Knowledge based threading approach to model the MHC-binders to MHC class I alleles in Hepatitis E Virus: a clue for epitope-based vaccine design

Abstract

Identification of cytotoxic T lymphocytes (CTL) is a crucial step for designing a peptide based vaccine. T-cell recognition of the peptide-MHC complex is a pre-requisite for initiating the immunological events which leads to the immune response. In the present study CD8+ T-cell epitope for capsid protein of hepatitis E virus (HEV) were identified and knowledge based threading approach has been implemented for MHC binding peptides. The study demonstrated structural analysis of interactions in protein–peptide complexes can lead to insight into the mode of substrate recognition. The compatibility of the peptide to bind to MHC complex is evaluated by pairwise amino acid contact potential. Threading approach has been applied for peptide binding to two MHC class I alleles for the capsid protein of HEVwhose crystal structure is available in Protein Data Bank. The threading approach could be extended to screen a large number of MHC alleles for the prediction of Tcell epitopes using data generated for molecular modeling of peptide MHC complex.