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.

We present the thermal and conformational states of the spike glycoprotein (S-protein) of SARS-CoV-2 at six temperatures ranging from 3℃ to 95℃ by all-atom molecular dynamics (MD) µs-scale simulations. While corroborating with clinical results of the temperature impact on the COVID-19 infection, we examine the potential phase transitions of the S-protein in the temperature range and our simulation results revealed the following thermal properties of the S-protein: (1) It is structurally stable at 3℃, agreeing with observations that the virus stays active for more than two weeks in the cold supply chain; (2) Its structure varies more significantly for temperature window of 60℃ to 80℃ than in all other windows; (3) The sharpest structural variations occur near 60℃, signaling a plausible critical temperature nearby; (4) The maximum deviation of the receptor-binding domain at 37°C suggests the anecdotal observation 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.