Prediction of Antigenic MHC Peptide Binders and TAP Binder of COX1 Protein through In Silico Approach

Abstract

In the current analysis Cytochrome c oxidase subunit I (CO1 or MT-CO1) protein sequence from GWD has been used to study the MHC binding antigenic peptide, antigenic peptide prediction through different B cell prediction method, protein solvent accessibility, polar and nonpolar residue to analyze the regions which are probably exposed on the protein surface. From the protein the peptide fragment can be used to analyze and specific nonamer can be selected for the rational vaccine designing. In this investigation, PSSM and SVM algorithms are applied for finding of MHC I and MHC II binding peptides. We also predicted the high affinity TAP binding peptides of CO1 protein from GWD, having 205 amino acids which show 197 nonamers. From the opted outcomes we predict that, the possibilities that, the antigenic peptide of cytochrome c oxidase subunit I (mitochondrion) protein might play a major role and could be the most suitable candidate for subunit vaccine development on the bases of the finding that, with single epitope, the immune response can be generated in large population.