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

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...

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Main Authors: Su, Chinh Tran To., Schönbach, Christian., Kwoh, Chee Keong.
Other Authors: School of Computer Engineering
Format: Article
Language:English
Published: 2013
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DRNTU::Engineering::Computer science and engineering
Online Access:https://hdl.handle.net/10356/84316
http://hdl.handle.net/10220/18334
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Institution: Nanyang Technological University
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spelling sg-ntu-dr.10356-843162022-02-16T16:27:34Z 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. School of Computer Engineering Bioinformatics Research Centre DRNTU::Engineering::Computer science and engineering 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. 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. 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. Published version 2013-12-19T02:44:29Z 2019-12-06T15:42:40Z 2013-12-19T02:44:29Z 2019-12-06T15:42:40Z 2013 2013 Journal Article 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 https://hdl.handle.net/10356/84316 http://hdl.handle.net/10220/18334 10.1186/1471-2105-14-S2-S21 23368875 en BMC Bioinformatics 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. © 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. application/pdf application/pdf application/vnd.ms-excel application/pdf application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
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
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.
author2 School of Computer Engineering
author_facet School of Computer Engineering
Su, Chinh Tran To.
Schönbach, Christian.
Kwoh, Chee Keong.
format Article
author 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 https://hdl.handle.net/10356/84316
http://hdl.handle.net/10220/18334
_version_ 1725985560439291904

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