356, was selected as a probiotic strain to produce biosurfactant. The SDS-PAGE methodand
FTIR assay was used for the determination of biosurfactant. Antiadhesive activities was
determined by pre-coating and co- incubating methods. The FTIR analysis and SDS-PAGE of
derived biosurfactant revealed one band with approximate size of 10 kDa. Due to the release of
such biosurfactants, L. acidophilus was able to interfere with the adhesion and biofilm formation
of the Serratiamarcescens strains. This biosurfactant in 2.5 mg/ml concentration showed
antiadhesive activity against of S. marcescensstrains. Our results showed that this biosurfactant
can be used as a preventive strategy to interrupt the onset of pathogenic biofilm growth on
catheters and other medical insertional materials.
Keywords: Serratiamarcescens, Biofilm formation, Biosurfactant, SDS-PAGE.
HTTP://UI.CNF.IR/PPS 197
Fermentative production of lysine by Corynebacterium glutamicum
from different nitrogen sources
Hanieh Ebrahimi1, Jamshid Fooladi1, Majid Mamhad Heravi2
1 Laboratory of Industrial Microbiology, Faculty of Biology, Alzahra University, Tehran, Iran.
2 Faculty of Science, Department of Chemistry, Alzahra University, Tehran, Iran.
Abstract
Amino acids are the basic building blocks of proteins. Among the 20 Proteinogenic L-amino
acids, L-lysine has been recognized as one of the most deficient essential amino acids which are
nutritionally necessary for humans and animals. It has also got various pharmaceutical
applications in the formulation of diets with balanced amino acids concentration and in amino
acids infusions. In this research, production of lysine by Corynebacterium glutamicum (ATCC
13032) from different nitrogen sources including: ammonium nitrate, ammonium sulphate,
ammonium chloride, ammonium dihydrogen phosphate and urea on lysine accumulation were
investigated. For this purpose, beet molasses was selected as a constant carbon source. The
production of L-lysine was examined qualitatively using Thin Layer Chromatography (TLC).
The results of fermentation experiments showed that ammonium sulphate was the best nitrogen
source for lysine production and for other substrates the yield of lysine was lower.
Keywords: Lysine, Fermentation, Corynebacterium glutamicum, TLC, Ammonium sulphate.
HTTP://UI.CNF.IR/PPS 198
Optimization of different carbon sources for production of L-lysine
by Corynebacterium glutamicum
Hanieh Ebrahimi1, Jamshid Fooladi1, Majid Mamhad Heravi2
1 Laboratory of Industrial Microbiology, Faculty of Biology, Alzahra University, Tehran, Iran.
2 Faculty of Science, Department of Chemistry, Alzahra University, Tehran, Iran.
Abstract
Amino acids are the basic bioelements of proteins. Out of the 20 standard L-amino acids, L-
lysine is one of the 9 amino acids which are essential for human and animal nutrition. L-lysine is
useful as medicalment, chemical agent, food material and feed additive. In this research,
Corynebacterium glutamicum (ATCC13032) were used as a biocatalyst of lysine production.
The effect of different carbon sources including: glucose, sucrose, beet molasses, malt extract
and whey on lysine production were investigated.For this purpose, ammonium sulphate was
selected as a constant nitrogen source. The production of L-lysin was examined qualitatively
using Thin Layer Chromatography (TLC). The results of fermentation experiments showed that
beet molasses and malt extract have the maximum yield of lysine production while other carbon
sources consist of lower yield of lysine.
Keywords: Lysine, Fermentation, Corynebacterium glutamicum, TLC.
HTTP://UI.CNF.IR/PPS 199
In silico comparison of structural features of envelope protein of
zika virus with the homologous proteins of two close viruses
Samira Ebrahimi and Hassan Mohabatkar
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Abstract
This days, world has been facing valid separation of Zika virus outside its geographical zone.
Investigations prove a relationship between Zika virus and microcephaly in newborn babies.
Working on important proteins of this virus could be useful for struggling against this virus. In
the present investigation, computational study of envelope protein of Zika virus (ZIKV) was
performed and the results were compared with envelope protein of two close related viruses,
Dengue virus (DENV), and Spondweni virus (SPOV). In the present study important structural
properties of envelope protein of Zika virus were predicted. Prediction was performed by means
of bioinformatics tools such as T-COFFEE, PseAAC, Virus-PLoc, Signal-3L, GOR IV,
MemBrain, DiANNA, BCPREDS, MHCPred, and GlycoEP. Similarities and differences
between these envelope proteins were predicted and discussed.
Keywords: Zika virus, Flavivirus, Envelope protein, Bioinformatics, Microcephaly, Zoonosis.
HTTP://UI.CNF.IR/PPS 200
Activation of EF-hand II of photoproteinaequorin by replacement of
its calcium-binding loop
Mahsa Ebrahimi1, Reza Hassan Sajedi2, Khosro Khalifeh 1, Bijan Ranjbar3
1Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
2Department of Biochemistry, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.
3Department of Biophysics, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.
Abstract
Aequorin, a calcium-binding photoprotein, was originally isolated from the jellyfish
Aequoreavictoria that emits light in the presence of Ca2+, decomposing into apoaequorin,
coelenteramide and CO2. This protein has four EF-hand motifs which consist of a helix–loop–
helix structure with a high affinity for calcium ions and are critical for calcium sensitivity and
triggering bioluminescence activity. This protein contains four EF-hand structural domains I, II,
III, and IV from the N to C terminus that tree of them (I, III, IV) bind to calcium. In this study,
we designed a new structure of aequorin by replacing loopII with loop III. This substitution was
purposed in order to investigate the calcium dependent behaviors of this modified protein then
was modeled and energy minimization performed by MODELLER. In this work, the encoding
gene of the photoprotein was synthesized into pUC57 and inserted into the EcoRI/XhoIsite of the
pET28a vector . Protein expression was carried out successfully in E. coli BL21 (DE3). Activity
determination revealed that, the expressed protein is active and its calcium dependent features
changed compared to native aequorin.
Keywords: Aequorin, EF-hand, Calcium-binding, Replacement.
HTTP://UI.CNF.IR/PPS 201
Bioinformatics design of deoxyribozyme 10-23 targeted to beta-
lactamase mRNA for inhibition of ampicillin-resistant bacteria
Nasrin al-Sadat Ahmadi1, Abolghasem Esmaeili 2, Fatemeh Javadi-Zarnaghi3
1MSc student; Cellular and Molecular Biology Division; Department of Biology; Faculty of Sciences, University of
Isfahan; Isfahan; Iran. 2 PhD, Cellular and Molecular Biology Division; Department of Biology; Faculty of Sciences, University of Isfahan;
Isfahan; Iran.
PhD, Cellular and Molecular Biology Division; Department of Biology; Faculty of Sciences, University of Isfahan;
Isfahan; Iran.
Abstract
Deoxyribozymes (DZ) can play a role as gene expression inhibitors at the mRNA level. Among
them 10-23 deoxyribozymes have a significant potential in treatment of diseases. Designed DZ
includes a catalytic core made of 15 deoxyribonucleotides and two diagnostic arms consist of 9
nucleotides for binding to target RNA and hydrolyzing it. The catalytic feature of this
deoxyribozyme cause cutting of RNA between an unpaired purine (A) and a pyrimidine pair. For
this purpose the first sequence of plasmid with beta –lactamase genewas taken through the
www.addgene.com database. The secondary structure of the ampicillin resistance gene was also
taken via Mfold software. Then intended gene region which is situated in target zone was found.
In another hand ORF sequence was taken from expasy server and due to the protein sequence
related to intend region of the gene, the ORF with the most related sequence similarity was
chosen. Subsequently the complete DNA sequence was taken from expasy and the DZ was
designed based on the reverse complement sequence of mRNA. Results show that the designed
DZ targets the mRNAs involved in several diseases pathways.Their enhanced biological
stability, small size; negligible side-effects in vivo caused by high specificity and lack of
immunogenicity, have paved the way for DZs to enter clinical trials.
Keywords: Deoxyribozyme 10-23, Gene expression, Ampicillin-resistant bacteria.
HTTP://UI.CNF.IR/PPS 202
Prediction of the mode of interaction between monoterpenes and the
nitroreductase from Enterobacter cloacae by docking simulation
Zeynab Ahmadianpour
Department of Biochemistry, sanandaj Branch, Islamic Azad University, Sanadaj, Iran.
Abstract
Monoterpenes from the essential oils of several plants have been shown to enhance the
bactericidal activities of nitrofurantoin and furazolidone against the bacteria of
Enterobacteriaceae family. In this study, computer-aided molecular mode ling and docking
techniques have been employed to simulate the theoretical mode of interaction between
monoterpenes and Enterobacter cloacae nitroreductase. Enhancement of nitro drug potency in
the presence of mono terpenes may be the result of modulation of nitroreductase activity.
Binding nitroreductase with monoterpenes may decrease the efficient conversion of toxic
reactive intermediates to final products lacking bactericidal activity.
Keywords: Enterobacter cloacae, Docking simulation, Nitroreductase, Molaecular modeling.
HTTP://UI.CNF.IR/PPS 203
Molecular modeling, docking and molecular dynamics simulation
approaches to assessment binding of coumarin to β-casein
Zahra Adibipour, Abdol-KhaleghBordbar, Mehdi Sahihi, Najme Fani
Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Abstract
Low solubility of hydrophobic drugs is a major problem in pharmaceutics industry. In the
present work, a comprehensive computational study has been done on the interaction of
coumarin as a hydrophobic drug with bovine β-casein protein (βCN) as a nano-carrier by using
molecular modeling, molecular docking and molecular dynamics (MD) simulation procedures.
This study revealed the possible application of this nano particle as an efficient and
biocompatible drug carrier of coumarin. First, 3D structure of βCN was modeled using I-
TASSER server, and then to accomplish more stable and better structure of the model obtained
from I-TASSER, a 50 ns MD simulation using GROMACS 4.5.4 software package was
performed on the βCN structure. Using the obtained structure from MD simulation for βCN a
molecular docking calculation was performed to find the binding site of βCN for coumarin.
Docking results showed that coumarin binds to the hydrophobic core of βCN and is in contact
with Leu 103, Pro 101, Pro 100, Phe 102, Phe 48, Ile 45, Pro 168, Glu 51, Glu 46 and Lys 47
residues. Moreover, coumarin is able to form a hydrogen bond interaction with Phe 102 amino
acid residue. Finally, another MD simulation on the ligand-protein complex was done to examine
the effect of coumarin on the conformation of βCN protein. MD simulation results showed that
coumarin can interact with βCN through van der Waals and hydrogen bond interactions without
affecting the secondary structure of this protein.
Keywords: β-casein, Coumarin, Molecular modeling, Molecular docking, Molecular dynamic
simulation.
HTTP://UI.CNF.IR/PPS 204
Exploring binding properties of coumarin with Bovine β-Casein:
multispectroscopic and chemometrics studies
Zahra Adibipour, Abdol-KhaleghBordbar, Mehdi Sahihi, Najme Fani
Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Abstract
Several studies have been done through encapsulation of hydrophobic drugs in protein
nanoparticles to increase their aqueous solubility.Coumarin is a compound that belongs to benzo-
α-pyrone group and reveals high antibacterial effect. β-casein (βCN) is a protein which is found
in bovine milk and can be used as natural nano-delivery vehicles for hydrophobic drugs. In the
present study, we load βCN with coumarin and then explored the binding properties of coumarin
to βCN by using absorption and fluorescence spectroscopies and chemometrics analysis. The
spectrofluorometric titration experiment was run at four different temperatures from 293K to
308K and at two excitation wavelengths of 280nm and 295nm. The results show the quenching
effect of coumarin on fluorescence spectrum of βCN. The binding and Stern-Volmer constant
values at the excitation wavelentgth of 295nm were in the order of 104M-1 magnitude and
decreased with temperature which indicates high strength of binding and static quenching
mechanism for Tryptophan residue of βCN. Also data analysis represented the formation of 1:1
complex, negative values of entropy and enthalpy changes and the essential role of hydrogen
bonding and van der Waals interactions in binding of coumarin to βCN. The Förster’s distance
value (4.078nm) represents the static quenching mechanism of βCN by coumarin and significant
binding affinity. A positive deviation from linearity was observed for Stern-Volmer plot at the
excitation wavelength of 280nm, which demonstrate the dynamic quenching mechanism for
tyrosine and phenylalanine residues. Chemometrics analysis of UV-Vis spectroscopic titration
data showed the presence of three different species in the solution with the binding affinity of
105M-1 order of magnitude and the formation of 1:1 complex of coumarin with βCN.
Keywords: β-casein, Coumarin, Spectrofluorometric, Chemometrics.
HTTP://UI.CNF.IR/PPS 205
Measurement of dioxin contamination in water samples by a
bioluminescence method
SeyedePegah Azarchehry1, Farangis Ataei1, Saman Hosseinkhani2
1Biochemestry department of TarbiatModares University, Tehran. 2 Biochemistry department of TarbiatModares University, Tehran. The head of bioluminescence Laboratory.
Abstract Dioxins have harmful effect in environment. Dioxins include the group of molecules which have
same structure and same function in different organisms. The measurement of Dioxin‘s
concentration was obligated by World Health Organization (WHO). Dioxins has been produced
during the production of certain chlorinated phenols and their derivatives, and as a result of high
temperature pyrolysis and combustion of organic compoundsContaining halogens. This
compounds are very resistance in the environment. Because of its high lipophilicity and water
insolubility, dioxin concentrates in sediments and is incorporated into food chains.The traditional
method for measuring the concentration of dioxins in samples was gas chromatography-high
resolution mass spectrometry. Although it was very accurate technique, it is costly and of
limitation in number of tests done in a distinctive period of time.Cell based screening methods
such allow high throughput screening and are cheaper than last methods.In this study, according
to importance of water quality, we have tried to screen dioxins-like compounds in water samples
using bioluminescence method, extraction and clean up the dioxins with silica chromatography
column were set, and detection and measurement the concentration of dioxins in different water
samples by cells will be reported.
