5 VISEGRAD SYMPOSIUM ON STRUCTURAL SYSTEMS BIOLOGY · 5th VISEGRAD SYMPOSIUM ON STRUCTURAL SYSTEMS...

5th VISEGRAD SYMPOSIUM ON

STRUCTURAL SYSTEMS

BIOLOGY

PROGRAM & ABSTRACTS

17th- 20th June 2015

Szeged

Hungary

1

2

Organization

Department of Chemical Informatics, University of Szeged

Partners

Institute of Nanobiology and Structural Biology Global Change Research Centre Academy of Sciences of the Czech Republic Comenius University Bratislava University of Warsaw Jagellonian University in Krakow Medical University of Vienna Academy and University Center of Nove Hrady Infrastructure for System Biology Europe

Scientific Organizing Committee Babak Minofar

Rüdiger Ettrich

David Řeha,

Ján Urban

Béla Viskolcz

Imre G. Csizmadia

Thomas Stockner

Marta Pasenkiewicz-Gierula

Joanna Sułkowska

Local Organizing Team Béla Viskolcz

Imre G. Csizmadia

Csaba Hatvani

Anita Rágyanszki

János J. Szórád

Balázs Jójárt

Milán Szőri

3

5th Visegrad Symposium on Structural System Biology program Wednesday June 17 10.00-18.00 Registration

13:30-13:45 Béla Viskolcz: Conference opening

13:45-14:00 Imre G. Csizmadia: Past, present and future of V4 Opening session Chairperson: Richard Buchner 14:00-14:45 Maxim Fedorov (Glasgow): Modelling solvation properties of bio-active

molecules by molecular theory: achieving chemical accuracy 14.45-15:30 Pál Jedlovszky (Budapest): Effect of anaesthetics on the properties of a lipid

membrane in the biologically relevant phase. A computer simulation study 15:30-16:15 Joanna Sułkowska (Warsaw): Free energy landscape of protein with

complex topology, Tadpoles: new entangled motifs in proteins

16:15-16:30 Coffee break

1st Session Chairperson: Babak Minofar 16:30-17:00 Christian Schröder (Vienna): Computational dielectric spectroscopy of

proteins in various solvents 17:00-17:30 Richard Buchner (Regensburg): Dielectric Spectroscopy of Hydration and

Ion Binding 17:30-18:00 Svend Knak Jensen (Aarhus): The quest for methane on Mars – Methane as

a biomarker for past or present life

19:00 - Welcome party, buffet dinner (Jósika Pince)

Thursday June 18 2nd Session Chairperson: Jost Ludwig 09:00-09:30 Michelle A. Sahai (London): Exploring a Common Thread between

Addiction and Disease: The Dopamine Transporter 09:30-10:00 Michael C. Owen (Jülich): The Study of Oxidative Stress in

Alzheimer's Disease: A Theoretical Approach 10:00-10:30 Pavel Grinkevich (Nové Hrady): Structure and function of C-terminal

helical domain of the motor subunit HsdR from the type I restriction-modification system EcoR124I


3rd Session Chairperson: Joanna Sułkowska 11:00-11:30 Giorgia Brancolini (Oristano): Computational Strategies for

Amyoloidogenic Proteins interacting with Gold Nanoparticles 11:30-12:00 Jost Ludwig (Nové Hrady): The roles of conserved residues in the

Saccharomyces cerevisiae K+-translocation protein Trk1 analyzed by theoretical and experimental approaches

12:00-12:30 Ben Luisi (Cambridge): The structure and mechanism of a molecular

4

machine of drug transport 12:30-12:45 Anita Rágyanszki (Szeged): Analytical functional representation of quantum

chemical potential energy curves and surfaces

12:45-14:00 Lunch

4th Session Chairperson: Ján Urban

14:00-14:30 James J. Valdés (České Budějovice): Ticks as venomous animals: a

pharmacological perspective

14:30-15:00 Szilárd Fejér (Szeged): Cooperative rearrangements in clusters of anisotropic

particles

15:00:15.30 Nacer Idrissi (Oran): Luteolin- organic solvent interactions. A

moleculardynamics simulation analysis

15:30-16:00 Coffee break 5th Session Chairperson: Giorgia Brancolini 16:00-16:30 Milan Melicherčí: Changes induced by ligand binding to arginine repressor

from Bacillus subtilis

16:30-17:00 Stefan Balint (Timisoara): Prediction of the pollution due to a pesticide

17:00-17:30 Imre Jákli (Budapest): Extraordinary thermal stability of Trp-cage

miniproteins observed by chiroptical and NMR spectroscopy

18:00 - Dinner, Freetime Activities, Walk around Town, Poster Session

Friday June 19 6th Session Chairperson: Ben Luisi

09:00-09:15 Balázs Fábián (Budapest): Floating Patches of HCN at the Surface of Their

Aqueous Solutions – Can They Make “HCN World” Plausible?

09:15-09:30 Zsófia Borbála Rózsa (Szeged): Mapping out the 366 shades of the C4H8O2

isomers

09:30-10:00 Caroline Lynn Kamerlin (Uppsala):


7th Session Chairperson: Caroline Lynn Kamerlin

10:30-11:00 Ján Urban (Bratislava): Computational study concerning RNA or DNA

aptamers

11:00-11:30 Sebastian Kmiecik (Warsaw): Protein-peptide docking with significant

conformational changes and without prior knowledge of the binding site using

the CABS-dock web server

11:30-12:00 Balázs Jójárt (Szeged): MODYDB – just an other database?

5

12:30-13:30 Lunch

8th Session Chairperson: Nacer Idrissi 13:30-13:45 Lily Hunnisett (Szeged): The Cannabinoids: Does Cooperative Interplay

Underlie Their Therapeutic Nature? 13:45-14:15 Piotr Setny (München): Hydration in discrete water - from bulk free energies

to localised water molecules 14:00-14:30 Giancarlo Franzese (Barcelona): How water contributes to pressure and

cold denaturation of proteins

15:30-18:30 Trip around Szeged finished at the Monastery

20:00 - Conference dinner at the Monastery

Saturday June 20

Morning Departure

6

Abstracts of oral presentations

The authors of the abstracts bear the full responsibility for the scientific and

linguistic content.

7

Modelling solvation properties of bio-active molecules by molecular

theory: achieving chemical accuracy

Maksim Misin1, David S. Palmer2, Maxim V. Fedorov1* 1Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow, G4 0NG, UK

2Department of Pure and Applied Chemistry, University of Strathclyde, 16 Richmond Street, Glasgow, G4 0NG,

UK

Corresponding author: [email protected]

Keywords: Free energy, solvents, integral equations, chemical potential, correlation functions.

Molecular integral equations theories (IETs) provide an alternative way to molecular simulations

to calculate properties of biomolecular solvation [1,2]. In this report we will overview recent

developments in IETs with particular focus on IET-based methods for predicting thermodynamic

properties of bioactive molecules.

We recently developed a new model for computing hydration free energies based on the 3D

Reference Interaction Site Model (3D-RISM) [3]. The new adjustment to 3D-RISM theory

significantly improves hydration free energy predictions for various classes of organic molecules

at both ambient and non-ambient temperatures. An extensive benchmarking against experimental

data shows that, at least for uncharged compounds, the accuracy of the model is comparable to

(much more computationally expensive) molecular dynamics simulations.

Accuracy of predictions of other properties (aqueous solubility, octanol-water partition

coefficients, caco-2 cell permeability) by IET-based methods will be also discussed.

References

[1] E.L. Ratkova, D.S. Palmer and M.V. Fedorov, Chem. Rev., 2015, available online, DOI:

10.1021/cr5000283.

[2] D.S. Palmer, A.I. Frolov, E.L. Ratkova and M.V. Fedorov, Molecular Pharmaceuticals, 2011,

8, 1423-1429.

[3] M. Misin, M.V. Fedorov and D.S. Palmer, J. Chem. Phys., 2015, 142, 091105.

mailto:[email protected]

8

Effect of anaesthetics on the properties of a lipid membrane in the

biologically relevant phase. A computer simulation study

Balázs Fábián1, Mária Darvas2, Sylvain Picaud3, Marcello Sega4, and Pál

Jedlovszky1,5,6

1Institute of Chemistry, ELTE University, Budapest, Hungary 2SISSA, Sector of Molecular and Statistical Biophysics, Trieste, Italy

3Institut UTINAM Université de Franche-Comté, Besançon, France 4Institut für Computergestützte Biologische Chemie, University of Vienna, Austria

5MTA-BME Research Group of Technical Analytical Chemistry, Budapest, Hungary 6EKF Department of Chemistry, Eger, Hungary

Molecular dynamics simulations of the fully hydrated neat dipalmitoylphosphatidylcholine

(DPPC) membrane as well as DPPC membranes containing four different general anaesthetic

molecules, namely chloroform, halothane, diethyl ether and enflurane have been simulated at two

different pressures, i.e., at 1 bar and 1000 bar, at the temperature of 310 K. At this temperature

the model used in this study is known to be in the biologically most relevant liquid crystalline

(L) phase. To find out which properties of the membrane might possibly be related to the molecular

mechanism of anaesthesia, we have been looking for properties that change in the same way in

the presence of any general anaesthetic molecule, and change in the opposite way by the increase

of the pressure. This way, we have ruled out the density distribution of various groups along the

membrane normal axis, orientation of the lipid heads and tails, self-association of the

anaesthetics, as well as the local order of the lipid tails as possible molecular reasons of

anaesthesia. On the other hand, we have found that the molecular surface area, and hence also the

molecular volume of the membrane is increased by the presence of any anaesthetic molecule, and

decreased by the pressure, in accordance with the more than half a century old critical volume

hypothesis. We have also found that anaesthetic molecules prefer two different positions along

the membrane normal axis, namely the middle of the membrane and the outer edge of the

hydrocarbon region, close to the polar headgroups. This dual preference is explained by the

interplay of steric and electrostatic effects. The increase of the pressure is found to decrease the

former, and increase the latter preference, and hence it might also be related to the pressure

reversal of anaesthesia.

9

Free energy landscape of protein with complex topology, Tadpoles:

new entangled motifs in proteins

Joanna Sułkowska1

1 Chemistry Department and Center of New Technology, University of Warsaw

Pasteura 1, Warsaw, Poland


We identify new entangled motifs in proteins that we call tadpoles. Tadpoles arise in proteins

with disulphide bridges (or in proteins with amide linkages), when termini of a protein backbone

pierces through an auxiliary surface of minimal area, spanned on a covalent loop. We find that

as much as 18\% of all proteins with disulphide bridges in a non-redunant subset of PDB form

tadpoles, and classify them into five distinct geometric classes. Based on biological classification

of proteins we find that tadpoles are much more common in viruses, plants and fungi than in

other kingdoms of life. During the talk I will also discuss possible functions of tadpoles. Tadpoles

and associated surfaces of minimal area provide new, interesting geometric characteristics not

only of proteins, but also of othery biomolecules, with many potential applications.

10

Computational dielectric spectroscopy of proteins in various

solvents

Christian Schröder, Michael Haberler, Gregor Neumayr, Tibor Rudas, Othmar

Steinhauser

Department of Computational Biological Chemistry, Währingerstrasse 17, A-1090 Vienna (Austria)

Dielectric spectroscopy is a wide-spread used experimental technique to study relaxation in

amorphous media, in particular liquid systems. As compared to nuclear magnetic resonance,

inelastic neutron scattering and similar techniques, dielectric experiments probe the complete

sample, i.e. they measure collective translational and rotational motion in systems governed by

electrostatic forces.

-helices are characteristic for a parallel alignment of peptide dipoles. Therefore, in this case the

collective dipole reaches its maximum value. In contrast, -sheets are typical for dipole

compensation whereas coil structures exhibit a certain residual correlation of dipoles [1-2]. In

addition, the interaction with ions, solvation water and bulk water complicates the dielectric

spectrum of these systems [1-4]. However, in computational dielectric spectroscopy, the overall

frequency-dielectric spectrum can be decomposed into its major contributions which can be

analyzed separately.

In here, we would like to present our results concerning the interaction of ubiquitin with water at

a molecular [1] and mesoscopic resolution [2] as well as solvation shell resolved [3]. Particular

interactions with ionic liquid/water mixtures and their effects on the protein structure and

dynamics are also discussed [4]. In a recent study we combined experimental and dielectric

spectroscopy to investigate the oligomerization of insulin monomers in aqueous solution [5]

showing the importance of pre-aggregated states.

