Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein

Cecylia S. Lupala; Xuanxuan Li; Jian Lei; Hong Chen; Jianxun Qi; Haiguang Liu; Xiao-dong Su

After energy minimization using the steepest descent algorithm, each system was equilibrated at human body temperature 310.15 K, which was maintained by Nose-Hoover scheme with 1.0 ps coupling constant in the NVT ensemble (constant volume and temperature) for 125.0 ps under periodic boundary conditions with harmonic restraint forces applied to the complex molecules (400 kJ mol −1 nm −2 on backbone and 40 kJ mol −1 nm −2 on the side chains) 16, 17 . In the subsequent step, the harmonic restraints were removed and the NPT ensembles were simulated at one atmosphere pressure (10 5 Pa) and body temperature. The pressure was maintained by isotropic Parrinello-Rahman barostat 18 Three independent trajectories starting from random velocities based on Maxwell distributions were simulated for both CoV2-RBD/ACE2 and SARS-RBD/ACE2 complex systems in their wild types. In all simulations, a time step of 2.0 fs was used and the PME (particle mesh Ewald) 20 was applied for long-range electrostatic interactions beyond 12.0 Å.