Keywords: Dioxins, Biosensor, Bioluminescence, Water sample, Contamination detection.
HTTP://UI.CNF.IR/PPS 206
Role of the pre- molten globule structure in amyloid fibril formation
Ali Es-haghi1, Azadeh Ebrahim-Habibi2, Mohsen Nemat-Gorgani3
1Faculty of Science, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran.
2Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran
University of Medical Sciences, Tehran, Iran.
3Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.
Abstract
The major factor that caused extensive research on the protein fibrillation is their crucial roles in
important diseases known as the amyloidosis diseases. Neurodegenerative diseases, including
Alzheimer's, Parkinson's, diabetes and Huntington are the most important types of this disease.
Understanding the mechanisms of fibril formation and ways of treatment can be useful in
reducing this type of disorder. In this project, the fibrillation of carbonic anhydrase protein was
investigated as a model. Carbonic anhydrase creates two stable intermediated known as pre-
molten and molten globule, in different pH solution. This protein at pH between pH 3-4 molten
globule structures was formed while the pre- molten form took place under pH 3. In our tests at
pH 3.5 when the protein in molten globule structures only the amorphous aggregates were
formed. Instead, at pH 2.4 in pre- molten globule structure amyloid fibrils formed in the protein.
There some reports, indicated the protein from pre- molten globule structure go toward amyloid
assembly. Even intrinsically unstructured proteins such as alpha-Synuclein first took a structure
similar to pre- molten globule and then made amyloid fibrils. It seems pre- molten globule
structure have the major role in promoting to amyloid fibrils. Perhaps drugs that prevent the
formation of pre- molten globule structure have an important role in inhibiting amyloid fibrils.
Keywords: Pre-molten globule, Carbonic anhydrase, Amyloid fibril.
HTTP://UI.CNF.IR/PPS 207
Nano-liposomal lipid peroxidation as a consequence of the diabetic
albumin glycation
Maha Asadi1, Hamzeh Maleki1, Mehran Habibi-Rezaei1, 2
1College of Science, University of Tehran.
2Nano-biomedicin Center of Excellence.
Abstract
Glycation is a non-enzymatic reaction between reducing sugar and bio-macromolecules. This
reaction leads to distruction or activity defection in biomolecules and produces glycation end
products (AGE) and reactive oxygen species (ROS). Albumin that is a more important serum
protein, glycated by high glucose in diabetic condition and raises AGE and ROS in blood. In this
study, the effect of diabetic protein glycation on membrane lipid peroxidation is reported using
constructed nono-liposomes. Liposomes prepared using lecitin and cholesterol then incubated in
the presence of the bovine serum albumin (BSA) in diabetic condition for 40 days. The lipid
peroxidation (LPO) induced by diabetic protein glycation is monitored by AGE and ROS using
intrinsic AGE dependent auto-fluorescence and malondialdehid (MDA) measurement,
respectively. The amount MDA was increased as increasing the time of incubation of liposomes
under diabetic glycation of albumin by carbohydrate, however, a rate increase was observed at
after 20th day. The protein glycation produces AGE and ROS. The ROS generation and LPO are
highlighted as a causative mechanism in diseases such as cardiovascular, neuropathies,
nephropathies, retinopathies etc.
Keywords: Nano-liposomes, Peroxidation, Glycation, Reactive oxygen radicals, Diabets.
HTTP://UI.CNF.IR/PPS 208
Gold nanoparticles-capped mesoporous silica for enzyme responsive
controlled release of doxorubicin in cancer therapy
Parvaneh Eskandari1, Ali Akbar Saboury1, Mehdi Khoobi2
1Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran. 2Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran.
Abstract
Mesoporous silica nanoparticles (MSN), as prominent candidates for next generation therapeutic
carriers, have a great deal of attention because contain parallel pores with two unique openings
that anticancer drug load in this pores. Therefore, this characterization makes it as an ideal
delivery system that can controlled release simultaneously, in which, the pores can be closed
using a cap and opened with internally or externally stimuli. Matrix metalloproteases (MMPs)
are a family of extracellular proteolytic enzymes that are overexpression in cancerous tissues.
We studied the stimuli-responsive release profiles of doxorubicin loaded gold nanoparticles-
capped MSNs delivery systems by using peptide cleavable linker that sensitive to overexpressed
matrix metalloproteinase in extracellular of cancer cells.In this nanosystem high dose of
doxorubicin deliver to cancer cells without effect on healthy tissues.
Keywords: MMP-cleavable peptides, Mesoporous silica, Responsive systems, Doxorubicin.
HTTP://UI.CNF.IR/PPS 209
Isolation of ACE-inhibitory peptide produced by enzymatic activity
of goat milk whey proteins
Mehrnaz Esmaeilpour1, Mahmood Aminlari 2, Mohammad Reza Ehsani 3, Shahram
Shekarforoush 4, Ebrahim Hoseini 3
1 Department of Food Science and Technology, Fasa Branch, Islamic Azad University, Fasa, Iran. 2 Department of Biochemistry, School of Veterinary Medicine, Shiraz University, Shiraz, Iran. 3Department of Food Science and Technology, Science and Research Branch, Islamic Azad University, Tehran,
Iran.
4 Department of Food Hygiene and Public Health, School of veterinary Medicine, Shiraz University, Shiraz, Iran.
Abstract
In this study, goat milk whey proteins was hydrolyzed by trypsin, ficin and a combination of the
two to isolate angiotensin I-converting enzyme (ACE) inhibitory peptides. The hydrolysates
were fractionated using ultrafiltration membranes. The hydrolysate obtained by trypsin with
molecular weight <3 kDa exhibited the highest ACE-inhibitory activity that purified with reverse
phase high performance liquid chromatography (RP-HPLC). Among the fractions, fraction 2 had
the highest ACE inhibitory activity (IC50: 160 µg/ml). The results of this study indicate that
peptides produced by trypsin and ficin treatment could be considered as natural antihypertensive
agents alternatives to chemical counterparts used in food and pharmaceutical industries.
Keywords: Goat milk whey proteins, Bioactive peptide, ACE inhibitory activity, Ficin, Trypsin.
HTTP://UI.CNF.IR/PPS 210
The presence of JC virus VP1 capsid of genotype 2B in rheumatoid
arthritis patients in Isfahan, Iran
Sayyedeh Rahmaneh Atyabi1and Majid Bouzari1
1Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
Abstract
Opportunistic JC virus (JCV) infection is an asymptomatic latent infection that in
immunosuppressed individuals (patients undergo immunosuppressive treatment) such as
rheumatoid arthritis cases may lead to progressive multifocal leukoencephalopathy (PML). This
disorder causes demyelination of the white matter of brain. VP1 capsid of genotype 2B is an
aggressive form of the virus specially can be excreted from urine. In this study 43 patients with
rheumatoid arthritis and 100 healthy individuals were tested for the presence of JCV in urine.
PCR with specific primers were performed on urine pellet for detection of VP1 gene. All of the
positive PCR products of both patients and healthy individuals were sequenced. Fisher's exact
test was used for statistical analyses, then DNA and translated DNA sequences detected in this
study and the same from different countries obtained from GenBank with phylogenetic tree
constructed. JCV was detected in 18.60%, and 7% of rheumatoid arthritis patients and healthy
individuals respectively. Genotypes 1, 3 and 4 were detected in 2(25%), 5(62. 5%) and 1(12.5%)
of the rheumatoid arthritis patients and genotype 1 was found in 2(28.57%) and genotype 3 was
found in 5(71.42%) of healthy individuals respectively. The frequency of infection in the urine of
rheumatoid arthritis patients was higher. This may increase the risk of PML in them. On the
other hand only genotypes 1, 3 and 4 were detected that compare to genotype 2B are less
aggressive and so less chance of causing PML.
Keywords: JC virus, Progressive multifocal leukoencephalopathy, VP1, Rheumatoid arthritis,
Isfahan.
HTTP://UI.CNF.IR/PPS 211
In Silico analysis of single nucleotide polymorphisms (SNPs) and
screening of mutations affecting protein stability and function of
KRAS protein
Fatemeh Arabi Jeshvaghaniand Mohamad Reza Ganjalikhany
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
Abstract The human KRAS gene is the member of the RAS family of oncogenes with cytogenetic location
of 12p12.1 that encodes KRAS protein, a small GTP-binding protein which plays a critical role
in RAS/RAF/MEK/ERK pathway in fundamental cellular processes such as proliferation,
differentiation, apoptosis, and survival. Single nucleotide polymorphisms (SNPs) can influence
protein function, structure and stability. In this analysis we use five in silico SNP prediction
algorithms, SIFT, PolyPhen, nsSNPAnalyzer, SNPs&GO and PROVEAN to identify functional
SNPs in coding regions of KRAS gene and predicts the effect of these variants on KRAS
function and stability. This study is the first extensive in silico analysis of the highly
polymorphic KRAS gene. Polymorphism data for the KRAS gene were retrieved from NCBI
database of SNPs (dbSNP) then used as inputs in SIFT (Sorting Intolerant from Tolerant) and
PolyPhen (Polymorphism phenotyping) algorithms and the other tools that predict the potential
impact of amino acid substitutions on protein function and structure. The dbSNP-NCBI database
revealed a total of 2717 SNP for human KRAS gene which comprised of 73 missense SNPs. We
selected the missens SNPs for our further investigations. It has been predicted that 45 missens
SNPs (61.64%) are deleterious by SIFT analysis, 43 missens SNPs (58.9%) are predicted to be
possibly damaging to KRAS function according to our Polyphen-2 results. nsSNPAnalyzer,
SNPs&GO and PROVEAN show the diseases and natural SNPs in KRAS gene separately with
their related specific scores. We find GLY12ASP, GLY13ASP, GLY60ARG and VAL14ILE as
the most deleterious mutation by these tools. Then these four mutations were analyzed by Align-
GVGD that combines the biophysical characteristics such as side chain composition, polarity and
volume of amino acids and protein multiple sequence alignments (Grantham Variation (GV) and
Grantham Deviation (GD) scores) to predict where amino acid substitutions fall in a spectrum of
deleterious to neutral. Biophysical analysis indicates a clear insight of stability loss due to these
mutation in KRAS protein. As there are numerous SNPs in KRAS gene our computational
analysis can be effective for further study in linkage and association of genetic studies to
understand the changes affect protein functions and stability for diagnosis KRAS related disease,
design and development of new drugs particularly the inhibitors of RAS/RAF/MEK/ERK
pathway.
Keywords: Single nucleotide polymorphism (SNP), In silico analysis, KRAS protein, Stability.
HTTP://UI.CNF.IR/PPS 212
Computational molecular docking studies of bioactive peptides from
milk proteins as angiogenesis converting enzyme inhibitors with
antihypertensive effects
Fatemeh Arabi Jeshvaghani1 and Mohamad Reza Ganjalikhany
Department of Biology, Faculty of science, University of Isfahan, Isfahan, Iran.
Abstract
Milk represents a unique source of nutrients and biologically active proteins and peptides that
secreted into milk and released by proteolytic action. There are many milk protein-derived ACE
inhibitory peptides with antihypertensive activity to avoid undesirable side effects of synthetic
drugs. Hypertension is the most common worldwide risk factor for stroke, kidney disease and
several cardiovascular disorders. The renin-angiotensin system (RAS) activation plays a key role
in hypertension. Inhibition of RAS with angiotensin converting enzyme (ACE) inhibitors by
blocking the enzyme that catalyses the conversion of angiotensin I to angiotensin II can lead to
reduce blood pressure by blood vessels dilation. The aim of this study is to analyse the potential
ACE inhibitory action of four bioactive peptides in milk by computational docking studies and
campary with synthetic ACE inhibitor drug. Molecular docking study of benazepril (FDA
approved ACE inhibitor drug) and APTLtetrapeptides, IPP and VPP tripeptides and YP
dipeptides with ACE (PDB ID: 1O86) has been done using Autodock 4.2.6. The results have
indicated that among these bioactive peptides in milk IPP showed higher binding affinity
compared to others with the lowest binding energy (-6.65kcal/mol) and the high potential effect
for hypertension treatment. While, the lowest binding energy was observed in YP (-
5.28kcal/mol). The binding energy of benazepril to ACE was -8.75kcal/mol. Our findings clearly
demonstrate the potency of milk bioactive peptides for discovery and development of new ACE
inhibitors from natural sources with less toxicity and more selectivity than chemical inhibitor and
prove that dietary foods like milk can be effective for treatment of hypertension and other
cardiovascular disorders.
Keywords: Molecular docking, Bioactive peptides, Milk, Angiotensin converting enzyme,
Hypertension.
HTTP://UI.CNF.IR/PPS 213
Molecular docking and quantitative structure--activity
relationships(QSAR) studies of herbal compounds in Iris
pseudopumila (Iridaceae)asacetylcholinesterase inhibitorsin
alzheimer's disease treatment
Fatemeh Arabi Jeshvaghani1, Mohamad Reza Ganjalikhany2
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
Abstract
Alzheimer's disease (AD) a progressive neurological disorder is the most common cause of
dementia. Acetylcholinesterase inhibitors can be applied in neurodegenerative disorders
treatment like alzheimer's disease by inhibition of acetylcholinesterase (AChE) enzyme that is
encoded by the ACHE gene on chromosome 7 which catalysis the hydrolysis of neurotransmitter
ACh into acetate and choline in conducting tissue specially in motor neurons. Natural herbal
products that have been used traditionally as nutrition or medicine may also act as AChE
inhibitors.Iris pseudopumila (Iridaceae)flowers and rhizomes extract consist of two non-
alkaloidal compounds including isoorientin and isovitexin that can have significant AChE
inhibitory effect. The aim of this study is to analyse the potential AChE inhibitory action of
natural compunds in Iris pseudopumila by computational docking studies. Molecular docking
study of Donepezil and PyridostigmineAChE chemical inhibitor drugs and Isoorientin and
isovitexin with AChE (PDB ID:4PQE) has been done using Autodock 4.2.6.QSAR studies have
been implemented to predict the biological properties of the bioactive compounds. The
molecular descriptors such as molecular weight, hydrogen donor, acceptors, LogP, Total
Polar Surface Area (TSPA), were obtained using FAF drugs ADME/Tox filtering . The
results have indicated that among these two compounds in Iris, isovitexin showed higher binding
affinity compared to another with the lowest binding energy (-6.49kcal/mol) and the high
potential effect for AD treatment that is more than Pyridostigmine inhibition effect. Donepezil
showed the lowest binding energy (-8.25kcal/mol). Our findings clearly demonstrate thepotency
of these herbal compounds for discovery and development of new AChE inhibitors with less
toxicity and more selectivity than chemical inhibitors and prove that natural herbal compounds
like Iris pseudopumila can be effective for treatment of Alzheimer's disease and other
nurological disorders.
