Title: Extrapolating the effect of non-synonymous SNP in bread wheat HSP16.9B gene: a molecular modelling and dynamics study
Authors: Bharati Pandey; Saurabh Gupta; Atmakuri Ramakrishna Rao; Dev Mani Pandey; Ravish Chatrath
Addresses: Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand – 835215, India ' Department of Bioinformatics, Indian Institute of Information Technology, Allahabad – 211015, India ' Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi – 110012, India ' Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand – 835215, India ' ICAR-Indian Institute of Wheat & Barley Research (IIWBR), Karnal – 132001, India
Abstract: Small heat shock proteins (sHSP) are molecular chaperons which play a key role in protein homeostasis under stress conditions. Point mutation of aspartic acid (D) substitution for asparagine (N) at residue 11 (D11N) in HSP16.9B protein was predicted in HSP16.9B gene in wheat. However, its impact on protein function and structural consequences has not been explored. In this study, we examined the effect of point mutation using molecular modelling and molecular dynamics (MD) simulations. Moreover, point mutation induced addition of beta-sheet before the mutation position in the mutant protein. Three-dimensional homology protein modelling, structure validation, and molecular dynamics were carried out to investigate the conformational transitions and dynamics of the HSP16.9B protein due to D11N non-synonymous single nucleotide polymorphism (nsSNP). The MD results indicated that the stability of the mutant protein structure during entire simulation runs. Altogether, our investigation will provide useful understanding related to structural and functional basis of HSP16.9.
Keywords: molecular dynamics simulations; heat shock protein; molecular modelling; secondary structure.
International Journal of Bioinformatics Research and Applications, 2020 Vol.16 No.1, pp.101 - 116
Accepted: 23 Dec 2017
Published online: 02 Feb 2020 *