The invariant chain derived fragment CLIP is an efficient in vitro inhibitor of peptide binding to MHC class II molecules.

The invariant chain derived peptide CLIP inhibits association of peptides to the class II peptide binding site. Two DR3 specific peptides, the microbacterial heat shock protein 65 derived peptide hsp3-13 and the naturally occurring invariant chain derived peptide Ii131-149 were employed to study binding inhibition by CLIP (Ii82-102) in a series of combinations. Incubation of detergent solubilized DR polypeptides from Ii-free cells with 500 microM of synthetic CLIP almost completely prevents binding of 50 microM subsequently added DR3-specific peptides. When CLIP and the peptides were added simultaneously to DR3 molecules, binding of hsp3-13 was abolished, whereas binding of Ii131-149 was only partially blocked. This indicates apparent affinity differences of the peptides. The addition of CLIP to preformed DR-peptide complexes substantially reduced binding of hsp3-13,while there was little effect on the DR associated Ii131-149. The profound inhibitory ability of CLIP, which in vivo would diminish binding of antigenic peptides, suggests an intracellular mechanism that abrogates the persistence of the CLIP-DR complex. The HLA-DM molecules have been suggested as candidates for this function. The strong in vitro binding of the naturally occurring peptide Ii131-149 to DR3 may suggest that only limited amounts of this peptide are available in vivo for competition of exogenous peptide binding to class II molecules.