The MHC class II-associated invariant chain-derived peptide clip binds to the peptide-binding groove of class II molecules.

Major Histocompatibility Complex (MHC) class II proteins bind to peptides derived from processed foreign antigens, and display them on the cell surface of antigen presenting cells for recognition by CD4+ regulatory T lymphocytes. Prior to their binding to antigenic peptides in endosomal compartments, class II molecules are associated with a nested set of peptides CLIP derived from amino acids 80 to 107 of the invariant chain (Ii). Currently the interaction between the CLIP peptide and class II molecules is not clear. Using an FITC-labeled CLIP peptide and soluble empty class II molecules synthesized in insect cells, we have investigated the direct binding of the CLIP peptide to class II molecules, and the influence of localized polymorphic residues in the peptide-binding groove on the binding. We found that the human class II HLA-DR1 molecule contains a single-binding site for the CLIP peptide as well as the antigenic peptide MP19-31, as analysed by Scatchard analysis. Further studies also showed that occupancy of the peptide-binding groove by antigenic peptides inhibited the binding of CLIP to DR1 molecules and vice versa. Most importantly, the polymorphic residues beta 85 and 86, which define the major peptide-binding pocket, strikingly influence the CLIP-DR1 interaction, as assayed by the SDS-stability of class II-peptide complexes and the affinity of class II-peptide interactions. These data indicate that the peptide-binding pocket and thus the peptide-binding groove of the class II molecule are directly involved in the association with the CLIP peptide.