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Peptides shorter than a minimal CTL epitope may have a higher binding affinity than the epitope for the class I Kk
J Cossins1, K Gould, G G Brownlee
1Sir William Dunn School of Pathology, University of Oxford, United Kingdom.
Abstract:
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.