Keywords: Molecular Docking, QSAR studies, Alzheimer's disease, Acetylcholinesterase
Inhibitor, Iris pseudopumila.
HTTP://UI.CNF.IR/PPS 214
Study of the binding of warfarin drug to β- lactoglobulin by UV-
visible and isothermal titration calorimetry techniques
Afshari Sahar, Zeyni – Esfahani Asghar, Rastegari Aliasghar
Department of Molecular and Cell Biochemistry, Islamic Azad University, Falavarjan, Esfahan, Iran
Abstract
β- lactoglobulin is one of the lipocalin family's members and the major protein of cow's milk.
It comprised two disulphide bridges and one free Cys121. The biological function of β-
lactoglobulin remains unknown yet but it was suggested that this protein has a potential role in
fatty acid transportation through digestive tract. Thus, it can be used as a transporter for
hydrophobic molecules for controlled delivery applications. Warfarin is a hydrophobic molecule
and an anticoagulant preventing the clot formation in blood vessels. In this study, the interaction
of warfarin with β-lactoglobulin was investigated by the ultraviolet-visible (UV –Vis) and
circular dichroism (CD) spectroscopy. The results of UV-vis titration in different temperatures
(25, 30, 35, 40℃ ) showed that the warfarin/ β-lactoglobulin interaction was exothermic and
spontaneous. The binding constant was 103M-1. The protein was more stable at low temperatures
and the results of CD Spectroscopy did not demonstrate any significant structural changes for
warfarine binding to β-lactoglobulin.
Keywords: β-lactoglobulin, interaction, Hydrophobic, warfarin, UV–Vis spectroscopy, Circular
dichroism.
HTTP://UI.CNF.IR/PPS 215
Fabrication of gold nanorod assemblies on BSA amyloid fibril
scaffolds
YasinAkhtari1, Mina Sadat Eghbal2, Tahereh Tohidi Moghadam3, Bijan Ranjbar2, 3
1 Department of Biomedical Engineering, Faculty of High Technology, TarbiatModares University, Tehran, Iran.
2 Department of Biophysics, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.
3 Department of Nanobiotechnology, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.
Abstract
Today, gold nanorods have attracted significant attention due to their optical, thermal and
catalytic properties, promising variety of applications in conjugation with proteins and
nucleic acid. This effort has focused on simultaneous exploitation of dual properties presented by
hybrid scaffolds of nano and bio counterparts, leading to fabrication of interesting biotemplates.
Gold nanorods (GNRs) were interacted with bovine serum albumin (BSA) amyloid fibrils to
design a nanowires-like scaffold. To obtain amyloid fibril structures of BSA, different
concentrations of protein were dissolved in 0.1 M phosphate buffer (pH 8.9). Samples were
incubated at 62 ˚C, with continuous stirring for 12 hours. GNRs were synthesized via seed
mediated growth protocol and characterized by TEM and UV-Vis spectroscopy. Monitoring of
the amyloid fibril formation by Thioflavin T (ThT), far and near-ultraviolet Circular Dichroism
(CD) spectropolarimetry indicated conformational changes in BSA and transformation into
amyloid fibril structures. SEM images of the nanostructures treated with BSA amyloid fibrils
also depicted ordered aggregates of GNRs on the biotemplate. Results of this investigation
highlighted possibility of fabricating directed nanostructured assemblies on amyloid fibril based
scaffolds, as a novel candidate for future biomedical and biosensing applications in tissue
engineering and hybrid drug delivery systems.
Keywords: Gold nanorods, Nanostructures, Biotemplate, Amyloid fibrils.
HTTP://UI.CNF.IR/PPS 216
The effect of modified tryptophan residues on kinetic,
thermodynamic and structure of mashroomtyrosinase
Saeed Emami1and Nematollah Gheibi2
1Department of Biology, Faculty of Basic Sciences, Islamic Azad UniversityScience and Research Branch, Tehran,
Iran.
2 Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.
Abstract
MashroomTyrosinase (MT) is a metalloenzyme and is a good model in mechanistic point of
view for the study of tyrosinase as the key enzyme in melanogenesis. To recognizing mechanism
of MT’s activity its inhibition, activation, mutation and modification are important methods of
investigations. Here, the chemical modification of MT tryptophan residues have been done by N-
bromosuccinimide (NBS) and the activity, stability and structure of native and modified enzyme
were comprised. Chemical modification of MT tryptophan residues induced by enzyme
incubation with different concentrations of NBS. The relative activity of native and modified MT
were investigated through catecholase reaction of enzyme by L-Dopa as substrate.
Thermodynamic parameters including: ∆G25°C and Tm obtained from thermal denaturation of the
native and modified enzyme. The circular dichroism and intrinsic fluorescence techniques have
been used for study of secondary and tertiary structure of MT respectively. The relative activity
reduced from 100% for native to 10%, 7.9% and 6.4% for modified MT with different 2, 10 and
20 mM concentrations of NBS, respectively. Thermal stability of modified enzyme were
emphasized by decreasing in Tm and ∆G25°C values.In accordance with kinetic and
thermodynamic studies the lower stability of modified MT was observed from the changes of its
secondary and tertiary structures. Chemical modification of tryptophan residues with NBS
reduces activity and stability of MT in line with its structural changes. So this study emphasized
to the crucial role of tryptophan residues in the structure-function relationship of the enzyme.
Keywords: Chemical Modification, MashroomTyrosinase, N-Bromosuccinimide, Kinetic,
Structure.
HTTP://UI.CNF.IR/PPS 217
Covalent immobilization of glucoamylase on superparamagnetic
nanocomposites4 O3graphene oxide Fe
Mahkame Amirbande and Asghar Taheri-Kafrani
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan.
Abstract Recently, highly soluble enzymes in physiological environment and hydrophilic has been
noticable. Graphene oxide is a nontoxic material and selective modulator for enzyme activity and
is also a thermostable molecule that is important in large-scale nanostructure sheet applicatoins.
Nanostructures of hybrid graphene oxide-Fe3O4-cyanuric chloride (GO-MNP-CC) have
adjustable surface chemistry that is an excellent candidate for covalence immobilization
enzyme.Glucoamylase is used in industrial food products and other applications. The interaction
of GO-MNP-CC with a bioactive molecule, such as a glucoamylase enzyme, hasn't been
explored. The results of this study indicated that the reusability and stability of immobilized
enzyme have been obviously improved compared to the free enzyme. The optimum condition of
immobilized glucoamylase determine at pH 6.5 and 60oC. The apparent Km and Vmax for free
and immobilized glucoamylase were also determined. These properties make them a good
candidate to improve the practicality and further the development of the capacity enzyme
attachment. Thus, magnetic nanoparticles GO–Fe3O4 can be used in various applications with an
industrial purpose. The structure properties of the immobilized glucoamylase and support were
characterized by transmission electron microscopy (TEM), X-ray photoelectron spectroscopy
(XPS), Fourier-transform infrared spectra (FTIR), thermo-gravimetric analysis (TGA) and
vibrating sample magnetometer (VSM) analysis.
Keywords: Graphene oxide, GO-Fe3O4, Cyanoric chloride, Glucoamylase, Enzyme
immobilization.
HTTP://UI.CNF.IR/PPS 218
Functionalized superparamagnetic chitosan nanoparticles in enzyme
engineering: A highly dispersive, stable and robust biocatalyst
Mahkame Amirbande, Asghar Taheri-Kafrani
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan.
Abstract
Glucoamylase (EC 3.2.1.3) from Aspergillus Niger was immobilized on chitosan
superparamagnetic nanoparticles (SPCh-CC) by covalent binding after activation with cyanuric
chloride to produce glucose from starch. The important parameters such as temperature, pH,
reaction time, enzyme concentration and other parameters have been studied and optimum values
were detected. The activity recovery of immobilized glucoamylase was over than 80% and this
result showed that immobilization processcouldn’t significantly inhibit enzyme-substrate
interaction and thus the enzymatic activity. The Michaelis-Menton constant (Km) and vmax values
were improved and this suggested that SPCh-CC nanocarriers can be an ideal choice for
immobilization of glucoamylase. The structure properties of the synthesized SPCh-CC and
immobilized glucoamylase, was characterized using TEM, XRD, and FT-IR analyses.
Keywords: Chitosan nanoparticles, Glucoamylase, Cyanuric chloride, Enzyme immobilization,
Robust biocatalyst, Enzyme activity.
HTTP://UI.CNF.IR/PPS 219
Investigation on physicochemical properties of [Ni (FIP) 2] (OAC)2
complex and its interaction with ct-DNA and Its effect on ct-DNA
stability
Alireza Amini Khozani and Nasrin Sohrabi
Department of Chemistry, Payame Noor University, PO. Box 19395-3697, Tehran, Iran.
Abstract
Deoxyribonucleic acid (DNA) is an important genetic substance in the organism, which carries
most of hereditary information and facilitates the biological synthesis of proteins and enzymes
through replication and transcription of this information. It is one of the most important
biological molecules targeted by natural and synthetic compounds. Investigation on the
interactions of small molecules with DNA has been an intensive topic over the past years in the
scope of life science, chemistry, clinic medicine and genetics. These studies are beneficial for
screening new and more efficient drugs targeting to DNA, investigating the structure and
biological function of DNA, and elucidating the damage mechanism of DNA. In this study, the
physicochemical properties of [Ni(FIP)2](OAC)2complex and its interaction with calf thymus
DNA at different temperature were investigated using UV/Vis and fluorescence spectroscopies,
viscosity and denaturation methods. The results show that the shape and position of the bonds
did not change significantly. So, this complex has suitable stability and doesn’t show any
aggregate and the interaction with calf thymus DNA is endothermic and the driving force is
entropy and the binding mode of [Ni(FIP)2](OAC)2 complex to calf thymus DNA is electrostatic
mode.
Keywords: Calf thymus DNA, [Ni (FIP)2](OAC)2, UV/Vis spectra, Denaturation, Fluorescence
emission.
HTTP://UI.CNF.IR/PPS 220
An in-silico investigation on the structure and function of the
Phenanthrene degradative bacteria enzymes, an introduction to
development of anti-cancer probiotics Elnaz Enferadi-Moghadam1 and Aliakbar Haddad-Mashadrizeh 2, 3
1Department of Biology, Science and Research Branch, Islamic Azad University, Khorasan Razavi, Neyshabur,Iran.
2Cell and Molecular Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of
Mashhad,Iran.
3Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
Abstract
Gut flora, as an organ with extensive known and unknown capabilities, containing different
kinds of bacteria with various properties. Some of these bacteria recognized as probiotics which
in turn have beneficial effects on the health via digestion facilitation and or production some
complex compounds such as vitamins and antibiotics. In this regard, the performance of these
bacteria in prevention and treatment of a range of diseases have been revealed. So, absorption
and digestion the aromatic hydrocarbons (AH), which are in food, could be a promising strategy
for the prevention of a wide range of diseases such as cancer via equipping the probiotics to the
corresponding genes of AH catabolism or dairy enrichment with related enzymes. Bearing in
mind, profiling and characterization the competent corresponding enzymes of AH metabolism
would be providing approaches for cancer prevention, which are considered in this study through
Phenanthrene. For this purpose, a profile of bacterial enzymes with capacity in Phenanthrene
degradation has been gathered and then corresponding nucleotide and protein sequence were
retrieved from related databases such as NCBI and UniProt. CD Search, motif Scan,
InterProScan, Blast, MEGA6, Hex and ClusPro2.0 were then used for molecular analysis of the
selected sequences. Structural modeling carried out via Modeller program and assessment by
MOE. Moreover, thermal stability of the selected domains performed via Gromacs program. The
results of this study whilst presents a profile of the bacterial enzymes involved in Phenanthrene
degradation, provided a series of efficient of domains with high binding affinity to Phenanthrene
as well as other HA other hydrocarbons with temperature stability in some cases. Overall, these
results led to provide a series of data for designing new genetic construct for probiotic
development as well as chimeric enzymes production for AH, especially Phenanthrene,
catabolism.
Keywords: Aromatic hydrocarbons, Phenanthrene, Cancer, Probiotics.
HTTP://UI.CNF.IR/PPS 221
The effect of time and temperature incubation on bacterial phytase
activity
SarehAnvari1, Jamshid Fooladi1, Parichehr Hanachi1
1Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.
Abstract
Phytase [myo-inositol hexakisphosphate hydrolase] initiates the step-wise removal of phosphate
from phytate [myo-inositol hexakis phosphate]. Phytate is the major storage form of
phosphorous in cereals, legumes, oil seeds, and nuts. This enzyme has been used widely in
animal feeding to improve phosphorus nutrition, and reduce phosphorus pollution of animal
waste. The bacterial phytase isolated from soil, and grew on PSM (Phytase Specific Medium).
