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SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain
Open accessPreprint — published as 10.1038/s42003-023-05332-w · Paper page
Abstract
The COVID-19 pandemic and SARS-CoV-2 variants have dramatically illustrated the need for a better understanding of antigen (epitope)-antibody (paratope) interactions. To gain insight into the immunogenic characteristics of epitopic sites (ES), we systematically investigated the structures of 340 Abs and 83 nanobodies (Nbs) complexed with the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. We identified 23 distinct ES on the RBD surface and determined the frequencies of amino acid usage in the corresponding CDR paratopes. We describe a clustering method for analysis of ES similarities that reveals binding motifs of the paratopes and that provides insights for vaccine design and therapies for SARS-CoV-2, as well as a broader understanding of the structural basis of Ab-protein antigen (Ag) interactions.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Metadata
- Authors
- Jiang, J., Boughter, C., Ahmad, J., Natarajan, K., Boyd, L., Meier-Schellersheim, M., & Margulies, D.
- Affiliations
- National Institutes of Health (US)
- National Institute of Allergy and Infectious Diseases
- Corresponding author
- Jiang, Jiansheng
- Margulies, David
- ORCID
- Venue
- Communications Biology
- Published
- 2023-05-18
- Volume
- 6
- Issue
- 1
- Pages
- 953-953
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC10509263
- OpenAlex
- W4386847605
- Cited by
- 24
- References
- 1
- Citations by year
- 2026: 7 · 2025: 9 · 2024: 8
- FWCI
- 4.97
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Communications Biology (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (-0001)
- National Institute of Allergy and Infectious Diseases
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Immunology and Microbiology › Immunology › Monoclonal and Polyclonal Antibodies Research
- Keywords
- SARS-CoV-2, spike protein receptor-binding domain, antibody paratope, nanobodies, binding motifs, antigen-antibody reaction, vaccine design, COVID-19 pandemic
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