References

[1] C. Schröder, T. Rudas, S. Boresch, and O. Steinhauser „Simulations studies of the protein-

water interface. I. Properties at the molecular resolution”, J. Chem. Phys. 124 (2006), 234907

[2] T. Rudas, C. Schröder, S. Boresch, and O. Steinhauser „Simulations studies of the protein-

water interface. II. Properties at the mesoscopic resolution”, J. Chem. Phys. 124 (2006), 234908

[3] G. Neumayr, T. Rudas, and O. Steinhauser “Global and local Voronoi analysis of solvation

shells of proteins”, J. Chem. Phys. 133 (2010), 084108

[4] M. Haberler, C. Schröder, and O. Steinhauser „Solvation studies of a zinc finger protein in

hydrated ionic liquids“, Phys. Chem. Chem. Phys. 13 (2011), 6924

[5] C. Schröder, O. Steinhauser, P. Sasisanker and H. Weingärtner „Orientational alignment of

amyloidogenic proteins in pre-aggregated solutions“, Phys. Rev. Lett. 114 (2015), 128101

11

Dielectric Spectroscopy of Hydration and Ion Binding

Richard Buchner1

1Institute of Physical and Theoretical Chemistry, University of Regensburg, Regensburg, Germany


Our understanding of the physiological action of many small organic solutes, like urea or TMAO,

in water is still rather patchy. For instance, in the case of urea it is still debated whether its

denaturating effect on proteins arises from direct interaction or through its disturbing effect on

protein hydration [1,2]. Clearly, the balance of hydrophilic and hydrophobic moieties on the

molecule and their respective hydration is of major importance for the behavior of these

substances. Of at least similar relevance is the interaction of biomolecules with ions since the

latter are always present under physiological conditions.

Dielectric relaxation spectroscopy in the microwave region is a convenient tool to study hydration

as well as ion-binding phenomena [3,4]. In particular, this technique can detect various types of

ion pairs and distinguishes between bulk-like, moderately-bound (slow) and “frozen”

(irrotationally bound) water molecules. After a short introduction into the basics of DRS, its

advantages and pitfalls, we will discuss what kind of information can be deduced from dielectric

spectra and how this is linked to results from other techniques. In particular, the connections to

computer simulations and statistical mechanics will be highlighted, focusing on our recent

investigations of aqueous solutions of methylated ureas and of the osmolyte ectoine as examples.

References

[1] Funkner, S.; Havenith, M.; Schwaab, G.; Urea, a Structure Breaker? Answers from THz

Absorption Spectroscopy, J. Phys. Chem. B 116, 13374-13380 (2012).

[2] Hunger, J.; Ottosson, N.; Mazur, K.; Bonn, M.; Bakker, H.J.; Water-mediated interactions

between trimethylamine-N-oxide and urea, Phys. Chem. Chem. Phys. 17, 298-306 (2015).

[3] Buchner, R.; Hefter, G.; Interactions and dynamics in electrolyte solutions by dielectric

spectroscopy, Phys. Chem. Chem. Phys. 11, 8984-8999 (2009).

[4] Rahman, H.M.A; Hefter, G.; Buchner, R.; Hydrophilic and Hydrophobic Hydration of

Sodium Propanoate and Sodium Butanoate in Aqueous Solution, J. Phys. Chem. B 117, 2142-

2152 (2013).


12

The quest for methane on Mars. Methane as a biomarker for past

or present life.

Ebbe N. Bak1, Kai Finster1,2, Per Nørnberg1, and Svend J. Knak Jensen3 1Department of Bioscience, Aarhus University, Denmark

2Stellar Astrophysics Center, Department of Physics and Astronomy, Aarhus University, Denmark 3Department of Chemistry, Aarhus University, Denmark


The observation of methane on Mars is of much interest as it may indicate past or present life on

the planet. The concentration of methane shows a substantial spatial and temporal variation. The

source of methane on Mars is unknown; likewise, a fast destruction mechanism is needed to

understand the observations [1, 2]. Here we present experiments that mimic the wind mediated

erosion of surface material. The erosion creates activated sites that can react with methane and

account for the fast disappearance of methane from the Martian atmosphere [3]. A preliminary

quantum mechanical based mechanism is presented for the reaction of activated material with

methane.

References

[1] C. R. Webster et al., Low Upper Limit to Methane Abundance on Mars. Science 342 355-356

(2013)

[2] C. R. Webster et al., Mars methane detection and variability at Gale crater. Science 347 415-

417 (2015)

[3] S. J. K. Jensen et al., A sink for methane on Mars? The answer is blowing in the wind. Icarus

236 24-27 2014


13

Exploring a Common Thread between Addiction and Disease: The

Dopamine Transporter

Dr. Michelle A. Sahai1

1 University of Roehampton, Whitelands College, Holybourne Avenue, London, SW15 4JD, United Kingdom


Dopamine neurotransmission has been the subject of research for nearly half a century. However,

it was not until the late eighties, when it was implicated with the reinforcing effects of cocaine,

that the dopamine transporter (DAT) was identified as a potential target for pharmacological

treatments of cocaine abuse. Despite intensive pharmacological investigations, no effective

pharmacotherapy for cocaine abuse has demonstrated efficacy for long-term use, but tremendous

scientific advances have been made toward understanding DAT and its role in a variety of

neurological disease states and disorders. This includes Parkinson’s disease, schizophrenia,

attention-deficit/hyperactivity disorder and drug abuse [1, 2]. With the aid of sophisticated

mathematical/molecular modelling methods such as Quantitative Structure-Activity Relationship

models (QSAR) and molecular dynamics simulations we aim to assess novel psychoactive

substances (NPS) as potential treatments for the stimulant effects of cocaine in DAT. The results

that characterise the stimulant potential of the screened NPS will be compared with those derived

from the so-far used experimental techniques, such as autoradiography and voltammetry [3].

References

[1] F. H. Hansen, T. Skjørringe, S. Yasmeen, N. V. Arends, M. A. Sahai , K. Erreger, T. F.

Andreassen, V. Neergheen, M. Karlsborg, A. H. Newman, S. Pope, S. Heales, L. Friberg, L. H.

Pinborg, C. Loland, L. Shi, H.Weinstein, A. Galli, L. E. Hjermind, L. B. Møller and U. Gether.

Missense dopamine transporter mutations associate with adult parkinsonism and ADHD, J. Clin.

Invest . 124(7); 3107-3120. (2014)

[2] P. J. Hamilton, N. G. Campbell, S. Sharma, K. Erreger, F. H. Hansen, C. Saunders, A. N.

Belovich, NIH Autism Seq. Consort., M. A. Sahai , E. H. Cook, U. Gether, H. S. Mchaourab, H.

J. G. Matthies, J. S. Sutcliffe and A. Galli. De novo mutation in the dopamine transporter gene

associates dopamine dysfunction with autism spectrum disorder, Mol. Psychiatry. 18(12); 1315-

1323. (2013)

[3] M. Sahai, V. Barrese, N. Dutta, J. Opacka-Juffry and C. Davidson. The benzofuran 5-MAPB

(1-(benzofuran-5-yl)-n-methylpropan-2-amine) binds to the dopamine transporter and prolongs

dopamine efflux in rat nucleus accumbens. (in preparation)

14

The Role of Oxidative Stress in Alzheimer's Disease: A Theoretical

Approach

Michael C. Owen1, Waldemar Kulig2, Ilpo Vattulainen2, and Birgit Strodel.1,3

1 Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich,

Germany

2 Department of Physics, Tampere University of Technology, Tampere, Finland

3 Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf,

Germany


Alzheimer’s disease (AD) is the most common form of dementia in the elderly. In AD, the

amyloid-β peptide (Aβ) has been identified as a clinical hallmark in its disease pathology. A

conformational transition of the native Aβ peptide conformation into a β-sheet-rich state results

in the formation of toxic oligomers, which is believed to be a crucial event in the initiation of

AD. Aβ has been shown to induce pore formation in neuronal membranes, which subsequently

disrupts neuronal Ca2+ ion homeostasis [1]. However, neither the relationship between the

conformational change and oligomerization nor that between Aβ-membrane interactions and pore

formation are properly understood. Free radicals, produced either by A, respiration, or the

Fenton reaction, can oxidize the lipids that form the plasma membrane, a result which has shown

to promote A-membrane interactions. Meanwhile, free radicals have also been shown to abstract

hydrogen from the C of Gly and Ala residues, which initiated the to unfolding of oxidized

model peptides [2,3].

In an effort to dilineate the role of oxidation AD pathology we monitored the changes to the

structure of oxidized A peptides in different solvents and a bilyer comprised of oxidized 1-

palmitoyl-2-oleoylphosphatidylcholine (POPC) and cholesterol using MD simulations. An

oxidized Gly25 caused A to form -sheets in a solvent-dependent manner, whereas oxidized

POPC affected the membrane curvature, bilayer thickness, and the area per lipid in a dose-

dependent manner. These ongoing studies are an attempt to dilineate the role of oxidative stress

in the pathology of AD as it relates to A conformational change and A-membrane interactions.

References

[1] J. Nasica-Labouze, et al. Amyloid protein and Alzheimer's disease: When computer

simulations complement experimental studies. Chem. Rev. 115, 3518-3563 (2015).

[2] M. Owen, B. Viskolcz, I. G. Csizmadia. Quantum chemical analysis of the unfolding of a

penta-alanyl 310-helix initiated by HO, HO2 and O2-. J. Phys. Chem B 115, 8014-8023 (2011).

[3] M. C. Owen, M. Szori, I. G. Csizmadia, B. Viskolcz Conformation-dependent OH/H202

hydrogen abstraction reaction cycles of Gly and Ala residues: A comparative theoretical study.

J. Phys. Chem. B 116, 1143-1154 (2012).

15

Structure and function of C-terminal helical domain of the motor

subunit HsdR from the type I restriction-modification system

EcoR124I

Pavel Grinkevich1,2, Amanda Li3, Tatsiana Baikova1,2, Mikalai Lapkouski1, Alena

Guzanova4, Eva Csefalvay1,2, Marie Weiserova4 and Rüdiger Ettrich1,2 1 Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Nove

Hrady, Czech Republic 2 Faculty of Sciences, University of South Bohemia, Czech Republic

3 Chemistry Department, Princeton University, Princeton, New Jersey, USA 4 Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic

The structure of the HsdR subunit of EcoR124I [1] suggests that the motor subunit is a planar

array of four functionally integrated domains, with the fourth, C-terminal domain being all helical

and implied to play a role in complex assembly and/or DNA binding. However, the last 150

amino acids of this domain are unresolved in the crystal structure.

A single point mutation lead to a new crystal structure that allowed to trace the backbone of the

unresolved C-terminal residues, and homology and energetic modeling was applied to generate

an all-atom 3-D model of wild-type HsdR, complemented by in vivo and in vitro studies to

establish the function of the helical domain.

In vitro DNA cleavage assays, gel mobility shift assays and in vivo restriction tests were

performed on the wild-type and mutant HsdRs with selectively deleted parts of the helical

domain. In addition, further techniques, such as screening for stably expressing HsdRs with

Exoluclease III mediated random-length deletions of N-terminus, and the fusion of HsdR’s C-

terminus with green fluorescent protein, are being developed in effort to obtain a higher-

resolution crystal structure.

Our results strongly support the role of the C-terminal domain of HsdR in subunit interaction and

demonstrate the importance of the C-terminus in complex assembly.

Reference

[1] M. Lapkouski, S. Panjikar, P. Janscak, I. Kuta Smatanova, J. Carey, R. Ettrich, E. Csefalvay,

Structure of the motor subunit of type I restriction-modification complex EcoR124I, Nat Struct

Mol Biol. 16, 94-95 (2009).

16

Computational Strategies for Amyoloidogenic Proteins interactingwith

Gold Nanoparticles

Stefano Corni1 and Giorgia Brancolini1

1CNR-NANO S3, Institute of Nanoscience, via Campi 213/A, 41100 Modena, Italy Corresponding author: [email protected]

Nanoparticles (NPs) are recognized to exhibit distinct physical and chemical properties

compared with the same materials in the bulk form. [1] NPs have been repeatedly reported to interact with proteins, and this interaction can be exploited to affect processes undergone by

proteins, such as fibrillogenesis. Fibrillation is common to many proteins, and in living organisms, it causes tissue-specific or systemic amyloid diseases.

I will review our recent computational modeling advances which were pursued in the quest for a

theoretical framework elucidating the association mechanisms and the ability to design and

control the recognition events of interfaces between amyloidogenic protein and nanoparticles.

