Protein protein interaction, functional proteomics

Introduction��Types of Protein-protein interactions��Effects of Protein-Protein Interactions��Protein-Protein Interaction Identification Methods :��- Experimental (In vivo) Yeast two hybrid system�- Experimental (In vitro) Co-immunoprecipitation, ChIP, Affinity Blotting, Protein Probing �- Computational (In silico) Database of interacting proteins, VisANT etc.

Conclusion�References

1. FUNCTIONAL PROTEOMICS Protein-Protein interaction By KAUSHAL KUMAR SAHU Assistant Professor (Ad Hoc) Department of Biotechnology Govt. Digvijay Autonomous P. G. College Raj-Nandgaon ( C. G. )

2. CONTENTS Introduction Types of Protein-protein interactions Effects of Protein-Protein Interactions Protein-Protein Interaction Identification Methods : - Experimental ( In vivo ) Yeast two hybrid system - Experimental ( In vitro ) Co-immunoprecipitation, ChIP , Affinity Blotting, Protein Probing - Computational ( In silico ) Database of interacting proteins, VisANT etc. Conclusion References

3. FUNCTIONAL - having a special activity, purpose, or task. PROTEOMICS - the study of proteomes and their functions. the full complement of proteins that occur within a cell, tissue, or organism Word Origin - protein + gen  ome. Protein often work together i.e. in combination with other proteins. So, one single protein cannot give the information of its working because to be in action proteins need to interact with other proteins. Hence, to understand the function we simply need to understand the interaction and links between them which further gives the idea of how it works. INTRODUCTION

4. PROTEIN-PROTEIN INTERACTIONS Understanding of biological activities understanding of diseases the basis for new therapeutic approaches

5. TYPES OF PROTEIN-PROTEIN INTERACTIONS On the basis of their composition : HOMOLIGOMERS HETEROLOIGOMERS ex : PPIs in muscle contraction ex : PPI between Cytochrome Oxidase and TRPC3

6. TYPES OF PROTEIN-PROTEIN INTERACTIONS On the basis of duration : STABLE TRANSIENT ex : Hemoglobin structure ex : muscle contraction

7. EFFECTS OF PROTEIN-PROTEIN INTERACTION Protein interactions are one common mechanism to allow for substrate channeling. Can result in the formation of a new binding site. • Can inactivate a protein • Can change the specificity of a protein for its substrate • Identify the different interactions, understand the extent to which they take place in the cell, and determine the consequences of the interaction.

8. PROTEIN-PROTEIN INTERACTION IDENTIFICATION METHODS

9. PROTEIN-PROTEIN INTERACTION IDENTIFICATION METHODS Another way of classification for methods for identification of PPIs The first is ‘atomic observation ’ in which the protein interaction detected using, for example, X-ray crystallography . These experiments can yield specific information on the atoms or residues involved in the interaction. • The second is a ‘ direct interaction observation ’ where protein interaction between two partners can be detected as in a two-hybrid experiment. • At a third level of observation, multi-protein complexes can be detected using methods such as immuno-precipitation or mass specific analysis . This type of experiment does not reveal the chemical detail of the interactions or even reveal which proteins are in direct contact but gives information as to which proteins are found in a complex at a given time .

10. Experimental ( In vivo ) YEAST TWO HYBRID SYSTEM

11. Experimental ( In vitro ) CO-IMMUNOPRECIPITATION (co-IP) Co-immunoprecipitation (co-IP) is a popular technique for protein interaction discovery. Co-IP is conducted in essentially the same manner as an immunoprecipitation (IP) of a single protein, except that the target protein precipitated by the antibody, also called the “bait”, is used to coprecipitate a binding partner/protein complex, or “prey”, from a lysate. Gives the idea of two things : Presence of a particular protein. Interaction idea between proteins. A Protein Complex

12. Experimental ( In vitro ) CHROMATIN-IMMUNOPRECIPITATION (Ch-IP) Chromatin immunoprecipitation (Ch-IP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or other DNA binding sites. Cross link Shear DNA Immunoprecipitate Isolate antibody-protein-DNA complex Isolate DNA Sequence the nucleotide fragment

13. Experimental ( In vitro ) AFFINTY BASED INTERACTION Analogous to the use of affinity columns, proteins can be fractionated by PAGE transferred to a nitrocellulose membrane, and identified by their ability to bind a protein, peptide, or other ligand. Gives the idea of two things : Presence of a particular protein. Interaction idea between proteins. Affinity Chromatography Affinity Blotting

14. Experimental ( In vitro ) PROTEIN PROBING A labeled protein can be used as a probe to screen an expression library in order to identify genes encoding proteins that interact with this probe.   Interactions occur on nitrocellulose filters between an immobilized protein and the labeled probe protein.

15. Computational ( In silico ) Protein–protein interactions are only the raw material for networks. To build a network, researchers typically combine interaction data sets with other sources of data and develop interaction maps. Primary databases that contain protein–protein interactions include : DIP ( http://dip.doe-mbi.ucla.edu ) BioGRID IntAct ( http://www.ebi.ac.uk/intact ) MINT ( http://mint.bio.uniroma2.it ) How to Build Biological Networks?   • Search/Retrieve from knowledge bases • Predict from genome sequences • Predict from “omics” data • Predict from literature • Integrate and analyze • Meta-networks from genome scale data analysis

16. Computational ( In silico ) Nodes represents proteins     Edges represents interaction/connections Biological Networks – Basic Features: 1) Degree • Number of connections that a node has. 2) Distance • Number of connections between two nodes, in a shortest path. 3) Path • A sequence of connections • Is there a path (reachability) • Mean Shortest Path distance(closeness) • In how many shortest paths(betweenness). 4) Size of a network (Number of nodes) • Density of a network on of the connections • Motifs/Cliques/Clusters/Sub-networks

17. Computational ( In silico ) Why Build/Analyze Biological Networks? Types of Biological Networks :   DNA-Protein RNA-RNA RNA-Protein Protein-Protein

18. Computational ( In silico ) Integrated Data Sources Available Interaction Network Data

19. Experimental ( In vitro ) Database of Interacting Proteins (DIP)   Study : Protein function, Protein-protein relationship, Evolution of protein-protein interaction, The network of interacting proteins, The environments of protein-protein interactions   Predict : Unknown protein-protein interaction, The best interaction conditions   The current status of DIP   • Number of proteins: 6978 • Number of organisms: 101 • Number of interactions:18260 • Number of distinct experiments describing an interaction: 22229 • Number of articles: 2203

20. Experimental ( In vitro ) BioGRID https://thebiogrid.org/ The  Biological General Repository for Interaction Datasets  ( BioGRID ) is a biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID) by Mike Tyers , Bobby-Joe Breitkreutz, and Chris Stark at the Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital.

21. CONCLUSION Proteins are the building blocks of our body. Study of their interaction is necessary to understand its working. Simply two or more proteins cannot reveal of how they actually work. So, there is need to understand the complete interaction of a protein at a time and at a particular situation in which bioinformatics and its tools play a vital role.

22. REFERENCES Bioinformatics and Functional Genomics, Second Edition, Jonathan Pevsner Bioinformatics and Functional Genomics, Third Edition, Jonathan Pevsner https://thebiogrid.org/ YOUTUBE LINKS https://www.youtube.com/watch?v=dlBAf8CEG_o https://www.youtube.com/watch?v=8F_SFymyMCw https://www.youtube.com/watch?v=vp9r3rkGv1Q https://www.youtube.com/watch?v=QpZ5Cv7YVvk https://www.youtube.com/results?search_query=CO-IMMUNOPRECIPITATION