Fig. 1: Scheme of the spatially distributed subdomains of the SARS-CoV-2 spike RBD and designment of the RBD chimeric mutants of specific swapped subdomains to disclose structural determinants governing SARS-CoV-2 RBD/hACE2 interaction.
A WT SARS-CoV-2’s spike RBD, especially RBM can be spatially partitioned into three subdomains owing to their specific hACE2 contact resides and spatial arrangement. Similar RBD structural organizational patterns are detected in SARS-CoV-2 Omicron (B.1.1.529), SARS-CoV-1 and bat coronavirus RaTG13; The RBD structures as presented above are from spike RBD/hACE2 crystal structures with PDB# 6M0J, 7TN0, 2AJF, and 7DRV31,37,44,51. B SPR measurement of RBDs’ binding to hACE2(1-740)-FC immobilized on Series S Sensor Chip (Protein A), which cover those from above sarbecovirus species, but not that of RaTG13. The equilibrium dissociation constants (KD) from triplicate measurements were calculated with BIAcore@ 8 K Evaluation Software (GE Healthcare) by fitting to a 1:1 Langmuir binding model. C RBD protein sequence alignment between WT SARS-CoV-2, Omicron (B.1.1.529), SARS-CoV-1 and bat coronavirus RaTG13. The secondary structures as discovered in WT SARS-CoV-2 RBD is labeled on top of sequence alignment; Black filled triangles point to the direct contact resides in WT SARS-CoV-2 RBD/hACE2 complex. D Experimental design of chimeric mutants of swapped subdomains with WT SARS-CoV-2 RBD as the template. For each partitioned subdomain of wild type SARS-CoV-2 RBD, key residues of polar or non-polar contact within 4 Å cutoff between spike RBD and hACE2 interfacing chains are identified and those different residues are swapped with homologous counterparts identified from above selected crystal structures. For each swapped subdomain mutant, the mutated residues corresponding to each subdomain are marked in red color.