The effects of two different systems on 2-microglobulin, namely gold nanoparticles covered with

hydrophilic surfactants and gold nanoparticles functionalized with hydrophobic ligands, are

presented. Recent simulations at multiple levels (enhanced sampling molecular dynamics,

Brownian dynamics, and Poisson_Boltzmann electrostatics) and NMR measurements have

explained the origin of the observed protein perturbations, showing that in the presence of

citrate-capped gold NPs at physiological-like conditions, the interaction is weak and it is not able

to induce protein fibrillation (Fig.1). [2] On the contrary, the interactions with hydrophobic

ligands can block active sites of the protein domain from binding to another protein, thus

potentially inhibiting the fibrillation activity.[3]

The interaction of the gold-nanoparticles with two amyloidogenic variants of 2-microglobulin is

further discussed, namely (a) the truncated N6 and (b) the mutated D76N, and a fibrillization pathway

is proposed. The results offer possible strategies for controlling the desired effect of NPs on the

conformational changes of amyloidogenic proteins, which have crucial roles in the fibrillation

process.[4]

Fig. 1 Monomeric protein interacting with citrate-capped gold nanoparticle: (left) 20 ns of T-REMD

simulations (right) NMR protein signal intensities [1] Kumar et al., 2013. Manual on Critical Issues in Nanotechnology R&D Management: An Asia-

Pacific Perspective. APCTT-ESCAP

[2] Brancolini, G. et al. Nanoscale, 2014, 6, 7903-7911

[3] (i) Brancolini, G. et al. ACS NANO, 2015, 9, 2600-2613 (ii) Brancolini, G. et al. ACS Nano,

2012, 6, 9863-9878

[4] (i) Mangione, P. P. et al., J. Biol. Chem. 2013, 288, 30917-30930 (ii) G. Esposito et al. Subcell

Biochem. 2012, 65, 165-83.

17

The roles of conserved residues in the Saccharomyces cerevisiae

K+-translocation protein Trk1 analyzed by theoretical and

experimental approaches.

Vasilina Zayats, Thomas Stockner, Saurabh Kumar Pandey, Katharina Wörz,

Rüdiger Ettrich, Jost Ludwig

Institute of Nanobiology & Structural Biology, GCRC, v.v i., Nove Hrady, Czech Republic and IZMB / Molecular

Bioenergetics, University of Bonn, Bonn, Germany

Potassium ion (K+) uptake in yeast is mediated mainly by the Trk1/2 proteins that enable cells to

survive on external K+ concentration as low as a few µM. Yeast (and other fungal) Trks are

related to prokaryotic TRK and Ktr and plant HKT K+ transport systems. Based on the (weak)

similarity of these proteins to prokaryotic K-channels, homology models were developed (Durell

& Guy, 1999) after the first K-channel structure was available. Crystal structures of prokaryotic

TrkH and KtrB that are more closely related to yeast Trks were published recently (Cao et al.,

2011, Vieira-Pires et al., 2013) and allowed to develop more precise homology models. Overall

sequence similarity is however very low, thus requiring experimental verification of homology

models. Here a refined structural model of the Saccharomyces cerevisiae Trk1 is presented that

was obtained by combining homology modeling, molecular dynamics simulation and

experimental verification through functional analysis of mutants. The structural models and the

experimental results showed that glycines within the selectivity filter, conserved amongst the K-

translocation protein family are not only important for protein function, but are also required for

correct folding/ membrane targeting. Furthermore, the roles of several conserved charged

residues were analyzed. An earlier proposed interaction was verified and another -yet not

considered- interaction identified that might enhance folding and stability of yeast Trk1. The

model could provide the structural basis for addressing the long standing question if Trk1 is a

passive or active ion-translocation system.

References

[1] S.R. Durell, H.R. Guy, Structural models of the KtrB, TrkH, and Trk1,2 symporters based on

the structure of the KcsA K+ channel, Biophys. J. 77 (1999) 789-807.

[2] Y. Cao, X. Jin, H. Huang, M. G. Derebe, E.J. Levin, V. Kabaleeswaran, Y. Pan, M. Punta, J.

Love, J. Weng, M. Quick, S. Ye, B. Kloss, R. Bruni, E. Martinez-Hackert, W.A. Hendrickson,

B. Rost, J.A. Javitch, K.R. Rajashankar, Y. Jiang, M. Zhou, Crystal structure of a potassium ion

transporter TrkH, Nature 471 (2011) 336-40.

[3] R.S. Vieira-Pires, A. Szolloressi, J.H. Morais-Cabral, The structure of the KtrAB potassium

transporter, Nature 496 (2013) 323–328.

18

Structure and mechanism of a bacterial multi-drug efflux pump

Dijun Du1 , Zhao Wang2, Nathan R. James1 , Jarrod E. Voss1 , Ewa Klimont1 ,

Thelma Ohene-Agyei1 , Henrietta Venter1 , Wah Chiu2 , and Ben Luisi1

1 Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK

2Department of Bichemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA


Microorganisms encode several classes of transmembrane molecular pumps that can expel a wide

range of chemically distinct toxic substances. These machines contribute to the capacity of the

organisms to withstand harsh environments, and they help to confer resistance against clinical

antimicrobial agents. In Gram-negative bacteria, the pumps comprise tripartite assemblies that

actively transport drugs and other harmful compounds across the cell envelope. We describe

recent structural and functional data that have provided insights into the architecture and transport

mechanism of the AcrA-AcrB-TolC pump of Escherichia coli. This multi-drug efflux pump is

powered by AcrB, a member of the resistance/nodulation/cell division (RND) family of

transporters, which are energised by proton electrochemical gradients. Crystallographic data

reveal how a small protein AcrZ is engaged in a concave surface in the transmembrane domain

of AcrB, and we discuss how this interaction may affect the efflux activities of AcrB and other

RND family members.

References

[1] Du, D., Wang, Z., James, N.R., Voss, J.E., Klimont, E., Ohene-Agyei, T., Venter, H. Chiu,

W. and Luisi, B.F. (2014). Structure of the AcrAB-TolC multidrug efflux pump. Nature. 509,

512-515. Doi:10.1038/nature13205

[2] Du, D., van Veen, H.W. and Luisi, B.F. (2015) Assembly and operation of bacterial

tripartite multidrug efflux pumps. Trends in Microbiology . doi:10.1016/j.tim.2015.01.010.

19

Analytical functional representation of quantum chemical potential

energy curves and surfaces

Anita Rágyanszki1, Svend J. Knak Jensen2, Imre G. Csizmadia1, Béla Viskolcz1, 1 Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary

2 Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark


The long term aims for the present research is to find mathematical functions which describe the

folding of the peptide residues. In order to find eventually the solution to solve the protein folding

problem and to build up the conformational network for the folding but it is reasonable to start

with the description of small compounds (I-V), and aim for a bottom up solution.

C

CC

HH

HH

Propane

I

HHH H

C

CC

CC

H

HH

H

H H

HH

HH HH

n-Pentane

II

C

CN

HH

H

NC

O

CC

HH

HH HH O

HIII IV

N-Acetyl-Glycine

N-methylamide

C

CN

H

NC

O

CC

HH

HH HH O

H

N-Acetyl-Alanine

N-methylamide

HH3C

V

C

CN

H

NC

O

CC

HH

HH HH O

H

N-Acetyl-Valine

N-methylamide

CH

CC

H H

H

H H

HH

The aims for the present research:

to achieve a reasonable accuracy of the fitted functions for the folding of the internal rotation

of typical organic functional groups which have only one independent variable [1],

to extend the one dimensional mathematical functions to describe the folding of the molecules

which have two independent torsional angles and they are include peptide bonds [2],

the fitted functions, which are describe the conformational spaces, can be analyzed to obtain

the critical points, minima, transition states and maxima.

References

[1] A. Rágyanszki, A. Surányi, I.G. Csizmadia, A. Kelemen, S. J. K.k Jensen, S. Y. Uysal, B.

Viskolcz. Fourier type potential energy function for conformational change of selected organic

functional groups. Chem. Phys. Lett. 599 (2014) 169–174

[2] A. Rágyanszki, K. Z. Gerlei, A. Surányi, I. G. Csizmadia, A. Kelemen, S. J. K. Jensen, B.

Viskolcz. Big Data reduction by fitting mathematical functions. A search for appropriate

functions to fit Ramachandran surfaces. Chem. Phys. Lett. 625 (2015) 91-97

20

Ticks as venomous animals: a pharmacological perspective James J. Valdés1

1Institute of Parasitology, Biology Centre of ASCR, Branišovská 1160/31 České Budějovice, Czech Republic

37005

Ticks are considered ectoparasites, but, according to the criteria revised by Fry et al. [1], ticks

are venomous animals [2]. Tick saliva contains an arsenal of macromolecules that target host

defense mechanisms to obtain a blood meal. Kunitz peptides are expressed by venomous animals

and are one of the major families encoded in tick salivary glands. Tick salivary Kunitz are diverse

in their primary sequence, but maintain a conserved tertiary structural motif. Some tick salivary

Kunitz modulate an array of targets. We were able to hypothesize on this target promiscuity by

analyzing the molecular dynamics of two Kunitz salivary peptides from two geographically

distinct tick species [3]. Understanding the promiscuity of tick salivary macromolecules may

benefit the drug industry.

Ticks also secrete lipocalins that sequester histamine during blood feeding. By sequestering

histamine, these lipocalins prevent host inflammatory responses by competing with the host’s

native receptor for histamine. Competition for ligand/drug binding between two proteins (or

pharmacological promiscuity) is extensively studied experimentally, but there are no studies on

the all-atom exploration of this competition. A novel method was developed to simulate, visualize

and analyze this competition at the host-tick interface [4] using an algorithm developed at the

Barcelona Supercomputing Center [5]. Pharmacological promiscuity is an obstacle in the drug

industry and simulating the host-tick interface may aid in rational drug design.

References:

[1] Fry, B.G. et al. (2009). The Toxicogenomic Multiverse: Convergent Recruitment of

Proteins Into Animal Venoms. Annu. Rev. Genomics Hum. Genet. 10:483.

[2] Cabezas-Cruz, A., Valdés, J.J. (2014) Are ticks venomous animals? Frontiers in Zoology.

11:47.

[3] Valdés, J.J., et al. (2013). Tryptogalinin is a tick Kunitz serine protease inhibitor with a

unique intrinsic disorder. PLoS ONE. 8(5):e62562.

[4] Valdés, J.J. (2014). Antihistamine response: a dynamically refined function at the host-

tick interface. Parasites & Vectors. 7:491.

[5] Borrelli, K.W., Vitalis, A., Alcantara, R., Guallar, V. (2005) PELE: Protein energy

landscape exploration. A novel Monte Carlo based technique. J Chem Theory Comput.

1(6):1304-1311

21

Cooperative rearrangements in clusters of anisotropic particles

Szilard Fejer1, Dwaipayan Chakrabarti2 and David J. Wales3

1University of Szeged, Faculty of Education, Department of Chemical Informatics, H-6725 Szeged,

Boldogasszony sgt. 6, Hungary 2School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom

3University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom


The shape and interaction anisotropy of building blocks defines not only the way such particles

aggregate, but their dynamical properties as well. The building block anisotropies are therefore

of particular importance in the functioning of biological systems and the design of mesoscale

structures with well-defined properties. Low-energy aggregates of simple anisotropic building

blocks usually interconvert via highly cooperative motions that are specific to the system itself.

I will present different mechanisms specific to complex structures such as sliding rearrangements

in open tubes, hinge-moves in Bernal spirals, string bends in clusters of triblock Janus particles

etc. Among these, some can be seen experimentally, but in nanoscale structures such mechanisms

are yet to be confirmed.

22

Luteolin- organic solvent interactions. A molecular dynamics

simulation analysis

Khadidja Smail1, Noureddine Tchouar2, B. Marekha3, A. Sietsonen4, M. Barj,3

A. Idrissi3 1 Département de Biotechnologie, Faculté SNV, Université des Sciences et de la Technologie Université des Sciences

et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB), BP 1505 El M'naouer, Oran 31000, Algeria. 2 Laboratoire de Modélisation et Optimisation des Systèmes Industriels (LAMOSI), Université des

Sciences et de la Technologie d'Oran- Mohamed Boudiaf (USTO-MB), BP 1505 El M'naouer, Oran 31000,

Algeria. 4Ecole Normale Supérieure, UMR CNRS-ENS-UPMC n 8640, 24 rue Lhomond, F-75005 Paris, France

3 Université Lille 1 Sciences et Technologies, UMR 8516, LASIR, Villeneuev d'Ascq, France 59650.

Flavonoid biological activity is correlated with the structural elements of these molecules,

including the number and position of hydroxyl groups, It is also affected by the molecular

environment (polar or non-polar solvent, cellular environment).1 For this reason the current

theoretical investigation is carried out using molecular dynamics (MD) simulation on a

flavonoid molecule (Luteolin: Lut) in various solvents. The idea is to characterize the local

structure around the C=O and the various OH groups of Lut in these environments. Indeed,

previous works have shown the correlation between the different patterns of the local structure

around the OH moieties of quercetine and its solubility in various solvent such as chloroform,

water, acetone and ter-butanol.2 Furthermore, one of the important issues in the study of the

photochemistry of flavonoids and particularly Lut is to rationalize to what extent the nature of the

solvent determines their photochemistry, and more precisely how the nature of the solvent may

induce a special local organization around the OH and C=O moieties. As a consequence, the MD

simulations of Lut in four alcohols (methanol, 1-propanol, 2- propanol, 1-butanol), in

dimethylsulfoxide, acetone and hexane have been performed with a dual purpose: first, to

characterize the local structure around the OH and C=O moieties of Lut and particularly to

investigate the effect of these solvents on the intra molecular H-bonding between the OH and

the C=O groups of Lut, and, second, to correlate these data with the experimental properties of

Lut in these solvents.3 To this end the behavior of radial distributions (RDF), nearest neighbor

RDF, Voronoi polyhedra as well as the behavior of the number of H-bonding as a function of the

type the solvent, have been analyzed.

