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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
Authors: Su, Chinh Tran To.
Schönbach, Christian.
Kwoh, Chee Keong.
Keywords: DRNTU::Engineering::Computer science and engineering
Issue Date: 2013
Source: 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.
Series/Report no.: BMC Bioinformatics
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.
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.
ISSN: 1471-2105
DOI: 10.1186/1471-2105-14-S2-S21
Rights: 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:  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.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCSE Journal Articles

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File Description SizeFormat 
2013 BMC-Bioinformatics_H1N1 paper_Chinh.pdfMain Article356.86 kBAdobe PDFThumbnail
1471-2105-14-s2-s21-s1.pdfMAFFT multiple sequence alignment of pandemic strains (2009 - the top 7 sequences) HA proteins to HA (1918 - South Carolina) and WHO vaccine HA (the last 3 sequences)494.24 kBAdobe PDFThumbnail
1471-2105-14-s2-s21-s2.xlsPredicted HA T cell epitopes of H1N1 2009 strains compared to 1918 and WHO-1999-2006-2007 strains.38.5 kBMicrosoft ExcelView/Open
1471-2105-14-s2-s21-s3.pdfPhysicochemical properties of NetCTL-predicted HLA-B44 restricted T cell epitope candidates (A) and non-epitopes (B).93.41 kBAdobe PDFThumbnail
1471-2105-14-s2-s21-s4.pdfResidues of domain α1, α2 of HLA-B*4405 interacting with DM1-TCR.66.99 kBAdobe PDFThumbnail


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