Natural ligand motifs of H-2E molecules are allele specific and illustrate homology to HLA-DR molecules

Motifs of peptides naturally associated with H-2E(k) and E(d) molecules were determined by (i) pool sequencing of natural ligand mixtures and (ii) sequencing of individual natural ligands followed by their alignment to the basic motif suggested by pool sequencing. The data reveal nine amino acid motifs with interaction sites at relative positions P1, P4, P6 and P9, with specificities that are identical at some but different at other anchor positions between E(d) and E(k) motifs, illustrating the different requirements for peptides to be presented by these two MHC molecules. The anchors with the most restricted specificity are P1 and P9. P1 is aliphatic for E(k) and predominantly aromatic for E(d). P9 is positively charged for both molecules. P4 and P6 show a totally different amino acid preference between E(k) and E(d) ligand motifs. An alignment of E(d) and E(k) protein sequences to the recently reported HLA-DR1 pocket residues is in agreement with observed anchor residues in E(k) and E(d) motifs, thus confirming the predicted similarity of mouse class II E molecules with human DR molecules. Furthermore, this alignment was extended to the putative pockets of class II E(b) and E(s) molecules, and allowed, together with sequence information of previously identified natural ligands of E(b) and E(s) molecules, a prediction of their respective motifs. The information obtained by this study should be useful to identify putative class II E epitopes in proteins and to design peptides for blocking class II E molecules.