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Interfacial residues in protein�protein complexes are in the eyes of the beholder

Parvathy, J and Yazhini, A and Srinivasan, N and Sowdhamini, R (2023) Interfacial residues in protein�protein complexes are in the eyes of the beholder. In: Proteins: Structure, Function and Bioinformatics .

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Official URL: https://doi.org/10.1002/prot.26628


Interactions between proteins are vital in almost all biological processes. The characterization of protein�protein interactions helps us understand the mechanistic basis of biological processes, thereby enabling the manipulation of proteins for biotechnological and clinical purposes. The interface residues of a protein�protein complex are assumed to have the following two properties: (a) they always interact with a residue of a partner protein, which forms the basis for distance-based interface residue identification methods, and (b) they are solvent-exposed in the isolated form of the protein and become buried in the complex form, which forms the basis for Accessible Surface Area (ASA)-based methods. The study interrogates this popular assumption by recognizing interface residues in protein�protein complexes through these two methods. The results show that a few residues are identified uniquely by each method, and the extent of conservation, propensities, and their contribution to the stability of protein�protein interaction varies substantially between these residues. The case study analyses showed that interface residues, unique to distance, participate in crucial interactions that hold the proteins together, whereas the interface residues unique to the ASA method have a potential role in the recognition, dynamics, and specificity of the complex and can also be a hotspot. Overall, the study recommends applying both distance and ASA methods so that some interface residues missed by either method but crucial to the stability, recognition, dynamics, and function of protein�protein complexes are identified in a complementary manner. © 2023 Wiley Periodicals LLC.

Item Type: Journal Article
Publication: Proteins: Structure, Function and Bioinformatics
Publisher: John Wiley and Sons Inc
Additional Information: The copyright for this article belongs to author.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 04 Mar 2024 09:27
Last Modified: 04 Mar 2024 09:27
URI: https://eprints.iisc.ac.in/id/eprint/84307

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