In silico prediction of MHC binding peptides and epitopes from Tobacco streak virus coat protein to develop immuno-diagnostics for virus

Tobacco streak virus (TSV), a member of Ilarvirus genus, infect broad range of vegetables, oilseed and fiber crops. The genome consisted of tripartite, positive-sense single-stranded RNA. The coat protein of TSV serve as an excellent source of antigenic peptides (epitopes) that binds to the major histocompatability complex (MHC) and influence the antibody production in mice/rabbit. With the advancement in computational studies, the most effective peptides that bind the cell surface glycoproteins, MHC, to mediate immune response by way of antigen presentation and T cell activation can be elucidated. Among the 16 high affinity binders listed, KFYRLLIGF sequence was ranked highest by TAPPred as coat protein binding protein TAP transporters. It was observed that peptide regions RMTAPIPW, GTFGMVDGV, RGCPAHAPA and TRKASECLA were ranked first from MHCII-IAb, MHCII-IAd, MHCII-IAg7 and MHCII-RT1.B alleles at positions 71, 149, 41 and 101 as possible predicted binders of class II MHC from coat protein of TSV. Eight antigenic determinants were predicted from the Predicting Antigenic Peptides tool where the highest pick was AKTSLKLPNNQVWVTRKASECLAK sequence with 87th start position and 110th end position. Average antigenic propensity for this protein was 1.0184 which indicated it to be potentially antigenic. The fragments observed in the present study can be used as efficient antigenic determinants with further verification from the wet lab studies. Therefore, these fragments can be used to develop specific antibodies against Tobacco streak virus infecting pumpkin