References

[1] Gould, K. S.; Lister, C., Flavonoid Functions in Plants. CRC Press, Taylor and Francis: Boca Raton,

2006.

[2]. Chebil, L. et al. J. Phys.Chem. B 2010, 114 (38), 12308-12313.

[3] Peng, B. et al. J. Chem. Eng. Data 2006, 51 (6), 2038-2040.

23

Changes induced by ligand binding in arginine repressor from Bacillus

subtilis

Milan Melicherčík,1,2 Saurabh Pandey2,3, Thomas Stockner4, Jannette Carey5,

Rüdiger Ettrich2,3

1 Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, Mlynská dolina, SK-842 48,

Bratislava, Slovak Republic

2 Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the

Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic

3 Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33, Nove Hrady,

Czech Republic

4 Medical University of Vienna, Vienna, Austria

5 Chemistry Department, Princeton University, Princeton, NJ, 08544-1009, USA


The arginine repressor protein is main regulon of whole arginine metabolism in procaryotic cells.

The whole protein is functional as hexamer (as two trimers) composed of six identical monomers

(each has approx. 150 aminoacids). Each monomer has two domains connected thru short linker.

Domain at the C end (C domain) is responsible for hexamer forming and ligand binding. The

domain at the N end (N domain) binds to the DNA.

The most studied protein is from Escherichia coli. Previously we simulated this system and

shown the ligand binding induces the allosteric changes in domain positions – the trimer stop

rotation around the axis, which goes through their centers of mass. [1, 2] Unfortunately for E.

coli protein there are no crystal structures of whole protein (only independent N domain and

hexamer of C domains). Because of this missing structure, we can’t study the DNA-protein

binding. We used structures from Bacillus subtilis species, whose are available in PDB database

with codes 1F9N, 2P5L and 2P5M. The primary structure is very similar, although there are some

important differences. B. subtilis doesn’t have arginine residue in position to compete with ligand

(in E. coli the ligand competes with Arg110 for creating a salt bridge with Asp125 and the ligand-

Asp salt bridges stop the trimers rotation), has one helix (H4) inserted just after linker and has

arginine residue in linker instead E. coli, which it has on the very beginning of N domain.

We have simulated above mentioned structures to find out what are the differences between B.

subtilis and E. coli proteins. In apo state of protein the H4 has similar function as the salt bridge

between E. coli's Arg110-Asp125 – keeping together the trimers. Also the missing arginine

results in different rotation of trimers after ligand binding. In simulations with the whole protein

the biggest movements were done by N domains. They were able to switch their beta-turn-beta

structures, which allow binding to the DNA molecule.

References

[1] Rebecca Strawn, Milan Melichercik, Michael Green, Thomas Stockner, Jannette Carey,

Rudiger Ettrich (2010) Symmetric allosteric mechanism of hexameric Escherichia coli arginine

repressor exploits competition between L-arginine ligands and resident arginine residues PLOS

Computational Biology 6:6.e1000801.

[2] S K Pandey, D Reha, V Zayats, M Melichercik, J Carey, R Ettrich (2014) Binding-competent

states for L-arginine in E. coli arginine repressor apoprotein. Journal of Molecular Modeling 20

(7):2330.


24

Prediction of the pollution due to a pesticide

Agneta M. Balint1 and Stefan Balint1

1West University of Timisoara


In this paper the cause of the pollution is a pesticide. The degradation of the pesticide as well the

spatial concentration distribution in soil of its toxic by-products is investigated . A mathematical

model is presented in which the degradation of the pesticide and the migration in soil of the toxic

by-products is described. This model facilitates the understanding and prediction of the pollution

caused by a pesticide. Based on the model, numerical simulations are presented.

25

Extraordinary thermal stability of Trp-cage miniproteins

observed by chiroptical and NMR spectroscopy

Viktor Farkas1, Imre Jákli1, András Perczel1,2

1MTA-ELTE Protein Modelling Research Group, H-1117 Budapest, Pázmány Péter sétány 1/A 2Loránd Eötvös University, Institute of Chemistry, Laboratory of Structural Chemistry and Biology, H-1117

Budapest, Pázmány Péter sétány 1/A

The temperature induced folding/unfolding properties of the twelve N-terminal helix-elongated

(E0…E11) variants of Exenatide-4 analogue Tc5b_N1R (E0) Trp-cage miniprotein was studied

by UV-ECD and NMR spectroscopy. These miniproteins have folded structure stabilized by

hydrophobic interactions, hydrogen bond network and a salt bridge. Beside the temperature

dependent NMR experiments, both far- and near-UV ECD spectra were recorded from 5 to 85°C

(by 5°C incremens). These data were analyzed using the in house developed CCA+

deconvolution software to extract the folding information. NMR and ECD experiments showed

increased helical content of the structure as the N-terminal was elongated, reaching a plateau at

the E7 structure. From there the helical content didn’t increased significantly. As the temperature

increased, N-terminal helix of these miniproteins unwinds linearly, but thermal unfolding of the

Trp-cage is made in two consecutive steps, first the fold resists against T induced unfolding

(between 5 and 35 °C), then unfolds gradually.

020

4060

80-1 0 1 2 3 4 5 6 7 8 9 1011

0.2

0.4

0.6

0.8

1.0

Model peptides

R2

T / °C

26

Floating Patches of HCN at the Surface of Their Aqueous Solutions

– Can They Make “HCN World” Plausible?

Balázs Fábián1,2, Milán Szőri3, Pál Jedlovszky1,4,5

1 Laboratory of Interfaces and Nanosize Systems, Institute of Chemistry, Eötvös Loránd University, Pázmány P.

Stny 1/A, H-1117, Budapest, Hungary 2 Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt.

Gellért tér 4, H-1111 Budapest, Hungary 3 Department of Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725

Szeged, Hungary 4 MTA-BME Research Group of Technical Analytical Chemistry, Szt. Gellert tér 4, H-1111 Budapest, Hungary

5 EKF Department of Chemistry, Leényka utca 6, H-3300 Eger, Hungary

Corresponding author: [email protected], [email protected]

The liquid/vapor interface of the aqueous solutions of HCN of different concentrations has been

investigated using molecular dynamics simulation and intrinsic surface analysis. Although HCN

is fully miscible with water, strong interfacial adsorption of HCN is observed at the surface of its

aqueous solutions, and, at the liquid surface, the HCN molecules tend to be located even at the

outer edge of the surface layer. It turns out that in dilute systems the HCN concentration can be

about an order of magnitude larger in the surface layer than in the bulk liquid phase. Furthermore,

HCN molecules show a strong lateral self-association behavior at the liquid surface, forming thus

floating HCN patches at the surface of their aqueous solutions. Moreover, HCN molecules are

staying, on average, an order of magnitude longer at the liquid surface than water molecules, and

this behavior is more pronounced at smaller HCN concentrations. Because of this enhanced

dynamical stability, the floating HCN patches can provide excellent spots for polymerization of

HCN, which can be the key step in the prebiotic synthesis of partially water-soluble adenine. All

of these findings make the hypothesis of “HCN world” more plausible.

Reference

[1] B. Fábián, M. Szőri, P. Jedlovszky, Floating Patches of HCN at the Surface of Their

Aqueous Solutions – Can They Make “HCN World” Plausible? J. Phys. Chem. C 118, 21469-

21482 (2014).



27

Mapping out the 366 shades of the C4H8O2 isomers

Zsófia Borbála Rózsa1, Milán Szőri1

1 Department of Chemical Informatics, University of Szeged, H-6725, Szeged, Boldogasszony sgt 6.


Constitutional isomers of the oxygen containing organic compounds can make a huge variety of

molecules and complexes. In this study all possible 366 singlet state constitutional isomers of the

C4H8O2 formula had been examined, including all molecules, bi-, tri- and tetramolecular

complexes, by comparing their thermodynamic properties, trying to find correlation between

their stability and structural features. This specific chemical formula includes molecules such as

butyric acid, which is a preferred substrate for colonocytes [1], or dioxanes which are used as

industrial solvents and may cause xenobiotic contamination of waters [2]. By using graph theory

all these molecules and multi-molecular complexes can be made, where atoms make the nodes

of the graph, and bonds make the edges. With this technique we can generate all the isomers of

a given formula by taking into consideration the binding specificities of the atoms using valence

shell electron pair repulsion coded by general MM2 force field parameters. After the creation of

the isomers the structures were optimized and the thermodynamic values were computed using

the G3MP2B3 ab initio computational methods. In order to validate our method, atomization

scheme was used to calculate heat of formation to compare the results with literature values. The

chemical species were ranked according to their Gibbs free energy and entropy which resulted a

thermodynamic map of molecules. This map can be divided into domains where great difference

can be found based on the types of the isomers, like their number of fragments. The Guinness

molecules of the system [3] were also described in details as well as the effect of structural

elements such as the size and the oxygen content of the ring.

[1] D. L. Topping and P. M. Clifton, “Short-Chain Fatty Acids and Human Colonic Function: Roles

of Resistant Starch and Nonstarch Polysaccharides,” Physiol Rev, vol. 81, no. 3, pp. 1031–1064, Jul.

2001.

[2] H. Barndõk, D. Hermosilla, L. Cortijo, E. Torres, and a Blanco, “Electrooxidation of industrial

wastewater containing 1,4-dioxane in the presence of different salts.,” Environ. Sci. Pollut. Res. Int., vol.

21, no. 8, pp. 5701–12, Apr. 2014.

[3] M. A. Suhm, “Guinness molecules: identifying lowest-energy structures.,” Angew. Chem. Int.

Ed. Engl., vol. 53, no. 7, pp. 1714–5, Feb. 2014.

28

The Effect of High Density Lipoprotein (HDL) on the Catalytic

Activity of Serum Paraoxonase-1 (PON1)

Klaudia Szeler,1 Moshe Ben-David,2,3 Joel L. Sussman,3 Dan S. Tawfik2, Shina

Caroline Lynn Kamerlin1

1Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden 2Departments of Structural Biology

3Biological Chemistry, Weizmann Institute of Science, Israel


Serum paraoxonase 1 (PON1) is a calcium-dependent lipo-lactonase that promiscuously

catalyzed the hydrolysis of various organophosphate pesticides and nerve agents [1]. PON1

interacts with high-density lipoprotein (HDL) affecting both PON1's stability and activity [2,3]

(Fig. 1). However, how PON1-HDL interactions regulate PON1's activity remains unclear. We

present here a combination of kinetic, crystallographic and computational work (using the

empirical valence bond approach) of the PON1 catalyzed hydrolysis of phosphotriester and

lactone substrates. We provide a detailed structural and mutational analysis for the native

lactonase activity of the enzyme, and for the promiscuous phosphatase activity using paraoxon as

a model substrate. Our results provide a detailed model for the activation of PON1 by HDL and

demonstrate the detrimental role too much flexibility can play on an enzyme's catalytic activity. Figure 1: Proposed model for the anchoring of PON1 to HDL based on the substrate-free crystal

structure of rePON1 (PDB ID:3SRE).

