A negatively charged anchor residue promotes high affinity binding to the MHC class II molecule I-Ak

An allele-specific peptide-binding motif for the murine MHC class II molecule I-Ak has proven elusive. Here we demonstrate that the I-Ak molecule preferentially binds peptides that contain negatively charged amino acids at the primary anchor position (Asp or Glu at P1), and that I-Ak can also bind peptides with polar residues at P1 (Cys, Ser, Asn, Gin, or Thr), although with lower affinity. This preference for a negatively charged anchor residue is so pronounced that polyalanine peptides containing a single Asp can bind to I-Ak. Eight naturally processed peptides were found to use an Asp, as demonstrated by a drop in the I-Ak binding affinity of these peptides after Ala substitution. The chemical identity of the amino acid in the anchor position was also important in determining the ability of peptide-I-Ak complexes to resist denaturation on SDS-polyacrylamide gels. The P1 binding pockets of HLA-DR and H-2E molecules are reported to be large and hydrophobic, and these class II molecules prefer to bind peptides with large aliphatic or aromatic side chains at P1. Our results suggest that the structure of the I-Ak P1 binding pocket is different. Based on sequence comparisons, we suggest that the P1 binding pockets of H-2A molecules may prove more polymorphic than the P1 binding pockets of H-2E molecules, and that this additional polymorphism will cause H-2A molecules to display larger intra-allelic differences in peptide binding specificities.