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
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, espe...
Published in: | BMC Bioinformatics |
---|---|
Main Authors: | , , |
Other Authors: | , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
2013
|
Subjects: | |
Online Access: | http://hdl.handle.net/10220/18334 https://doi.org/10.1186/1471-2105-14-S2-S21 |
id |
ftnanyangtu:oai:dr.ntu.edu.sg:10220/18334 |
---|---|
record_format |
openpolar |
spelling |
ftnanyangtu:oai:dr.ntu.edu.sg:10220/18334 2023-05-15T15:34:29+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 Tran To. Schönbach, Christian. Kwoh, Chee Keong. Bioinformatics Research Centre School of Computer Engineering 2013 http://hdl.handle.net/10220/18334 https://doi.org/10.1186/1471-2105-14-S2-S21 en eng BMC Bioinformatics Su, C. T., Schönbach, C., & Kwoh, C. K. (2013). 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. BMC Bioinformatics, 14(Suppl 2), S21. 1471-2105 http://hdl.handle.net/10220/18334 http://dx.doi.org/10.1186/1471-2105-14-S2-S21 © 2013 The Author(s), licensee BioMed Central Ltd. This paper was published in BMC Bioinformatics and is made available as an electronic reprint (preprint) with permission of The Author(s). The paper can be found at the following official DOI: http://dx.doi.org/10.1186/1471-2105-14-S2-S21. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. BioMed Central's Open Data policy. Unless otherwise stated, data included in published open access articles are distributed under the terms of the Creative Commons CC0 1.0 Public Domain Dedication waiver. This applies to data included in the article, its reference list(s) and its additional files. PDM CC0 DRNTU::Engineering::Computer science and engineering Journal Article 2013 ftnanyangtu https://doi.org/10.1186/1471-2105-14-S2-S21 2019-05-24T19:26:58Z 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. Published version Article in Journal/Newspaper Avian flu DR-NTU (Digital Repository at Nanyang Technological University, Singapore) BMC Bioinformatics 14 Suppl 2 S21 |
institution |
Open Polar |
collection |
DR-NTU (Digital Repository at Nanyang Technological University, Singapore) |
op_collection_id |
ftnanyangtu |
language |
English |
topic |
DRNTU::Engineering::Computer science and engineering |
spellingShingle |
DRNTU::Engineering::Computer science and engineering Su, Chinh Tran To. 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 |
topic_facet |
DRNTU::Engineering::Computer science and engineering |
description |
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. Published version |
author2 |
Bioinformatics Research Centre School of Computer Engineering |
format |
Article in Journal/Newspaper |
author |
Su, Chinh Tran To. Schönbach, Christian. Kwoh, Chee Keong. |
author_facet |
Su, Chinh Tran To. Schönbach, Christian. Kwoh, Chee Keong. |
author_sort |
Su, Chinh Tran To. |
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 |
publishDate |
2013 |
url |
http://hdl.handle.net/10220/18334 https://doi.org/10.1186/1471-2105-14-S2-S21 |
genre |
Avian flu |
genre_facet |
Avian flu |
op_relation |
BMC Bioinformatics Su, C. T., Schönbach, C., & Kwoh, C. K. (2013). 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. BMC Bioinformatics, 14(Suppl 2), S21. 1471-2105 http://hdl.handle.net/10220/18334 http://dx.doi.org/10.1186/1471-2105-14-S2-S21 |
op_rights |
© 2013 The Author(s), licensee BioMed Central Ltd. This paper was published in BMC Bioinformatics and is made available as an electronic reprint (preprint) with permission of The Author(s). The paper can be found at the following official DOI: http://dx.doi.org/10.1186/1471-2105-14-S2-S21. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. BioMed Central's Open Data policy. Unless otherwise stated, data included in published open access articles are distributed under the terms of the Creative Commons CC0 1.0 Public Domain Dedication waiver. This applies to data included in the article, its reference list(s) and its additional files. |
op_rightsnorm |
PDM CC0 |
op_doi |
https://doi.org/10.1186/1471-2105-14-S2-S21 |
container_title |
BMC Bioinformatics |
container_volume |
14 |
container_issue |
Suppl 2 |
container_start_page |
S21 |
_version_ |
1766364858905788416 |