Journal of Proteomics & Bioinformatics
Open Access

Abstract

Prediction of MHC Binding Peptides and Epitopes from Coat Protein of Mungbean Yellow Mosaic India Virus-Ub05

Sarika, Mohd. Akram, M. A. Iquebal and Naimuddin K

Mungbean yellow mosaic India virus (MYMIV) is recognized as one of the most economically important viruses that affects several leguminous crops like mungbean, urdbean, cowpea, pigeonpea etc. and occurs in Indian subcontinent. In the present study, coat protein of MYMIV is being used to fi nd out highly suitable MHC binding peptides and epitopes. Thirty nine peptide regions were found to have high af fi nity to TAP binding peptides using cascade support vector machine (SVM). Few of these coat protein TAP transporters are 201- NRFFKVNNY with score 9.208, 108- KRFCIKSVY with score 8.817, 44-RWTNRPMWR with score 8.790, 134- NTVMFKLCR with score 8.672 and 41- KRRRWTNRP with score 8.498 where the scores are based on the average af fi nity of an amino acid at particular position. The SVM based method for prediction of promiscuous MHC Class II binders reported MHCII-IAb peptide regions, 30- PASAGGVPT, 127-IKSKNHTNT, 44-RWTNRPMWR, 6-YDTAFSTPI, (optimal score 1.220); MHCII-IAd peptide regions, 226-NALLLYMAC, 30-PASAGGVPT, 32-SAGGVPTNM, 236- HASNPVYAT, (optimal score 0.620); MHCII-IAg7 peptide regions, 13-PISNARRRL, 212- YNHQEAAKY, 221-ENHTENALL, 209-YVVYNHQEA, (optimal score 1.569) and MHCII- RT1.B peptide regions, 223- HTENALLLY, 188- TGGQYACKE, 168- TVKNDLRDR, 4-RTYDTAFST, (optimal score 0.932) as possible predicted binders from coat protein. The most suitable predicted segments in coat protein of MYMI virus for developing speci fi c antibodies found in this study are 56-FYRLYRSPDVPRGCEGPCKVQSF–78, 206-VNNYVVYNHQ-215 and 108-KRFCIKSVYITG-119. Fragments identi fi ed through this approach tend to be high- ef fi ciency binders, in which larger percentage of their atoms are directly involved in binding as compared to larger molecules. These fragments may, therefore, be used in cross protection and to develop begomovirus speci fi c antibodies that can be exploited in sero-diagnostics.