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INTRODUCTION TO PROTEINPROTEIN INTERACTION
PRATIK DUTTA,1621CS05,
AINLPML Group,CSE Dept, IIT PATNA
Guidance By: Dr. Sriparna Saha
OUTLINE OF THE PRESENTATION What is Protein?? Protein Structure RNA/DNA/ Gene/ Protein Central Dogma of Biology Microarray and Gene Expression Data Proteinprotein Interaction Protein Interaction Network Conclusion
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WHAT IS PROTEIN Protein are large biomolecules that consisting of one or more long
chains of amino acids A protein contains at least one long polypeptide( chain of amino
acids) Primarily the sequence of amino acid differs the protein from
each other
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3D structure of protein myoglobin
AMINOACIDS AND POLYPEPTIDE Amino acid are biologically important organic compound that
consists of Amine group( NH2) Carboxylic Acid group (COOH) and a side chain( R)
Therefore the key elements of amino acid are carbon (C) , hydrogen(H) , oxygen(O) and nitrogen(N)
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Amine group
Carboxylic group
Structure of an amino acidα
AMINOACIDS AND POLYPEPTIDE Though there are about 500 amino acids, only 20 amino acid
appear in genetic code When two or more amino acid is connected through peptide bond
it is called polypeptide(amino acid chain)
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STRUCTURAL ELEMENTS OF PROTEIN
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3d structure of protein
chain of Amino acid Molecular structure
of peptide
Molecular structure of amino acid
Key elements of protein
PROTEIN STRUCTURE Protein structure is the threedimensional arrangement of
atoms in a protein molecule To perform several biological functions, protein folds into one or
more specific spatial conformations Several noncovalent interactions are responsible for this
confirmations Levels of protein structure
Primary structure: linear sequence of amino acids in the polypeptide chain
Secondary structure : helical structure due to hydrogen bond between the mainchain peptide groups. E.g helix and sheetsα β
Tertiary structure: folded into a compact globular structure due to hydrophobic interactions
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THE CENTRAL DOGMA Relation between DNA, RNA and proteins
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CENTRAL DOGMA Explains the flow of genetic information from DNA to RNA, to make
a functional product Protein Stages of Central Dogma
Replication: Fundamental step of central dogma, make a new DNA from existing DNA by DNA polymerase
Transcription: Make new mRNA from DNA by RNA polymerase
Translation: Make new protein from mRNA by ribosome
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CENTRAL DOGMA
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Transcription
Translation
Central Dogma of Molecular Biology
GENE EXPRESSION VALUES
† AINLPML GROUP, IIT PATNA †
GENE EXPRESSION VALUE In the field of molecular biology, gene expression profiling is the
measurement of the activity of thousands of genes at once Gene expression values of large genes are measured by microarray Gene expression can be quantified by measuring either mRNA or
protein Gene Expression Measurement Method
Single Channel Arrays: Give estimations of the absolute levels of gene expression compare two set of condition for each gene requires two separate singledye hybridizations
Two Channel Arrays: Two hybridized cDNA samples (e.g. diseased tissue versus healthy tissue) and labelled with
two different fluorescentdyes(Cy5 and Cy3)
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GENE EXPRESSION VALUE
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GENE EXPRESSION DATASET
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Gene expression level of gene i in mRNA sample j
( http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS1388 )
Single Channel Arrays: (normalized) Log2(Intensity)
Double Channel Arrays: )3(
)5(log2 CyIntensity
CyIntensity
PROTEINPROTEIN INTERACTION
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PROTEINPROTEIN INTERACTION Lasting and specific physical contacts established between two or
more proteins for carried out some specific biological activity Represents pair wise protein interactions of the organisms Example of PPI
Muscle Contraction Cellular Transportation
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protein1
protein2
ProteinproteinInteraction
PROTEINPROTEIN INTERACTION Interaction between two proteins is carried out by several
biochemical events Electrostatic Forces: Force interacting between static electrically
charged particles
Hydrogen bonds: electrostatic attraction between hydrogen(H) and highly electronegative atom(e.g. O, N)
Van der Waals forces: residual attractive or repulsive forces between molecules or atomic groups
Hydrophobic interactions: Maximize hydrogen bond
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TYPES OF INTERACTION Stability
Stable: Always stable and active e.g. Hormones, Hemoglobin Transient: Control the majority of cellular processes, can be strong or weak, fast
or slow
Structural Homooligomer : Same type of subunits e.g. Enzymes Heterooligomer: Different types of subunits e.g. Gproteins
Chemical Bonding Covalent Bonding: Share electron pairs Noncovalent Bonding: Rather sharing electrons , involves in some
electromagnetic forces
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IMPORTANCE OF PPI NETWORK Useful for isolating groups of interacting proteins
that participate in the same biological process Helps to understand the mechanism of
regulating cell life Useful to predict the biological functions of
uncharacterized proteins
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REFERENCES http://www.medicalnewstoday.com/articles/196279.php http://www.chemistry.uoguelph.ca/educmat/phy456/456lec02.htm http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aliph
atic.html http://www.particlesciences.com/news/technicalbriefs/2009/protein
structure.html http://www.slideshare.net/NaghmehPoorinmohamma/proteinprotein
interactionppi http://www.clearbiology.com/biochemistryreviewactivity/proteins/ http://worldofbiochemistry.blogspot.in/2013_09_01_archive.html http://www.ch.embnet.org/CoursEMBnet/Pages3D07/documents/3Di
ntro07.pdf http://www.ch.embnet.org/CoursEMBnet/PagesTR08/slides/EmbNe
t_CleanEx_1.pdf https://en.wikipedia.org/wiki 08/02/17
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THANK YOU