Download Introduction to Protein-protein Interaction

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
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Protein are large biomolecules that consisting of one or more long chains of amino acids
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A protein contains at least one long polypeptide( chain of amino acids)
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Primarily the sequence of amino acid differs the protein from each other
3D structure of protein myoglobin
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AMINO­ACIDS AND POLYPEPTIDE
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Amino acid are biologically important organic compound that consists of 
Amine group( ­NH2)
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Carboxylic Acid group (­COOH)
and a side chain(­ R) 
Carboxylic group
Amine group
Structure of an α­amino acid
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Therefore the key elements of amino acid are carbon (C) , hydrogen(H) , oxygen(O) and nitrogen(N)
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AMINO­ACIDS AND POLYPEPTIDE
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Though there are about 500 amino acids, only 20 amino acid appear in genetic code
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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
Key elements of protein
3d structure of protein
Molecular structure of amino acid
chain of Amino acid
Molecular structure of peptide
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PROTEIN STRUCTURE
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Protein structure is the three­dimensional arrangement of atoms in a protein molecule
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To perform several biological functions, protein folds into one or more specific spatial conformations
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Several non­covalent interactions are responsible for this confirmations
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Levels of protein structure
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Primary structure: linear sequence of amino acids in the polypeptide chain
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Secondary structure : helical structure due to hydrogen bond between the main­chain peptide groups. E.g α­helix and β­sheets
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
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Explains the flow of genetic information from DNA to RNA, to make a functional product Protein
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Stages of Central Dogma
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Replication: Fundamental step of central dogma, make a new DNA from existing DNA by DNA polymerase
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Transcription: Make new mRNA from DNA by RNA polymerase
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Translation: Make new protein from mRNA by ribosome
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CENTRAL DOGMA
Transcription
Translation
Central Dogma of Molecular Biology
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GENE EXPRESSION VALUES
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GENE EXPRESSION VALUE
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In the field of molecular biology, gene expression profiling is the measurement of the activity of thousands of genes at once
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Gene expression values of large genes are measured by microarray
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Gene expression can be quantified by measuring either mRNA or protein
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Gene Expression Measurement Method
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Single Channel Arrays: 
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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
( http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS1388 )
Gene expression level of gene i in mRNA sample j
Single Channel Arrays: (normalized) Log2(Intensity)
Intensity (Cy 5)
Double Channel Arrays: log 2
Intensity (Cy 3)
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PROTEIN­PROTEIN INTERACTION
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PROTEIN­PROTEIN INTERACTION
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Lasting and specific physical contacts established between two or more proteins for carried out some specific biological activity
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Represents pair wise protein interactions of the organisms
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Example of PPI
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Muscle Contraction
Cellular Transportation
protein1
protein2
Protein­protein
Interaction
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PROTEIN­PROTEIN INTERACTION
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Interaction between two proteins is carried out by several biochemical events
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Electrostatic Forces:­ Force interacting between static electrically charged particles
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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
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Hydrophobic interactions:­ Maximize hydrogen bond
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TYPES OF INTERACTION 
Stability
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Structural
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Stable:­ Always stable and active e.g. Hormones, Hemoglobin
Transient:­ Control the majority of cellular processes, can be strong or weak, fast or slow 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
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http://www.medicalnewstoday.com/articles/196279.php
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http://www.chemistry.uoguelph.ca/educmat/phy456/456lec02.htm
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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/
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http://worldofbiochemistry.blogspot.in/2013_09_01_archive.html
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http://www.ch.embnet.org/CoursEMBnet/Pages3D07/documents/3Di
ntro07.pdf
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http://www.ch.embnet.org/CoursEMBnet/PagesTR08/slides/EmbNe
t_CleanEx_1.pdf
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https://en.wikipedia.org/wiki
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THANK YOU
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