Binding of longer peptides to the H-2K(b) heterodimer is restricted to peptides extended at their C terminus: Refinement of the inherent MHC class I peptide binding criteria

MHC class I molecules usually bind short peptides of 8-10 amino acids, and binding is dependent on allele-specific anchor residues. However, in a numb er of cellular systems, class I molecules have been found containing peptid es longer than the canonical size. To understand the structural requirement s for MHC binding of longer peptides, we used an in vitro class I MHC foldi ng assay to examine peptide variants of the antigenic VSV 8 mer core peptid e containing length extensions at either their N or C terminus. This approa ch allowed us to determine the ability of each peptide to productively form K-b/beta(2)-microglobulin/ peptide complexes, We found that H-2K(b) molecu les can accommodate extended peptides, but only if the extension occurs at the C-terminal peptide end, and that hydrophobic flanking regions are prefe rred. Peptides extended at their N terminus did not promote productive form ation of the trimolecular complex, ii structural basis for such findings co mes from molecular modeling of a H-2K(b)/12 mer complex and comparative ana lysis of PI IHC class I structures, These analyses revealed that structural constraints in the A pocket of the class I peptide binding groove hinder t he binding of N-terminal-extended peptides, whereas structural features at the C-terminal peptide residue pocket allow C-terminal peptide extensions t o reach out of the cleft, These findings broaden our understanding of the i nherent peptide binding and epitope selection criteria of the MHC class I m olecule, Core peptides extended at their N terminus cannot bind, but peptid e extensions at the C terminus are tolerated.