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The alteration of structural network upon transient association between proteins studied using graph theory
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  • Ramanathan Sowdhamini,
  • Vasam Prabantu,
  • Himani Tandon,
  • Sankaran Sandhya,
  • Narayanaswamy Srinivasan
Ramanathan Sowdhamini
Indian Institute of Science Molecular Biophysics Unit

Corresponding Author:mini@ncbs.res.in

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Vasam Prabantu
Indian Institute of Science Molecular Biophysics Unit
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Himani Tandon
Indian Institute of Science Molecular Biophysics Unit
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Sankaran Sandhya
Indian Institute of Science Molecular Biophysics Unit
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Narayanaswamy Srinivasan
Indian Institute of Science Molecular Biophysics Unit
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Abstract

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 optimised 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 analysed. 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.
31 May 2023Submitted to PROTEINS: Structure, Function, and Bioinformatics
31 May 2023Submission Checks Completed
31 May 2023Assigned to Editor
31 May 2023Review(s) Completed, Editorial Evaluation Pending
06 Jun 2023Reviewer(s) Assigned
17 Jul 2023Editorial Decision: Revise Minor
01 Sep 20231st Revision Received
01 Sep 2023Submission Checks Completed
01 Sep 2023Assigned to Editor
01 Sep 2023Review(s) Completed, Editorial Evaluation Pending
04 Sep 2023Reviewer(s) Assigned
14 Sep 2023Editorial Decision: Accept