In contrast to
HLA-B*2705, B*2709 is weakly or not associated to
ankylosing spondylitis. Both allotypes differ by a single D116H change. We compared the B*2705- and B*2709-bound
peptide repertoires by mass spectrometry to quantify the effect of B*2709 polymorphism on
peptide specificity. In addition, shared and differentially bound
ligands were sequenced to define the structural features of the various
peptide subsets. B*2705 shared 79% of its
peptide repertoire with B*2709. Shared
ligands accounted for 88% of the B*2709-bound repertoire. All B*2705
ligands not bound to B*2709 had C-terminal basic or Tyr residues. Most B*2709-bound
peptides had C-terminal aliphatic and Phe residues, but two showed C-terminal Arg or Tyr. The B*2709-bound repertoire included 12% of
peptides not found in B*2705. These had aliphatic C-terminal residues, which are also favored in B*2705. However, these
peptides bound weakly B*2705 in vitro, indicating distinct contribution of secondary anchor residues in both subtypes. Differences in
peptide binding did not affect the ratio of native to beta2-microglobulin-free
HLA-B27 heavy chain at the cell surface. Our results suggest that weaker association of B*2709 with
ankylosing spondylitis is based on differential binding of a limited subset of natural
ligands by this allotype.