Molecular dynamics of the P.1 variant of SARS-CoV-2

All molecular dynamics simulations were performed in GROMACS 2019.1 software by Prof. Dr. Jonathas N. Silva. The time interval for each simulation is 50ns. Among the crystallographic structures, we have the antibody-antigen complex containing the P.1 variant (PDB ID: 7NXB), and the respective wild-type structure (PDB ID: 7NX6) In preparing the topology, Na+ and Cl- ions were inserted to neutralize the system at a concentration of 0.15 mol/L. Trajectory files were simulated based on the CHARMM36 force field. We use a cubic solvation box, by the TIP3P water model. The production of trajectories was carried out using the NPT canonical cycle. The Parrinello–Rahman barostat was adopted to keep the pressure constant at 1 atm, while the Berendsen algorithm acted as a thermostat to keep the system temperature at 300 K.

Simulations were also performed in NAMD3 over 50 ns for the ACE2-RBD complex (PDB ID: 6M0J). In silico mutagenesis for the P.1 variant (K417T, E484K, N501Y) was performed in the PyMOL software. All input files for the simulation were automatically generated by the QwikMD plugin with the CHARM36 force field. The simulation files are in .psf (topology) and .dcd (trajectory) format.