Fig. 3: MD simulation of the RBD—ACE2 of WT and VoCs.
From: Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants
a Ribbon-like representation of the RBD—ACE2 complex and highlight of residues mutated in VoCs. b Total energies and c Lennard−Jones energies for all RBD—ACE2 complexes. d Average frequencies of contacts from 7.5 μs of MD trajectory of SARS-CoV-2 WT (gray) and VoCs Alpha (blue), Beta (green), Gamma (orange), and Kappa (purple). High-frequency contacts are shown in the form (ACE2 residue number)—(RBD residue number) for seven contacts involving relevant mutations. Zoom-in on the RBD—ACE2 region around e RBD residue 501 and f around RBD residues 484 and 417 for the WT and the 4 VoCs. Sidechains are represented by sticks. Residues 38, 42, and 355 in ACE2 contacting RBD residue 501 (e) and residues 30, 31, 34, and 75 in ACE2 contacting RBD 417 or 484, respectively, are shown. Data in b, c show the mean and the whiskers are the s.d. of the mean value obtained from N = 3130 (WT), N = 2851 (Alpha), and N = 3130 (Beta and Kappa).
