Shaking the β-Bulges

Craveur, P and Narwani, TJ and Srinivasan, N and Gelly, J-C and Rebehmed, J and De Brevern, AG (2021) Shaking the β-Bulges. In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19 (1). pp. 14-18.

PDF IEEE-ACM_tra_com_bio_bio_19-1_14-18_2022.pdf - Published Version Restricted to Registered users only Download (689kB) | Request a copy

Abstract

β-bulges are irregularities inside the β-sheets. They represent more than 3 percent of the protein residues, i.e., they are as frequent as 3.10 helices. In terms of evolution, β-bulges are not more conserved than any other local protein conformations within homologous protein structures. In a first of its kind study, we have investigated the dynamical behaviour of β-bulges using the largest known set of protein molecular dynamics simulations. We observed that more than 50 percent of the existing β-bulges in protein crystal structures remained stable during dynamics while more than1/6th were not stable at all and disappeared entirely. Surprisingly, 1.1 percent of β-bulges that appeared remained stable. β-bulges have been categorized in different subtypes. The most common β-bulges' types are the smallest insertion in β-strands (namely AC and AG); they are found as stable as the whole β-bulges dataset. Low occurring types (namely PC and AS), that have the largest insertions, are significantly more stable than expected. Thus, this pioneer study allowed to precisely quantify the stability of the β-bulges, demonstrating their structural robustness, with few unexpected cases raising structural questions.

Item Type:	Journal Article
Publication:	IEEE/ACM Transactions on Computational Biology and Bioinformatics
Publisher:	Institute of Electrical and Electronics Engineers Inc.
Additional Information:	The copyright for this article belongs to the Institute of Electrical and Electronics Engineers Inc.
Keywords:	Molecular dynamics, Dynamical behaviours; Homologous proteins; Protein conformation; Protein molecular dynamics simulation; Protein residues; Structural robustness, Proteins, protein, beta sheet; genetics; molecular dynamics; protein conformation; protein secondary structure, Molecular Dynamics Simulation; Protein Conformation; Protein Conformation, beta-Strand; Protein Structure, Secondary; Proteins
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	14 Jul 2022 04:56
Last Modified:	14 Jul 2022 04:56
URI:	https://eprints.iisc.ac.in/id/eprint/74356

Actions (login required)

View Item