Zeitschrift für Proteomik und Bioinformatik
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Prediction of MHC Binding Peptides and Epitopes from Groundnut Bud Necrosis Virus (GBNV)

Gomase V.S, Kale K.V and Shyamkumar K

A virus disease caused of crop losses to groundnut in Andhra Pradesh during kharif in the year 2000. It was presumed to be caused by Groundnut bud necrosis virus (GBNV), a virus known to be widely distributed in India. It is one among the important infestations affecting groundnut cultivation especially during summer. Nucleocapsid peptides of groundnut bud necrosis virus are most suitable for subunit vaccine development because with single epitope, the immune response can be generated in large population. Analysis shows MHC class II binding peptides of coat protein from SMV are important determinant for protection of many plants form viral infection. In this assay we predicted the binding affinity of SMV genome polyprotein having 276 amino acids, which shows 268 nonamers. In this analysis, we found the SVM based MHCII-IAb peptide regions, 171- PLAYYQNVK, 95- RTEAFIRTK, 90- DWTFKRTEA, 37- KAFYDANKT, (optimal score is 1.059); MHCII-IAd peptide regions, 159- LSSMTGLAP, 68- KSGKYVFCG, 11- KIKELLAGG, 49- TFTNCLNIL, (optimal score is 0.702); MHCIIIAg7 peptide regions, 128- PLVAAYGLN, 127- LPLVAAYGL, 18- GGSADVEIE, 39- FYDANKTLE, (optimal score is 1.551); and MHCII- RT1.B peptide regions, 49- TFTNCLNIL, 247- DKAFSASLS, 110- KSKNDAAKQ, 92- TFKRTEAFI , (optimal score is 1.092) which represented predicted binders from nucleocapsid protein. The method integrates prediction of peptide MHC class I binding; proteasomal C terminal cleavage and TAP transport efficiency of the nucleocapsid protein of GBNV. Thus a small fragment of antigen can induce immune response against whole antigen. This theme is implemented in designing subunit and synthetic peptide vaccines.