To investigate the effect of incubation conditions on phytase activity, sodium phytate as substrate
incubated with extracellular phytase at various periods of time (10, 20,30,40,50 and 60 min) and
temperatures (4, 25,37,42,56 °C). The activity of phytase was assayed by measuring increased
rate of inorganic orthophosphate (Pi) using ammonium heptamolybdate. The reaction mixture
consisted of 500 µl acetate buffer (0.2 M, pH 5.5 containing 2.5 mM sodium phytate), and 500 µl
of the supernatant. After incubation, the reaction was stopped by adding 500 µl of 15%
trichloroacetic acid (TCA). Assay mixture mixed with 1000 µl of ammonium heptamolybdate
reagent. The amount of released free phosphate was determined spectrophotometrically at 750
nm. Results showed the optimum time for incubation was 30 minutes. It possessed a temperature
optimum of 42 °C. Soil and water micro-organisms are capable of hydrolyzingphytic acid.
Utilizing of these micro-organisms in animal feed helps to decrease environmental pollution, and
raise the uptake of mineral materials.
Keywords: Phytase, Phytate, Incubation conditions, Animal feed.
HTTP://UI.CNF.IR/PPS 222
Thermal stability of lactoperoxidase stabilized on modified magnetic
nanoparticle
Narges Babadaie Samani1, Hashem Nayeri1, Gholamreza Amiri2
1Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran.
2Falavarjan Branch, Islamic Azad University, Isfahan, Iran.
Abstract Immobilized enzymes are drawing significant attention for potential commercial applications as
biocatalysts by reducing operational expenses and by increasing process utilization of the
enzymes. Typically, immobilized enzymes have greater thermal stability and are more resistant
to denaturation that the soluble native form of the enzyme. Magnetic nanoparticles provide
advantages as the supporting material for immobilized enzymes, and magnetic modified
nanoparticles have more ability instead of not modified one such as: higher surface area that
allows for greater enzyme loading, lower mass transfer resistance, less fouling effect, and
selective, nonchemical separation from the reaction mixture by an applied a magnetic field. In
this study at the first, we synthesized Fe3O4 and then was coverage by SiO2 by co-precipitation
and sol-gel respectively. Lactopeoxidase in an optimum situation was immobilized on to Fe3O4@
SiO2 NPs, after that its thermal stability was studied in different temperatures (40-100) at various
times (5min-1h). The results of this study showed that in all temperatures (40-100) and times
(5min-1h) activity of free and immobilized enzyme were decreased, but in all situations activity
of immobilized enzyme was more than free enzyme. According to the results of this study it can
be concluded that stabilized of lactoperoxidase on Fe3O4@ SiO2 NPs can be increase its thermal
stability and preparation of this enzyme for industry.
Keywords: Fe3O4@ SiO2 NPs, Lactoperoxidase, Enzyme immobilization, Thermal stability.
HTTP://UI.CNF.IR/PPS 223
Effect of over-expressing Apaf-1 on apoptosis induction
Maisam Bakhshoudeh, Farangis Ataei, Saman Hosseinkhani
Department of Biochemistry, Faculty of biological sciences, TarbiatModares University, Tehran, Iran.
Abstract
Cancer is the second main cause of death in Iranian women. Out of different kinds, breast cancer
is the most dominant. The rate of apoptosis decreases significantly in breast cancer leading to
metastasis stage of cancer. Apoptotic protease activating factor 1 (Apaf-1) and cytochrome c are
key players in formation of apoptosome, which subsequently activates the cascades of caspase
activities. In most malignant cells, rate of expression of Apaf-1 is low compared to normal cells,
which results in lower rate of apoptosis. In addition, in recent studies it was determined that in
presence of “p53 associated Parkin-like cytoplasmic protein” (PARC/CUL9), cytochrome c is
targeted for ubiquitination, while there is low Apaf-1 availability. This, results in decreased rate
of apoptosis. In this study, we have demonstrated that exogenous expression of Apaf-1 in MCF-7
cell line caused higher caspase 3/7 activity compared to untreated MCF-7 cells after induction of
apoptosis by doxorubicin. As it was expected, since the MCF-10A cell line has higher levels of
Apaf-1 in comparison to MCF-7 cell line, a greater caspase 3/7 activity was observed.Therefore,
it seems that Apaf-1 levels and apoptosis rate are in positive correlation. More conclusive results
will need to be gathered to further prove this claim.
Keywords: Apoptosis, Apaf-1, Breast cancer, Doxorubicin.
HTTP://UI.CNF.IR/PPS 224
Studying the presence of hemolysin BL and NHE subunit genes in
Iranian native Bacillus strains with probiotic potential by PCR
NastaranBahrami Gahrooei1, Mohsen Golnari Maranni2, Mohammad Ali Asadollahi2, SeyedSafa
Ali Fatemi3
1Microbiology group, NourDanesh non-profit higher education institute of Meymeh, Isfahan, Iran.
2 Biotechnology Department, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
3Systeme Biology Group, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
Abstract
A tripartite hemolytic heat-labile enterotoxin designated HBL is responsible for the diarrheal
food poisoning syndrome caused by some strains of Bacillus spp. HBL is the product of an
operon containing hblA, hblD, and hblC, which encode the binding subunit (B) and the L1 and
L2 lytic components, respectively. Additionally, a non-hemolytic enterotoxin (NHE) operon has
recently been characterized. NHE also consists of three proteinaceous subunits including nheA,
nheB and nheC, two lytic factors and a binding factor. Consumption of enterotoxigenicBacillus
spp. at high cell densities results in symptoms of diarrhea, with possible vomiting from a
separate heat-stable emetic toxin. In the present study, we investigated the presence of HBL &
NHE subunit genes in Bacillus isolates by PCR. Thirty-nine Bacillus strains were isolated from a
variety of dairy products, soil samples, vinegar, livestock excreta and poultry excreta samples.
Isolates were identified by biochemical and molecular methods. These Bacillus strains were
screened for probiotic characteristics and finally 16 strains were selected to investigate the
presence of HBL & NHE subunit genes. These strains belong to the B. subtilis, B. licheniformis,
B. toyonensis, B. pumilus, B. coagulans B. amiloliquifaciens, B. endophitycusand B.
siamensisspecies. The results showed that among the 16 strains, seven contained HBL & NHE
subunit genes. This study suggested that HBL & NHE subunit genes could be detected among
Bacillus spp. outside the Bacillus cereus group.
Keywords: Enterotoxin, Hemolysin BL, Non-hemolytic enterotoxin, Bacillus, Probiotic.
HTTP://UI.CNF.IR/PPS 225
Inhibition of angiogenesis signaling pathways by synergic
administration of VEGF antibody along with endostatin derived
peptide in the human umbilical vein endothelial cells
Hossein Bayat1, Reza H. Sajedi1, Kamran Mansouri2, Seyed Mohsen Asghari3
1Department of Biochemistry, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran. 2Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran. 3Department of Biology, Faculty of Basic Sciences, University of Guilan, Rasht, Iran.
Abstract
Angiogenesis is one of the most important stages in tumor growth, though it is a very suitable
target for drug designing. Inhibition of tyrosine kinase receptors like VEGFR-1 and VEGFR-2
by recruiting a monoclonal antibody called bevacizumab (Avastin) and removing its VEGF
ligand (a kind of mitogen for endothelial cells and necessary for angiogenesis process), leads to
angiogenesis inhibition. On the other side, endostatin derived peptide is able to inhibit
endothelial cell growth through an especial integrin receptor. The main goal of this research is
investigating the synergic effect of VEGF antibody (as a specific inhibitor), and endostatin
derived peptide (as a general inhibitor), in order to achieve efficient angiogenesis inhibition and
reduce the dosage of drug administration. The proliferation assay on Human Umbilical Vein
Endothelial Cells (HUVEC) showed the best synergic effect in 400 ng/ml of peptide along with
400 µg/ml of Avastin with 95% inhibition, while single administration of peptide in 400 ng/ml
concentration and anti-VEGF antibody in 400 µg/ml concentration, led to 62% and 48%
angiogenesis inhibition, respectively. The estimation of cytosolic Ca2+ by fluorescence Ca2+
indicator, Fura-2 and tube formation assay confirmed MTT data. Therefore, we concluded that
synergic administration of these two drugs effectively inhibits the endothelial cell growth.
Keywords: Cancer, Angiogenesis, Avastin, Endostatin, Synergic effect.
HTTP://UI.CNF.IR/PPS 226
Evaluation of antioxidant activity in peptides of fermented soybean
meal by Lactobacillus rhamnosus
Maryam Bigdeli, Fakhri-Sadat Hosseini, Mohammad Reza Soudi, Zahra Moosavi-nejad
Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.
Abstract
Soybean meal is a byproduct of vegetable oil industry that can use for livestock feeding. Solid-
state fermentation (SSF) has received great attention because this bioprocess has potential to
successfully convert inexpensive agro industrial residues, as well as plants, in a great variety of
valuable compounds, such as bioactive peptides .The aim of this study was the production of
antioxidant peptides from fermented soybean meal by Lactobacillus rhamnosus. Lactobacillus
rhamnosus was used to produce antioxidant peptides at 30 °C under appropriate humidity during
different incubation time from 24 hours to 72 hours .Antioxidant activity was studied by DPPH
(2, 2-diphenyl-1-picrylhydrazyl) radical scavenging .The result indicated more than 91 % radical
scavenging property in fermented soybean meal .
Keywords: Antioxidant activity, Antioxidant peptides, Lactobacillus rhamnosus, Soybean meal,
Soli state fermentation.
HTTP://UI.CNF.IR/PPS 227
Production of antioxidant peptides from soybean meal by Bacillus
subtilis
Maryam Bigdeli1, Fakhri-Sadat Hosseini1, Mohammad Reza Soudi2, Zahra Moosavi-nejad3
1 Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.
2Department of Microbiolgy, Faculty of Biological Science, Alzahra University, Tehran, Iran.
3 Department of Biochemistry, Faculty of Biological Science, Alzahra University, Tehran, Iran.
Abstract
Oxidative stress has been assumed as one of the most important reasons for increasing
occurrence of different diseases such as cancer, diabetes, hypertension, and asthma. Antioxidant
peptides are produced from different dietary proteins which provide defense against oxidative
stress. Soybean meal is a byproduct of vegetable oil Industry. Solid state fermentation of soybean
meal by Bacillus subtilis subsp. subtilis was used to produce antioxidant peptides at 30 °C under
appropriate humidity within 72 h incubation time. Antioxidant activity was measured by radical
scavenging test using DPPH (2, 2-diphenyl-1-picrylhydrazyl). The results indicated greater than
82% radical scavenging property in fermented soybean meal.
Keywords: Antioxidant peptides, Soybean meal, Bacillus subtilis, Scavenging activity, Solid
state fermentation.
HTTP://UI.CNF.IR/PPS 228
Theoretical design of a new vaccine for multiple sclerosis (MS)
Karim Mahnam1, Nasrin Payab1, Mohsen Mobine Dehkordi2, Mostafa Shakhsi-Niaei2
1. Biology Department, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.
2. Department of Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran.
Abstract
Multiple sclerosis (MA) is an autoimmune demyelinating disease targeting the human central
nervous system. It is believed that the activation of T cells reacting with the CNS antigens is the
first autoimmune event in MS. MOG and MBP are the myelin sheath proteins and highly
pathogenic antigen epitopes involved in immune response. Today, more researchers are looking
for drugs with high specificity to function on the immune system. Tolerogenic vaccines are a
new class of drugs that reduce the immune response to the MS antigens by presenting the
associated antigens. This study aims to model a fusion protein vaccine using the combination of
MOG(1-20) and MBP(147-166) linked to interlukine-16 and examine its antigenic properties. For this
propose at first model MOG(1-20) linked to MBP(147-166) was made by modeler 10 and. The best
obtained model connected to C-terminal domain of IL-16 and was used for 10 ns molecular
dynamics simulation via Gromacs 5 package. Also free MOG and MBP antigens were simulated
separately for 10 ns. The results revealed that the solvent accessible surface areas of MOG and
MBP epitopes are almost the same in both free and in fusion protein. Then we can conclude that
this fusion protein preserve antigenic property of MOG and MBP epitopes.
Keywords: Multiple sclerosis, Vaccine, Fusion protein, Protein engineering, Molecular dynamics
simulation.
HTTP://UI.CNF.IR/PPS 229
The effect of temperature on the formation rate of liposome of
DSPC and CHOL by coarse-grained molecular dynamics
simulations studies
and Majid Taghdir parchekanichoozaki Jalil
Faculty of Biological Science, TarbiatModares University, Jalal Ale Ahmad Highway, P.O.Box: 14115-111, Tehran,
Iran
.
Abstract
In general, the importance of liposomes in medical and pharmaceutical can be divided into two
areas of treatment and diagnosis of diseases. The application of liposomes as a tool, a model or a
reagent in basic research such as cell interactions, cognitive processes is notable. The stability of
liposomes containing pharmaceuticals are also very important and heavily influenced by the type
of their phospholipids and the general composition of phospholipids that are more unsaturated.
Based on thermodynamic concepts and chemical-physical properties of phospholipids these
molecules in aqueous media tend to that form vesicle structures. In this study coarse-grained
simulations were done at different temperatures to simulate the liposome DSPC and CHOL. The
structure analysis showed that the liposomes is formed as well as.The further analysis showed
that temperature has an important effect on the formation rate of liposomes.These results showed
that the formation of the liposome in higher rate is happen in higher temperature. These findings
revealed that the temperature tune the balance of van der waals and electrostatic interactions in
the formation of liposome.
Keywords: Self-assembled liposome, Liposome stability, Temperature effect, Coarse-grained
simulations.
HTTP://UI.CNF.IR/PPS 230
Purification of sugar beet pulp induced pectinase from P. indica by
chitosan-PVA magnetic beads
ParisaFathi Rezaei1, Somayeh Kiani1, Saleh Shahaabivand1, Gholamreza Mahdavinia2
1Department of Biology, Faculty of Science, University of Maragheh, Maragheh, Iran. 2Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh, Iran.
