In order to characterize peptide binding motifs of MHC class II molecules HLA-DR3, we have sequenced pool or single peptides eluted from the binding groove. Anchor residues identified are in agreement with peptide binding and sequencing studies reported by different groups. Four positions seem to be dominant (i, i + 3, i + 5, i + 8) while 2 secondary positions (i + 1, i + 2) could cooperate to facilitate binding. According to all the criteria define here and the literature, we propose an anchor motif specific for DR3, which has been tested on the sequence of an antigen from Schistosoma mansoni. Three out of 6 putative epitopes identified share common sequences with immunodominant regions determined in humans and by experimental immunizations in animal models. Extended to other alleles, this approach could be suitable to define potentially immunodominant peptides useful for vaccines.
Amino Acid Sequence Animals