Residue 116 determines the C-terminal anchor residue of HLA-B*3501 and -B*5101 binding peptides but does not explain the general affinity difference.

HLA-B3501 and -B5101 molecules, which belong to the HLA-B5 cross-reactive group, bind peptides carrying similar anchor residues at P2 and the C-terminus, but differences are observed in the preference for a Tyr residue at the C-terminus and the affinity of peptides. A recent study of HLA-B3501 crystal structure suggested that residue 116 on the floor of the F-pocket determines a preference for anchor residues at the C-terminus. In order to evaluate the role of the residue 116 in the peptide binding to both HLA-B3501 and HLA-B5101 molecules, we generated HLA-B3501 mutant molecules carrying Tyr at residue 116 (B3501-116Y) and tested the binding of a panel of nonamer peptides to the B3501-116Y molecules by a stabilization assay with RMA-S transfectants expressing the mutant molecules. The substitution of Tyr for Ser at residue 116 markedly reduced the affinity of nonamer peptides carrying Tyr at P9, while it enhanced that of nonamer peptides carrying Ile and Leu at P9. On the other hand, the affinity of peptides carrying aliphatic hydrophobic residues at P9 to B3501-116Y molecules was much higher than that to HLA-B3501 and HLA-B5101 molecules. These results indicate that residue 116 is critical for the structural difference of the F-pocket between HLA-B3501 and HLA-B5101 which determines the C-terminal anchor residues, while leaving other residues which differ between HLA-B3501 and HLA-B*5101 may be responsible for the low peptide binding property of the latter.