Abstract
Pectinases or pectinolytic enzymes are one of the upcoming commercial enzymes that are
produced by higher plants and microorganisms such as fungi, bacteria, yeasts. These enzymes
have a wide range of industrial applications including fruit processing, tea and coffee
fermentation, in paper and textile, waste water treatment and plant oil extraction. Pectins are
complex polysaccharides which present in cell wall of plants and degraded by pectinase to
simple substances such as galacturonic acid. Because of the vast industrial applications of
pectinases, all over the world many groups are searching to find new efficient methods for
purification and immobilization of pectinase. In line with other attempts, here the efficiency of
chitosan-PVA magnetic beads for purification of P. indicaproduced pectinase was evaluated.
Sugar beet pulp (SBP) as a by-product of sugar factory was used to induce production of
pectinase by P. indicain submerged fermentation. For this reason, P. indica was cultured on
Kaefer medium supplemented with SBP. The slurry was filtered by centrifugation at 10,000 rpm
at 4 ºC for 15 min. Then the supernatant was incubated with chitosan-PVA magnetic beads at 4
ºC overnight with continues shaking. The enzyme was desorbed from magnetic beads by 0.5 mM
CaCl2 (PH= 5.9). The protein content of samples was determined by Bradford assay. Based on
the results, the protein content of the solutions treated with chitosan-PVA magnetic beads was
increased significantly. In conclusion, chitosan-PVA magnetic beads could be a good candidate
to purify pectinase, but further optimization is required.
Keywords: Piriformosporaindica, Pectinase, Pectin, Sugar beet pulp, Chitosan-PVA magnetic
bead.
HTTP://UI.CNF.IR/PPS 231
Investigating the role of DADLE on 6-OHDA-induced cell toxicity in
human neuroblastoma cells SH-SY5Y as an in vitro model of
Parkinson’s disease
Elham Pooresmaeili-Babaki, Saeed Smaeili-Mahani, Mehdi Abbasnejad
Department of Biology, Faculty of Sciences, ShahidBahonar University of Kerman, Kerman, Iran.
Abstract
Parkinson’s disease is a common neurodegenerative disorder characterized by the loss of
dopaminergic neurons in the substantia nigra pars compacta and the accumulation of
proteinacousintraneuronal inclusions known as Lewy bodies. Pharmacologic treatment of PD can
be divided into symptomatic and neuroprotective therapies. DADLE ([D-Ala2, D-Leu5]-
Enkephalin) is a syntheticopioid peptide with analgesic properties. It prevents and reverses
methamphetamine (METH)-induced damage of dopaminergic terminals of brain. It prevents
naltrexone-sensitive PC12 cell apoptosis in serum deprivation conditions. Thus, it might play an
essential role in the survival of neurons and organs.Therefore, the present study was designed to
investigate the effects of DADLE on 6-OHDA-induced SH-SY5Y cells toxicity as an in vitro
model of Parkinson disease. To induce cell toxicity, the SH-SY5Y cells were treated with 150
µM 6-OHDA. In treatment groups, different doses of DADLE (1, 5, 10 and 50 μM) were used to
investigate its possible protective mechanisms. Cell toxicity was determined by MTT assay.The
results suggested that DADLE doesn't have any neuroprotective effects against 6-OHDA-
induced apoptosis in dopaminergic cells.
Keywords: DADLE, MTT assay, 6-OHDA, SH-SY5Y cell.
HTTP://UI.CNF.IR/PPS 232
Interactions of β-lactoglobulin with Lovastatin
Asghar Ali Asghar, Rategari Isfahani -Zeini, NajafabadiFerdos-Pouresmaeili
Department of Molecular and Cell Biochemistry, Islamic Azad University, Flavarjan, Iran.
Abstract
The major protein in bovine milk whey, 𝛽-Lactoglobulin (𝛽-LG), has several binding sites for
ligands. The biological function of 𝛽 − 𝐿𝐺 is not clear, but its potential role in carrying fatty
acids through the digestive tract has been suggested. 𝛽-LG has been found in complexes with
lipids such as butyric and oleic acids and has a high affinity for a wide variety of compounds.
Lovastatin (Lvt), is an important anticholesterolemic drug which inhibits the conversionof HMG-
CoA to mevalonate in the biosynthesis of cholesterol. In this study, the interaction of Lvt with 𝛽-
LG was investigated using circular dichroism (CD) and UV–vis spectroscopic. The results of
UV–visshowedincrease in absorbance during its interaction with Lvt and this ligand interacts
with 𝛽 -LG forming equimolar complexes. The binding and thermodynamicparameters were
calculated. Hydrophobic interactions were proved to play significant role in theinteraction of Lvt
with 𝛽-LG. According to far- and near-UVCD results, this ligandhas no apparent influence on 𝛽-
LG secondary structure, however they partially destabilize its tertiary structure.
Keywords: β-lactoglobulin, Lovastatin, Circular dichroism, UV-vis spectroscopy.
HTTP://UI.CNF.IR/PPS 233
Efficient synthesis and purification of buserelin acetate
Somayeh Ahadi1, Samane Poursan1, Saeed Balalaie1,2
1Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416, Tehran, Iran. 2Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
Abstract
Buserelin Acetate (Brand name: Suprefact®) is a potent luteinizing hormone releasing hormone
(LHRH) and (GnRH) agonist analogue, that is categorized as antineoplastic drugs. It is used for
men, to lower levels of testosterone which is the palliative treatment of advanced (metastatic)
prostate cancer. Buserelin acetate works by blocking the production of testosterone that reduces
the growth and reproduction of prostate cancer cells. In women, it lowers levels of estrogens and
progesterone and has been studied as a treatment in estrogen receptor positive breast cancer.
Buserelin acetate is administered by subcutaneous injection or as a nasal solution. Herein, we
report an efficient novel approach based on the use of suitable protected amino acid and the type
of deprotection methods to access the pure product. The synthesis was done based on SPPS
method and Fmoc protected amino acids. The structure of buserelin acetate was confirmed based
on HRMS (ESI) data.
Keywords: Buserelin acetate, LHRH analogue, FH, FSH.
HTTP://UI.CNF.IR/PPS 234
A thermodynamic approach of the interaction between human
serum albumin and a new synthesized platinum complex
Atefeh Poursoleiman1, Adeleh Divsalar2, Ali Akbar Saboury1, MahboubeEslami Moghadam3
1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
2Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
3Chemistry & Chemical Engineering Research Center of Iran, Tehran, Iran.
Abstract
Human serum albumin (HSA) can interact, reversibly or irreversibly with macromolecules such
as proteins, drugs, smaller organic compounds and inorganic ions. Platinum-based drugs are
frequently used in the clinical practice to treatment of various cancers. Because of some serious
side effects in these complexes, we are looking for other platinum complexes with lower toxicity.
In this study, we investigated the binding properties of a new platinum complex (Pt (NH3)2) Gly-
Amyl) as an anti-cancer compound to HSA under simulative physiological conditions via
spectroscopic techniques of fluorescence and circular dichroism (CD). Results of fluorescence
study showed that the considerable quenching in intrinsic fluorescence of HSA upon binding of
this complex. The values of binding constant (Ka) and the corresponding numbers of binding
sites (n) measured according quenching methods, respectively. In addition, far-UV-CD results
show that this complex did not induce any significant changes in the secondary structure of HSA.
These findings provide a molecular-level understanding of complex-HSA binding interactions,
which can be used as a useful guideline for further drug design.
Keywords: Anti-tumor component, Platinum complex, Human serum albumin, Fluorescence.
HTTP://UI.CNF.IR/PPS 235
Computational analysis of miR-423 mediated drug response in
breast cancer
Nadia pourmoshir and SadeqVallian
Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR Iran.
Abstract
MiRNAs play a significant role in pharmacogenomics by down-regulating genes that are
important for drug function. These interactions can be described as triplet sets consisting of a
miRNA, a target gene and a drug associated with the gene. In the present study we aim to
investigate the association of miR423 expression and cyclophosphamide function by combining
data on miRNA targeting and protein-drug interactions. In this study, miR-423 targeting
information was derived from miRanda database and information of cyclophosphamide and
cdkn1a were obtained from drug bank and PDB databases, respectively. Then, cdkn1a-
cyclophosphamide interactions were annotated by PharmGKB database. Finally, all the data
were investigated and validated by Pharmaco-miR database. The data showed that miR-423
could inhibit CDKN1A expression, which functions as a master downstream effector of tumor
suppressors. Together, a miRNA, a target gene and a drug that interacts with the product of the
target gene, form a miRNA pharmacogenomics set.
Keywords: MiR-423, Drug response, Breast cancer.
HTTP://UI.CNF.IR/PPS 236
Evaluation of dioxin contaminations in fish oil samples by
bioluminescence method
ElnazTajabadiEbrahimi, Saman Hosseinkhani, Farangis Ataei, ElhamTahmasbi
Department of Biochemistry, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.
Abstract
In determination of contaminants (dioxins, polychlorinated biphenyls, polyaromatic
hydrocarbons), cell-based assays are useful methods for screening purposes: they are mainly
characterized by high sample throughput and lower costs than Mass Spectrometry (MS)-based
methods. Cell-based assays are highly sensitive for the determination of dioxins. Fish oil has
been identified as one of the most important contributors to the levels of polychlorinated
biphenyls (PCBs) in food and feed products. In this study dioxins are extracted from fish oil by
an extraction solution of 97% Hexane and 3% Diethyl ether. An ultrasonic process is used to
ensure intimate contact of the matrix with the extraction solution. Then, the extracted sample is
passed on an activated silica gel column, resulting in the purification of dioxin, which can be
exposed on dioxin responsive-chemically activated luciferase gene expression cells. The cells are
incubated for 24 hour at 37⁰C with 5% CO2. After incubation, the cells are lysed with lysis
reagent and luciferase activity is measured. Upon exposure to dioxin-like compounds, the cells
express luciferase in a dose-dependent manner. The measured luminescence resulting from
exposure to a chemical or chemical mixture is converted into a bioassay toxic equivalency value
by the direct comparison of the response for a given sample to a dose-response curve obtained
with 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD or dioxin).
Keywords: Dioxin, DR-CALUX, Fish oil, Bioluminescence.
HTTP://UI.CNF.IR/PPS 237
Characterization of electrospun gelatin nanofibers crosslinked with
tannic acid
Elham Tavassoli-Kafrani1, Sayed Amir Hossein Goli1, Milad Fathi1, Asghar Taheri-Kafrani2
1Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan
84156-83111, Iran.
2Department of Chemistry, Laboratory of Biophysical Chemistry, University of Isfahan, Isfahan 81746-73441, I.R.
Iran.
Abstract
This work was aimed to prepare crosslinked electrospun gelatin nanofibers. As a natural phenolic
compound, tannic acid was used to crosslink gelatin and subsequently electrospinning was
fabricated using acetic acid/ water mixture (60:40) as solvent. The properties of gelatin solution
were characterized measuring electrical conductivity, viscosity, and surface tension. The
prepared gelatin fibers were analyzed by SEM, DSC, and FTIR tests. Electrical conductivity and
viscosities of crosslinked gelatin solutions were both higher than that of non-crosslinked gelatin
solution and surface tension showed no major difference. Using SEM, crosslinked gelatin was
determined to maintain fiber morphology. However, the fiber mean diameter showed an increase
in crosslinked samples in comparison to non-crosslinked gelatin nanofibers. FTIR spectra
revealed that tannic acid probably interacted with C-N-C groups of gelatin molecules and DSC
analyses proved that crosslinking led to an increase in thermal stability of gelatin nanofibers.
Keywords: Electrospinning, Gelatin, Tannic acid, Crosslinking.
HTTP://UI.CNF.IR/PPS 238
Kinetics and spectrofluorimeteric the studies of catalase in presence
of spermidine
Fateme Tavakoli Chalespari and Behzad Shareghi
Department of biology, Faculty of science, University of shahrekord, P. O. Box 115, Iran.
Abstract
Catalase (CAT) is one of the most important enzymes of antioxidantdefense systems, which
could protect cell againstoxidative stresses induced by reactive oxygen species. Catalase is an
oligomeric enzyme (MW=240000Da) with four identical subunits.In this study, the effects of
different concentrations of spermidine was investigated on the catalytic activity of catalase by
using spectrophotometer (UV-Visible) at pH=7.4 and 370C. Moreover, we used fluorescence
spectroscopic method for investigating the changes in tertiary structure of enzyme at different
temperatures based on the changes in intrinsic emission. The kinetic parameters of the enzyme
activity showed that the increased concentrations of spermidine lead to decrease in the enzyme
activity as a non-competitive inhibitor. In addition, fluorescence data represented the decreasing
in intrinsic emission of enzyme with increase inspermidine concentrations, which indicates that
changeshave been done at three dimensional environments around the enzyme chromophores.
These results demonstrated that fluorescence quenching of spermidine occur through a static
mechanism. The thermodynamic data suggested that electrostatic interactions were the
predominant intermolecular forces in the binding reaction.
Keywords: Catalase, Spectrophotometer, Spectrofluorimeter, Spermidine.
HTTP://UI.CNF.IR/PPS 239
Effect of TiO2 nanoparticle on structural stability and activity of
catalase
Fateme Tavakoli Chalespari and Behzad Shareghi
Department of biology, Faculty of science, University of shahrekord, P. O. Box 115, Iran.
Abstract
Catalase, is an important antioxidant enzyme that has numerous industrial and medical
applications. TiO2 nanoparticles, the most widely used metal oxide nanoparticles, have been
increasingly employed in a variety of industrial applications. These lead to increasing human
exposure and to affecting human health and the environment. As a result the study of interaction
between enzyme and nanoparticles is important. In this experimental study, the alterations in
catalase activity were measured in the absence and the presence of different concentrations of
TiO2 nanoparticle by using spectrophotometer (UV-Visible) at pH=7.4 and 370c. Moreover, we
used fluorescence spectroscopic methods for investigating the changes in tertiary structure and
binding properties of enzyme at different temperatures based on the changes in intrinsic
emission.Analyzing the kinetic of the enzyme showed that increasing the concentrations of TiO2
lead to decrease in the enzyme activity. TiO2 acts as un-competitive inhibitor. In addition,
fluorescence data represented the decreasing in intrinsic emission of enzyme in the presence
ofTiO2 nanoparticle, which indicates that the environment of tryptophans changed. This result
demonstrated that the static type of quenching mechanism is involved in the intrinsic quenching
of enzyme on TiO2.
