N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, China
- Institute of Botany, Jiangsu Province, China
- Chinese Academy of Sciences, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, China
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, China
Figures
Figure 1
Two SARS-CoV-2 variants bind to ACE2 with higher affinity.
(A) Domain architecture of the SARS-CoV-2 spike monomer. NTD, N-terminal domain; RBD, receptor-binding domain; SD1, subdomain 1; SD2, subdomain 2; FP, fusion peptide; HR1, heptad repeat 1; CH, …
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Figure 1—source data 1
Source cell-surface-binding data used for Figure 1G,H.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig1-data1-v2.xlsx
Figure 2 with 1 supplement
Kinetics of the binding of the receptor-binding domain (RBD) and of RBD mutants to the ACE2 protein.
(A–C) Surface plasmon resonance (SPR) sensorgrams (thin black lines) with fits (thick gray lines). ACE2 protein concentrations of 50, 20, 10, 5, 2, and 1 nM were used. Values were fitted to the 1:1 …
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Figure 2—source data 1
Source data describing the kinetics of each receptor-binding domain (RBD) bound to ACE2 protein used for Figure 2 and Figure 2—figure supplement 1.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Kinetics of RBDK417N and RBDE484K binding to ACE2 protein.
(A, B) Surface plasmon resonance (SPR) sensorgrams (thin black lines) are shown with fits (thick gray lines). Concentrations used for ACE2 protein were 50, 20, 10, 5, 2, and 1 nM, respectively. …
Figure 3 with 4 supplements
Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) experiment to quantify the strength of binding between the receptor-binding domains (RBDs) and ACE2 in living cells.
(A) Schematic of the AFM-SMFS measurement process showing how the interaction is quantified. RBD with an N-terminal NGL recognition sequence is immobilized on a GL-coated AFM tip by the ligase OaAEP1…
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Figure 3—source data 1
Source data for the histograms of unbinding force for different RBD–ACE2 complexes used in Figure 3C and Figure 3—figure supplement 3.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig3-data1-v2.xlsx
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Figure 3—source data 2
Binding probabilities for different RBD–ACE2 complexes used for Figure 3D.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig3-data2-v2.xlsx
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Figure 3—source data 3
Force mapping results for the different complexes used for Figure 3E and Figure 3—figure supplement 4.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig3-data3-v2.xlsx
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Figure 3—source data 4
Loading rates for different RBD–ACE2 complexes used for Figure 3F.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig3-data4-v2.xlsx
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Figure 3—source data 5
The spring constant (k) for all 15 cantilevers.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig3-data5-v2.xlsx
Figure 3—figure supplement 1
Representative force-extension curves for different RBD–ACE2 complexes involving (A) RBD, (B) RBDN501Y, (C) RBDTriple, (D) RBDK417N, or (E) RBDE484K.
A clear unbinding peak with force higher than 20 pN is present.
Figure 3—figure supplement 2
The force mapping results for the three different complexes in a 2 × 2 µm area: (A) blank on untransfected normal HEK293 cell, (B) RBD, (C) RBDN501Y, and (D) RBDTriple.
Figure 3—figure supplement 3
Histograms of unbinding force for RBDK417N–ACE2 (A) and RBDE484K–ACE2 (B) under a pulling speed of 5 µm/s.
The rupture forces are 40 ± 11 pN (RBDK417N, n = 894) and 41 ± 9 pN (RBDE484K, n = 606), respectively.
Figure 3—figure supplement 4
Plots of raw unbinding force against the loading rate of the three different complexes: (A) RBD, (B) RBDN501Y, and (C) RBDTriple.
The gray symbols are the forces required for an individual unbinding event under a specific loading rate. The five solid markers in each graph are the most probable unbinding forces under the five …
Figure 4 with 4 supplements
SMD simulations of RBD–ACE2 complex dissociation.
(A–C) Force-extension traces of RBD–ACE2 (violet), RBDN501Y–ACE2 (orange), and RBDTriple–ACE2 (green) complexes pulled apart at 5 Å/ns. The curves represent the average results from 20 simulations, …
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Figure 4—source data 1
Rupture forces for the three complexes from 20 SMD simulations.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig4-data1-v2.xlsx
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Figure 4—source data 2
Distances between key residues in the RBDs–ACE2 complexes used for Figure 4D,E.
- https://cdn.elifesciences.org/articles/69091/elife-69091-fig4-data2-v2.xlsx
Figure 4—figure supplement 1
SMD simulations of the dissociation of the different RBD–ACE2 complexes involving (A) RBD, (B) RBDN501Y or (C) RBDTriple.
Figure 4—video 1
Representative SMD simulation of the RBD (violet)–ACE2 complex at a constant velocity of 5.0 Å/ns.
ACE2 is colored in cyan. Residues 500, 501, 417, 484, and 487 of RBD, and contacting residues from ACE2 (D355, K353, Y41, D30, and Y83) are labeled and shown as sphere models. The distances between …
Figure 4—video 2
Representative SMD simulation of the RBDN501Y(orange)–ACE2 complex at a constant velocity of 5.0 Å/ns.
ACE2 is colored in cyan. Residues 500, 501, 417, 484, and 487 from RBD, and contacting residues from ACE2 (D355, K353, Y41, D30, and Y83) are labeled and shown as sphere models. The distances …
Figure 4—video 3
Representative SMD simulation of the RBDTriple (green)–ACE2 complex at a constant velocity of 5.0 Å/ns.
ACE2 is colored in cyan. Residues 500, 501, 417, 484, and 487 from RBD, and contacting residues from ACE2 (D355, K353, Y41, D30, and Y83) are labeled and shown as sphere models. The distances …
