Proteomics approach for prediction of immunogenic site from Footand- mouth disease virus

Gomase V.S¹*, Phadnis A. C.², Tripathi A.K.^3
1Proteomics Unit, Department of Bioinformatics, Padmashree Dr. D. Y. Patil University, Plot No-50, Sector-15, CBD Belapur, Navi Mumbai, 400614, MS, India
²Proteomics Unit, Department of Bioinformatics, Padmashree Dr. D. Y. Patil University, Plot No-50, Sector-15, CBD Belapur, Navi Mumbai, 400614, MS, India
³Proteomics Unit, Department of Bioinformatics, Padmashree Dr. D. Y. Patil University, Plot No-50, Sector-15, CBD Belapur, Navi Mumbai, 400614, MS, India
* Corresponding Author : virusgene1@ yahoo.co.in

Received : -     Accepted : -     Published : 15-06-2009
Volume : 1     Issue : 1       Pages : 1 - 3
Int J Biotechnol Appl 1.1 (2009):1-3
DOI : http://dx.doi.org/10.9735/0975-2943.1.1.1-3

Keywords : Antigen, Epitope, PSSM, SVM, MHC, Peptide vaccine
Conflict of Interest : None declared

Foot-and-mouth disease is caused by FMDV, an Aphthovirus of the viral family Picornaviridae. Peptide fragments of Foot-and-mouth disease virus protein can be used to select nonamers for use in rational vaccine design and to increase the understanding of roles of the immune system in infectious diseases. Analysis shows MHC class II binding peptides of protein from Footand-mouth disease virus are important determinant for protection of host form viral infection. In this assay we predicted the binding affinity of protein having 213 amino acids, which shows nonamers. These peptides are from a set of aligned peptides known to bind to a given MHC molecule as the predictor of MHC-peptide binding. MHCII molecules bind peptides in similar yet different modes and alignments of MHCII-ligands were obtained to be consistent with the binding mode of the peptides to their MHC class, this means the increase in affinity of MHC binding peptides may result in enhancement of immunogenicity of protein nonamers. Binding ability prediction of antigen peptides to major histocompatibility complex (MHC) class I & II molecules is important in vaccine development from Foot-and-mouth disease virus.

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