Keywords: Catalase, Kinetic parameter, Intrinsic quenching, TiO2 nanoparticle.
HTTP://UI.CNF.IR/PPS 240
Separation and precipitation of β –lactoglobulin from commercial
whey preparations by NaCl salting out at low pH
Rezvan Kazemi, Reihaneh Kordsedehi, Asghar Taheri-kafrani
Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.
Abstract Whey is a by-product of cheese production process that its proteins (wp) have many valuable
functional properties such as foaming and emulsifying ability or gel formation. Cheese
production on an industrial scale causes to produce a large volume of whey. WP, well known for
their nutritional value and versatile functional properties, are widely utilized in the food industry.
WP provides health benefits to humans of all ages by providing specific bioactive components.
The most important of whey protein is β –lg which constitute 48-58 %. (wt) and its
characteristics prevail over the other ones and significantly define the properties of whey.
Technologies currently used for β –Lg isolation combine methods of ion-exchange
chromatography, enzymatic hydrolysis, complex formation, precipitation, electrodialysis and
membrane separation. Although these fractionation techniques can provide effective protein
precipitation at the laboratory scale, most have not been widely implemented for commercial
scale because of their relatively high cost complexity, low productivity, poor selectivity and/or
unacceptable denatured products. The objective of this study was separation of β –Lg fractions
from the other whey proteins, without heat denaturation in both fractions, by a salting out
procedure suitable for scaling up and compatible with food industry requirements. It has been
showed that the greatest protein contents were obtained using salt treament methods.
Keyword: Whey, WP, Precipitation, β –Lg.
HTTP://UI.CNF.IR/PPS 241
Proteins and peptides in camel milk
Mohammad Rabbani Khorasgani and Reihaneh Amini
Department of Biology, Faculty of Sciences, University of Isfahan.
Abstract
Camel milk is an important nutrientin some countries and it has many valuable ingradients with
benificient nutritional, immunological and growth effects. In this article some impotant proteins
and peptids of camel milk are presented as the following: Casein (CN): It is the major protein in
camel milk and the β-CN is the main camel milk casein. Camel milk is similar to human milk in
that it contains a high percentage of β -CN; this high percentage could reflect its higher
digestibility rate and lower incidence of allergy induction in the gut of infants. Glycine and
cystine were found to be significantly lower in dromedary milk caseinCompared to bovine's
milk.Camel milk κ-CN was reported to contain an extra proline residue in its sequence (Pro95).
This additional proline residue is expected to play an important role in the stability of camel milk
κ -CN sequence compared with bovine milk κ –CN sequence .Other properties of camel milk
proteins (casein and whey proteins) compared to bovine milk :- lower electrophoretic mobility,
higher molecular size, broader size distribution of casein particles, more of average micelle
diameter, higher quantity of whey proteins ,higher heat stability and a lower degree of hydrolysis
after reaction with pancreatic enzymes.Whey: antimicrobial agents : Camel milk was reported to
have an antimicrobial effect against gram positive and gram negative bacteria, this inhibitory
activity was attributed to the presence of antimicrobial substances such aslysozyme, hydrogen
peroxide, lactoferrin, lactoperoxidase and immunoglobulins .Other components :Camel milk
whey contains other main components such as serum albumin, and peptidoglycan recognition
protein andinsulin like protein. The intake of camel milk reduced the excessive need for insulin
whichcan help in regulating the blood glucose levels. It is hoped to progress research about
camel milk and beneficial uses of it for human health.
Keywordes: Camel milk, Proteins, Peptides, Casein.
HTTP://UI.CNF.IR/PPS 242
Efficient synthesis and purification of octreotide acetate as a
somatostatin agonist analogue
Fatemeh Baghestani1, Sorour Ramezanpour1, Ali Nikbakht1, Saeed Balalaie1, 2
1Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416.
Tehran, Iran. 2Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
Abstract
Pharmaceutical peptides are known as natural drugs with superior characteristics such as high
target affinity, low side effects. Due to these characteristics, they gained a major interest for their
synthesis. Octreotide is an octapeptide that mimics natural somastostatin pharmacologically,
though it is a more potent inhibitor of growth hormone, glucagon. Meanwhile, there are some
radiopeptide based on octreotide.A distinguished point of this compound is the presence of
disulfide bridge in its structure. Recently, it was shown that the number of disulfide bridge in the
structure of peptides has an important role in their activities. In continuation of our research for
the developing of the know-how for the synthesis of pharmaceutical peptides, and especially the
peptides with disulfide bondwe wish to report the synthesis of octreotide acetate as active
pharmaceutical ingredient (API). Octreotide acetate was synthesized through solid phase peptide
synthesis(SPPS) approach, after cleavage, disulfide bridge was introduced followed by final
deprotection, the crude peptide was purified using preparative HPLC.The structure of product
was approved using HR-MS(ESI) data.
Keywords: Somastostatin analogue, Disulfide bridge, Radiopeptide.
HTTP://UI.CNF.IR/PPS 243
Optimization of carbon source for phytase production in submerged
fermentation of a strain of Aspergillus niger and comparison of
enzyme activity between immobilized and free spores
Atefeh Hamzeh 1, Jamshid Fooladi 1, FakhriSadat Hosseini 2
1 Laboratory of Industrial Microbiology, Faculty of Biology, AlzahraUniversity, Tehran, Iran.
2 Faculty of Biology, Alzahra University, Tehran, Iran.
Abstract
The main storage form of phosphorous in plant seeds is Phytic acid (Lopez et al, 2002).6
phosphate groups allow phytate to form complexes with multivalent cations (Dost and Tokul,
2006) and proteins. Therefor phytic acid as an anti-nutrient factor creates various digestion
problems. Phytase is an enzyme that is able to hydrolyzephytic acid and releases inorganic
phosphate and increases bioavailability of minerals. Simple stomached animals have no or very
little amount of this enzyme (Gargova et al.2002). Excreted phytate can be decomposed in soil
and causes environnmental problems.We examined submerged fermentation of Aspergillus niger
for phytase production. Media prepared according to a report (Gonita and Mishra, 2013) but with
4 different carbon sources: glucose 1 %, Malt extract 1%, molasses 1%and sucrose 1 %. The best
carbon source was used for submerged fermentation for comparison between immobilized and
free spores. Then immobilized spores of this study were used for another submerged
fermentation with wheat bran 1 % but without using sodium phytate. Enzyme activity was
determined according to the methodexplained by Engelen et al. (1994). Among 4 differrent
carbon sources,Malt extract 1% had the maximum phytase activity and glucose had minimum
activity because of its inhibitory effect. Vats and Banerjee reported glucose inhibition in 2002.
The immobilized spores indicated higher phytase activity than free spores.Furthermore
immobilized spores in the second media (wheat bran 1 %) showed the maximum phytase
production after 96 hours; therefore wheat bran induced phytase production in immobilized
spores.
Keywords: Phytase ,phytic acid , Submerged fermentation , Aspergillus niger, Immobilization.
HTTP://UI.CNF.IR/PPS 244
An investigation on the structure and function of the cell surface
prostate-specific antigens for development a new generation of
immunotoxins
Mohammad Rastegar Moghadam Baghestani1, Aliakbar Haddad-Mashhadrizeh2, Javad Baharara3
1Department of Biology, Science and Research branch, Islamic Azad University, Khorasan Razavi, Neyshabur, Iran.
2 Celland molecular biotechnology research group, institute of biotechnology, and Department of Biology, Faculty
of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
3 Department of Biology, Mashhad Branch, Islamic Azad University.
Abstract:
Prostate cancer, which is originated from malignancy in prostate tissue, is one of the most
common types of cancer among men. This type of disease, which in the past 20 years is one of
the basic factors of death in the men of the society, led to serious attention for development
prognostic and therapeutic approaches in the health system. Among these strategies,
immunotoxinstherapy with the ability to target specific cancer cells, have momentous position.
However, the development of this type of medication is required to the characterization of the
cancer cell specific antigens. Bearing in mind, cell surface prostate-specific antigens profiling as
well as characterization of them were considered in this study. In this regard, at the first step 15
specific antigen of prostate tissue was collected based on literature review. In-silico expression
assay of the selected antigens were performed via proteinatlas program, on the several of
cancerous and non-cancerous tissue. The nucleotide and protein sequences as well as 3D
structure of the selected antigens were extracted from related databases. Meanwhile,
corresponding ligands of the selected antigens were detected by String, and then evaluated based
on binding assays via Clusproprograms. The results of this research led to reveal some cell
surface prostate-specific antigenswith high expression on the prostate malignancies including
PAGE3, KDM5D, FOLH1as key targets for immunotoxins development of this type of
cancer.On the other hand, among of the 40 kinds of corresponding detected ligandsof these
antigens, HPA062248, HPA049086, HPA010593, HPA000764 with high binding affinity, short
in length and limited in post-translational modification raised as favorable candidate for the
development of this type of medication. However, this capacity would be evaluated after
designing and simulation of the newimmunotoxins in laboratory conditions, which are
considered in our group.
Keywords: Cancer, Prostate, Immunotoxins, Antigen, Ligand.
HTTP://UI.CNF.IR/PPS 245
A comparative study of effects of canola meal bioactive peptides,
antibiotic, probiotic and prebiotic on growth performance, some
blood parameters, intestinal morphology and gut microflora in
broiler chicks
Sadegh Karimzadeh, Mansour Rezaei , Asadolah Teimouri Yansari
Department of Animal Sciences, Faculty of Animal Science and Fisheries, Sari University of Agricultural Sciences
& Natural Resources.
Abstract
The aim of the present study was to evaluate the effects of canola meal bioactive peptides (CBP)
produced by enzymatic hydrolysis of canola meal, antibiotic (Virginiamycin®), probiotic
(Bactocell®) and prebiotic (Agrimos®) on growth performance, some blood parameters, gut
microflora and intestinal morphology of broiler chicks. A total of 200 one-day-old Ross 308
male broiler chicks were randomly allocated to 5 dietary treatments with 4 replicates of 10 birds
per each. Birds were fed with a basal diets (Control), 250 mg CBP/kg, 200 mg antibiotic/kg,
0.01% prebiotic and 0.1% probiotic for a 42 d feeding trial. Results indicated that addition of
CBP and probiotic diet increased (P<0.05) body weight gain (BWG) and decresed feed
conversion ratio (FCR) (1-28 d, 29-42 and 1-42 d) (P<0.05). In comparison to the other group,
adding CBP diet improved serum total protein, phosphorus and calcium concentrations (P<0.05).
Also, adding CBP to diet decreased serum cholesterol and triglyceride concentrations (P<0.05).
The villus height, the ratio of villus height to crypt depth of duodenum, jejunum and ileumin in
chicks fed by CBP and probiotic increased and crypt depth significantly decreased (P<0.05).
Adding CBP and probiotic decreased gram negative bacteria’s counts in ileum and caecum
compared to the control group. Results of the present study suggested that CBP probiotic might
use as a functional additive in broiler chicks diet.
Keywords: Canola meal Bioactive Peptides, Probiotic, Prebiotic, Performance, Some blood
Parameters, Intestinal morphology, Broilers.
HTTP://UI.CNF.IR/PPS 246
The investigation of stability of functionalized alkyl-peptide self-
assembly innanofiber form by molecular dynamics simulation
Havva Mehralitabar, Majid Taghdir, Hossein Nadrimanesh
Faculty of Biological Science, TarbiatModares University, Jalal Ale Ahmad Highway, P.O.Box: 14115-111, Tehran,
Iran.
Abstract
The design of amphiphilic alkyl-peptides which can assemble into architectures like nanofiber
and liposomes is applicable in the field of tissue engineering and drug delivery. Nanofiber
formatted fromalkyl-peptidescan reorganize hydrogelswith different physical properties to
mimicthe extracellular matrix of different types of tissues. The aim of this research is to
investigate the stability of the nanofiber structure of alkyl-
peptideFAQRVPPEEEGGGAAAAK(C16) which is functionalized by the sequence of
FAQRVPP with the property of differentiating of neural stem cell to neurons. The all atom
molecular dynamic (MD) simulation applied to simulate a pre-constructed structure of nanofiber
with radially arranging of 9 alkyl-peptides in one layer and 16 numbers of those layers in one
cylindrical structure. The result of 50 ns simulation by Amber package showed that this
functionalized alkyl-peptides cannotconstruct stable structures in fiber form andis broken to two
smaller micelles likeshape. So that it can be proposed, space prevention of bulky structure of
functional group in alkyl-peptide causes the disruption.Therefore, selection of longer alkyl chain
to have a balance between hydrophobic and hydrophilic forces in the fiber or choosing a
combination of functionalized and non-functionalized alkyl-peptide in fiber structure to reduce
the space prevention of functional group in fiber surfacecan increase the stability.These
findingscan help to design the fiber structures with deferent softness or stiffness.
Keywords: Alky-peptide, Self-assembled nanofiber, Tissue engineering, Softness, Stiffness.
