THE IMPORTANCE OF SECONDARY ANCHOR RESIDUES OF HLA CLASS-I PROTEINS BINDING PEPTIDES - DEVELOPMENT OF A SYNTHETIC PEPTIDE WITH HIGH BINDING AFFINITY TO HLA-B27 MOLECULES

Crystallographic studies of MHC class I proteins with peptides bound and sequence analysis of the released peptides have revealed that the allele specificity is governed by the complementary interaction of the side chains of several amino acid residues of the bound peptide ("anchor residues") with the corresponding peptide side chain-binding pockets of MHC class I proteins. The role of the secondary anchor residues in the interaction with MHC class I molecules can be studied by a chemometric approach to Quantitative Structure-Activity Relationship (QSAR). In the present work, we have applied this approach to the study of the role of the secondary anchor residues in HLA-B27 peptide binding. Nine nonapeptides were designed by this method and synthesized. All of these carried a primary HLA-B27 anchor motif, Arg in P2 and Lys in P9, while position P3, P5, P6 and P7 were varied using selected representative amino acids. The relative binding affinity of these peptides was determined quantitatively by a direct binding assay, provisionally called HLA class I alpha chain refolding assay. The relative importance of the amino acid structural factors in each of the varied position was then estimated and used to design peptides optimized for their binding to HLA-B27 class I molecules. In conclusion, the paper has shown the usefulness of the chemometric strategy for studying peptides of interest in molecular immunology.