Truncation analysis of several DR binding epitopes

Peptide regions crucial for binding to four different DR alleles (DR1, DR2, DR5, and DR52a) have been localized in five unrelated DR binding peptides (dynorphin 1-13, sperm whale myoglobin 132-153, influenza hemagglutinin 307-319, pigeon cytochrome c 88-104, and tetanus toxoid 830-843) by testing panels of truncated analogs for DR binding. It was found that in most cases, different DR alleles recognize almost identical, albeit distinct, core regions, suggesting that different DR alleles may recognize similar structures on their peptide ligands. Furthermore, it was found that these core regions, notwithstanding their derivation from unrelated sequences, share a common structural pattern. When the sequences of several other unrelated determinants were scrutinized, the structural motif identified was present in some, but absent in other good DR binders, suggesting that good DR binding capacity of peptide molecules may be compatible with more than one single sequence pattern.