IR spectra of COVID-2019 virus (SARS-CoV-2) protein.

The source of the MD simulation trajectories and structures we use to simulate the IR spectra of SARS-CoV-2 virus were obtained from Komatsu and co-workers (MD simulation trajectories of SARS-CoV-2) and D. E. Shaw research (MD simulation trajectories of SARS-CoV-1-ACE2, SARS-CoV-2-ACE2 and trimeric SARS-CoV-2 spike glycoprotein, receptor-binding domain of the SARS-CoV-2 spike and the human ACE2 receptor), respectively. The criteria of the snapshots chosen and the time steps of the obtained snapshots were stated as below:<br> (1) For the snapshots of SARS-CoV-1 were chosen from 2 ns MD simulation, in total 1000 configurations were extracted with a 2 ps time step interval for calculating the IR spectra.<br> (2) For the snapshots of SARS-CoV-2 were chosen from 10 us MD simulation, in total 10000 configurations were extracted with a 1 ns time step interval for calculating the IR spectra. <br> (3) For the snapshots of SARS-CoV-1-ACE2 were chosen from 10 us MD simulation, in total 8334 configurations were extracted with a 1.2 ns time step interval from start time 1200ps – 10us for calculating the IR spectra. <br> (4) For the snapshots of SARS-CoV-2-ACE2 were chosen from 10 us MD simulation, in total 8334 configurations were extracted with a 1.2 ns time step interval from start time 1200ps – 10us for calculating the IR spectra.<br> (5) For the snapshots of Trimeric SARS-CoV-2 spike glycoprotein (closed state) were chosen from 10 us MD simulation, a total of 8334 configurations were extracted with an 1.2 ns interval from start time 1200ps – 10us (contains 9 trajectories, 1000 snapshots for No.1-8 trajectories, 334 snapshots for No.9 trajectory). We chose the first 800 snapshots in each of No.1-8 trajectories (6400 in total) to calculate the IR spectra.<br> (6) For the snapshots of Trimeric SARS-CoV-2 spike glycoprotein (opened state) were chosen from 10 us MD simulation, a total of 8334 configurations were extracted with a 1.2 ns interval from start time 1200ps – 10us(contains 9 trajectories,1000 snapshots for No.1-8 trajectories, 334 snapshots for No.9 trajectory). We chose the first 800 snapshots in each of No.1-8 trajectories (6400 in total) to calculate the IR spectra. <br>