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