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

  1. Fang Tian
  2. Bei Tong  Is a corresponding author
  3. Liang Sun
  4. Shengchao Shi
  5. Bin Zheng
  6. Zibin Wang
  7. Xianchi Dong  Is a corresponding author
  8. Peng Zheng  Is a corresponding author
  1. Nanjing University, China
  2. Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, China

Abstract

SARS-CoV-2 is 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), sharing a key mutation N501Y on the RBD, appear to be more infectious to humans. To understand the underlying mechanism, we performed cell surface binding assay, kinetics study, single-molecule technique, and 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 slower dissociation rate. Consistently, atomic force microscopy-based single-molecule force microscopy quantifies their strength showing a higher binding probability and unbinding force for the mutation. Molecular dynamics simulations of RBD-ACE2 complexes indicated that the N501Y introduced additional π-π and π-cation interaction for the higher force/interaction. Taken together, we suggested that the reinforced interaction from N501Y mutation in RBD should play an essential role in the higher transmission of SARS-CoV-2 variants and future mutations in the RBD of the virus should be under surveillance.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have provided for Figures 1-4.

Article and author information

Author details

  1. Fang Tian

    School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Bei Tong

    Institute of Botany, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
    For correspondence
    beitong@cnbg.net
    Competing interests
    The authors declare that no competing interests exist.
  3. Liang Sun

    School of Life Sciences, Nanjing University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Shengchao Shi

    Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Bin Zheng

    Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Zibin Wang

    School of Life Sciences, Nanjing University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Xianchi Dong

    School of Life Sciences, Nanjing University, Nanjing, China
    For correspondence
    xianchidong@nju.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
  8. Peng Zheng

    Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
    For correspondence
    pengz@nju.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4792-6364

Funding

National Key Research and Development Program of China (2020YFA0509000)

  • Xianchi Dong

Fundamental Research Funds for the Central Universities (14380205)

  • Peng Zheng

Natural Science Foundation of Jiangsu Province (BK20200058)

  • Peng Zheng

Natural Science Foundation of Jiangsu Province (BK20202004)

  • Peng Zheng

Natural Science Foundation of Jiangsu Province (BK20190275)

  • Xianchi Dong

National Natural Science Foundation of China (21771103)

  • Peng Zheng

National Natural Science Foundation of China (21977047)

  • Peng Zheng

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2021, Tian et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 6,835
    views
  • 936
    downloads
  • 273
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Fang Tian
  2. Bei Tong
  3. Liang Sun
  4. Shengchao Shi
  5. Bin Zheng
  6. Zibin Wang
  7. Xianchi Dong
  8. Peng Zheng
(2021)
N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2
eLife 10:e69091.
https://doi.org/10.7554/eLife.69091

Share this article

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

Further reading

    1. Structural Biology and Molecular Biophysics
    Manming Xu, Sarath Chandra Dantu ... Shozeb Haider
    Research Article

    The relationship between protein dynamics and function is essential for understanding biological processes and developing effective therapeutics. Functional sites within proteins are critical for activities such as substrate binding, catalysis, and structural changes. Existing computational methods for the predictions of functional residues are trained on sequence, structural, and experimental data, but they do not explicitly model the influence of evolution on protein dynamics. This overlooked contribution is essential as it is known that evolution can fine-tune protein dynamics through compensatory mutations either to improve the proteins’ performance or diversify its function while maintaining the same structural scaffold. To model this critical contribution, we introduce DyNoPy, a computational method that combines residue coevolution analysis with molecular dynamics simulations, revealing hidden correlations between functional sites. DyNoPy constructs a graph model of residue–residue interactions, identifies communities of key residue groups, and annotates critical sites based on their roles. By leveraging the concept of coevolved dynamical couplings—residue pairs with critical dynamical interactions that have been preserved during evolution—DyNoPy offers a powerful method for predicting and analysing protein evolution and dynamics. We demonstrate the effectiveness of DyNoPy on SHV-1 and PDC-3, chromosomally encoded β-lactamases linked to antibiotic resistance, highlighting its potential to inform drug design and address pressing healthcare challenges.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Andrew P Latham, Longchen Zhu ... Bin Zhang
    Research Article

    The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences to the physical properties of condensates, that is, the molecular grammar, are hampered by a lack of effective approaches for probing high-resolution structural details. Using a combination of multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored a series of systems consisting of diblock elastin-like polypeptides (ELPs). The simulations succeeded in reproducing the variation of condensate stability upon amino acid substitution and revealed different microenvironments within a single condensate, which we verified with environmentally sensitive fluorophores. The interspersion of hydrophilic and hydrophobic residues and a lack of secondary structure formation result in an interfacial environment, which explains both the strong correlation between ELP condensate stability and interfacial hydrophobicity scales, as well as the prevalence of protein-water hydrogen bonds. Our study uncovers new mechanisms for condensate stability and organization that may be broadly applicable.