References

[1] M. I. Mackness, S. Arrol, C. Abbot and P. N. Durrington, Protection of high-density lipoprotein against oxidative modification by high-density lipoprotein associated paraoxonase. Atherosclerosis 104 129-135 (1993). [2] L. Gaidukov L and D. S. Tawfik, High affinity, stability and lactonase activity of serum paraoxonase PON1 anchored on HDL with ApoA-I. Biochemistry 44, 11843-11854 (2005). [3] L. Gaidukov, R. I. Viji, S. Rosenblat, M. Aviram and D. S. Tawfik, ApoE induces serum paraoxonase PON1 activity and stability similar to ApoA-I. Biochemistry 49, 532-538 (2010). [4] M. Ben-David, J. L. Sussman, K. Szeler, C. I. Maxwell, S. C. L. Kamerlin and D. Tawfik,

Catalytic stimulation by restrained active-site floppiness - the case of high-density lipoprotein-bound serum paraoxonase 1. J. Mol. Biol. 427, 1359-1374 (2015)

29

Computational study concerning RNA or DNA aptamers

Katarína Skúpa1, Milan Melicherčík1 and Ján Urban1

1Department of nuclear physics and biophysics

Faculty of Mathematics, Physics and Informatics

Comenius University in Bratislava, Slovakia

Aptamers are short nucleic acid segments, which can bind with high affinity and specifity to a wide

range of molecules. The RNA/DNA aptamers form an attractive class of molecules which are widely

applicable. They can be used in medicine, pharmaceutics, environmental and food analytics as

diagnostic and therapeutic agents and as recognition elements. Our contribution is oriented to the

application of theoretical methods for the study of properties of dopamine and RNA/DNA

nucleosides molecular systems.

For the description of these systems molecular dynamics simulations (MD) and quantum

chemical calculations have been applied. The obtained results are discussed.

Acknowledgements: Support from the VEGA 1/0878/15 grant is acknowledged.

30

Protein-peptide docking with significant conformational changes

using the CABS-dock web server

Mateusz Kurcinski, Michal Jamroz, Maciej Blaszczyk, Andrzej Kolinski and

Sebastian Kmiecik*

University of Warsaw, Warsaw, Poland

*Corresponding author: [email protected]

Protein-peptide interactions play a key role in cell functions. Their structural characterization,

although very challenging, is important for discovery of new drugs. Based on our methodology

for highly efficient simulation of proteins [1, 2], we developed the CABS-dock web server for

protein-peptide molecular docking [3]. While other docking algorithms require pre-defined

localization of the binding site, CABS-dock doesn’t require such knowledge. Given a protein

receptor structure and a peptide sequence (and starting from random conformations and positions

of the peptide), CABS-dock performs simulation search for the binding site allowing for full

flexibility of the peptide and small fluctuations of the receptor backbone [3-5]. This protocol was

extensively tested over the largest dataset of non-redundant protein-peptide interactions available

to date (including bound and unbound docking cases) [3]. For over 80% of the dataset cases, we

obtained models with high or medium accuracy (sufficient for practical applications). CABS-

dock method for coupled binding site search and protein-peptide docking can be easily

complemented by other computational tools (e.g. high-resolution docking refinement protocols)

or experimental data to improve the results of the docking experiment. CABS-dock web server

is freely available at http://biocomp.chem.uw.edu.pl/CABSdock

References

[1] Jamroz M, Kolinski A, Kmiecik S. (2013) CABS-flex: Server for fast simulation of protein

structure fluctuations. Nucleic Acids Res. 41, W427-31.

[2] Blaszczyk M, Jamroz M, Kmiecik S, Kolinski A. (2013) CABS-fold: Server for the de novo

and consensus-based prediction of protein structure. Nucleic Acids Res. 41, W406-11.

[3] Kurcinski M, Jamroz M, Blaszczyk M, Kolinski A, Kmiecik S. (2015) CABS-dock web

server for the flexible docking of peptides to proteins without prior knowledge of the binding

site. Nucleic Acids Res. doi: 10.1093/nar/gkv456.

[4] Kurcinski M, Kolinski A, Kmiecik S. (2014) Mechanism of Folding and Binding of an

Intrinsically Disordered Protein As Revealed by ab Initio Simulations. Journal of Chemical

Theory and Computation. 10, 2224-2231.

[5] Blaszczyk M, Kurcinski M, Kouza M, Wieteska L, Debinski A, Michal J, Andrzej K,

Kmiecik S. (2015) Modeling of protein-peptide interactions using the CABS-dock web server

for binding site search and flexible docking. Methods (submitted), preprint at

arXiv:1505.01138.

http://biocomp.chem.uw.edu.pl/CABSdock

31

MoDyDB – just an other database?

Béla Fiser1, László Müller2, Béla Viskolcz2, Balázs Jójárt2

1Department of Organic Chemistry I, University of the Basque Country/UPV-EHU, Manuel de Lardizabal 3,

Donostia-San Sebastián, Spain-20018

2Department of Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, Szeged,

Hungary-6725


In this lecture we introduce a new database – called Molecular Dynamics and Docking DataBase,

will be freely available at modydb.org - containing parameter and coordinate files for molecular

dynamics and docking calculations of receptor – ligand complexes. AMBER related parameters

were assigned for the complexes, and for docking calculations files are in AutoDock and

AutoDock Vina format. The database provides a coherent, standardized set of structures which

is useful in different fields of computational chemistry.

32

Cannabinoids. Does Cooperative Interplay Underlie Their

Therapeutic Nature?

Lily M. Hunnisett1,2 , Kun V. Tian3 , Bela Viskolcz1 , Imre G. Csizmadia1,4,

Gregory A. Chass2

1 Department of Chemical Informatics, University of Szeged, Szeged, Hungary

2 School of Biological and Chemical Sciences, Queen Mary University of London, London, UK 3 Materials Science Research Institute, Semmelweis University, Budapest Hungary

4 Department of Chemistry, University of Toronto, Toronto, Ontario, Canada

The regulation of cannabinoid ratios existing in cannabis samples, and therefore the

accompanying psychological side effects, is a major concern when considering its use as a

therapeutic or recreational drug. It is therefore of great interest to understand, on a molecular

level, their interconverting-abilities, and molecular behaviour in biologically-relevant media.

This work presents exploratory structural and energetic analyses of neutral models of Δ8 and Δ9

isomers of Tetrahydrocannabinol (THC) and Cannabidiol (CBD), completed at the B3LYP/6-

311++G(d,p) level of theory in H2O solvent.

Free-energy results showed Δ8-THC to be ~9 and ~22 kJ.mol-1 more stable than Δ9-THC and

CBD respectively, a result in agreement with previous experimental data. High sensitivity to

cannabinoid conformation was observed, in particular for the alkyl side chain, suggesting a

potentially significant influence over their pharmacological activities. Overlap of relative free-

energies of the three cannabinoids, complemented by energetically-accessible barriers to inter-

conversion supports the hypothesis that they co-exist, and that their dynamic switching plays an

important role in their bio-activites. Complementary methodological development allowed for

effective general dissemination of the multi-dimensional analyses carried out.

33

Hydration in discrete water – from bulk free energies to localised

water molecules

Piotr Setny1

1Centre of New Technologies, University of Warsaw

Banacha 2c, 02-097 Warsaw, Poland


Biomolecules typically exist and function in water. The influence of aqueous environment needs

to be taken into account in all theoretical and computational studies of living matter at atomistic

level. Approaches, such as computer simulations, involving water in explicit, all-atom

representation are often prohibitively expensive, while the existing simplified, so called implicit

solvent models are only moderately successful.

Here, we will present a new method for modeling of biomolecular hydration. It is based on

discrete solvent representation and mean field description of solute-water and water-water

interactions. While maintaining computational efficiency of typical implicit solvent models, it

avoids many of their important deficiencies. The proposed model correctly reproduces

experimental hydration free energies for an extensive set of roughly 700 diverse organic

compounds, including atomic and molecular ions. At the same time it accurately predicts the

distribution and binding free energies of isolated water molecules buried within protein

structures. The combination of such unique capabilities, makes it a useful tool for receptor-ligand

docking as well as a valuable aid for experimental methods aimed at the prediction of

macromolecular structures such as X-ray crystallography or NMR.

34

How water contributes to pressure and cold denaturation of

proteins

Giancarlo Franzese1 1Universitat de Barcelona, Spain


The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are

commonly understood as due to water-mediated interactions. Here we study several cases of

proteins, with or without a unique native state, with or without hydrophilic residues, by means of

a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that

taking into account how water at the protein interface changes its hydrogen bond properties and

its density fluctuations is enough to predict protein stability regions with elliptic shapes in the

temperature-pressure plane, consistent with previous theories. Our results clearly identify the

different mechanisms with which water participates to denaturation and open the perspective to

develop advanced computational design tools for protein engineering [1-5].

References

[1] K. Stokely, M. G. Mazza, H. E. Stanley, and G. Franzese, Proc. Natl. Acad. Sci. 107, 1301 (2010).

[2] V. Bianco, S. Iskrov, and G. Franzese, J. Biol. Phys. 38, 27 (2012). [3] G.

Franzese and V. Bianco, Food Biophys. 8, 153 (2013). [4] V. Bianco and G.

Franzese, Sci. Rep. 4, 4440 (2014).

[5] V. Bianco and G. Franzese, "How water contributes to pressure and cold denaturation of

proteins", arXiv:1505.07594 (2015)

35

Abstracts of poster presentations

The authors of the abstracts bear the full responsibility for the scientific and

linguistic content.

36

Computational study of hydrophilic ephedrine derivatives

(C10H16NO2) and interactions with β2-adregeneric receptor

Joshua Campbell1, János J. Szórád3, Lily M. Hunnisett3, Béla Fiser3,4, Anita

Rágyanszki3, Balázs Jójárt3, Milán Szőri3, Imre G. Csizmadia2,3, Béla Viskolcz4

1-Department of Chemical &Physical Sciences, University of Toronto Mississauga, L5L6A2, Ontario Canada

2-Department of Chemistry, University of Toronto, M5S 3H6 Toronto, Ontario, Canada 3-Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary

4-Department of Organic Chemistry I, University of the Basque Country, Manuel Lardizábal 3, 20018 Donostia-

San Sebastian, Gipuzkoa, Spain

As a preliminary step to drug design, the interactions that promote the formation of stable

complex should be considered. Activation of the G-coupled protein, specifically the β2-

adregeneric receptor (β2AR) is used to treat asthma and preterm labour as these receptors exist at

higher densities in smooth muscles.[1,2] One such known agonist is ephedrine, however it is

unselective in binding to this G-coupled protein.[3,4]

As such, this study explored the binding affinity of the isomers with stoichiometry C10H16NO2

and the human β2AR. Generation of the molecular library constrained the isomers to include a

phenyl ring and protonated amine nitrogen. Probing the depth of the library within the constraints,

the various protonation states and stereoisomers were included. Simulation of physiological pH

(Protein preparation wizard in Schrödinger suites) determined the protonation stated of the

various residues.

After which they were sequentially docked (with Glide apart of the Schrödinger suites) with

increasing precision. From the docking scores and interaction energies (Eint) it was observed that

the Asp113 accounts for approximately 60% of the total Eint.

References:

[1] Solanki, P.; Yadav, P.; Kantharia, N. Ephedrine: Direct, Indirect or Mixed Acting

Sympathomimetic? Int. J. Basic Clin. Pharmacol. 2014, 3 (3), 431

[2] Barnes, P. J. Beta-Adrenoceptors on Smooth Muscle, Nerves and Inflammatory Cells. Life

Sci. 1993, 52 (26), 2101–2109.

[3] Butz, P.; Kroemer, R. T.; Macleod, N. a.; Simons, J. P. Conformational Preferences of

Neurotransmitters: Ephedrine and Its Diastereoisomer, Pseudoephedrine. J. Phys. Chem. A

2001, 105 (3), 544–551.

[4] Ahlquist, R. . A Study of Adrenotopic Receptors. Am. J. Physiol 1948, 153, 586–600.

37

Molecular recognition of constitutional isomers of epinephrine by

GPCR Balázs Fábián1, János J. Szórád2, Lily M. Hunnisett2, Béla Fiser2,3, Anita


1Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics,

Műegyetem rkp. 3-9 H-1111 Budapest, Hungary 2Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary

3Department of Organic Chemistry I, University of the Basque Country, Manuel Lardizábal 3, 20018 Donostia-San

Sebastian, Gipuzkoa, Spain 4Department of Chemistry, University of Toronto, M5S 3H6 Toronto, Ontario, Canada


Epinephrine (C9H13NO3), also known as adrenaline, is a hormone1 and neurotransmitter2

belonging to the group of catecholamines, that is, it is a monoamine having a benzene ring with

two hydroxyl side groups (catechol group). Epinephrine, along with other catecholamines like

norepinephrine and dopamine is produced in the adrenal medulla and is released into the blood-

stream as a part of the fight-or-flight response3. Epinephrine works as a nonselective agonist of

α and β adrenergic receptors, which are responsible the majority of cellular responses.

