2 DISTINCT HLA-A-ASTERISK-0101-SPECIFIC SUBMOTIFS ILLUSTRATE ALTERNATIVE PEPTIDE BINDING MODES

Previous studies have defined two different peptide binding motifs spe cific for HLA-A0101. These motifs are characterized by the presence o f tyrosine (Y) at the C-termini of 9-mer and 10-mer peptides, and eith er a small polar or hydrophobic (S, T, M) residue in position 2, or a negatively charged (D or E) residue in position 3. In this study, the structural requirements for peptide binding to A0101 have been furthe r analyzed by examining the binding capacity of large sets of peptides corresponding to naturally occurring sequences which bore one or the other of these two A0101-specific motifs. By correlating the presence of specific residue types at each position along the peptide sequence with increased (or decreased) binding affinity, the prominent influen ce of secondary anchor residues was revealed. In most cases, the two a nchors in positions 2 and 3 appear to act synergistically. With the ex ception of the DE(3) submotif in 9-mer peptides, a positive role for a romatic residues in position 1 and the center of the peptide (position s 4 or 5 of 9- or 10-mer peptides, respectively), and proline at C-3, were also consistently detected. However, secondary anchor residues al so appear to differ significantly between the two different submotifs, demonstrating that A0101 can utilize alternative modes in binding it s peptide ligands. According to these analyses, specific refined submo tifs were also established, and their merit verified by independent se ts of potential A0101 binding peptides. Besides providing useful insi ght into the nature of the interaction of the A0101 allele with its p eptide ligands, such refined motifs should also facilitate accurate pr ediction of potential A0101-restricted peptide epitopes.