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
Methods
Experimental
In Vitro
In Vivo
Computational

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_Pr
otein-Protein_Interaction
 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8641042/#:~:text=Protein%
2Dprotein%20interactions%20(PPIs),the%20functions%20of%20unknown%2
0proteins
 https://www.csb.pitt.edu/ComputationalGenomics/Lectures/Lec26.pdf
 file:///C:/Users/dell/Downloads/2419-18135-1-PB.pdf