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

Bei Tong,Fang Tian,Liang Sun,Shengchao Shi,Bin Zheng,Xianchi Dong,Zibin Wang,Peng Zheng

doi:10.7554/elife.69091

Bei Tong, Fang Tian + Show 6 more

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https://doi.org/10.7554/elife.69091

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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.

Highlights

Over the past 20 years, coronaviruses have posed severe threats to public health
ACE2–mCherry-positive cells were stained with AlexaFluor488 labeled-receptor-binding domain (RBD), and the overlay images showed the co-localization of RBD and ACE2 on the cell surface (Figure 1F), validating their interaction
We combined cell- surface-binding assays, mechanical manipulation by Atomic force microscopy (AFM)-single-molecule force microscopy (SMFS), and molecular dynamics simulations to understand the behavior of key mutations recently detected in B.1.1.7 and B.1.351 variants that affect RBD binding

Summary

Introduction

Over the past 20 years, coronaviruses have posed severe threats to public health. In 2003, severe acute respiratory syndrome coronavirus (SARS-C oV-1) emerged in humans after being transferred from an animal reservoir and infected over 8000 people with a fatality rate of ~10% fatality rate (Ksiazek et al, 2003; Florindo et al, 2020). Middle East respiratory syndrome coronavirus (MERS-C oV) has infected over 1700 people with a fatality rate of ~36% since 2012 (Zaki et al, 2012). In late December 2019, a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-C oV-2), was identified as the cause of an outbreak of a new respiratory illness named COVID-19. SARS-C oV-2 has caused more than 4 million deaths to date. Considerable efforts have been made to understand its molecule mechanism

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