Precise prediction of a Kk-restricted cytotoxic T cell epitope in the NS1 protein of influenza virus using an MHC allele-specific motif.

The nonstructural protein NS1 of influenza A/PR/8/34 virus has previously been reported to be recognized by murine Kk-restricted cytotoxic T lymphocytes (CTL), although the sequence of the epitope was not defined. A Kk-specific motif has previously been published and consists of a glutamic acid or (less frequently) an aspartic acid at position 2 and an isoleucine at the carboxyl terminus of a peptide eight or nine residues long. This motif was used here to predict the sequence of the NS1 epitope, which was defined as a nonapeptide corresponding to amino acid residues 152-160, sequence EEGAIVGEI. This is the first CTL epitope to be defined within the NS1 protein of the influenza A virus. A model of how this epitope could bind to the Kk molecule was produced by homology modelling from an X-ray crystal structure of a human HLA/peptide complex.