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Comparative analysis of permanent and transient domain-domain interactions in multi-domain proteins
  • Ramanathan Sowdhamini,
  • Swayam Prakash Das Sidhanta,
  • Narayanaswamy Srinivasan
Ramanathan Sowdhamini
Indian Institute of Science Molecular Biophysics Unit

Corresponding Author:mini@ncbs.res.in

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Swayam Prakash Das Sidhanta
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

Protein domains are structural, functional, and evolutionary units. These domains bring out the diversity of functionality by means of interactions with other co-existing domains and provide stability. Hence, it is important to study intra-protein inter-domain interactions from the perspective of types of interactions. Domains within a chain could interact over short timeframes or permanently, rather like protein-protein interactions (PPIs). However, no systematic study has been carried out between two classes, namely permanent and transient domain-domain interactions (DDIs). In this work, we studied 264 two-domain proteins, belonging to either of these classes and their interfaces on the basis of several factors, such as interface area and details of interactions (number, strengths, and types of interactions). We also characterized them based on residue conservation at the interface, correlation of residue motions across domains, its involvement in repeat formation, and their involvement in particular molecular processes. Finally, we could analyse the interactions arising from domains in two-domain monomeric proteins, and we observed significant differences between these two classes of domain interactions and a few similarities. This study will help to obtain a better understanding of structure-function and folding principles of multi-domain proteins.
01 Jun 2023Submitted to PROTEINS: Structure, Function, and Bioinformatics
01 Jun 2023Submission Checks Completed
01 Jun 2023Assigned to Editor
01 Jun 2023Review(s) Completed, Editorial Evaluation Pending
05 Jun 2023Reviewer(s) Assigned
11 Jul 2023Editorial Decision: Revise Minor
10 Aug 20231st Revision Received
10 Aug 2023Submission Checks Completed
10 Aug 2023Assigned to Editor
10 Aug 2023Review(s) Completed, Editorial Evaluation Pending
11 Aug 2023Editorial Decision: Accept