Course Title
BCH 305/ Department of Biochemistry
Ogbonna, C. U.
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PROTEIN-PROTEIN
INTERACTION
Description
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Heading Title
• Almost all the cellular processes occur through Protein-Protein-Interactions
(PPIs) - physical and functional interactions between molecules in living
systems
• This calls for better understanding of the structural basis of PPIs remains
an important endeavor
• Advances in high throughput PPI identification techniques, has helped the
identification of the interface residues
• Such identification promotes drug development, elucidation of molecular
pathways, generation of protein mimetics and understanding of disease
mechanisms
Figure 1. Protein-protein interaction
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Figure 2. A pictorial representation of a protein-
protein interaction complex
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PPI Interface
• Protein-protein interaction is becoming one of the major objectives of
system biology.
• Noncovalent contacts between the residue side chains are the basis for
protein folding, protein assembly, and PPI
• Over 80% of proteins do not operate alone but in complexes
• Proteins involved in the same cellular processes are repeatedly found to be
interacting with each other
• The functions of unidentified proteins can be predicted on the evidence of
their interaction with a protein, whose function is already revealed
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Mediators of PPI
• PPI are mediated by a varied set of proteins but often done by the
proteins having a specific quaternary structure.
• They are found in the
• membranes (as transporters or channels or receptors etc.),
• cytosol (like ribosomes, carrier proteins, chaperones and several other enzymes)
and in different sub cellular organelles.
• Molecular interactions of proteins are diverse and are, according to the
affinity - strong or weak
• Interacting interface showed conserved amino acid residues at interacting
surfaces (like hydrophobic protein core with polar surfaces).
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Benefits
• Enzyme regulation, stability and activation
• Caspase-9 together with Apaf1, cofactor, and Cytochrome C and ATP forms an
apoptosome, an oligomeric form that helps the enzyme to produce its active form by
dimerization
• Channels and receptor functions
• Receptors like tyrosine kinase phosphates alpha present on the cell surface work
mainly as a weak homodimer,
• Allosteric regulation, activation and inhibition.
• While Hemoglobins are unloaded with O2, subunits of hemoglobin are in T (tense)
state and after loading of O2 it becomes to be in R (relaxed) state.
• Signal transmission
• Combination of different proteins to transmit signals.
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Classification of PPIs
• The categories depend on
• The type of interacting partners,
• Stability of the PPI complexes,
• Time-span of the interactions between the protein partners,
• Nature of the interface between the proteins
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Identity of Interacting Partners
• Identical interacting protein chains form homo-oligomer
• Non-identical partners form heterooligomers
• Eg. Haemoglobin forms homo-tetramer while G protein coupled receptors are
example of
• hetero-oligomers.
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Stability of Interacting Complexes
• Protomers that cannot exist in free form and only stable in multimeric
association form obligate oligomers (Homo-obligomers and/or heteroobligomers)
• They may be obligate or nonobligate
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Lifetime of PPI
• Permanent complexes highly stable association between protomers which
need help from molecular switches to break.
• Transient or permanent
• Transient interactions would form signaling pathways while permanent
interactions will form a stable protein complex.
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Nature of the Interaction Interface
• Protomers which use the same interacting interface to join each other are
called isologous complex
• Heterologous assembly protomers use different interfaces to form PPI
without any closed symmetry.
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PPIs can
• (i) Modify the kinetic properties of enzymes
• (ii) Act as a general mechanism to allow for substrate channeling
• (iii) Construct a new binding site for small effector molecules
• (iv) Inactivate or suppress a protein
• (v) Change the specificity of a protein for its substrate through interaction
with different binding partners
• (vi) Serve a regulatory role in either upstream or downstream level
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Classification of PPI Detection Methods
• The in vitro methods in PPI detection are tandem affinity purification,
affinity chromatography, coimmunoprecipitation, protein arrays, protein
fragment complementation assay, phage display, X-ray crystallography, and
NMR spectroscopy.
• The in vivo methods in PPI detection are yeast two-hybrid (Y2H, Y3H) and
synthetic lethality.
• The in silico methods in PPI detection are sequence-based approaches,
structure-based approaches, chromosome proximity, gene fusion, in silico 2
hybrid, mirror tree, phylogenetic tree, and gene expression-based
approaches.
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