Coarse-Grained Molecular Simulations

Coarse-grained (CG) models are computationally effective approaches for simulations of large systems over long time scales. In this study, CG-CABS model^100−104 was used for simulations of the crystal structures of the SARS-CoV-2 RBD complex with ACE2 (PDB id 6M0J)¹⁵ and complexes formed by the dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (PDB id 7A91, 7A92)³⁴ (Figure ​Figure11A–C). We also simulated the cryo-EM structure of the SARS-CoV-2 RBD complex with the Fab fragments of two neutralizing antibodies, REGN10933 and REGN10987 (PDB id 6XDG)¹⁰⁵ (Figure ​Figure11D–F). In this high-resolution model, the amino acid residues are represented by Cα, Cβ, the center of mass of side chains and another pseudoatom placed in the center of the Cα-Cα pseudobond. In this model, the amino acid residues are represented by Cα, Cβ, the center of mass of side chains and the center of the Cα-Cα pseudobond. The CABS-flex approach implemented as a Python 2.7 object-oriented standalone package was used in this study to integrate a high-resolution coarse-grained model with robust and efficient conformational sampling proven to accurately recapitulate all-atom MD simulation trajectories of proteins on a long time scale.¹⁰⁴ Conformational sampling in the CABS-flex approach is conducted with the aid of Monte Carlo replica-exchange dynamics and involves local moves of individual amino acids in the protein structure and global moves of small fragments.^100−102

Crystal structures of the SARS-CoV-2 RBD and S1 domain complexes with ACE enzyme and REGN-COV2 antibody cocktail. (A) Structural overview of the SARS-CoV-2 RBD complex with ACE2 (PDB id 6M0J). The SARS-CoV RBD is shown in cyan ribbons, and the RBM region is in blue ribbons. The subdomain I of human ACE2 is shown in red ribbons, and subdomain II is shown in green ribbons. The structure of ACE2 consists of the N-terminus subdomain I (residues 19–102, 290–397, and 417–430) and C-terminus subdomain II (residues 103–289, 398–416, and 431–615) that form the opposite sides of the active site cleft. (B) The crystal structure of the dissociated S1 domain form in the complex with ACE2 (PDB id 7A91). S1-RBD is in cyan ribbons, and ACE2 is in green ribbons. (C) The crystal structure of the fully dissociated S1 domain in the complex with ACE2 (PDB id 7A92). The S1 domain of the SARS-CoV-2 S protein is in cyan ribbons, and ACE2 is in green ribbons. (D) The cryo-EM structure of the SARS-CoV-2 RBD in the complex with REGN10933/REGN10987 antibody cocktail. The RBD region is shown by the green surface. REGN10933 Fab fragment is shown in ribbons with the heavy chain in cyan and the light chain in blue. REGN10987 is in ribbons with the heavy chain in orange and the light chain in purple. The positions of functional residues targeted by mutational variants and antibody-escaping mutations are E406, K417, E484, and N501 and are annotated and highlighted as black patches on the RBD surface. (E) A close-up of the SARS-CoV-2 RBD interactions with REGN10933. The RBD is shown on the green surface. REGN10933 Fab fragment is shown in ribbons with heavy chain in cyan and light chain in blue. The REGN10933 antibody epitope on RBD is highlighted in cyan patches on the surface. The positions of E406, K417, E484, F486, N501 are shown as black surface patches on the RBD. (F) A close-up of the SARS-CoV-2 RBD interface with REGN10987. The red patches correspond to the REGN10987 epitope. The positions of E406, K417, N439, E484, F486, N501 are shown as black surface patches on the RBD.

The default settings were applied in which soft native-like restraints are imposed only on pairs of residues fulfilling the following conditions: the distance between their C^α atoms was smaller than 8 Å, and both residues belong to the same secondary structure elements. A total of 1,000 independent CG-CABS simulations were performed for each of the studied systems. In each simulation, the total number of cycles was set to 10,000, and the number of cycles between trajectory frames was 100. MODELER-based reconstruction of simulation trajectories to the all-atom representation provided by the CABS-flex package was employed to produce atomistic models of the equilibrium ensembles for studied systems.