Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural Data
COVID-19, the illness caused by the SARS-CoV-2 virus, is now a worldwide pandemic with mortality in hundreds of thousands as infections continue to increase. Containing the spread of this viral infection and decreasing the mortality rate is a major challenge. Identifying appropriate antigenic epitop...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-03-01
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| Series: | Frontiers in Artificial Intelligence |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/frai.2021.630955/full |
| _version_ | 1818336789709979648 |
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| author | Sangeeta Khare Marli Azevedo Pravin Parajuli Kuppan Gokulan |
| author_facet | Sangeeta Khare Marli Azevedo Pravin Parajuli Kuppan Gokulan |
| author_sort | Sangeeta Khare |
| collection | DOAJ |
| description | COVID-19, the illness caused by the SARS-CoV-2 virus, is now a worldwide pandemic with mortality in hundreds of thousands as infections continue to increase. Containing the spread of this viral infection and decreasing the mortality rate is a major challenge. Identifying appropriate antigenic epitopes from the viral proteins is a very important task for vaccine production and the development of diagnostic kits and antibody therapy. A novel antigenic epitope would be specific to the SARS-CoV-2 virus and can distinguish infections caused by common cold viruses. In this study two approaches are employed to identify both continuous and conformational B-cell antigenic epitopes. To achieve this goal, we modeled a complete structure of the receptor binding domain (RBD) of the spike protein using recently deposited coordinates (6vxx, 6vsb, and 6w41) in the protein data bank. In addition, we also modeled the RBD-ACE2 receptor complex for SARS-CoV-2 using the SARS-CoV RBD-ACE2 complex (3D0J) as a reference model. Finally, structure based predicted antigenic epitopes were compared to the ACE2 binding region of RBD of SARS-CoV-2. The identified conformational epitopes show overlaps with the ACE2-receptor binding region of the RBD of SARS-CoV-2. Strategies defined in the current study identified novel antigenic epitope that is specific to the SARS-CoV-2 virus. Integrating such approach in the diagnosis can distinguish infections caused by common cold viruses from SARS-CoV-2 virus. |
| first_indexed | 2024-12-13T14:44:54Z |
| format | Article |
| id | doaj.art-c43bd3b395494891a854c24718b90248 |
| institution | Directory Open Access Journal |
| issn | 2624-8212 |
| language | English |
| last_indexed | 2024-12-13T14:44:54Z |
| publishDate | 2021-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Artificial Intelligence |
| spelling | doaj.art-c43bd3b395494891a854c24718b902482022-12-21T23:41:30ZengFrontiers Media S.A.Frontiers in Artificial Intelligence2624-82122021-03-01410.3389/frai.2021.630955630955Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural DataSangeeta KhareMarli AzevedoPravin ParajuliKuppan GokulanCOVID-19, the illness caused by the SARS-CoV-2 virus, is now a worldwide pandemic with mortality in hundreds of thousands as infections continue to increase. Containing the spread of this viral infection and decreasing the mortality rate is a major challenge. Identifying appropriate antigenic epitopes from the viral proteins is a very important task for vaccine production and the development of diagnostic kits and antibody therapy. A novel antigenic epitope would be specific to the SARS-CoV-2 virus and can distinguish infections caused by common cold viruses. In this study two approaches are employed to identify both continuous and conformational B-cell antigenic epitopes. To achieve this goal, we modeled a complete structure of the receptor binding domain (RBD) of the spike protein using recently deposited coordinates (6vxx, 6vsb, and 6w41) in the protein data bank. In addition, we also modeled the RBD-ACE2 receptor complex for SARS-CoV-2 using the SARS-CoV RBD-ACE2 complex (3D0J) as a reference model. Finally, structure based predicted antigenic epitopes were compared to the ACE2 binding region of RBD of SARS-CoV-2. The identified conformational epitopes show overlaps with the ACE2-receptor binding region of the RBD of SARS-CoV-2. Strategies defined in the current study identified novel antigenic epitope that is specific to the SARS-CoV-2 virus. Integrating such approach in the diagnosis can distinguish infections caused by common cold viruses from SARS-CoV-2 virus.https://www.frontiersin.org/articles/10.3389/frai.2021.630955/fullspike proteinSARS–CoV−2receptor binding domianconformational epitopeviral infection |
| spellingShingle | Sangeeta Khare Marli Azevedo Pravin Parajuli Kuppan Gokulan Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural Data Frontiers in Artificial Intelligence spike protein SARS–CoV−2 receptor binding domian conformational epitope viral infection |
| title | Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural Data |
| title_full | Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural Data |
| title_fullStr | Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural Data |
| title_full_unstemmed | Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural Data |
| title_short | Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural Data |
| title_sort | conformational changes of the receptor binding domain of sars cov 2 spike protein and prediction of a b cell antigenic epitope using structural data |
| topic | spike protein SARS–CoV−2 receptor binding domian conformational epitope viral infection |
| url | https://www.frontiersin.org/articles/10.3389/frai.2021.630955/full |
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