Our aim was to study molecules based on the same formula as the protonated epinephrine

(C9H14NO3) in order to evaluate their pharmacological potency as a stimulant of adrenergic

receptors. In the current work, extensive docking calculations were performed using the

Schrödinger program package to gain insight into properties of the possible ligands. The

molecules were suitably prepared and docked into the R chain of the 3SN6 β adrenergic receptor4

of the Protein Data Bank. Out of all possible isomers containing the pharmacophore benzene

ring, the top 10 scoring were analyzed in detail.

To the best of our knowledge, these structures are novel and also have better docking score than

the parent molecule epinephrine. The differences in their scores are within the accuracy of the

method. The molecules always interact strongly with the ASP 113, the SER and ASN residues

located at the binding site of the receptor. The stability of each molecule was assessed based on

their relative free energies. The comparison was made using Density Functional Theory (DFT)

with the B3LYP functional in water solvent. Based on this, most of the analyzed structures show

greater stability than the parent molecule epinephrine. Finally, the plot of the docking scores

against the DFT energies indicates 3 families of molecules. Although there were no obvious

structural similarities in these groups, this question needs to be investigated in detail.

References

[1] Babisch, W.; "Stress hormones in the research on cardiovascular effects of noise"; Noise &

Health; 2003, 5(18), 1-11

[2] Berecek, K. B. M.; Brody, M. J.; "Evidence for a neurotransmitter role for epinephrine

derived from the adrenal medulla"; American Journal of Physiology; 1982, 242 (4), H593–

H601

[3] "Catecholamines"; Health Library. San Diego: University of California.

[4] Rasmussen, S. G. F.; DeVree, B. T.; Zou, Y. et al.; "Crytal structure of the β2 adrenergic

receptor – Gs protein complex"; Nature, 2011, 477, 549-555

http://myhealth.ucsd.edu/library/healthguide/en-us/support/topic.asp?hwid=te7424

38

Development of Fluctuating Finite Element Analysis - Dynamics

and Kinetics of Mesoscale Biomolecules

Ben Hanson, Daniel Read, Oliver Harlen, Sarah Harris

University of Leeds

The increasing resolution capability of x-ray crystallography, and more recently cryo-em [1], is

leading to more interest in the structure and dynamics of larger and more complex proteins.

Proteins of this nature, such as molecular motors, arguably exist at the mesoscale in both the

spatial and temporal regimes. Fluctuating Finite Element Analysis (FFEA), a continuum

mechanical representation of biomaterial [2], has been previously reported to give insights into

the dynamical range of motors such as rotary ATPases [3]; i.e. the spatial mesoscale. Here we

present preliminary results of a kinetic scheme integrated with FFEA, implemented in order to

take FFEA fully into the temporal mesoscale. The molecule of study is cytoplasmic dynein, a

molecular motor powered by an ATP cycle which transports cargo along microtubules [4], and

for which a purely kinetic model currently exist [5].

References

[1] Kühlbrandt, W., Science 343, 1443-44 (2014)

[2] Oliver, R., Read, D. J., Harlen, O. G. and Harris, S. A., J. Comp. Phys. 239, 147-65 (2013)

[3] Richardson, R. A. et al., Proteins 82(12), 3298-311 (2014)

[4] Roberts, A. J., Kon, T., Knight, P. J., Sutoh, K. and Burgess, S. A., Nature Reviews Mol. Cell Biol. 14,

713-726 (2013)

[5] Sarlah, A. and Vilfan, A., Biophys. J. 107, 662-671 (2014)

39

Dynamics of protein ligand interactions – impact on drug discovery

Sarah Harris1 , Anastasia Zhuravleva1 and Outi Kamarainen1

1University of Leeds, Leeds, United Kingdom


Introducing a new drug to market is a lengthy and expensive process (10-15 years and

$1.2billion). Better understanding of how and why a drug molecule binds to a target and what

changes in the structure and chemistry could improve the binding affinity may help to shorten

the drug design process and in recent years the role of molecular motions in binding selectivity

and efficiency attracts an increasing attention from drug design research. Whilst calorimetric

methods can quantify the total free energy and entropy change, it is difficult to estimate

contributions from the different components of entropy, one of the largest unknowns being the

magnitude of the configurational entropy change.

Molecular dynamics simulations of the drug and target protein can provide more details of the

different atomistic movements contributing to the total entropy change, thus potentially providing

valuable clues for lead optimisation. However, the relatively short time scale of simulations (100

ns to few µs) and potential issues with obtaining suitable parameters for ligands remain a

challenge. For this study, we use the well-characterized N-terminal domain of the chaperone

protein Hsp90 as a model system to study the vibrational entropy of Hsp90 binding to different

small-molecule inhibitors. We employ the NMR spectroscopy to validate the data from molecular

dynamics simulations and improve our in silico methods. The aim of this project is to develop a

generic computational approach that can be used to predict dynamic features for different protein-

ligand/drug systems and thus, to improve drug design and lead optimisations processes in

pharmaceutical sector.

40

Synthesis and characterization of NGR peptides to design

radiopharmaceuticals

Z. Lovrity1, G. Mező2, D. Szikra3, I. Kertész3 1Department of Nanobiotechnology, University of Miskolc, Hungary

2Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, Hungary 3Department of Nuclear Medicine, University of Debrecen, Hungary

Angiogenesis is the formation of new blood vessels from preexisting vasculature. This process might be

triggered and enhanced by many human diseases including cancer, atherosclerotic plaque and peripheral

artery disease. Aminopeptidase N (APN, also known CD13) has been associated with the growth of the

new vasculatures and suggested as a suitable target for anti-cancerous therapy. An asparaginyl-glycinyl-

arginine (NGR) sequence containing peptides have been identified as a specific ligands of CD13.

Conjugation of NGR peptides with chemotherapeutic drugs might improve the tumor therapy.

Labeled NGR derivatives with 64Cu, 68Ga and 99mTc are useful radiotracers for the in vivo imaging of

CD13-expression of tumors and neovasculature by binding to APN.

The aim of this study was to design, synthetize different, chemically stable NGR derivatives for using them

radiotracers.

Cyclic NGR peptides with amide- and thioether bond were synthetized by development of precursor linear

peptides on Rink-Amide MBHE resin with standard Fmoc/tBu strategy. Cyclization was carried out in

solution. The linear semi-protected H-Lys(CIZ)-Asn-Gly-Arg-Glu-NH2 peptide was cleaved from the

resin using TFA mixture, which was cyclized: the amide bond was formed between the N-terminus

and side chain of Glu. The crude cyclic peptide was purified by RP-HPLC. The CIZ protecting group from

the side chain of Lys residue was removed by HF-p-cresol mixture. The cyclic peptides were dissolved

in sodium-carbonate buffer. p-SCN-Bn-NOTA (or p-NCS-benzyl NODAGA) was dissolved in

DMSO and was introduced to the cyclic peptide solution. The chelator-conjugated NGR derivate was

purified by semi-preparative RP-HPLC.

The pure products were identified by LC-MSMS (LCMS-IT-TOF, Shimadzu Co.). External mass

calibration, resolution and sensitivity of the ion trap and TOF analyzer were adjusted using a standard

TFANa solution. Mobile phase A was composed 5% acetonitrile in water, 0,1% TFA and B 5% water in

acetonitrile, 0,1% TFA. Isocratic elution was performed at a flow rate of 0,2 ml/min. During a 3-min

run, independent infusion analysis was carried out in the positive ionization mode. The MS operating

conditions were as follows: electrospray voltage 4,5 kV; CDL and heat block temperatures 200°C;

nebulizing gas flow 1,5 L/min, drying gas pressure 100 kPa. Mass spectra were acquired in the range of

m/z 100-1500 Da for MS1, 50-1000 for MS2 and MS3. The collision energy was set 50% both for MS2,

MS3. Shimadzu's Composition Formula Predictor software was used to provide chemical formula of

NGR peptides and their fragments.

41

Constitutional Isomers of Norepinephrine (C8H12NO3) Interactions

with β2-Adrenergic Receptor

Min-Yen Lu1, János J. Szórád2, Lily M. Hunnisett2, Béla Fiser23, Anita

Rágyanszki2, Balázs Jójárt2, Milán Szőri2, Imre G. Csizmadia12, Béla Viskolcz2

1: Department of Chemistry, University of Toronto, M5S 3H6 Toronto, Ontario, Canada

2: Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary

3: Department of Organic Chemistry I, University of the Basque Country, Manuel Lardizábal 3, 20018 Donostia-San Sebastian, Gipuzkoa,

Spain

Norepinephrine is a catecholamine with multiple roles often acting as a hormone or

neurotransmitter. It often plays a role in adrenergic agonism as a drug through the activation by

ligand binding of GPCRs. Most of the known noradrenaline effects such as regulation of vascular

tone and sympathetic system are carried out via common bindings to α1 and α2-adrenergic

receptors instead of β subclass. Therefore, our investigation of Norepinephrine (C8H12NO3)

structure and its isomers is a key element to discover a new binding endogenous ligand. Due to

the difference of ligand specificity and signalling process, this structural-based approach will

identify the potential ligands through examination of docking score and interaction energy.

Approximately 7000 isomeric structures of C8H12NO3 are generated by Schrödinger program

including Molgen, Stereoizoer and Epik. By performing molecular docking against β2-adrenergic

receptors with Glide utilizing levels of HTVS, SP and XP precison , the top 10 XP high-rankig

molecules display binding affinities with targeted receptor. Of the 10 structures, 5 molecules

were unknown, displaying low docking scores and favorable interaction energy values. Among

the best docking hits, interactions of the neibouring amino acids residues are examined to

determine the most favorable structure. The XP results of the new discovered ligand structures

can be further synthesized for potential pharmaceutical research.

This computational data induced through experimentation may create new opportunities for

therapeutic drug development.

References:

[1] S. Ferguson, R. Feldman; “Beta-Adrenoceptors as Molecular Targets in the treatment of

Hypertension” Canadian Journal of Cardiology, 2014, vol 30, pps3-s8

[2] S. Rasmussen, B. Devree, Y. Zou, A. Kruse, K. Chung, T. Kobilka, F. Thian, P. Chae, E. Pardon,

D. Calinski, J. Mathiesen, S. Shah, J. Lyons, M. Caffrey, S. Gellman, J. Steyaerr, G. Skinitotis, W. Weis,

R, Sunahara; Cyrstal structure of the beta 2 adenergic receptor-Gs protein complex; Nature, 2011, vol477

pp549-555

[3] P. Kolb, D. Rosenbaum, J. Irwin, J. Fung, B. Kolbllka, B. Schoichet, “Structure-based discovery

of beta 2-adrenergic receptor ligands”, PNAS 2009, vol 16, pp6843-6848

[4] D. Vassilatis, J. Hohmann, H. Zeng, F Li, J Rachalis, M. Mortrud, S Rodriquez, J weller, A

Wright, J Bergmann, G Gaitanaris; “The G protein-coupled receptor repertoires of human and mouse”

PNAS, 2003, vol 100, pp4903-4908

42

Binding-Competent States for L-arginine in E. coli Arginine

Repressor Apoprotein

Saurabh K. Pandey1,2, David Reha 1,2, Vasilina Zayats 1,2, Milan Melichercik 1,3,

Jannette Carey 4,

Rudiger Ettrich 1,2 1Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic

2 University of South Bohemia, Nove Hrady, Czech Republic

3 Comenius University, Bratislava, Slovakia

4 Princeton University, Princeton, NJ, USA.

Arginine repressor of E. coli is a multifunctional hexameric protein that provides feedback

regulation of arginine metabolism upon activation by the negatively cooperative binding of L-

arginine. A molecular mechanism of allostery has been described earlier in which

conservedarginine and aspartate residues in each ligand-binding pocket promote rotational

oscillation of the trimers within the hexameric domain that binds L-arginine by engagement and

release of hydrogen-bonded salt bridges. Binding of exogenous L-arginine displaces resident

arginine residues and arrests oscillation, shifting the equilibrium quaternary ensemble and

promoting motions that maintain the configurational entropy of the system [1]. Interpretation of

this complex system requires an understanding of the protein's conformational landscape. In this

work the ~50 kDa hexameric C-terminal domain was studied by 100 ns molecular dynamics

simulations in presence and absence of the six L-arg ligands that bind at the trimer-trimer

interface. A rotational shift between trimers followed by rotational oscillation occurs in the

production phase of the simulations only when L-arg is absent. Analysis of the system reveals

that the degree of rotation is correlated with the number of hydrogen bonds across the trimer

interface. The trajectory presents frames with one or more apparently open binding sites into

which one L-arg could be docked successfully in three different instances, indicating that a

binding-competent state of the system is occasionally sampled. Simulations of the resulting

singly-liganded systems reveal for the first time that the binding of one L-arg results in a

holoprotein-like conformational distribution.

