TitleThe alteration of structural network upon transient association between proteins studied using graph theory.
Publication TypeJournal Article
Year of Publication2023
AuthorsPrabantu VManjveekar, Tandon H, Sandhya S, Sowdhamini R, Srinivasan N
Date Published2023 Oct 30

Proteins such as enzymes perform their function by predominant non-covalent bond interactions between transiently interacting units. There is an impact on the overall structural topology of the protein, albeit transient nature of such interactions, that enable proteins to deactivate or activate. This aspect of the alteration of the structural topology is studied by employing protein structural networks, which are node-edge representative models of protein structure, reported as a robust tool for capturing interactions between residues. Several methods have been optimized to collect meaningful, functionally relevant information by studying alteration of structural networks. In this article, different methods of comparing protein structural networks are employed, along with spectral decomposition of graphs to study the subtle impact of protein-protein interactions. A detailed analysis of the structural network of interacting partners is performed across a dataset of around 900 pairs of bound complexes and corresponding unbound protein structures. The variation in network parameters at, around, and far away from the interface are analyzed. Finally, we present interesting case studies, where an allosteric mechanism of structural impact is understood from communication-path detection methods. The results of this analysis are beneficial in understanding protein stability, for future engineering, and docking studies.

Alternate JournalProteins
PubMed ID37902388
Grant ListBT/PR40187/BTIS/137/9/2021 / / Department of Biotechnology, Ministry of Science and Technology, India /
IBAB/MSCB/182/2022 / / Institute of Bioinformatics and Applied Biotechnology /
JBR/2021/000006 / / Science and Engineering Research Board /