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Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach
This is an article published in Infection, Genetics and Evolution 91 (2021) 104815; https://doi.org/10.1016/j.meegid.2021.104815
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Infection, Genetics and Evolution
2024
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| _version_ | 1867613136945676288 |
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| access_status_str | Open Access |
| author | Kwarteng, Alexander Asiedu, Ebenezer Sylverken, Augustina Angelina Larbi, Amma Sakyi, Samuel Asamoah Asiedu, Samuel Opoku |
| author2 | 0000-0002-0893-2908 |
| author_browse | 0000-0002-0893-2908 Asiedu, Ebenezer Asiedu, Samuel Opoku Kwarteng, Alexander Larbi, Amma Sakyi, Samuel Asamoah Sylverken, Augustina Angelina |
| author_facet | 0000-0002-0893-2908 Kwarteng, Alexander Asiedu, Ebenezer Sylverken, Augustina Angelina Larbi, Amma Sakyi, Samuel Asamoah Asiedu, Samuel Opoku |
| author_sort | Kwarteng, Alexander |
| collection | Thesis |
| description | This is an article published in Infection, Genetics and Evolution 91 (2021) 104815; https://doi.org/10.1016/j.meegid.2021.104815 |
| format | Article |
| id | oai:ir.knust.edu.gh:123456789/15692 |
| institution | KNUST (Ghana) |
| language | English |
| last_indexed | 2026-06-10T12:31:21.331Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from KNUSTSpace — Kwame Nkrumah University of Science & Technology (Ghana) |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Infection, Genetics and Evolution |
| publisherStr | Infection, Genetics and Evolution |
| record_format | dspace |
| source_str | KNUSTSpace — Kwame Nkrumah University of Science & Technology (Ghana) |
| spelling | oai:ir.knust.edu.gh:123456789/15692 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach Kwarteng, Alexander Asiedu, Ebenezer Sylverken, Augustina Angelina Larbi, Amma Sakyi, Samuel Asamoah Asiedu, Samuel Opoku 0000-0002-0893-2908 0000-0003-2867-1984 0000-0002-7691-914X 0000-0002-3814-6924 0000-0001-5168-4762 0000-0002-0352-3195 This is an article published in Infection, Genetics and Evolution 91 (2021) 104815; https://doi.org/10.1016/j.meegid.2021.104815 The D614G variant of SARS-CoV-2 S-protein emerged in early 2020 and quickly became the dominant circulating strain in Europe and its environs. The variant was characterized by the higher viral load, which is not associated with disease severity, higher incorporation into the virion, and high cell entry via ACE-2 and TMPRSS2. Previous strains of the coronavirus and the current SARS-CoV-2 have demonstrated the selection of mutations as a mechanism of escaping immune responses. In this study, we used molecular dynamics simulation and MM-PBSA binding energy analysis to provide insights into the behaviour of the D614G S-protein at the molecular level and describe the neutralization mechanism of this variant. Our results show that the D614G S-protein adopts distinct conformational dynamics which is skewed towards the open-state conformation more than the closed-state conformation of the wild-type S-protein. Residue-specific variation of amino acid flexibility and domain specific RMSD suggest that the mutation causes an allosteric conformational change in the RBD. Evaluation of the interaction energies between the S-protein and neutralizing antibodies show that the mutation may enhance, reduce or not affect the neutralizing interactions depending on the neutralizing antibody, especially if it targets the RBD. The results of this study have shed insights into the behaviour of the D614G S-protein at the molecular level and provided a glimpse of the neutralization mechanism of this variant. KNUST 2024-04-18T10:44:06Z 2024-04-18T10:44:06Z 2021 Article Infection, Genetics and Evolution 91 (2021) 104815; https://doi.org/10.1016/j.meegid.2021.104815 https://doi.org/10.1016/j.meegid.2021.104815 https://ir.knust.edu.gh/handle/123456789/15692 en application/pdf Infection, Genetics and Evolution |
| spellingShingle | Kwarteng, Alexander Asiedu, Ebenezer Sylverken, Augustina Angelina Larbi, Amma Sakyi, Samuel Asamoah Asiedu, Samuel Opoku Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach |
| title | Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach |
| title_full | Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach |
| title_fullStr | Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach |
| title_full_unstemmed | Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach |
| title_short | Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach |
| title_sort | molecular characterization of interactions between the d614g variant of sars cov 2 s protein and neutralizing antibodies a computational approach |
| url | https://doi.org/10.1016/j.meegid.2021.104815 https://ir.knust.edu.gh/handle/123456789/15692 |
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