Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions

Abstract

Molecular dynamics and free energy simulations have been carried out to elucidate the structural origin of differential protein-protein interactions between the common receptor protein angiotensin converting enzyme 2 (ACE2) and the receptor binding domains of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [A. E. Gorbalenya et al., Nat. Microbiol. 5, 536-544 (2020)] that causes coronavirus disease 2019 (COVID-19) [P. Zhou et al., Nature 579, 270-273 (2020)] and the SARS coronavirus in the 2002-2003 (SARS-CoV) [T. Kuiken et al., Lancet 362, 263-270 (2003)] outbreak. Analysis of the dynamic trajectories reveals that the binding interface consists of a primarily hydrophobic region and a delicate hydrogen-bonding network in the 2019 novel coronavirus. A key mutation from a hydrophobic residue in the SARS-CoV sequence to Lys417 in SARS-CoV-2 creates a salt bridge across the central hydrophobic contact region, which along with polar residue mutations results in greater electrostatic complementarity than that of the SARS-CoV complex. Furthermore, both electrostatic effects and enhanced hydrophobic packing due to removal of four out of five proline residues in a short 12-residue loop lead to conformation shift toward a more tilted binding groove in the complex in comparison with the SARS-CoV complex. On the other hand, hydrophobic contacts in the complex of the SARS-CoV-neutralizing antibody 80R are disrupted in the SARS-CoV-2 homology complex model, which is attributed to failure of recognition of SARS-CoV-2 by 80R.

Keywords: SARS-CoV-2; molecular dynamics; protein–protein interaction; relative free energy of binding.

Fig. 1.

Crystal structures (A) and computed electrostatic potentials (B) of ACE2 and the RBD. In A, the RBD–ACE2 complex is shown (Left), along with the designation of binding contact regions CR1, CR2, and CR3 for the RBD of SARS-CoV-2 (Center) and SARS-CoV (Right); the RBM is colored in yellow, and key residues are shown in stick model. The contact residues in ACE2 is colored in red. In B, the van der Waals surface of residues within 3.8 Å between RBD and receptor atoms are colored blue to indicate positive potential and red for negative potential. Crystal structures (PDB ID codes 6LZG and 6ACG) are used for the schematic depiction.

Fig. 2.

Characteristic dynamic fluctuations of the RBD–ACE2 complexes of SARS-CoV-2 and SARS-CoV depicted by the two lowest-frequency principal components (PC1 and PC2) in A, and dynamic conformations projected on to the two principal vectors (C). (B) The rmsd and contact areas of the receptor-binding motif in both complexes during the 200-ns MD simulations. (D) The tilt angles of the two RBD–ACE2 complexes, defined by vectors from the Cα atom of His34 near the center of the N-terminal helix to the centers of mass (C.O.M) for RBD and ACE2, respectively.

Fig. 3.

Computed averages and fluctuations of interaction distances of selected residues (A) and structural depiction of key interfacial interactions between ACE2 and the RBM of SARS-CoV-2 (B) and SARS-CoV (C) in the three contact regions at the N-terminal end of ACE2 (CR1), the central region (CR2) of the RBM, and the β-turn contact region of ACE2 (CR3). Key hydrogen bonds and salt bridges are highlighted with dashed lines, and hydrophobic contacts are shaded in yellow background. Legends for A are colored light blue for residues in the ACE2–SARS-CoV complex, light maroon for residues in ACE2–SARS-CoV-2, and black for conserved residues found in both sequences at the corresponding sites.

Fig. 4.

Homology model of the antibody 80R and RBD of SARS-CoV-2 (A), computed averages and fluctuations of interatomic distances of selected residues (B), and structural details of key interfacial interactions between the SARS-CoV neutralizing antibody 80R and the RBM of SARS-CoV (C) and SARS-CoV-2 (D) in the three contact regions designated in Fig. 1. In A, the CDR loops H2 and H3, mimicking the β-turn binding region of ACE2, and the framework region (FR) loop L3 on 80R are highlighted in red. Key hydrogen bonds and salt bridges are highlighted with dashed lines, and hydrophobic contacts are shaded in yellow background. Legends for B are colored light blue for residues in the 80R–SARS-CoV complex, light maroon for residues in 80R–SARS-CoV-2, and black for conserved residues found in both sequences at the corresponding sites.