S373P Mutation Stabilizes the Receptor-binding Domain of Spike Protein in Omicron and Promotes Binding

Abstract

A cluster of several newly occurring mutations on Omicron are found at the {beta}-core region of spike proteins receptor-binding domain (RBD), where mutation rarely happened before. Notably, the binding of SARS-CoV-2 to human receptor ACE2 via RBD happens in a dynamic airway environment, where mechanical force caused by coughing or sneezing occurs and applies to the proteins. Thus, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of RBDs and found that the mechanical stability of Omicron RBD increased by ~20% compared with the wild-type. Molecular dynamics simulations revealed that Omicron RBD showed more hydrogen bonds in the {beta}-core region due to the closing of the -helical motif caused primarily by mutation S373P, which was further confirmed experimentally. Moreover, the binding ability of Omicron to ACE2 is promoted with a stabilized RBD. This work reveals the effect of the highly conserved mutation S373P which is present in most Omicron subvariants, including BA.1-5, BQ. 1, XBB, and CH.1.1.