ROLE OF THE POLYMORPHIC RESIDUES IN HLA-DR MOLECULES IN ALLELE-SPECIFIC BINDING OF PEPTIDE LIGANDS

Analysis of peptide binding to a set of HLA-DR alleles has allowed the proteins to be segregated into functional subsets, depending on the a mino acids at positions 57 and 86 of the beta-chain. DR proteins with glycine at 86 beta and aspartic acid at 57 beta bound a simplified pep tide with significantly lower IC50 values than alleles that did not ha ve this combination of amino acids. The size of the amino acid at 86 b eta seemed to modify the steric requirements for the single most impor tant side chain of the peptide. Within each of the four subgroups, oth er polymorphic amino acids define allele-specific binding requirements . These were explored by analyzing the ability of eight different DR a lleles to bind 13 known T cell determinants. The side chains in the pe ptides that seemed to be responsible for allele specificity were deter mined by correlating their common structural features with complementa ry polymorphic residues in the binding site. The importance of these r esidues was tested by incorporating them into a polyalanine backbone, and was confirmed by the ability of these residues to transfer allele specificity to these simplified analogues. Even though polymorphic con tacts affected peptide affinity, the majority of the free energy of bi nding in all cases arose from interactions with the peptide backbone a nd the single hydrophobic amino acid at the third position. These cons traints seem to orient all peptides in a similar location, forcing the m to adopt a closely related conformation in the binding site. The cor responding side chain in each peptide contacts the same pocket in the binding site, regardless of the allele. This apparent similarity shoul d allow any DR allele to be analyzed by extrapolation from the DR1 cry stal structure.