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The alteration of structural network upon transient association between proteins studied using graph theory

Prabantu, VM and Tandon, H and Sandhya, S and Sowdhamini, R and Srinivasan, N (2023) The alteration of structural network upon transient association between proteins studied using graph theory. In: Proteins: Structure, Function and Bioinformatics .

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Official URL: https://doi.org/10.1002/prot.26606


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. © 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.
Keywords: allosterism; article; case report; clinical article; decomposition; human; protein protein interaction; protein stability; protein structure; spectroscopy
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 04 Mar 2024 09:39
Last Modified: 04 Mar 2024 09:39
URI: https://eprints.iisc.ac.in/id/eprint/84377

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