HTTP://UI.CNF.IR/PPS 247
Beta keratin solubilization: a new method for blocking sulfydryl
groups
Fateme Rezaei Sadrabadi and Zahra Moosavi-Nejad
Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
Abstract
Feathers are rich sources of beta keratin which are important byproducts of poultry industries
causing environmental disposal problems. Feather is made up of 90% protein which keratin is its
main protein. Due to the highly crosslinkes, it is the fibrous protein, therefore it is resistant to
proteolytic enzymes and has high mechanical stability. Keratinouse materials have been
considered due to essential qualities such as, inherently biocompatibility, biodegradability,
mechanical resistance and frequency. In the present study proteins of feather are dissolved by
urea and β-mercaptoethanol. To prevent aggregation of protein, cysteine residues blocked with
some blocking agent such as iodoacetamide, iodoacetic acid and bromosuccinic acid. In the
present study iodoacetamide and H2O2 were used as blocking agent. After dialysis, the qualities
of antioxidant and the chelating ability of extracted protein were tested by 2, 2-diphenyl-1-
picrylhydrazyl (DPPH) radical scavenging ability and metal chelating assay. 2, 2-diphenyl-1-
picrylhydrazyl radical scavenging abilities of feather keratin that blocked with iodoacetamide
and H2O2 81.71% and 87.78% respectively. Fe2+-chelating ability oftheir was 82.74%
and78.36% respectively. According our results, hydrogen peroxide can be introduced as a
cheaper and more accessible blocking agent for preparing keratin solution.
Keywords: Keratin, Iodoacetamide, H2O2, DPPH, Metal chelating ability.
HTTP://UI.CNF.IR/PPS 248
Antioxidant and metal chelating ability of feather keratin
Fateme Rezaei Sadrabadi and Zahra Moosavi-Nejad
Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
Abstract
Feathers are rich sources of beta keratin which are important byproducts of poultry industries
causing environmental disposal problems. Feather is made up of 90% protein which keratin is its
main protein. Due to the highly crosslinkes it is the fibrous protein, therefore it is resistant to
proteolytic enzymes and has high mechanical stability. Keratinouse materials have been
considered due to essential qualities such as, inherently biocompatibility, biodegradability,
mechanical resistance and frequency. In the present study, feather proteins were dissolved by
urea and β-mercaptoethanol at the temperature of 50 o C. After dialysis, the quantities of
antioxidant and the chelating ability of extracted protein were measured by 2, 2-diphenyl-1-
picrylhydrazyl (DPPH) radical scavenging ability and metal chelating assay respectively. 2,2-
diphenyl-1-picrylhydrazyl radical scavenging abilities of feather keratin was 79.21 % and its
Fe2+-chelating ability was 92.06 %. Therefore the feather protein can be used as a cheap
antioxidant and reducing agent without any digestion.
Keywords: Keratin, DPPH, Antioxidant ability, Chelating ability.
HTTP://UI.CNF.IR/PPS 249
Binding of carbon nanotube to carcinoembryonic antigen: A the
oretical approach
Behafarid Ghalandari1,2 and Nazila Eyvazzadeh1,2
1Radiation Research Center, Faculty of Paramedicine, AJA University of Medical Sciences, Tehran, Iran.
2Department of Radiology, Faculty of Paramedicine, AJA University of Medical Sciences, Tehran, Iran.
Abstract
The overexpression of characteristic proteinsin cancer cells provide an opportunity for early
diagnosis of cancer. Among them carcinoembryonic antigen (CEA) is a well-known biomarker
for colorectal cancer diagnosis. On the other hand, the remarkable physicochemical properties of
single walled carbon nanotubes (SWCNTs) make them as one of the most promising materials
for applications in the fast electrochemical technique of biomarker sensing. In addition, SWCNT
is a good candidate for biomarker detection whereas it has complementary structure with
proteins. In this study, the ability of SWCNT with low diameter was investigated as a detector
for CEA. The computational study on CEA/SWCNT system was performed using Gaussian 98
program based on HF method of ab initio at theoretical level of 6-31G basis set at temperature of
25°C. The physical properties of interaction such as predominant binding force, charge
distribution and interaction energy have been investigated. The results show that SWCNT
interaction with CEA has minimum value of interaction energy and electrostatic interaction has
effective role in place of interaction. The results also show significant changes in electrochemical
properties such as charge distribution, dipole moment and polarity of CEA that are detectable
and measurable variables in presence of SWCNT. So, SWCNT with low diameter is a suitable
electrochemical sensor especially for CEA detection and measurement. As a result, this study
develops electrochemical sensorspresence in the early diagnosis of colorectal cancer.
Keywords: CEA, SWCNT, ab initio, Electrochemical properties.
HTTP://UI.CNF.IR/PPS 250
Peroxynitrite-modified human α-Crystallin subunits indicate
improved chaperone-like activity and enhanced protection against
copper-mediated ascorbic acid oxidation
Maryam Ghahramani and Reza Yousefi
Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
Abstract
Ascorbic acid (ASA) plays an important function to protect lens crystallins against oxidative
damages. In the cataractous lenses and during ageing, the increased lenticular level of copper ion
catalyzes, to important level, the conversion of ASA into dehydroascorbate and hydrogen
peroxide (H2O2) which are potentially two important modifying agents of lens proteins. This
study was performed with the aim to assess the structure, chaperone-like activity and protective
ability of peroxynitrite-modified human α-Crystallin subunits in a copper-mediated ASA
oxidation system. Depending on the extent of modification, αA- and αB-Crystallin display an
improved chaperone-like activity and enhanced protective ability against copper-mediated ASA
oxidation. Also, chaperone-like activities of both native proteins and their peroxynitrite-modified
counterparts were increased in the presence of copper ions. In addition, peroxynitrite
modification induced significant changes in structure of the recombinant proteins. Overall, the
enhancement of chaperone-like activity and the increase in ASA protective ability of human α-
Crystallin subunits upon peroxynitrite modification may suggest a new beneficial effect for this
oxidative and nitrative agent in the ocular system.
Keywords: α-Crystallin, Peroxynitrite, Copper ion, Ascorbic acid, Chaperone-like activity.
HTTP://UI.CNF.IR/PPS 251
Investigation the use of plants as host for protein production
Fereshteh Enami Mehmandoost and Hasan Mohabatkar
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Abstract
Most bacteria cannot proceed post translational modification properly and this is the reason for focusing
on plant hosts. Also, it reduces the cost of production, this procedure has high efficiency, for example
efficiency of Avidin production in a cluster of maize is higher than a tone of egg, the main aim of
pharming is production with high efficiency. The best plant for commercial use, is tobacco .The reason is
that this plant is well-established for gene transfer and expression, high biomass yield, prolific seed
production and the existence of large scale processing infrastructure. Alternative leafy crops that are
being investigated for pharming include: alfalfa, soybean, lettuce. The possibility of storage in room
temperature makes it more attractive in order not to waste energy. Fruits are major systems for production
of recombinant vaccines and antibody designed for topical application especially potatoes then it can be
replaced by tomato, banana, carrot, lettuce, maize, alfalfa and spinach. Because they are more palatable
than potato. Todays, maize can be used for Avidin, beta glocuronidase and trypsin production the
protein/recombinant protein production can be produced compatible with vermicular plants of each area.
This study compares different ways of transferring gene, growing efficiency in different plants. Also, it
considers ways to minimize potential risks for environment.
Keyword: Protein production, Different plant, Efficiency, Vaccine, Recombinant protein.
HTTP://UI.CNF.IR/PPS 252
Immobilization of human serum albumin on modified graphene
oxide nanosheets
Faransak Jafarian and Abdol Khalegh Bordbar
Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Abstract
Graphene oxide (GO) was prepared by a modified Hummers method and functionalized by (3-
mercaptopropyl) trimethoxysilane and used for covalent immobilization of human serum
albumin (HSA). The immobilization was carried out by the site-specific covalent binding
between thiol groups of HSA and thiol sulfonate groups on modified GO.The structure of the
prepared nanosheets were characterized by X-ray powder diffraction (XRD). The immobilization
was confirmed by Fourier transform infrared spectroscopy (FT-IR). XRD analysis showed that
the binding process has done no phase change in GO.FT-IR proved the formation of such
GO−O−Si bonds. 2 hour was determined as the optimal time for immobilization and the
maximum amount of immobilized protein was 34.8 mg per gram of support.
Keywords: Immobilization, Graphene oxide, Nanosheets, Human serum albumin.
HTTP://UI.CNF.IR/PPS 253
A combined spectroscopic and molecular docking approaches to
probing binding of daidzein to β-lactoglobulin
Parisa Hatami, Najme .Fani, Abdol Khalegh Bordbar
Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Abstract
In the present study, the molecular mechanism of daidzein binding to β -lactoglobulin (BLG)
(variants A and B) was investigated by fluorescence quenching, absorption spectroscopy and
molecular docking procedures. Analysis of spectrofluorimetric titration data represented the
formation of 1:1 complex, significant binding affinity, negative value of enthalpy change and
positive value for entropy change and the essential role of hydrogen bonding and van der Waals
interactions in binding of daidzein to BLG. The value of determined Förster΄s distance represents
the static mechanism for quenching of BLG by daidzein. The results of fluorescence competitive
binding expriments characterize the location of daidzein binding site in the outer surface of BLG.
Molecular docking study showed that daidzein binds in the outer surface site of BLG which is
accompanied with some hydrogen bonds. The support of molecular docking results by
biochemical fluorescence experiments confirms the validity of docking calculation.
Keywords: β -lactoglobulin, Daidzein, Fluorescence quenching, Molecular docking,
Thermodynamics parameters.
HTTP://UI.CNF.IR/PPS 254
VEGF-A epitope prediction aim to exploiting in angiogenesis
stimulation in order to tissue restoration using magnetic
nanoparticles Sadegh Khorrami and Hasan Mohabatkar
Faculty Of New Sciences & Technology, University Of Isfahan.
Abstract
Vascular endothelial growth factor was discovered in 1987. Different isoforms of each VEGF
molecule are generated by alternative splicing mechanism. In the meantime VEGF-A is a
dimeric glycoprotein isoform that plays a significant role in the regulation of angiogenesis.
Probably, using magnetic nanoparticle we can target short peptides sequence of this factor
(epitopes) to many goals, such as tissues being destroyed in order to stimulate angiogenesis and
restoration them. For this aim, determination of the protein amino acid sequence and prediction
of epitopes are necessary. Epitopes are of particular interest to both clinical and basic biomedical
researchers as they hold huge potential for vaccine design, disease prevention, diagnosis, and
treatment. Nowadays bioinformatics approaches play a vital role on analyzing amino acid
sequence to select the protective epitopes. In this study VEGF-A amino acidic sequence was
selected from protein data base of NCBI (Accession: NP_001028928.1). Using ExPASy tools,
ProtParam and GOR-4, their physical and chemical parameters and secondary structure
prediction of this Protein were investigated respectively. Then epitope prediction based on
hydrophilicity, flexibility/mobility, accessibility, polarity, exposed surface and turns of each
region were performed by BcePred. According to result, this protein hase 371 amino acids
residue and consist of 18 % extended strand, 28.8 % alpha helix and 56 % random coil. Also B
cell epitope prediction shows in this sequence there are two main epitopes region that are gained
the higher value compared to others: (1) from 98the residue to 103the, EEEKEE, this region is
located in an alpha helix structure. (2) From 160the residue to 165the, PHSPSR, this sequence is
located in random coil region. Hence these peptides have the potential that after practical
experiments are conjugate with magnetic nanoparticles and exploit to stimulate angiogenesis in
tissues being destroyed.
Kaywords: Epitope prediction, VEGF-A, Magnetic nanoparticles, Tissue restoration.
HTTP://UI.CNF.IR/PPS 255
Molecular docking study of HCV proteins with phytochemical
compounds from Prangos uloptera DC
Parisa Dehghani, Masoomeh Alamdaran Mokhtar Nosrati, Mostafa Salehi Rozveh
Department of Biotechnology, Faculty of Advanced Science, University of Isfahan, Iran.
Abstract
Because of high virulence and medicinal resistance of HCV virus during the last decades, many
investigations have been performed to discover and the introduction of anti-HCV drugs. The
results of numerous researchers have been shown that plant derivatives, may control HCV
infection very effectively. The aim of this research is the Bioinformatics study of HCV proteins
(E1, E2) inhibition by phytochemical compounds from Prangos ferulacea plant.In the present
study, the 3D structure of P.uloptera compounds, and HCV proteins was retrieved from the
PubChem and proteins Data Bank (PDB) respectively. After that, molecular docking was
performed by Molegro 5.5 software. The result confirmed that phytochemicals from P. uloptera
especially Alfa-pinion and D-germacrene had appropriate and strong interaction with E1 and E2
protein. Finally, based on the results P. uloptera could be the good candidate for HCVtretment
and more in vitro and invivo investigation about most effective compounds.
Keywords: Molecular docking, HCV, Hepatitis C, E1 and E2proteins, Prangos uloptera.
HTTP://UI.CNF.IR/PPS 256
Investigation the antibacterial effect of peptides derived from cow's
milk protein (caseinate) hydrolysis by lactic acid bacteria
Reihane kordesedehi and Asghar taheri
Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.
Abstract
Milk is an excellent source of well balanced nutrients and also exhibits a range of biological
activities. Bioactive peptides have been defined as specific protein fragments that have a positive
impact on body functions or conditions and may ultimately influence health. The beneficial
health effects may be classified as antimicrobial, antioxidative, antithrombotic, antihypertensive
and immunomodulatory. Bioactive peptides can be generated during milk fermentation by the
proteolytic activity of lactic acid bacteria starter cultures. Antibacterial peptides have been
derived from milk proteins , lactoferrin, α- S 1 - casein , α-S2 - casein , k- casein ,a -lactalbumin ,
b- lactoglobulin , and lysozyme .These peptides have been found to be active against a broad
range of pathogenic organisms .With the rise of consumer concerns about the deleterious effects
of chemical preservatives and the increasing preference for natural components, bioactive
peptides have the potential to be used in the formulation of health enhancing nutraceuticals for
food preparations .Addition of these peptides to food products could improve consumer safety as
a result of their antimicrobial properties. In this investigation we show that peptides obtained
after hydrolysis of milk proteins(caseinate) by lactic acid bacteria isolated from Iranain cow's and camel's milk sampels have a high antibacterial activity (zone of inhibition) against E.coli,
salmonella and shigella only after 24-h growth.
