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Noneffect of SARS-CoV-2 spike glycoprotein Y217N mutation on affinity between the virus and ACE2

  • Takuma Hayashi
    Correspondence
    For correspondence: Takuma Hayashi
    Affiliations
    National Hospital Organization, Kyoto Medical Center, Kyoto, Japan

    Japan Science and Technology Agency (JST) START-Program Project Team, Tokyo, Japan
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  • Ikuo Konishi
    Affiliations
    National Hospital Organization, Kyoto Medical Center, Kyoto, Japan

    Department of Obstetrics and gynecology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Open AccessPublished:May 27, 2021DOI:https://doi.org/10.1016/j.jbc.2021.100725
      The interaction between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and angiotensin-converting enzyme 2 (ACE2), the primary entry receptor for SARS-CoV-2, is a key determinant of the range of hosts that can be infected by the virus. Zhang et al. (
      • Zhang H.L.
      • Li Y.M.
      • Sun J.
      • Zhang Y.Y.
      • Wang T.Y.
      • Sun M.X.
      • Wang M.H.
      • Yang Y.L.
      • Hu X.L.
      • Tang Y.D.
      • Zhao J.
      • Cai X.
      Evaluating angiotensin-converting enzyme 2-mediated SARS-CoV-2 entry across species.
      ) reportedly constructed human ACE2 (hACE2) with the Y217N mutation and found that this mutation completely blocked SARS-CoV-2 entry. Zhang et al. (
      • Zhang H.L.
      • Li Y.M.
      • Sun J.
      • Zhang Y.Y.
      • Wang T.Y.
      • Sun M.X.
      • Wang M.H.
      • Yang Y.L.
      • Hu X.L.
      • Tang Y.D.
      • Zhao J.
      • Cai X.
      Evaluating angiotensin-converting enzyme 2-mediated SARS-CoV-2 entry across species.
      ) performed an receptor binding domain (RBD) binding assay and found that WT hACE2 potently bound the RBD; however, hACE2 Y217N almost lost the ability to bind the RBD.
      Our experiment using Spanner, a structural homology modeling pipeline method, revealed that the three-dimensional structure of the binding region containing the investigated five amino acids, 353-KGDFR-357 of hACE2 N217 involved in binding interactions with the spike glycoprotein of SARS-CoV-2, was completely conserved in comparison with the structure of hACE2 Y217.
      Structural remodeling analyses using the PDBePISA tool and MOE project DB (MOLSIS Inc) also suggested that the Y217N substitution in amino acid residues in the subdomain II motif of hACE2 (
      • Wang Q.
      • Zhang Y.
      • Wu L.
      • Niu S.
      • Song C.
      • Zhang Z.
      • Lu G.
      • Qiao C.
      • Hu Y.
      • Yuen K.Y.
      • Wang Q.
      • Zhou H.
      • Yan J.
      • Qi J.
      Structural and functional basis of SARS-CoV-2 entry by using human ACE2.
      ) did not significantly decrease the binding affinity of the RBD of SARS-CoV-2 (Fig. 1, Appendix). As the binding free energy did not change, the affinity between the ligand and receptor is fairly constant. No reports show the essential of the amino acid residues of the subdomain II motif of hACE2 for the binding of ACE2 to RBD (Appendix) (
      • Wang Q.
      • Zhang Y.
      • Wu L.
      • Niu S.
      • Song C.
      • Zhang Z.
      • Lu G.
      • Qiao C.
      • Hu Y.
      • Yuen K.Y.
      • Wang Q.
      • Zhou H.
      • Yan J.
      • Qi J.
      Structural and functional basis of SARS-CoV-2 entry by using human ACE2.
      ,
      • Villoutreix B.O.
      • Calvez V.
      • Marcelin A.G.
      • Khatib A.M.
      In silico investigation of the new UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 variants with a focus at the ACE2-spike RBD interface.
      ).
      Figure thumbnail gr1
      Figure 1The complex structure of RBD of spike glycoprotein of SARS-CoV-2 bound to human ACE2. A cartoon representation of the complex structure is analyzed using the LigPlot + program (v.1.4.5) and MOE project DB (MOLSIS Inc). The core and external subdomains in RBD in the spike glycoprotein of SARS-CoV-2 are colored in blue purple. Human ACE2 (hACE2) subdomains I and II are green, respectively. Key contact sites are marked with the two right boxes in three-dimensional structures and are further delineated for interaction details, respectively. The homology modeling of hACE2 with SARS-CoV-2 RBD with Y217 (lower right) or N217 (upper right) residue is reported. Protein buried surface areas are analyzed using the PDBePISA tool and MOE project DB (MOLSIS Inc). As the binding free energy did not change, the affinity between ACE2 and RBD of spike glycoprotein of SARS-CoV-2 is fairly constant. RBD, receptor binding domain; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
      Overall, the virus–receptor engagement is dominated by polar contacts mediated by the hydrophilic residues (
      • Hayashi T.
      • Abiko K.
      • Mandai M.
      • Yaegashi N.
      • Konishi I.
      Highly conserved binding region of ACE2 as a receptor for SARS-CoV-2 between humans and mammals.
      ). In support of this hypothesis, a single Y217N substitution was sufficient to conserve these interactions.

      Supporting information

      This article contains supporting information.

      Conflict of interest

      The author declares no conflicts of interests with the contents of this article.

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      Linked Article

      • Evaluating angiotensin-converting enzyme 2-mediated SARS-CoV-2 entry across species
        Journal of Biological ChemistryVol. 296
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          The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic represents a global threat, and the interaction between the virus and angiotensin-converting enzyme 2 (ACE2), the primary entry receptor for SARS-CoV-2, is a key determinant of the range of hosts that can be infected by the virus. However, the mechanisms underpinning ACE2-mediated viral entry across species remains unclear. Using infection assay, we evaluated SARS-CoV-2 entry mediated by ACE2 of 11 different animal species.
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      • Reply to Hayashi and Konishi: Noneffect of SARS-CoV-2 spike glycoprotein Y217N mutation on affinity between virus and ACE2
        Journal of Biological ChemistryVol. 296
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          We thank Hayashi and Konishi for their comments and interest in our article (1). We agree that by structural modeling analysis, angiotensin-converting enzyme 2 (ACE2 [Y217N]) mutant shows no changes in binding with receptor-binding domain (RBD) when compared with WT ACE2, which is depicted in Figure 4 in our article. We think the lower binding affinity of human ACE2 N217 with RBD was due to the following reasons. First, cell surface abundance of ACE2 Y217N was less compared with WT ACE2 (Fig. 5 in our article).
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