Molecular modeling and dynamics study of nonsynonymous SNP in bread wheat HSP16.9B gene

Abstract

An ubiquitous molecular chaperon, small heat shock proteins (sHSP) maintain protein homeostasis under stress conditions. Single nucleotide polymorphism was predicted in HSP16.9B gene but so far its impact on protein structure has not been extensively studied. Keeping this point in mind, we applied computational methods and performed molecular dynamics simulation to examine the effect of aspartic acid substitution for asparagine at 11th position (D11N) in HSP16.9B. Furthermore, the secondary structural analysis revealed an addition of beta sheet before the mutation point in the mutant protein. Three dimensional protein structure modeling, validation of structures and molecular dynamics were performed to study the mechanism of the non-synonymous single nucleotide polymorphism on structural changes. The root mean square deviation (RMSD) result showed the stability of the mutated structure throughout simulations. Moreover, root mean square fluctuation (RMSF) of atoms and Hydrogen-bond patterns further supported our results.