Biophysical characterization of the SARS-CoV2 spike protein binding with the ACE2 receptor explains increased COVID-19 pathogenesis

Ratul Chowdhury; Costas D Maranas

This enables both of these tyrosine side-chains to form a strong electrostatic contact with Thr27 side chain of ACE2. It is thus unsurprising that mutation of either Tyr473 or Tyr489 to alanine results in a similar (58.5% and 59.1%, respectively -as shown in Figure 2 ) reduction in binding with ACE2. In contrast, in . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.015891 doi: bioRxiv preprint the energy minimized complex of SARS-CoV-1 RBDs with ACE2 both Tyr442 and Tyr475 (see Figure 3 ) only contribute to internal stability of the spike by forming strong electrostatic contacts with RBD residues Trp476 and Asn473. They are therefore unavailable (or too far > 6.0Ã…) for binding with the neighboring ACE2 residues. Next, we focus on the role of glycine residues (see Figure 4 ) in all three spike RBDs which form important electrostatic contacts with ACE2 as they lead to more than 55% loss of binding (on average) upon mutation to alanine. We chose to study in detail one such representative glycine from each spike protein RBD -Gly502 from SARS-CoV-2, Gly488 from SARS-CoV-1, and Gly220 from OC83. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.015891 doi: bioRxiv preprint Interestingly, in both SARS-CoV variants, the capture mechanism of the ACE2 residue Lys353 by glycine residues in the spike protein is the same. Atomic coordinates of both these complexes were independently, and experimentally confirmed by Song et al. 3 in 2018 and Wang et al. in 2020 (manuscript unpublished but structure deposited at -www.rcsb.org/structure/6lzg). In both cases the SARS-CoV spike RBD uses a combination of a cation-and a strong electrostatic interaction to bind with Lys353. The electrostatic interaction is mediated by Asn501 in SARS-CoV-2 and Thr487 in SARS-CoV-1. Two glycine residues and a short hydrophobic group together allows the Asn501 (and Thr487 for SARS-CoV-1) to be within strong electrostatic reach of Lys353 while ensuring a cation-interaction between Tyr505 (and Tyr491 for SARS-CoV-1) and Lys353. Mutation Y505A (or Y491A for SARS-CoV-1) has no effect on ACE2 binding. However, mutation to alanine of either Gly502 or Asn501 (or their corresponding residues in SARS-CoV-1) leads to >70% loss of ACE2 binding. Thus, we recover a strong functional motif, which is conserved between the two SARS-CoV strains as seen in Figure 5 .