Binding of single substituted promiscuous and designer peptides to purified DRB1*0101

MHC class II molecules present antigenic peptides to T cells. The sequence characteristics of peptides associated with various class II alleles have been examined by analysis of peptide mixtures extracted from purified class II molecules as well by direct binding assays with substituted synthetic peptides and purified class II molecules. Here, in vitro binding assays with purified DRB1*0101 and glycine substituted analogues of H gamma 321-340 and alanine substituted analogues of TT948-967, universal CD4+ epitopes of the gamma subunit of the human nicotinic acetylcholine receptor and tetanus toxin, respectively, were able to compete for binding to an extent similar to that of the unsubstituted peptides. Testing whether this is a property of promiscuous, but not allele-specific peptide epitopes, a designer peptide containing the proposed anchor residues for binding DRB1*0101 was used in similar binding assays. As expected, the binding capacity of this designer peptide was much higher than that of the universal epitope peptides. However, substitution of the anchor residues for alanine in the context of this designer peptide did not abrogate binding to DRB1*0101 and, in fact, enhanced it. Therefore, it appears that for both class II allele-specific and universal epitope peptides, binding is a result of the combinatory effects of a few residues. The individual replacement of these residues with the sterically and electrostatically neutral residue alanine does not negatively affect binding in the continued presence of other anchor residues.