Structural and molecular analysis of SARSCoV-2 spike protein following S494P point mutations using bioinformatics and molecular dynamics methods.

Subject Areas : bioinformatics

Mehr Ali  Mahmood Janlou ¹ (Department of Biophysics, Faculty of Biological science, Gorgan Branch, Islamic Azad University, Gorgan, Iran)
Hasan  Saheb jamii ² (Department of Biophysics, Faculty of Biological science, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran)
elham  tazikeh lemeski ³ (Department of Chemistry, Gorgan Branch, Islamic Azad University, Gorgan, Iran)

Received: 2022-02-19 Accepted : 2022-04-18 Published : 2021-11-22

Keywords: docking, MD simulation, SARS-CoV-2, S494P, Spike protein, RBD,

Abstract :

The emergence of some mutations in the SARS-CoV-2 receptor binding domain (RBD) can increase the spread and pathogenicity due to the conformational changes and increase the stability of Spike protein. Due to the formation of different strains of SARS-CoV-2 by mutations, and their catastrophic effect on public health, the study of the effect of mutations by scientists and researchers around the world is inevitable. According to available evidence, the S494P variant is observed in several SARS-CoV-2 strains from Michigan, USA. To investigate how the S494P natural mutation alters receptor binding affinity in RBD, we performed structural analysis of wild-type and mutant spike proteins using some bioinformatics and computational tools. The results show that S494P mutation increases the spike protein stability. Also, applying docking by HADDOCK displayed higher binding affinity to hACE2 for mutant spike than wild type possibly due to the increased β-strand and Turn secondary structures which increases surface accessibly surface area (SASA) and the chance of interaction. The analysis of S494P as a critical RBD mutation may provide the continuing surveillance of spike mutations to aid in the development of COVID-19 drugs and vaccines.