Long-range effects in protein-ligand interactions mediate peptide specificity in the human major histocompatibility antigen HLA-B27 (B*2701)

B*2701 differs from all other HLA-B27 subtypes of known peptide specificity in that, among its natural peptide ligands, arginine is not the only allow ed residue at peptide position 2. Indeed, B*2701 is unique in binding many peptides with Gln2 in vivo. However, the mutation (Asp74Tyr) responsible fo r altered selectivity is far away from the B pocket of the peptide binding site to which Gln/Arg2 binds. Here, we present a model that explains this e ffect. It is proposed that a new rotameric state of the conserved Lys70 is responsible for the unique B*2701 binding motif. This side chain should be either kept away from pocket B through its interaction with Asp74 in most H LA-B27 subtypes, or switched to this pocket if residue 74 is Tyr as in B*27 01. Involvement of Lys70 in pocket B would thus allow binding of peptides w ith Gln2. Binding of Arg2-containing peptides to B*2701 is also possible be cause Lys70 could adopt another conformation, H-bonded to Asn97, which pres erves the same binding mode of Arg2 as in B*2705. This model was experiment ally validated by mutating Lys70 into Ala in B*2701. Edman sequencing of th e B*2701(K70A) peptide pool showed only Arg2, characteristic of HLA-B27-bou nd peptides, and no evidence for Gln2. This supports the computational mode l and demonstrates that allowance of B*2701 for peptides with Gln2 is due t o the long-range effect of the polymorphic residue 74 of HLA-B27, by induci ng a conformational switch of the conserved Lys70.