Prediction of MHC Binding Peptides and Epitopes from Groundnut Bud Necrosis Virus (GBNV)

Gomase V S,Kale K V,Shyamkumar K

doi:10.4172/jpb.1000024

Abstract

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.

Highlights

This is a virus disease causing more damage to groundnut crop during kharif and summer
The disease is caused by the Groundnut bud necrosis virus (GBNV)
Gomase method (2007), B-EpiPred Server, Hopp and Woods, Welling, Parker, Kolaskar and Tongaonkar antigenicity scales were designed to predict the locations of antigenic determinants in Groundnut bud necrosis virus

Summary

Materials and Methods

The nucleocapsid protein sequence of Groundnut bud necrosis virus was analyzed to study the antigenicity (Saritha and Jain, 2007), solvent accessible regions and MHC class peptide binding, which allows potential drug targets to identify active sites against plant diseases. Finding the location in solvent accessible regions in protein, type of plot determines the hydrophobic and hydrophilic scales and it is utilized for prediction This may be useful in predicting membrane-spanning domains, potential antigenic sites and regions that are likely exposed on the protein surface (Sweet and Eisenberg, 1983; Kyte and Doolittle, 1982; Abraham and Leo, 1987; Bull and Breese, 1974; Guy, 1985; Miyazawa and Jernigen, 1985; Roseman, 1988; Wolfenden et al, 1981; Wilson et al, 1981; Aboderin, 1971; Chothia, 1976; Eisenberg et al, 1984; Manavalan and Ponnuswamy, 1978; Black and Mould, 1991; Fauchere and Pliska, 1983; Janin, 1979; Rao and Argos, 1986; Tanford, 1962; Cowan and Whittaker, 1990; Rose et al, 1985; Wilkins et al, 1999; Eisenberg et al, 1984). We predicts those MHCI ligands whose C-terminal end is likely to be the result of proteosomal cleavage (Brusic et al, 1998; Bhasin and Raghava, 2005; Gomase et al, 2008)

Result and Interpretation

Discussion and Conclusion