A CONTINUOUS CENTRAL MOTIF OF INVARIANT CHAIN PEPTIDES, CLIP, IS ESSENTIAL FOR BINDING TO VARIOUS I-A MHC CLASS-II MOLECULES

Invariant chain (Ii) associates with MHC class II molecules and perfor ms a number of crucial functions in antigen presentation, A nested set of class II-associated Ii peptides (CLIP) has been isolated, comprisi ng the Ii sequence between residues 82 and 107, Recently, X-ray crysta llographic analysis has revealed that residues 87-101 occupy the HLA-D R3 peptide-binding groove, Based on our previous results, Lee and McCo nnell have also proposed a model for the binding of CLIP to various mo use I-A molecules in the binding groove, CLIP sequences are able to bi nd many MHC class II molecules but the molecular basis of this promisc uity has not yet been resolved, We have shown recently that CLIP bindi ng to I-A class II molecules is generally tolerant to side chain subst itutions, suggesting that the backbone structure of CLIP may provide t he features critical for its interaction with class II. In pursuit of this, backbone stereochemical disruptions by serial D-alanine substitu tions in CLIP86-104 have been used in competitive binding assays to I- A class II molecules, These studies have revealed that the phylogeneti cally conserved central continuous region, CLIP91-99, is intolerant to such configurational substitutions, Experiments with truncated and fr ame-shift analogues of CLIP showed that for effective binding to class II, the sequence element CLIP90-100 must be incorporated into a pepti de of 13 or more residues including at least three residues N-terminal to this motif. Additionally, it appears that different I-A molecules accommodate CLIP in different binding frames, These investigations of the relationship between the structure and binding of CLIP analogues l ead us to propose that there Is a general backbone motif of a periodic nature within the CLIP sequence that minimizes deleterious contacts a nd allows promiscuous binding to class II molecules.