Determination of MHC Binding Peptides and Epitopes from Non- Structural Movement (NSm) Protein of Groundnut Bud Necrosis Virus

Sarika; M.      Akram; M.      A. Iquebal; K.      Naimuddin

Abstract

Groundnut bud necrosis virus (GBNV) is recognized as one of the most economically important viruses and is known to affect several crops including peanut, potato, tomato and soybean. For managing plant virus diseases, determination of their causal agents’ identity at an early stage of crop is a pre-requisite. In the present study, NSm protein of GBNV has been used to predict out MHC binding peptides and epitopes that are highly suitable for antigenicity. Eighteen peptide regions were found to have high affinity. Few of these NSm protein TAP transporters are 126- RRYMHISRL with score 11.638, 125- NRRYMHISR with score 10.280, 46- AIMNKAKTL with score 7.762, 120- PTWNSNRRY with score 7.632 and 171- ASLKDPMCF with score 7.277. The support vector machine (SVM) based approach predicted MHCII-IAb peptide regions, 45- SAIMNKAKT, 151- ASLIDPNKM, 23- PAVKKENNR, 229- PIAAENNTC, (optimal score 0.938); MHCII-IAd peptide regions, 208- YAKGVGFAS, 101- NDSLVGNGN, 55- NGKQYVSSG, 63-GDSSVLGTY, (optimal score 0.852); MHCII-IAg7 peptide regions, 277- LQKAAERLA, 145- SKNNVKASL, 228-TPIAAENNT, 276- SLQKAAERL, (optimal score 1.640); and MHCII- RT1.B peptide regions, 193- TPKQCMQLN, 195- KQCMQLNLT, 246- KVIQSAALI, 166- IISRQASLK, (optimal score 0.800) as binders from NSm protein. Themost suitable predicted segments in NSm protein of GBNV virus found in the study are 164 KIIISRQASLKDPMCFIFHLNWS-186 and 237-CDVVPINRAKVIQSAALIEACKLMIP-262. These two fragments, obtained from non-structural movement protein with average propensity 1.016, are high-efficiency binders and may, thereforebe used in cross protection to provide resistance against GBNV and develop GBNV specific antibodies that can be exploited in sero-diagnostics.

Keywords: Cross protection, Groundnut bud necrosis virus, epitope, MHC binders, non-structural movement protein, support vector machine, GBNV, Tospoviruses, Tomato spotted wilt virus, Bunyaviridae, RNA polymerase, PCR, RT-PCR, ELISA, PSSMs, Hopp-Woods scale, Hydrophobicity plot of Hopp, &, Woods, Hydrophobicity plot of Welling, al, Kolaskar and Tongaonkar antigenicity sites, Hydrophobicity Sweet plot of OMH, Hydrophobicity plot of Kyte, Doolittle, Hydrophobicity plot of Rao, Argos, MHC, TAP transporter, Peptide Binders, Movement Protein, Antigenic Epitopes