N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

Abstract

SARS-CoV-2 has been spreading around the world for the past year. Recently, several variants such as B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), which share a key mutation N501Y on the receptor-binding domain (RBD), appear to be more infectious to humans. To understand the underlying mechanism, we used a cell surface-binding assay, a kinetics study, a single-molecule technique, and a computational method to investigate the interaction between these RBD (mutations) and ACE2. Remarkably, RBD with the N501Y mutation exhibited a considerably stronger interaction, with a faster association rate and a slower dissociation rate. Atomic force microscopy (AFM)-based single-molecule force microscopy (SMFS) consistently quantified the interaction strength of RBD with the mutation as having increased binding probability and requiring increased unbinding force. Molecular dynamics simulations of RBD–ACE2 complexes indicated that the N501Y mutation introduced additional π-π and π-cation interactions that could explain the changes observed by force microscopy. Taken together, these results suggest that the reinforced RBD–ACE2 interaction that results from the N501Y mutation in the RBD should play an essential role in the higher rate of transmission of SARS-CoV-2 variants, and that future mutations in the RBD of the virus should be under surveillance.

Mechanisms of SARS-CoV-2 entry into cells

“…The SARS-CoV-2 variants Alpha (lineage B.1.1.7), Beta (B.1.351) and Gamma (P.1), which were first identified in the United Kingdom, South Africa and Brazil, respectively, carry a common N501Y mutation in addition to the D614G mutation (TAbLe 1). Residue 501 is one of the key sites within the RBD involved in ACE2 binding 2,178,179 , and recent preliminary reports demonstrate that N501Y mutation strengthens RBD interaction with hACE2 (refS 180,181 ) and increases the infectivity and virulence of variants containing the mutation [182][183][184] . Interestingly, data indicate that the N501Y substitution also lends the S protein the ability to utilize mouse and rat ACE2 orthologues 182,185,186 , raising concern for the potential of new rodent reservoirs.…”

A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy

“…K417N and E484K strongly disrupt binding of class 1 and class 2 antibodies, respectively (24). N501Y is in or proximal to the class 3 epitope, but does not strongly affect the binding or neutralization of polyclonal convalescent or vaccine-elicited antibodies (8,23), although it enhances the RBD's affinity for its receptor, angiotensin converting enzyme 2 (ACE2) (11,25,26).…”

Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants

“…This ACE-2 interaction drives the transmission efficacy. Since most vaccine strategies are based on different spike-related immunogens (6), the RBD residue changes might pose major challenges in vaccine immune evasion capacity and receptor affinity adaptation (7)(8)(9)(10)(11)(12).…”