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Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens
SARS-CoV-2-specific CD4 and CD8 T cells have been shown to be present in individuals with acute, mild, and asymptomatic Coronavirus disease (COVID-19). Toward the development of diagnostic and therapeutic tools to fight COVID-19, it is important to predict and characterize T cell epitopes expressed...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8757863/ https://www.ncbi.nlm.nih.gov/pubmed/35047875 http://dx.doi.org/10.3389/fmedt.2020.553478 |
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author | Nerli, Santrupti Sgourakis, Nikolaos G. |
author_facet | Nerli, Santrupti Sgourakis, Nikolaos G. |
author_sort | Nerli, Santrupti |
collection | PubMed |
description | SARS-CoV-2-specific CD4 and CD8 T cells have been shown to be present in individuals with acute, mild, and asymptomatic Coronavirus disease (COVID-19). Toward the development of diagnostic and therapeutic tools to fight COVID-19, it is important to predict and characterize T cell epitopes expressed by SARS-CoV-2. Here, we use RosettaMHC, a comparative modeling approach which leverages existing structures of peptide/MHC complexes available in the Protein Data Bank, to derive accurate 3D models for putative SARS-CoV-2 CD8 epitopes. We outline an application of our method to model 8–10 residue epitopic peptides predicted to bind to the common allele HLA-A(*)02:01, and we make our models publicly available through an online database (https://rosettamhc.chemistry.ucsc.edu). We further compare electrostatic surfaces with models of homologous peptide/HLA-A(*)02:01 complexes from human common cold coronavirus strains to identify epitopes which may be recognized by a shared pool of cross-reactive TCRs. As more detailed studies on antigen-specific T cell recognition become available, RosettaMHC models can be used to understand the link between peptide/HLA complex structure and surface chemistry with immunogenicity, in the context of SARS-CoV-2 infection. |
format | Online Article Text |
id | pubmed-8757863 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-87578632022-01-18 Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens Nerli, Santrupti Sgourakis, Nikolaos G. Front Med Technol Medical Technology SARS-CoV-2-specific CD4 and CD8 T cells have been shown to be present in individuals with acute, mild, and asymptomatic Coronavirus disease (COVID-19). Toward the development of diagnostic and therapeutic tools to fight COVID-19, it is important to predict and characterize T cell epitopes expressed by SARS-CoV-2. Here, we use RosettaMHC, a comparative modeling approach which leverages existing structures of peptide/MHC complexes available in the Protein Data Bank, to derive accurate 3D models for putative SARS-CoV-2 CD8 epitopes. We outline an application of our method to model 8–10 residue epitopic peptides predicted to bind to the common allele HLA-A(*)02:01, and we make our models publicly available through an online database (https://rosettamhc.chemistry.ucsc.edu). We further compare electrostatic surfaces with models of homologous peptide/HLA-A(*)02:01 complexes from human common cold coronavirus strains to identify epitopes which may be recognized by a shared pool of cross-reactive TCRs. As more detailed studies on antigen-specific T cell recognition become available, RosettaMHC models can be used to understand the link between peptide/HLA complex structure and surface chemistry with immunogenicity, in the context of SARS-CoV-2 infection. Frontiers Media S.A. 2020-11-17 /pmc/articles/PMC8757863/ /pubmed/35047875 http://dx.doi.org/10.3389/fmedt.2020.553478 Text en Copyright © 2020 Nerli and Sgourakis. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Medical Technology Nerli, Santrupti Sgourakis, Nikolaos G. Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens |
title | Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens |
title_full | Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens |
title_fullStr | Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens |
title_full_unstemmed | Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens |
title_short | Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens |
title_sort | structure-based modeling of sars-cov-2 peptide/hla-a02 antigens |
topic | Medical Technology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8757863/ https://www.ncbi.nlm.nih.gov/pubmed/35047875 http://dx.doi.org/10.3389/fmedt.2020.553478 |
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