Structural analysis of novel amino acid substitutions in SARS-CoV-2 spike protein receptor-binding domain

Abstract

There are several novel amino acid substitutions in SARS-CoV-2 spike protein, which could account for the increased infectivity of this newly emerged virus. Therefore, in this paper we aimed to evaluate the potential effects of these amino acid substitutions on protein structure and function. For this purpose, we made use of several state-of-the-art computational tools and performed in silico analyses on protein similarity, 2D and 3D structure, ligand binding and biological function. We found that some of the novel amino acid changes caused significant structural alterations both at the secondary and tertiary structure level, possibly affecting the interaction between the spike protein receptor-binding domain (RBD) and ACE2, as well as other ligands. In conclusion, data we provided here is a significant contribution to our current knowledge of the SARS-CoV-2 virus and will aid in having a better understanding of its molecular differences, mechanism of infection and the cellular processes it affects in the host in order to develop better therapies and vaccines.