References

[1] R Strawn, M Melichercik, M Green, T Stockner, J Carey, R Ettrich (2010) Symmetric

vallosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition

between L-arginine ligands and resident arginine residues. PLOS Computational Biology 6: 6.

e1000801

43

Molecular Recognition Involving Combinatorial Chemistry: A

Case Study of Norepinephrine Derivative, C8H12NO2

Seung Gwan Ryoo1, János J. Szórád2, Lily M. Hunnisett2, Béla Fiser2,3, Anita


1Department of Chemistry, University of Toronto, M5S 3H6 Toronto, Ontario, Canada

2Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary 3Department of Organic Chemistry I, University of the Basque Country, Manuel Lardizábal 3, 20018

Norepinephrine is a neurotransmitter responsible for regulating stress responses and autonomic

activity within the body[1]. It strongly binds α1, α2, and β1 adrenergic receptors (ARs) and weakly

binds β2AR[2]. For this study, receptor-ligand interactions between β2AR and norepinephrine

derivatives corresponding to the molecular formula, C8H12NO2, are investigated to discover

ligand structures with tight binding interactions with β2AR, and to see if they have relevance in

drug design. Constitutional isomers containing a phenyl ring and a protonated nitrogen atom are

generated using Molgen[3], and prepared using Schrödinger LigPrep module[4]. The β2AR

structure is retrieved from the PDB database (PDB ID: 3SN6) and prepared via Schrödinger

Protein Preparation Wizard[5]. Molecular docking is then performed to predict the orientation

and conformation of the receptor-ligand complex using Glide[6]. Three docking methods –

HTVS, SP, and XP – are used to yield the 10 most stable ligand structures with XP docking

scores ranging from -10.141 to -8.821. The average docking score of these 10 structures (-9.3414)

is higher than that of norepinephrine derivatives containing one less oxygen atom (-8.5742), and

lower than that of norepinephrine, which contains one more oxygen atom (-10.3224). This trend

suggests that the number of oxygen atoms is proportional to both the docking score and ligand

stability. Six residues, namely ASP113, PHE193, SER203, PHE289, PHE290, and ASN312,

interact with the ligand structures. ASP113 contributes most significantly by forming hydrogen

bonds with -OH groups.

References

[1] A. P. Kohm, and V. M. Sanders, Norepinephrine and beta 2-adrenergic receptor stimulation

regulate CD4+ T and B lymphocyte function in vitro and in vivo, Pharmacol. Rev. 4, 487-525

(2001)

[2] K. Mori, E. Ozaki, B. Zhang, L. Yang, A. Yokoyama, I. Takeda, N. Maeda, M. Sakanaka,

and J. Tanaka, Effects of norepinephrine on rat cultured microglial cells that express α1, α2, β1

and β2 adrenergic receptors, Neuropharmacology 43, 1026-1034 (2002)

[3] R. Gugisch, A. Kerber, A. Kohnert, R. Laue, M. Meringer, C. Rücker and A. Wassermann,

MOLGEN 5.0, a Molecular Structure Generator, Bentham Science Publishers Ltd., Bayreuth,

Germany (2012)

[4] LigPrep, version 3.4, Schrödinger, LLC, New York, NY (2015)

[5] G. M. Sastry, M. Adzhigirey, T. Day, R. Annabhimoju and W. Sherman, Protein and ligand

preparation: Parameters, protocols, and influence on virtual screening enrichments, J. Comput.

Aid. Mol. Des. 27, 221-234 (2013)

[6] R. A. Friesner, R. B. Murphy, M. P. Repasky, L. L. Frye, J. R. Greenwood, T. A. Halgren, P.

C. Sanschagrin and D. T. Mainz, Extra Precision Glide: Docking and Scoring Incorporating a

Model of Hydrophobic Enclosure for Protein-Ligand Complexes, J. Med. Chem. 49, 6177-6196

(2006)

44

The role of motif III and its extended region in positioning the two

helicase domains in the motor subunit of the restriction-

modification system EcoR124I

Sinha D.1, Bialevich V.1, Shamayeva K.1, Řeha D.1, Ettrich R.1

1INSB, Academy of Sciences of the Czech Republic

The type I restriction-modification enzymes differ significantly from the type II enzymes

commonly used as molecular biology reagents. On hemi-methylated DNAs type I enzymes act

as conventional adenine methylases at their specific target sequences, but unmethylated targets

induce them to translocate thousands of basepairs through the enzyme before cleaving distant

sites nonspecifically. EcoR124I belongs to the same superfamily as yeast dsDNA translocase

Rad54 and two RecA-like helicase domains are involved in translocation and contain the seven

characteristic motifs for DEAD box helicases. In Rad54 an extended region of motif III is

involved ATPase activity. In EcoR124I this extended region, although it bears sequence and

structural similarities with Rad54, does not influence ATPase activity nor restriction activity.

However, the conserved glycin residue in motif III plays a role in the positioning of the two

helicase domains towards each other and its mutation alters ATPase activity and cleavage

activity.

References

[1] Mikalai Lapkouski, et al.[2009]Structure of the motor subunit of type I restriction-

modification complex EcoR124I.,Nat Struct Mol Biol 16:1 94-95 Jan

[2] D Sinha, et al.[2014]Interdomain communication in the endonuclease/motor subunit of Type

I restriction-modification enzyme EcoR124I,Journal of Molecular Modeling20 (7):2334

[3] Eva Csefalvay, et al.[2015]Functional coupling of duplex translocation to DNA cleavage in

a type I restriction enzyme PLOS One accepted with minor revisions 21.1.2015.

[4] Bialevich V, et al.The role of motif III and its extended region in positioning the two helicase

domains in the motor subunit of the restriction-modification system EcoR124I [manuscript in

preparation]

Acknowledgements: We gratefully acknowledge support from the Czech Science Foundation

(project number GACR P207/12/2323), and the Grant Agency of the University of South

Bohemia (grant no. 170/2010/P). Some computations were performed in MetaCentrum

SuperComputer facility.

45

A computational study of the interaction between dopamine and

DNA/RNA nucleosides

Katarína Skúpa, Milan Melicherčík, Ján Urban

Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava

The interaction between protonated dopamine and neutral RNA and DNA nucleosides was

studied by means of density functional theory calculations in vacuum and in implicit water. On

the most stable complexes formed with each of the nucleosides, the vertical absorption excitation

energies were evaluated and compared with the values of separated dopamine and corresponding

nucleoside. The most stable complex was formed with guanosine and the spectral changes in this

complex resulted in a significant reduction of the oscillator strength of the first dopamine’s

transition. In the first guanosine’s transition, a redshift of 0.2 eV was found combined with a

reduction of the oscillator strength.

46

Molecular Recognition of Norepinephrine Derivatives C8H12NO by

GPCR

Cheng Min Sung,1 János J. Szórád,2 Lily M. Hunnisett,2 Béla Fiser,2,3 Anita

Rágyanszki,2 Balázs Jójárt,2 Milán Szőri,2 Imre G. Csizmadia,2,4 Béla Viskolcz.2

1Department of Immunology and Human Biology, University of Toronto, M5S 3H6 Toronto, Ontario, Canada 2Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary

3Department of Organic Chemistry I, University of the Basque Country, Manuel Lardizábal 3, 20018 Donostia-San

Sebastian, Gipuzkoa, Spain 4Department of Chemistry, University of Toronto, M5S 3H6 Toronto, Ontario, Canada

Norepinephrine with a protonated amino group, C8H12NO3, is an essential monoamine

neurotransmitter in human body that exerts its effect on several brain regions, resulting in fight-

or-flight response.[1] As a vasopressor, norepinephrine is used as an immediate treatment for

vasodilatory states such as septic shocks.[2] Norepinephrine has high affinity to α1 and α2

adrenergic receptors (AR); it also binds to β1 and β3, but only weakly binds to β2AR.[3]

In this study, molecular recognition of norepinephrine derivatives (C8H12NO) by β2AR was

performed by Maestro 10.1 software package. All of the possible isomers of C8H12NO were

generated, and β2AR structure (PDB name: 3sn6) was prepared.[4] After step-by-step precision

state calculations from HTVS to SP to XP, 10 conformations with the lowest docking scores were

analyzed. Optimizations of the 10 conformations were performed in solvation of water by

Gaussian 09, and free energies were calculated.

Figure1. The most stable norepinephrine derivative (C8H12NO) found to bind with β2AR

with the lowest docking score.

With computational method, the top 10 ligands for β2AR with molecular formula of C8H12NO

were found. Further synthesis and investigation can be used to visualize their drug potential.

References

[1] Katzung, BG, Trevor, AJ. (2014). Basic and clinical pharmacology 13th edition. McGraw-

Hill Education. ISBN: 978-0-07-182505-4.

[2] De Backer, D, Biston, P, Devriendt, J, Madl, C, Chochrad, D, Aldecoa, C, Brasseur, A,

Defrance, P, Gottignies, P, Vincent, J. (2010). Comparison of dopamine and norepinephrine in

the treatment of shock. New Engl. J. Med. 362(9):779-789

[3] Piascik, M.T., Perez, D.M. (2001). Alpha1-adrenergic receptors: new insights and

directions. J. Pharmacol. Exp. Ther. 298 (2):403–410.

[4] Rasmussen, S.G.F., DeVree, B.T., Zou, Y., Kruse, A.C., Chung, K.Y., Kobilka, T.S., Thian,

F.S., Chae, P.S., Pardon, E., Calinski, D.,Mathiesen, J.M., Shah, S.T.A., et al. (2011). Crystal

structure of the beta-2 adrenergic receptor-Gs protein complex. Nature. 477:549-557

http://en.wikipedia.org/wiki/International_Standard_Book_Number

http://en.wikipedia.org/wiki/Special:BookSources/978-0-07-182505-4

47

Where are the isopeptides?

Veronika Szentirmai1, Milán Szőri1

1 Department of Chemical Informatics, University of Szeged, H-6725, Szeged, Boldogasszony sgt 6.

Corresponding author: [email protected], [email protected]

Conventional peptide (amide) bond is covalent linkage of NH2 and COOH groups of α-carbons

of two essential amino acid residues, which can form proteins (e.g hormones, enzymes and

structural proteins) in the living cells. However, most of the essential amino acid have other

functional groups (e.g. COOH, NH2 groups in the cases of Asp and Lys, respectively) which is

suitable to form alternative linkage between amino acid residues in principles. These species are

called as isopeptides in general and the best known existing example for such is the disulfide

bond between two cysteine (Cys) residues. Several other types of isopeptides can be also found

in Nature. In cyanobacteria and a few heterotrophic bacteria, other multiple isopeptide bonds

(multi-Arg-poly-γAsp) can be found with function of temporary nitrogen and reserve.1 It also has

been found that Streptococcus pyogenes, like many other Gram-positive bacteria, contains

extracellular proteins stabilized by spontaneous formation of the intramolecular isopeptide bonds.

The reason of the relatively rare presence of the isopeptides in living cell is not quite understood,

since some of them can have higher thermodynamic stability than the conventional peptide

linkage between the amino acid residues (ΔrG0 (Gly-Ala) = 17.3 kJ/mol), as it is the case for

gluthatione (γ-Glu-Cys-Gly) in our previous work.2 In order to shed some more light on the

thermodynamic background of the isopeptide formations, they are described quantitatively by the

change of thermochemical functions (ΔrH0, ΔrS0 and ΔrG0). These calculations were carried out

using the combination of the G3MP2B33 composite model and SMD implicit solvent model.4

According to our preliminary results serine-γ-asparagine (Ser_Asn) and Nε-(γ-glutamyl)lysine

(Glu_Lys) show relative large thermodynamical stability (ΔrG0 < -30.5 kJ/mol, above the Gibbs

free energy of hydrolysis of 1 mol ATP). Amongst these isopeptides, Glu_Lys motif had also

been detected experimentally in the spore coat proteins of Bacillus Subtilis5 and during the action

of transglutaminases.6

References

(1) Krehenbrink, M.; Oppermann-Sanio, F. B.; Steinbüchel, A. Arch. Microbiol. 2002, 177

(5), 371–380.

(2) Fiser, B.; Jojart, B.; Szőri, M.; Lendvay, G.; Csizmadia, I. G.; Viskolcz, B. J. Phys. Chem.

B 2015, 119.

(3) Baboul, A. G.; Curtiss, L. a.; Redfern, P. C.; Raghavachari, K. J. Chem. Phys. 1999, 110

(16), 7650.

(4) Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2009, 5 (9),

2447–2464.

(5) Kobayashi, K.; Kumazawa, Y.; Miwa, K.; Yamanaka, S. FEMS Microbiol. Lett. 1996, 144

(2-3), 157–160.

(6) Steinert, P. M.; Marekov, L. N. Mol. Biol. Cell 1999, 10 (12), 4247–4261.

