Peptide selection by an MHC H-2K^b class I molecule devoid of the central anchor ('C') pocket

The peptide-binding site of the murine MHC class I molecule H-2K^b contains a deep C pocket, that is critical for peptide binding, as it accepts the anchor phenylalanine or tyrosine residue located in the middle (position 5, P5F/Y) of H-2K^b binding peptides. H-2K^b predominantly binds octameric peptides. By both criteria, H-2K^b is unique among the known murine and class I molecule, none of which have a deep C pocket or preferentially select octamers. We investigated the relative importance of the C pocket in peptide selection and binding by the MHC. An MHC class I H-2K^b variant, K(bW9), predicted to contain no C pocket, was engineered by replacing valine at MHC9 with tryptophan. This mutation drastically altered the selection of peptides bound to K(bW9). The K(bW9) molecule predominantly, if not exclusively, bound nonamers. New peptide anchor residues substituted for the loss of the P5F/Y:C pocket interaction. P3P/Y, which plays an auxiliary role in binding to K^b, assumed the role of a primary anchor, and P5R was selected as a new primary anchor, most likely contacting the E pocket. These experiments demonstrate that the presence of a deep C pocket is responsible for the selection of octameric peptides as the preferred ligands for K^b and provide insight into the adaptation of peptides to a rearranged MHC groove.