HIGH-AFFINITY BINDING OF SHORT PEPTIDES TO MAJOR HISTOCOMPATIBILITY COMPLEX CLASS-II MOLECULES BY ANCHOR COMBINATIONS

We have previously identified four anchor positions in HLA-DRB10101-b inding peptides, and three anchors involved in peptide binding to DRB1 0401 and DRB1*1101 molecules, by screening of an M13 peptide display library (approximate to 20 million independent nonapeptides) for DR-bi nding activity. In this study, high stringency screening of the M13 li brary for DRB10401 binding has resulted in identification of three fu rther anchor positions. Taken together, a peptide-binding moth has bee n obtained, in which six of seven positions show enrichment of certain residues. We have demonstrated an additive effect of anchors in two d ifferent ways: (i) the addition of more anchors is shown to compensate for progressive truncation of designer peptides; (ii) the incorporati on of an increasing number of anchors into 6- or 7-residue-long design er peptides is shown to result in a gradual increase of binding affini ty to the level of 13-residue-long high-affinity epitopes. The anchor at relative position 1 seems to be obligatory, in that its substitutio n abrogates binding completely, whereas the elimination of other ancho rs results only in partial loss of binding affinity. The spacing betwe en anchors is critical, since their effect is lost by shifting them on e position toward the N or C terminus. The information born out of thi s study has been successfully used to identify DR-binding sequences fr om natural proteins.