Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding

TLDR

The receptor binding domain of the SARS‑CoV‑2 spike protein mediates attachment to ACE2 and is a key determinant of host range and a dominant target of neutralizing antibodies. The study experimentally measures the effects of all amino acid mutations in the RBD on protein folding and ACE2 affinity, and provides an interactive visualization and open pipeline to aid vaccine design and mutation annotation. The authors performed comprehensive mutagenesis of the RBD, measuring expression and ACE2 binding for each variant, and developed an interactive visualization and open analysis pipeline. Most RBD mutations impair folding or ACE2 binding, identify constrained surface regions as potential vaccine or therapeutic targets, and show that although some mutations enhance ACE2 affinity, these have not been selected in circulating SARS‑CoV‑2 strains.

Abstract

The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor and is a major determinant of host range and a dominant target of neutralizing antibodies. Here, we experimentally measure how all amino acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity-enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.