HLA-B15 peptide ligands are preferentially anchored at their C termini

Therapies to elicit protective CTL require the selection of pathogen- and t umor-derived peptide ligands for presentation by MHC class I molecules. Edm an sequencing of class I peptide pools generates "motifs" that indicate tha t nonameric ligands bearing conserved position 2 (P2) and P9 anchors provid e the optimal search parameters for selecting immunogenic epitopes, To dete rmine how well a motif represents its individual constituents, we used a ho llow-fiber peptide production scheme followed by the mapping of endogenousl y processed class I peptide ligands through reverse-phase HPLC and mass spe ctrometry. Systematically mapping and characterizing ligands from B*1508, B *1501, B*1503, and B*1510 demonstrate that the peptides bound by these B15 allotypes i) vary in length from 7 to 12 residues, and ii) are more conserv ed at their C termini than their N-proximal P2 anchors. Comparative peptide mapping of these B15 allotypes further pinpoints endogenously processed li gands that bind to the allotypes B*'1508, B*1501, and B*1503, but not B*151 0. Overlapping peptide ligands are successful in binding to B*1501, B*1503, and B*1508 because these B15 allotypes share identical C-terminal anchorin g pockets whereas B*1510 is divergent in the C-terminal pocket. Therefore, endogenous peptide loading into the B15 allotypes requires that a conserved C terminus be anchored in the appropriate specificity pocket while N-proxi mal anchors are more flexible in their location and sequence. Queries for o verlapping and allele-specific peptide ligands may thus be contingent on a conserved C-terminal anchor.