Prediction of potential cytotoxic T lymphocyte epitopes of bovine herpesvirus 1 based on allele-specific peptide motifs and proteolytic cleavage specificities.

Major histocompatibility complex (MHC) class I molecules present endogenous peptides to cytotoxic T lymphocytes (CTLs). Elucidation of CTL epitopes of intracellular pathogens helps in designing better vaccines to control economically important human and animal diseases. In this study, candidate epitopes that are potentially available for presentation to the CTLs via five bovine MHC class I molecules have been identified. This was accomplished by using the computer programs "Find-patterns" and "Peptidestructure" of GCG package and applying the information on cleavage patterns of cytosolic and endoplasmic reticulum proteases and peptidases as well as MHC class I allele-specific peptide motifs on 23 bovine herpesvirus-1 (BHV-1) proteins available on protein sequence database. Several candidate peptides were found for each of the bovine lymphocyte antigens (BoLA)-A11, -A20, -HD1, and -HD6 whereas no peptide was found for BoLA-HD7. Majority of the candidate peptides were from the viral glycoproteins. The contribution of such studies towards the identification of CTL epitopes of BHV-1 and other intracellular pathogens is discussed.