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Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins
Li, Weiwei1,2; Xu, Zepeng1,3; Niu, Tianhui4; Xie, Yufeng1,5; Zhao, Zhennan1; Li, Dedong1; He, Qingwen1; Sun, Wenqiao1; Shi, Kaiyuan1; Guo, Wenjing1,2; Chang, Zhen6; Liu, Kefang1; Fan, Zheng7; Qi, Jianxun1,2; Gao, George F.1
2024-04
Source PublicationEMBO Journal
ISSN0261-4189
Volume43Issue:8Pages:1484-1498
Abstract

Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding and immune evasion are recognized as two major drivers for evolution of the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, the underlying mechanism of interplay between two factors remains incompletely understood. Herein, we determined the structures of human ACE2 complexed with BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5 RBDs. Based on the ACE2/RBD structures of these sub-variants and a comparison with the known complex structures, we found that R346T substitution in the RBD enhanced ACE2 binding upon an interaction with the residue R493, but not Q493, via a mechanism involving long-range conformation changes. Furthermore, we found that R493Q and F486V exert a balanced impact, through which immune evasion capability was somewhat compromised to achieve an optimal receptor binding. We propose a “two-steps-forward and one-step-backward” model to describe such a compromise between receptor binding affinity and immune evasion during RBD evolution of Omicron sub-variants.

KeywordImmune Evasion Omicron Receptor Binding Sars-cov-2 Sub-variants
DOI10.1038/s44318-024-00062-z
URLView the original
Indexed BySCIE
Language英語English
WOS Research AreaBiochemistry & Molecular Biology ; Cell Biology
WOS SubjectBiochemistry & Molecular Biology ; Cell Biology
WOS IDWOS:001220453300008
PublisherWILEY, 111 RIVER ST, HOBOKEN 07030-5774, NJ
Scopus ID2-s2.0-85187126375
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Citation statistics
Document TypeJournal article
CollectionFaculty of Health Sciences
Corresponding AuthorFan, Zheng; Qi, Jianxun; Gao, George F.
Affiliation1.CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
2.University of Chinese Academy of Sciences, Beijing, China
3.Faculty of Health Sciences, University of Macau, Macao
4.Air Force Medical University, Air Force Medical center, PLA, Beijing, China
5.Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
6.Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
7.Institutional Core Facility, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
Recommended Citation
GB/T 7714
Li, Weiwei,Xu, Zepeng,Niu, Tianhui,et al. Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins[J]. EMBO Journal, 2024, 43(8), 1484-1498.
APA Li, Weiwei., Xu, Zepeng., Niu, Tianhui., Xie, Yufeng., Zhao, Zhennan., Li, Dedong., He, Qingwen., Sun, Wenqiao., Shi, Kaiyuan., Guo, Wenjing., Chang, Zhen., Liu, Kefang., Fan, Zheng., Qi, Jianxun., & Gao, George F. (2024). Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins. EMBO Journal, 43(8), 1484-1498.
MLA Li, Weiwei,et al."Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins".EMBO Journal 43.8(2024):1484-1498.
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