48

Binding Affinities of Epinephrine Derivatives (C9H14NO2) to ß2

Adrenergic Receptors; A Computational Study

Wendy Wang1, János J. Szórád3, Lily M. Hunnisett3, Béla Fiser3,4, Anita

Rágyanszki3, Balázs Jójárt3, Milán Szöri3, Imre G. Csizmadia2,3, Béla Viskolcz2

1Department of Pharmacology and Toxicology, University of Toronto, M5S 3H6 Toronto, Ontario, Canada 2Department of Chemistry, University of Toronto, M5S 3H6 Toronto, Ontario, Canada

3Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary 4Department of Organic Chemistry I, University of the Basque Country, Manuel Lardizábal 3, 20018 Donostia-San

Sebastian, Gipuzkoa, Spain

Over the past decades, ß2 adrenergic receptors have garnered attention as drug targets for many

pharmacological developments. Combined with a number of G-protein coupled receptors, a well-

known ligand that binds to the cavity of this protein is epinephrine [1]. The depolarization of this

receptor plays a crucial role in the fight-or-flight response, smooth muscle contractions as well

as bradycardia [1]. Therefore, the investigation of the relationship between the epinephrine ligand

and its receptor has great implications upon the development of novel compounds, as epinephrine

today has known applications in medicine, particularly in the treatment of select cardiovascular

conditions—such as heart arrhythmia—as well as roles in inducing smooth muscle relaxation in

the bronchioles when coupled with ß2 adrenergic receptors [2].

The aim of this investigation is to generate all the possible isomeric forms given the molecular

formula: C9H14NO2. The relative lack of one oxygen atom compared to the epinephrine molecular

formula makes this compound an epinephrine derivative. Noting that the binding pocket of the

3SN6 receptor is hydrophobic, the aim is to investigate the elements that increase the affinity of

the ligand with its active site. Computational software along with elements from the Schrödinger

Suite 2015 will be used to generate the library of possible isomers of the epinephrine derivative

(C9H14NO2). Density functional theory techniques will be carried out in the end to finalize the

best structure that dock to this protein.

References

[1] Marki, Arpad, et al. "Phytoecdysteriods and anabolic-androgenic steroids-structure and

effects on humans." Curr. Med. Chem 15.1 2008 75-91.

[2] Packer, Milton. "Current role of beta-adrenergic blockers in the management of chronic

heart failure." Am. J. Med 110.7 2001 81-94.

49

Computational Molecular Modeling of Ephedrine and its Isomers

(C10H16NO) and Molecular Recognition by GPCR protein

Vivian Xie1, János J. Szórád2, Lily M. Hunnisett2, Béla Fiser2, 3, Anita

Rágyanszki2, Balázs Jójárt2, Milán Szőri2, Imre G. Csizmadia1, 2, Béla Viskolcz2

1Department of Chemistry, University of Toronto, M5S 3H6 Toronto, Ontario, Canada 2Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary

3Department of Organic Chemistry I, University of the Basque Country, Manuel Lardizábal 3, 20018 Donostia-San Sebastian,

Gipuzkoa, Spain

A computational chemistry approach was used to create a molecular library of isomers with the

molecular formula C10H16NO (ephedrine). These isomers were studied using computational

chemistry principles to find their respective binding affinities with the β2 adrenergic receptor

protein. Programs such as the Schrodinger Maestro suite [1] were used to prepare and dock the

isomers. The stability of the isomers were calculated by density functional theory using Gaussian

09 [2]. Ephedrine plays an important role as a sympathomimetic drug, mimicking transmitters such as

adrenaline [3]. This makes it an interesting molecule to study for the purpose of drug synthesis

which target the receptors of adrenaline. The target receptor, β2 adrenergic receptor, is linked to

cardiovascular and pulmonary functions [4]. The isomer with the highest docking score suggests

the highest binding affinity with this receptor.

Figure 1 The most stable isomer of C10H16NO

Results showed that Figure 1 had the highest binding affinity with the receptor due to

intermolecular hydrogen bonding with surrounding amino acids of the receptor. The stability of

the isomer in solvation was had a fair correlation with the docking score, highlighting why

some isomers docked with the receptor better than others.

References

[1] Schrödinger Release 2015-2: Maestro, version 10.2, Schrödinger, LLC, New York, NY, 2015.

[2] Gaussian 09, Revision D.01, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; et. al. Gaussian,

Inc., Wallingford CT, 2009.

[3] Casella, M., Russo, A.D., Izzo, G., Pieroni, M., Andreini, D., Russo, E., Colombo, D.,

Bologna, F., Bolognese, L., Zeppilli, P., Tondo, C. (2014). Ventricular arrhythmias induced by

long-term use of ephedrine in two competitive athletes. Heart Vessels. 30(10). 280-283

[4] Ramussen, S. G. F., Choi, H., Rosenbaum, D. M., Kobilka, T. S., Thian, F. S., Edwards, P.

C., Burghammer, M., Ratnala, V. R. P., Sanishvili, R., Fischetti, R. F., Schertler, G. F. X., Weis,

W. I., Kobilka, B. K. (2007). Crystal Structure of the human β2 adreneric G-protein-coupled

receptor. Nature. 10(1038). 1-6.

50

Interactions of epinephrine derivative (C9H14NO) with GPCR

protein

Rui Yue1, János J. Szórád2, Lily M. Hunnisett2, Béla Fiser2,3, Anita Rágyanszki2,

Balázs Jójárt2, Milán Szőri2, Imre G. Csizmadia1,2, Béla Viskolcz2 and the

presenting author Rui Yue1

1 Department of Chemistry, University of Toronto, M5S 3H6 Toronto, Ontario, Canada 2 Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6., H-6725 Szeged, Hungary

3 Department of Organic Chemistry I, University of the Basque Country, Manuel Lardizábal 3, 20018 Donostia-

San Sebastian, Gipuzkoa, Spain

Epinephrine (C9H13NO3) is a common primary treatment of anaphylaxis and cardiac arrest [1, 2].

When epinephrine binds to a β2 GPCR receptor in the human liver, heart and smooth muscle to

form a complex, it triggers second messages to increase glycogenosis, increase heart rate and

relax the smooth muscle [3]. In the interest of understanding the strength of biological activity of

a protein-ligand complex, determination of the docking score of the most stable complex of β2

G-protein coupled receptor and epinephrine derivative C9H14NO and analysis the interaction

energy are the purposes of the project. All possible benzene- ring containing constitutional

isomers were generated using Molgen 5.0, then all of them was docked into β2 GPCR by Maestro

Suits 2015-1 program package. The top 10 ranked structures were selected for further analysis.

Figure 1. Docking score comparison for top three most stable structures in epinephrine family.

Results suggest the non-covalent interactions between H atoms of the ligand and the oxygen atom

of the ASP113 residue form the most stable binding interaction. The increasing trend of the

stability of epinephrine family: epinephrine derivative (C9H14NO), another epinephrine

derivative (C9H14NO2) and epinephrine (C9H14NO3) suggests that increasing number of oxygen

in the formula increases chances of non-covalent interactions and the complex stability.

References

[1] M. C. Bhalla, et al, Predictors of epinephrine autoinjector needle length inadequacy.

American Journal of Emergency Medicine 31, 1671-1676 (2013)

[2] P. A. Greenberger, Epinephrine for anaphylaxis. Annals of Allergy, Asthma &

Immunology. 94 (5). 515-516 (2005)

[3] J. Pearce, Links between nerves and glands: the story of adrenalin. Advances in Clinical

Neuroscience & Rehabilitation 9: 22–28. (2009)

51

List of Participants

1 Agneta Balint [email protected] West University of Timisoara

2 Stefan Balint [email protected] West University of Timisoara

3 Paul Bauer [email protected] Department of Cell and Molecular Biology,

Uppsala University

4 Giorgia Brancolini [email protected] Center S3, CNR-NANO Institute Nanocience

5 Richard Buchner richard.buchner@

chemie.uni-regensburg.de

Institute of Physical and Theoretical Chemistry,

University of Regensburg

6 Jaroslav Burda [email protected] Charles University in Prague

7 Joshua Campbell [email protected] University of Szeged

8 Imre G. Csizmadia [email protected] University of Szeged

9 Balázs Fábián [email protected] University of Szeged

10 Maxim Fedorov [email protected] University of Strathclyde

11 Jacob Fondriest [email protected] Princeton University

12 Pavel Grinkevich [email protected] The University of South Bohemia in Ceske

Budejovice

13 Ben Hanson [email protected] University of Leeds

14 Pradeep Hiriyur

Nagaraj

[email protected] INSB, Czech Academcy of Sciences

15 Brianna Hnath [email protected] Princeton University

16 Lily Hunnisett [email protected] University of Szeged

17 Abdenacer Idrissi [email protected] University Lille1 Sciences and Technologies

18 Imre Jákli [email protected] MTA-ELTE Protein Modelling Research Group

19 Pál Jedlovszky [email protected] ELTE University

20 Balázs Jójárt [email protected] University of Szeged

21 Deepika Kale [email protected] Institute of Nanobiology and Structural Biology,

Global Change Research Center, Academy of

Sciences of the Czech Republic, Nove Hrady,

Czech Republic

22 Outi Kamarainen [email protected] University of Leeds

23 Lynn Kamerlin [email protected] Uppsala University, Department of Cell and

Molecular Biology

24 Sebastian Kmiecik [email protected] University of Warsaw

25 Sudhir Kumar Pal [email protected] Institute of Nanobiology and structural biology of

GCRC

26 Michal Kutý [email protected] The Institute of Nanobiology and Structural

Biology

27 Virginia Lane [email protected] Princeton University

28 Zita Lovrity [email protected] University of Miskolc, Department of

Nanobiotechnology

29 Min Yen Lu [email protected] University of Szeged

30 Jost Ludwig [email protected] INSB of GCRC, Academy of Sciences of the

Czech Republic, Nove Hrady, Czech Republic

31 Nicholas Luedtke [email protected] Princeton University

32 Ben Luisi [email protected] University of Cambridge

52

33 Mikael Lund [email protected] Lund University

34 John Martin [email protected] University of Cincinnati

35 Milan Melicherčík [email protected] Comenius University, Faculty of Mathematics,

Physics and Informatics

36 Babak Minofar [email protected] INSB

37 Wojciech Mrozik [email protected] Newcastle University

38 Judit Némethné

Sóvágó

[email protected] University of Miskolc

39 Martin Novák [email protected] Centrum výzkumu globání změny AV ČR, v.v.i.

40 Michael Owen [email protected] Forschungszentrum Jülich

41 Anna Pabis [email protected] Uppsala University, Department of Cell and

Molecular Biology

42 Saurabh

Kumar

Pandey [email protected] Institute of Nanobiology and Structural Biology

43 Miha Purg [email protected] Department of Cell and Molecular Biology,

Uppsala University

44 Anita Rágyanszki [email protected] University of Szeged

45 David Reha [email protected] INSB, Academy of Sciences of the Czech

Republic

46 Zsófia

Borbála

Rózsa [email protected] University of Szeged

47 Seung Gwan Ryoo [email protected] University of Szeged

48 Michelle Sahai [email protected] University of Roehampton

49 Christian Schröder [email protected] Department of Computational Biological

Chemistry

50 Dhiraj Sinha [email protected] INSB, Academy of Sciences of the Czech

Republic

51 Katarína Skúpa [email protected] Comenius University in Bratislava, Faculty of

Mathematics, Physics and Informatics

52 Emma Stavropoulos [email protected] Princeton University

53 Cheng Min Sung [email protected] University of Szeged

54 Veronika Szentirmai [email protected] University of Szeged

55 János Szórád [email protected] University of Szeged

56 Milán Szőri [email protected] University of Szeged

57 Laura Tociu [email protected] Princeton University

58 Jan Urban [email protected] Faculty of Mathematics, Physics and Informatics,

Comenius University in Bratislava

59 Andrea Vachová [email protected] Centrum výzkumu globání změny AV ČR, v.v.i.

60 James Valdés [email protected] Institute of Parasitology, Biology Centre of ASCR

61 Béla Viskolcz [email protected] University o Szeged

62 Jiawen Wang [email protected] University of Szeged

63 Daniel Wood [email protected] Princeton University

64 Vivian Xie [email protected] University of Szeged

65 Rui Yue [email protected] University of Szeged

Date post:	13-Jun-2018
Category:	Documents
Upload:	nguyenthuy
View:	216 times
Download:	0 times

5 VISEGRAD SYMPOSIUM ON STRUCTURAL SYSTEMS BIOLOGY · 5th VISEGRAD SYMPOSIUM ON STRUCTURAL SYSTEMS...

Documents