Keywords: Antibacterial effect, Peptides, Milk protein, Lactic acid bacteria.
HTTP://UI.CNF.IR/PPS 257
Immobilization of human serum albumin protein on metal-organic
framework material
Atefe Zare and Abdol Khalegh.Bordbar
Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
Abstract
In this study, one of the metal-organic frameworks, MIL-101-NH2(Cr), was synthesized by
solvothermal method and functionalized with 2,4,6-trichloro-1,3,5-triazine (TCT) and used for
covalent immobilization of human serum albumin (HSA). The effect of protein concentration
and the immobilization time for this process were examined and the values of 3 hour and 88.6
mg were obtained for optimal time and maximum amount of immobilized protein on a gram of
support, respectively. The immobilization was confirmed by Bradford method and Fourier
transforms infrared spectroscopy (FT-IR).
Keyword: HSA, Covalent immobilization, Metal-organic framework.
HTTP://UI.CNF.IR/PPS 258
Investigation the antibacterial effect of peptides derived from cow's
milk protein (Betalactaglobulin) hydrolysis by lactic acid bacteria
Rezvan Kazemi and Asghar taheri
Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.
Abstract
Milk is an excellent source of well balanced nutrients and also exhibits a range of biological
activities. Bioactive peptides have been defined as specific protein fragments that have a positive
impact on body functions or conditions and may ultimately influence health. The beneficial
health effects may be classified as antimicrobial, antioxidative, antithrombotic, antihypertensive
and immunomodulatory. Bioactive peptides can be generated during milk fermentation by the
proteolytic activity of lactic acid bacteria starter cultures. Antibacterial peptides have been
derived from milk proteins , lactoferrin, α- S 1 - casein , α-S2 - casein , k- casein ,a -lactalbumin ,
b- lactoglobulin , and lysozyme .These peptides have been found to be active against a broad
range of pathogenic organisms .With the rise of consumer concerns about the deleterious effects
of chemical preservatives and the increasing preference for natural components, bioactive
peptides have the potential to be used in the formulation of health enhancing nutraceuticals for
food preparations .Addition of these peptides to food products could improve consumer safety as
a result of their antimicrobial properties. In this investigation we show that peptides obtained
after hydrolysis of milk proteins(β-lactaglobulin) by lactic acid bacteria isolated from Iranain
cow's milk sampels have a high antibacterial activity (zone of inhibition) against E.coli,
salmonella and shigella only after 24-h growth.
Keywors: Antibacterial effect, Peptides, Milk protein, Lactic acid bacteria.
HTTP://UI.CNF.IR/PPS 259
Prediction of post-translational glycosylation of proteins
Masoomeh Alamdaran, Parisa Dehghani, Hassan Mohabatkar
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Abstract
Post translational modifications (PTMs) occur in the vast majority of proteins and are essential
for their functions. Most of the PTMs come in the form of proteolytic cleavage events or
covalent modifications at specific amino acid residues. One of the PTMs is protein glycosylation
which can be divided into four main categories mainly depending on the linkage between the
amino acid and the sugar. These are N-linked glycosylation, O-linked glycosylation, C-
mannosylation and glycophosphatidly inositol (GPI) anchors attachments. N-glycosylation is
characterized by the addition of a sugar to the amino group (NH2) of an asparagine. In O-
glycosylation, a sugar is attached to the hydroxyl group (OH2) of a serine or threonine. GPI
anchors refer to glycophosphatidyl-inositol groups attached near the C-terminal of a protein
chain that anchor the protein to the cell membrane. Identification of pair wise patterns
surrounding glycosylation sites and their usage in measure of ratio can be performed to weight
their propensity of association with modified residues. One of the new PTM prediction
programs is GPP (glycosylation prediction program), which predicts glycosylation sites with an
accuracy of 90.8% for serine sites, 92.0% for threonine sites and 92.8% for asparagine sites. This
is significantly better than other glycosylation predictors. GPP is available online at
http://comp.chem.nottingham.ac.uk/glyco/.
Keywords: Post-translational modification, Glycosylation, Glycosylation prediction program.
HTTP://UI.CNF.IR/PPS 260
Effectiveness of a number of natural product in improving viability
of probiotic bacteria in Iranian diary product
Afouz Khalili Samani and Asghar Taheri-Kafrani
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Abstract
Recognized to confer health benefits to consumers, probiotics such as Lactobacillus acidophilus
are commonly incorporated into fermented dairy products; among which yogurt is a popular
delivery vehicle. To materialize most of the putative health benefits associated with probiotics,
an adequate amount of viable cells must be delivered at the time of consumption. However, the
loss in their viabilities during refrigerated storage has been demonstrated previously. This study
focused on the effects of a number of natural product like citrus extract, Saffron extract, and
tomato extract in improving viability of probiotic bacteria in Iranian diary product such as yogurt
and cheese. For this purpose, inoculated samples were incubated aerobically at 42°C until milk
coagulation. Samples were examined for biomass and pH changes. Cell viability and post-
acidifying activity of strains were measured. The viability of yoghurt and probiotic bacteria was
assessed during manufacture and 35 days storage of yoghurt supplemented with four levels of
extracts, using four commercial starter cultures.
Keywords: Dairy product, Improving viability, Probiotic bacteria, Lactic acid bacteria.
HTTP://UI.CNF.IR/PPS 261
Effect of Polyoxometalates (POMs) on glioblastoma cancer cells
Laleh Ranjbaran1, Raheleh Masoudi1, Marjan Moghayedi2, Elaheh K.Goharshadi3
1Biology Department, College of Sciences, Shiraz University, Shiraz, Iran.
2 Department of Chemistry, Ferdowsi University of Mashhad, International Campus, Mashhad, Iran.
3 Department of Chemistry, Ferdowsi University of Mashhad, Mashhad 91779, Iran.
Abstract
Polyoxometalates (POMs) are stable metal-oxide inorganic compounds, which have shown a
great potential of antitumor and antiviral activities.The aim of this study was to investigate the
effects of POMs on glioblastoma cancer cell lines’ viability. For this aim, we treated the cells
with different concentrations of several POMs such as H3PW12O40, H3PMo12O40 and
H4SiW12O40and determined the viability of the cellsusing MTTassay. Our results showed that
POMs compoundshave different effects on the glioblastomacells. It was found that higher
concentrations of H3PMo12O40 are able to reduce the cancer cell survival while the two other
compounds did not show any effect on these cells.We conclude that POMs might be effective
compounds for treatment of glioblastoma.
Keyword: Polyoxometalates (POMs), Glioblastoma, Cell viability, Cancer.
HTTP://UI.CNF.IR/PPS 262
Prediction of phosphorylation sites of proteins from their amino
acid sequence
Parisa Rabiei and Hasan Mohabatkar
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Abstract
Post translational modification (PTMs) are of the most important modifications that can
significantly regulate the functionality of proteins. Glycosylation, methylation, hydroxylation,
phosphorylation and ubiquitylation are the most common PTMs than can control the metabolism
and activity of a cell. Experimentally, identification of PTMs is done by mass spectrometery
(MS) which is a very expensive and time consuming approach. Therefore, a computational
method based on a reliable dataset is demanded for in silico prediction the PTM of proteins from
their amino acid sequences. In the term of prediction several parameters are introduced to
evaluate the performance of these tools such as Sensitivity (Sn), Specificity (Sp), Matthew’s
correlation coefficient (MCC) and Accuracy(Acc) which are measured based on the number of
false positive (FP), false negative (FN), true positive (TP) and true negative (TN) predictions.
Additionally, to increase the evaluation efficiency of the predictions, some factors are important,
like having a valid training and testing datasets, using the appropriate and powerful algorithms or
operation engines, and performing a cross-validation test to examine the reliability of the server.
In this study, it is attempted to investigate and compare the state-of-the- art servers which present
user-friendly prediction tools for phosphorylation, such as PhosphoBase ELM, PhosphoSite,
NetPhosK and PhosphOrtholog. In addition their accuracy, specificity and sensitivity are
declared and discussed.
Keyword: Post translational modification, Phosphorylation, Prediction servers.
HTTP://UI.CNF.IR/PPS 263
Functionalized superparamagnetic graphene oxide nanoparticles as
a matrix for glucose oxidase immobilization
Mahkame Amirbande and Asghar Taheri-Kafrani
Department of Biotechnology, Faculty of Advanced Sciences and technologies, University of Isfahan, Isfahan, Iran.
Abstract
Glucose oxidase (β-D-glucose: oxygen 1-oxidoreductase; GOD) catalyzes the oxidation of β-D-
glucose to gluconic acid using oxygen as an electron acceptor. Nowdays, glucose oxidase is
receiving a lot of attention due to its extensive applications in pharmaceutical, food, beverage,
chemical, clinical chemistry, biotechnology and other industries. Superparamagnetic graphene
oxide nanoparticles were synthesised and then functionalized with cyanuric chloride to create a
biocompatible matrix for glucose oxidase immobilization. The structure attributes of the
immobilized glucose oxidase and support were characterized by transmission electron
microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared spectra
(FTIR), thermo-gravimetric analysis (TGA) and vibrating sample magnetometer (VSM) analysis.
These nanoparticles were improved the optimum conditions of immobilized enzyme rather than
free enzyme such as storage stability, thermostability, catalytic activity, pH dependence and the
half-life of an enzyme. Also, the apparent Km and ν max for free and immobilized glucose
oxidases were estimated. All these results reflects the success of the immobilization process.
Keywords: Glucose oxidase, Superparamagnetic graphene oxide, Cyanuric chloride,
Immobilization, Catalytic activity.
HTTP://UI.CNF.IR/PPS 264
Immobilization of glucose oxidase on superparamagnetic/chitosan
nanoparticles
Mahkame Amirbande and Asghar Taheri-Kafrani
Department of Biotechnology, Faculty of Advanced Sciences and technologies, University of Isfahan, Isfahan, Iran.
Abstract
Glucose oxidase enzyme (GOD) is an oxido-reductase that catalyses the oxidation of glucose to
hydrogen peroxide and D-glucono-δ-lactone. This enzyme was covalently immobilized onto
superparamagnetic chitosan nanoparticles using cyanuric chloride (CC), forming (SPCh-CC).
The size of the chitosan functionalized magnetic nanoparticles was measured using X-ray
diffraction (XRD) pattern and transmission electron microscopy (TEM). The enzyme activity
assays of the obtained bioconjugate showed an enhanced thermostability and pH-dependence
treatment in contrast with that of free glucose oxidase. The immobilized GOD maintained more
than half of its initial activity after 10 cycles. The free and immobilized glucose oxidase kinetic
parameters (Km and νmax) were determined by Michaelis-Menten equation and the results showed
an improvement in kinetic parameters. The results of this study showed that SPCh-CC
nanocarriers can be an ideal option for immobilization of glucose oxidase.
Keywords: Glucose oxidase, Superparamagnetic chitosan nanoparticle, Cyanuric chloride,
Enzyme activity.
HTTP://UI.CNF.IR/PPS 265
Comparing the physiochemical properties and alpha helix
percentages of different organisms’ Lactate dehydrogenases by
bioinformatics tool
Afrouz Khalili Samani, Parisa Rabiei and Hasan Mohabatkar
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Abstract
Lactate dehydrogenase (LD) has a significant role in metabolism, and is found nearly in all kind
of cells. LD converts the lactate to pyruvic acid reversibly by catalyzing the NAD+ to NADH in
the absence of O2. In this study, 20 sequences among different geniuses, including Lactobacillus
casei, Lactobacillus delbrueckii, Enterococcus faecium, Rhizopus oryzae, Amylomyces rouxii
and Homo sapiens were selected to compare properties. For this analysis Protparam was applied
which is a useful tool that represents the physiochemical features of proteins and is available at
(http://web.expasy.org/protparam/protparam-doc.htm). Furthermore, the secondary structure of
proteins was predicted using GOR4 (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=
npsa_gor4.html). A number of parameters including molecular weight (MW), isoelectric pH (pI)
and the percentage of alpha helix and cystein were measured and the respective diagrams were
drawn. Based on the results and diagrams, although, there is no evidence of significant
differences in the MW, alpha helix percentage and pI between lower to higher geniuses, the most
similarity was seen intrageniusly.
Keyword: Lactate dehydrogenase, Protparam, Physiochemical features, GOR4
HTTP://UI.CNF.IR/PPS 266
Studying the effect of changing the micro/nano roughness and
wettability of polypropylene (PP) films on the protein adsorption
Elham Shirani and Amir Razmjou
Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.
Abstract
Fouling is a result of the combination of sieving and the adsorption of particulates and
compounds onto a surface. Recently, the development of new materials or the
surface modification of sample to make them less prone to fouling has become a point of interest
for both researchers and industry. These new antifouling samples can be generated through either
anti-adhesion or anti-microbial approaches. In the anti-adhesion approaches, the surface
architecture of samples is changed to prevent or reduce the adsorption of foulants via changing
the roughness and the wettability or incorporating fouling release agents. The anti-microbial
approaches are based on killing the organisms, and suppressing the biofilm formation by
disrupting bacterial colonizations. Shifting the wettability of the surface toward
superhydrophobicity could reduce the interaction between feed water solution and surface
thereby reducing the risk of fouling. Considering the fact that protein adsorption is known as the
first stage of biofilm formation, reducing the protein adsorption is the key factor of excluding
biofilm formation. In this work, an attempt has been made to create
a superhydrophobic polypropylene (PP) surface with water contacts angle of above 150°. The PP
films were characterized by SEM, EDAX, AFM, contact angle goniometry, surface free energy,
Bradford and biofilm formation assay. Results showed a significantly low protein adsorption and
biofilm formation on the modified superhydrophobic surfaces. It should be pointed out here that
this modification promise a widespread application of PP sheets on industry and medicine fields.
Keywords: Protein adsorption, Biofilm formation, Superhydrophobicity, Bradford assay.