Work

Computational Analyses of Bifurcated Inter‐Protein Interactions in Protein–Protein Assemblies Reveal Their Pivotal Role in Conferring Stability

Year: 2025

Type: article

Abstract: Majority of the proteome is constituted by oligomers and their function is governed by underlying protein-protein interactions. Interfacial residues, namely residues right at the interface of two protein chains, are known to confer stability and specificity in dimers. However, other interactions play a significant role in the formation and maintenance of oligomers in protein assemblies as well. Inter-protein bifurcated interactions are those where one residue simultaneously interacts with two residues belonging to two neighboring protein chains. The characteristic features of such higher-order interactions remain largely unexplored and unknown. In this study, we focused on residues specifically involved in bifurcated interactions (referred as RBI). We examine the bifurcated inter-protein interactions by assembling a dataset of protein assemblies of known 3D structures. We have characterized the type of interactions and the residues involved in the interactions using parameters like energy contributions and conservation scores. We find that the residues participating in bifurcated inter-protein interactions contribute more to the stability of the complex than other interfacial residues. Furthermore, we have presented examples where mutation of a residue involved in a bifurcated interaction results in detrimental outcomes. This study highlights the significance of inter-protein bifurcated interactions that contribute to the stability of multiple interfaces in protein oligomers and hence contribute to the expansion of the understanding of protein assemblies.

Source: Proteins Structure Function and Bioinformatics

DOI: 10.1002/prot.70090

Authors: Sneha Bheemireddy, Revathy Menon, Sreenivas Chavali, Ramanathan Sowdhamini, Narayanaswamy Srinivasan

Institutions: Tata Institute of Fundamental Research, National Centre for Biological Sciences, Indian Institute of Science Bangalore, Indian Institute of Science Education and Research, Tirupati

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $4,550