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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
Chinh TT Su1, Christian Sch?nbach3,4* and Chee-Keong Kwoh1,2*
* Corresponding authors: Christian Sch?nbach schoen@bio.kyutech.ac.jp - Chee-Keong Kwoh asckkwoh@ntu.edu.sg
Author Affiliations
1 Bioinformatics Research Centre, School of Computer Engineering, Nanyang Technological University, Singapore 639798
2 Biomedical Engineering Research Centre, College of Engineering, Nanyang Technological University, Singapore 637553
3 Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
4 Biomedical Informatics Research Center, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
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BMC Bioinformatics 2013, 14(Suppl 2):S21 doi:10.1186/1471-2105-14-S2-S21
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/14/S2/S21
Published: 21 January 2013
? 2013 Su et al.; licensee BioMed Central Ltd.
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.
full text
http://www.biomedcentral.com/1471-2105/14/S2/S21
Chinh TT Su1, Christian Sch?nbach3,4* and Chee-Keong Kwoh1,2*
* Corresponding authors: Christian Sch?nbach schoen@bio.kyutech.ac.jp - Chee-Keong Kwoh asckkwoh@ntu.edu.sg
Author Affiliations
1 Bioinformatics Research Centre, School of Computer Engineering, Nanyang Technological University, Singapore 639798
2 Biomedical Engineering Research Centre, College of Engineering, Nanyang Technological University, Singapore 637553
3 Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
4 Biomedical Informatics Research Center, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
For all author emails, please log on.
BMC Bioinformatics 2013, 14(Suppl 2):S21 doi:10.1186/1471-2105-14-S2-S21
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/14/S2/S21
Published: 21 January 2013
? 2013 Su et al.; licensee BioMed Central Ltd.
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.
full text
http://www.biomedcentral.com/1471-2105/14/S2/S21