Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development
Abstract Background The pandemic 2009-H1N1 influenza virus circulated in the human population and caused thousands deaths worldwide. Studies on pandemic influenza vaccines have shown that T cell recognition to conserved epitopes and cross-reactive T cell responses are important when new strains emer...
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Online Access: | http://dx.doi.org/10.1186/1471-2105-14-s2-s21 https://link.springer.com/content/pdf/10.1186/1471-2105-14-S2-S21.pdf |
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crspringernat:10.1186/1471-2105-14-s2-s21 2023-05-15T15:34:30+02:00 Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development Su, Chinh TT Schönbach, Christian Kwoh, Chee-Keong 2013 http://dx.doi.org/10.1186/1471-2105-14-s2-s21 https://link.springer.com/content/pdf/10.1186/1471-2105-14-S2-S21.pdf en eng Springer Science and Business Media LLC BMC Bioinformatics volume 14, issue S2 ISSN 1471-2105 Applied Mathematics Computer Science Applications Molecular Biology Biochemistry Structural Biology journal-article 2013 crspringernat https://doi.org/10.1186/1471-2105-14-s2-s21 2022-01-04T07:55:17Z Abstract Background The pandemic 2009-H1N1 influenza virus circulated in the human population and caused thousands deaths worldwide. Studies on pandemic influenza vaccines have shown that T cell recognition to conserved epitopes and cross-reactive T cell responses are important when new strains emerge, especially in the absence of antibody cross-reactivity. In this work, using HLA-B*4405 and DM1-TCR structure model, we systematically generated high confidence conserved 2009-H1N1 T cell epitope candidates and investigated their potential cross-reactivity against H5N1 avian flu virus. Results Molecular docking analysis of differential DM1-TCR recognition of the 2009-H1N1 epitope candidates yielded a mosaic epitope (KEKMNTEFW) and potential H5N1 HA cross-reactive epitopes that could be applied as multivalent peptide towards influenza A vaccine development. Structural models of TCR cross-recognition between 2009-H1N1 and 2004-H5N1 revealed steric and topological effects of TCR contact residue mutations on TCR binding affinity. Conclusions The results are novel with regard to HA epitopes and useful for developing possible vaccination strategies against the rapidly changing influenza viruses. Yet, the challenge of identifying epitope candidates that result in heterologous T cell immunity under natural influenza infection conditions can only be overcome if more structural data on the TCR repertoire become available. Article in Journal/Newspaper Avian flu Springer Nature (via Crossref) BMC Bioinformatics 14 S2 |
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Applied Mathematics Computer Science Applications Molecular Biology Biochemistry Structural Biology |
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Applied Mathematics Computer Science Applications Molecular Biology Biochemistry Structural Biology Su, Chinh TT Schönbach, Christian Kwoh, Chee-Keong Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development |
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Applied Mathematics Computer Science Applications Molecular Biology Biochemistry Structural Biology |
description |
Abstract Background The pandemic 2009-H1N1 influenza virus circulated in the human population and caused thousands deaths worldwide. Studies on pandemic influenza vaccines have shown that T cell recognition to conserved epitopes and cross-reactive T cell responses are important when new strains emerge, especially in the absence of antibody cross-reactivity. In this work, using HLA-B*4405 and DM1-TCR structure model, we systematically generated high confidence conserved 2009-H1N1 T cell epitope candidates and investigated their potential cross-reactivity against H5N1 avian flu virus. Results Molecular docking analysis of differential DM1-TCR recognition of the 2009-H1N1 epitope candidates yielded a mosaic epitope (KEKMNTEFW) and potential H5N1 HA cross-reactive epitopes that could be applied as multivalent peptide towards influenza A vaccine development. Structural models of TCR cross-recognition between 2009-H1N1 and 2004-H5N1 revealed steric and topological effects of TCR contact residue mutations on TCR binding affinity. Conclusions The results are novel with regard to HA epitopes and useful for developing possible vaccination strategies against the rapidly changing influenza viruses. Yet, the challenge of identifying epitope candidates that result in heterologous T cell immunity under natural influenza infection conditions can only be overcome if more structural data on the TCR repertoire become available. |
format |
Article in Journal/Newspaper |
author |
Su, Chinh TT Schönbach, Christian Kwoh, Chee-Keong |
author_facet |
Su, Chinh TT Schönbach, Christian Kwoh, Chee-Keong |
author_sort |
Su, Chinh TT |
title |
Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development |
title_short |
Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development |
title_full |
Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development |
title_fullStr |
Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development |
title_full_unstemmed |
Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development |
title_sort |
molecular docking analysis of 2009-h1n1 and 2004-h5n1 influenza virus hla-b*4405-restricted ha epitope candidates: implications for tcr cross-recognition and vaccine development |
publisher |
Springer Science and Business Media LLC |
publishDate |
2013 |
url |
http://dx.doi.org/10.1186/1471-2105-14-s2-s21 https://link.springer.com/content/pdf/10.1186/1471-2105-14-S2-S21.pdf |
genre |
Avian flu |
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Avian flu |
op_source |
BMC Bioinformatics volume 14, issue S2 ISSN 1471-2105 |
op_doi |
https://doi.org/10.1186/1471-2105-14-s2-s21 |
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BMC Bioinformatics |
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14 |
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S2 |
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1766364868655448064 |