SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain
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 o...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-023-05332-w |
| _version_ | 1797557090200322048 |
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| author | Jiansheng Jiang Christopher T. Boughter Javeed Ahmad Kannan Natarajan Lisa F. Boyd Martin Meier-Schellersheim David H. Margulies |
| author_facet | Jiansheng Jiang Christopher T. Boughter Javeed Ahmad Kannan Natarajan Lisa F. Boyd Martin Meier-Schellersheim David H. Margulies |
| author_sort | Jiansheng Jiang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T17:12:16Z |
| format | Article |
| id | doaj.art-a054579999df4ca3962667ef9a71ae44 |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2024-03-10T17:12:16Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-a054579999df4ca3962667ef9a71ae442023-11-20T10:36:38ZengNature PortfolioCommunications Biology2399-36422023-09-016111510.1038/s42003-023-05332-wSARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domainJiansheng Jiang0Christopher T. Boughter1Javeed Ahmad2Kannan Natarajan3Lisa F. Boyd4Martin Meier-Schellersheim5David H. Margulies6Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIHComputational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIHMolecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIHMolecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIHMolecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIHComputational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIHMolecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIHAbstract 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.https://doi.org/10.1038/s42003-023-05332-w |
| spellingShingle | Jiansheng Jiang Christopher T. Boughter Javeed Ahmad Kannan Natarajan Lisa F. Boyd Martin Meier-Schellersheim David H. Margulies SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain Communications Biology |
| title | SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain |
| title_full | SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain |
| title_fullStr | SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain |
| title_full_unstemmed | SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain |
| title_short | SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain |
| title_sort | sars cov 2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain |
| url | https://doi.org/10.1038/s42003-023-05332-w |
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