DEFINITION OF SPECIFIC PEPTIDE MOTIFS FOR 4 MAJOR HLA-A ALLELES

Allele-specific motifs for the human MHC class I molecules, HLA-A1, A3 , A11, and A24 were characterized by three complementary approaches. F irst, amino acid sequence analysis of acid eluted peptide pools from a ffinity purified class I molecules defined putative motifs 9 or 10 ami no acids in length and bearing critical anchor residues at position 2 and at the COOH-terminal. These motifs were distinct, with the excepti on of the HLA-A3 and A11 motifs that were very similar to each other. Second, the correctness of these putative motifs was verified by analy zing the binding capacity of polyalanine peptide analogues to purified HLA-A molecules. Several alternative anchor residues that were not ob vious from the pooled peptide sequencing analysis were identified. Thi rd, sequences of individual peptides eluted from HLA-A1, A11, and A24 were determined by tandem mass spectrometry. Nonamers were the predomi nant species, although peptides of 8, 10, 11, and 12 amino acids in le ngth were also identified. These peptides displayed anchor residues pr edicted by the specific motifs at position 2 and at the COOH-terminal, regardless of peptide length. Synthetic versions of the naturally pro cessed peptides were shown to bind to the appropriate HLA-A alleles wi th IC50 values in the 0.3- to 200-nM range. A rational approach to sea rch Ags with known amino acid sequences for epitopes restricted by som e of the most common HLA-A types and of potential clinical importance is now feasible.