Modeling of the thermal properties of SARS-CoV-2 S-protein

Ziyuan Niu, Karin Hasegawa, Yuefan Deng, Ziji Zhang, Miriam Rafailovich, Marcia Simon, Peng Zhang

Research output: Contribution to journalArticlepeer-review

Abstract

We calculate the thermal and conformational states of the spike glycoprotein (S-protein) of SARS-CoV-2 at seven temperatures ranging from 3°C to 95°C by all-atom molecular dynamics (MD) µs-scale simulations with the objectives to understand the structural variations on the temperatures and to determine the potential phase transition while trying to correlate such findings of the S-protein with the observed properties of the SARS-CoV2. Our simulations revealed the following thermal properties of the S-protein: 1) It is structurally stable at 3°C, agreeing with observations that the virus stays active for more than two weeks in the cold supply chain; 2) Its structure varies more significantly at temperature values of 60°C–80°C; 3) The sharpest structural variations occur near 60°C, signaling a plausible critical temperature nearby; 4) The maximum deviation of the receptor-binding domain at 37°C, corroborating the anecdotal observations that the virus is most infective at 37°C; 5) The in silico data agree with reported experiments of the SARS-CoV-2 survival times from weeks to seconds by our clustering approach analysis. Our MD simulations at µs scales demonstrated the S-protein’s thermodynamics of the critical states at around 60°C, and the stable and denatured states for temperatures below and above this value, respectively.

Original languageEnglish (US)
Article number953064
JournalFrontiers in Molecular Biosciences
Volume9
DOIs
StatePublished - Sep 27 2022

Keywords

  • conformational state
  • molecular dynamics
  • S-protein
  • SARS-CoV-2
  • thermodynamics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

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