Protein modeling
Homology structural models of viral spike protein from SARS-CoV-2 (QHO62112.1) and Bat-CoV (AAZ67052.1) were built by using the tools of the SWISS-MODEL modeling server and the DeepView/Swiss-PdbViewer 4.01 software (Arnold et al., 2006[1]). Several models were obtained and the quality of each structure was evaluated. The best model for SARS-CoV-2 spike was obtained using the crystal structure of SARS-CoV spike protein (PDB code 6ACC). On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD. These models were subjected to further protein structure optimization. Hydrogen atoms were added and the partial charges were assigned for energy refinement. The protein model was embedded in a 100 Å water box. Then, energy minimization was performed while applying constraints to the protein backbone to preserve global folding and optimizing the relative position of the water molecules and protein. The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]). All MD simulations described in this study were performed with NAMD 2.12 (Phillips et al., 2005[10]), Vega ZZ 3.1.0.21 (Pedretti et al., 2004[9]). CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used. The obtained structures represent the lowest energy frame of the MD simulations. The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]).