Peptides shorter than a minimal CTL epitope may have a higher binding affinity than the epitope for the class I Kk molecule.

A previously published Kk-specific motif was used to predict that an optimal Kk-restricted epitope within the nucleoprotein (NP) of influenza A/PR/8/34 virus corresponds to sequence SDYEGRLI (residues 50-57). Although this is the minimal epitope recognized by murine cytotoxic T lymphocytes (CTL), its binding affinity for the Kk molecule is increased following removal of either the N-terminal amino acid residue (S) or the N-terminal dipeptide (SD). A possible explanation for this unexpected result is that interactions between the C-terminus of the epitope and the Kk molecule contribute to the binding energy to a much greater extent than interactions between the N-terminus of the epitope and the Kk molecule.