Protein protein interactions.pptx

protein protein interaction

1. Protein-protein interactions Submitted By: AKANKSHA 2204631 BIOCHEMISTRY (ZOM802 )

2. Protein - protein interactions Protein-protein interactions (PPIs) are the physical contacts between two or more proteins to perform complex biological functions. These interactions are stabilized by covalent or non-covalent forces . PPI are often mediated by the proteins having a specific quaternary structure. These types of proteins are generally found in plasma membranes, cytosol and in cellular organelles. Protein 1 Protein 2

3. Examples of ppi Muscle contraction Actin, Myosin, Troponin, Tropomyosin

4. Biosignalling MAP Kinase Pathway JAK-STAT Pathway

5. Forces involved in ppi a. Hydrogen Bonding H-bonding is a polar bond which arises due to polar interaction of two polar partners viz. a donor (having more electron affinity) and an acceptor (more electronegative). b. Salt bridges Salt bridges are formed between oppositely charge amino acid residue interaction. Salt bridges are relatively less in frequency at PPI interface. c. Disulphide bonds Disulfide bonds are the links between the sulfur atoms of 2 cysteine amino acid residues in proteins.

6. d. Hydrophobic interaction The hydrophobic interaction is the tendency of non-polar groups or molecules to aggregate in water solution. e. Van der waal’s force Van der Waals force is interaction of proteins with other molecules or with surfaces when they come close to each other. Salt bridges

7. Types of ppi a. Identity of Interacting Partner Homo- oligomers   If interacting protein chains are identical, they form homo-oligomer. Eg . Haemoglobin forms homo-tetramer Hetero- oligomers   If interacting protein chains are non-identical, they form hetero-oligomer. Eg . G protein coupled receptors are hetero- oligomers . Haemoglobin Serpentine Receptor

8. b. Lifetime of PPI Permanent complexes When an association between proteins is highly stable and need help from molecular switches to break them, they are permanent complexes. Eg . Hetero- trimeric G protein ( Gα , Gβγ and GDP) Transient complexes When a protein interacts briefly and in a reversible manner with other proteins in only certain biochemical cascade, they form transient complexes. Eg . Actin and myosin cross bridges

9. c. Types of interactions Covalent interactions Covalent interactions are those with the strongest association and are formed by disulphide bonds or electron sharing. Eg . Post-translational modifications such as methylation Non-covalent interactions Non-covalent bonds are usually established during transient interactions by the combination of weaker bonds, such as hydrogen bonds, ionic interactions, Van der Waals forces, or hydrophobic bonds.

10. d. Stability of Interacting Complexes Obligate partners If proteins cannot exist in free form and only stable in multimeric association, they form obligate oligomers . Eg . The Arc repressor dimer where dimerization is essential for DNA binding. Non-obligate partners If proteins can exist in free form as well, they are non obligate partners. Eg . Antigen-antibody complex Arc Repressor Dimer

11. Methods to study ppi

12. EXPERIMENTAL METHODS: In-vivo studies a. Yeast two hybrid system It detects the interactions between the query protein of interest and the known protein in yeast system. The Y2H is based on the functional reconstitution of the yeast TF Gal4 and subsequent activation of a selective reporter such as His3. Protein of interest (X) + Binding domain (BD) of a TF (Gal4) = Bait Known protein (Y) + Activation domain (AD) of a TF (Gal4) = Prey The constructed plasmids are transferred into yeast. Bait (BD-X) + Prey (AD-Y) = Transcription of reporter genes and form a functional Gal4 TF = Protein products = yeast growth in selective media Limitations: 1. Interactions of proteins outside nucleus are difficult to be studied. 2. Proteins, requiring post-translational modifications, are not suitable to study using this method.

13. YEAST TWO HYBRID SYSTEM

14. b. Fluorescence Resonance Energy Transfer FRET is a physical phenomenon of energy transfer from an excited donor- fluorophore to an acceptor- fluorophore . The transfer is non radiative and highly dependent on the distance between the two fluorophores (below 10 nm). The donor fluorophore typically emits at shorter wavelengths that overlap with the absorption spectrum of the acceptor molecule. The real time micro-imaging of interacting tagged protein partners in living cells can be done by modern microscopes.

15. In-vitro studies a. Affinity chromatography It is based on highly specific interactions between an immobilized ligand and its binding partner. The undesired molecules get eluted first and the purified solution contains only the targeted molecules.

16. b. Nuclear Magnetic Resonance (NMR) NMR is a method to study molecules by recording the interaction of radio waves with the nuclei of molecules placed in a strong magnetic field. NMR spectrum provides detailed information about the structure, dynamics and reaction state.

17. c. X-ray Diffraction (XRD) XRD is a non-invasive method to analyze the atomic structure of molecules. The basic principle behind XRD is the diffraction of X-rays when they interact with the atoms of the sample. X-rays are focused on the sample and the direction of x-rays change from the original direction to an angle θ . This is known as angle of diffraction. The angle of diffraction is used to determine the structure of a molecule.

18. computational METHODS:

19. Protein-protein interaction databases Importance of ppi The study of PPIs are important for development of new drugs. Eg . Maraviroc , inhibitor of the CCR5-gp120 interaction, is used as anti-HIV drug .  

20. References https://www.researchgate.net/publication/283897859_An_Overview_of_Protein-Protein_Interaction https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8641042/#:~:text=Protein%2Dprotein%20interactions%20(PPIs),the%20functions%20of%20unknown%20proteins https://www.csb.pitt.edu/ComputationalGenomics/Lectures/Lec26.pdf file:///C:/Users/dell/Downloads/2419-18135-1-PB.pdf