Protein protein interactions

Proteins folding and denaturation

1. PROTEIN-PROTEIN INTERACTIONS

2. Definition; Protein–protein interactions  ( PPI s ) are physical contacts of high specificity established between two or more protein molecules   to carry out their biological functions effectively as result of these interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect.

3. Introduction; Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. The protein –protein interaction have commonly been termed the ‘ INTERACTOME’ by scientists. French researchers first coined the term "interactome" in 1999; the first protein-protein interactome data appeared in 2000.     Why we study PPI? Protein-protein interactions determine outcome of most cellular processes. Proteins which are close homologues often interact in the same way

4. Protein-protein interactions provide evolutionary history of protein sequence and structural divergence PPIs are Pre-cursor to networks. Finding interactions between proteins involved in common cellular functions is a way to get a broader view of how they work cooperatively in a cell. Experimental studies indicate that many diseases that are related to molecular events occur due to lack of protein-protein interactions. Studying protein interactions, especially disease-related, beneficial for the process of drug design.

5. Protein b unknown Protein a known Interaction Better understanding of protein b’s function

6. Protein b Function b Protein a Function a Interaction Detecting relationship between pathways Detecting new pathways

7. Signal Transduction

8. Importance of PPIs Important field in cell biology & biochemistry. Posttranslational modifications. Signaling networks. Important field in viral replication which is very difficult to predict. Crucial for the understanding of the biological pathways, like cell signaling . PPI dysfunctions may lead to disease situations. Important targets for therapy  and drug designing.

9.   PPIs Classification Based on Affinity Obligate Non-obligate On The Basis of Stability\Duration of interaction Permanent Transient On The Basis Of Composition Homo- Oligomers Hetero-oligomers On The Basis Of Bonding Covalent Non-covalent

10. Role Of Water in PPIs Water molecules play a significant role in the interactions between proteins.  The crystal structures of complexes, obtained at high resolution from different but homologous proteins, have shown that some interface water molecules are conserved between homologous complexes. The majority of the interface water molecules make hydrogen bonds with both partners of each complex. Some interface amino acid residues or atomic groups of one protein partner engage in both direct and water mediated interactions with the other protein partner.

11. Indirect interactions, mediated by two water molecules, are more numerous in the homologous complexes of low affinity. Thus, water molecules may facilitate the interactions .

12. Yeast Two Hybrid System Also known as Y2H or two-hybrid screening. Molecular biology technique used to discover protein-protein interactions and protein–DNA interactions . Testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. Pioneered by Stanley Fields and Ok-kyu Song in 1989 .

13. Yeast two hybrid system Simple transcription Reporter Gene Transcription Complex Transcription DBD DBD = DNA Binding Domain AD AD = Activation Domain Upstream Activating Sequence UAS

14. Yeast two hybrid system Hybrid proteins DBD Bait AD fish

15. Reporter gene Transcription Complex transcription UAS DBD BAIT AD FISH Yeast two hybrid system Hybrid proteins

16. Yeast two hybrid system plasmids Plasmid A promoter DBD bait Plasmid B promoter AD fish Yeast

17. Applications Of PPI s Many PPIs are being used as therapeutic targets as they exhibit properties such as allosteric sites. Maraviroc, a drug that inhibits CCR5 gp 120 interaction and is a prominent anti HIV drug. Recently , a group of scientists were able to develop 30 peptides using protein–protein interaction studies to inhibit telomerase recruitment towards telomeres. PPIs have been used to identify the functions of unknown proteins. It is based on the assumption that uncharacterized proteins have similar functions as their interacting proteins

18. Protein concentration, which in turn are affected by expression levels and degradation rates. Protein affinity for proteins or other binding ligands. Ligands concentrations (substrates, ions, etc.). Presence of other proteins, nucleic acids, and ions. Electric fields around proteins. Occurrence of covalent modifications.

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