Abstract:
The binding motives of 18 different MHC class I and five different MHC class II molecules (HLA-DR17 and four HLA-DR4-subtypes) have been identified by multiple sequence analyses. A non-radioactive peptide binding assay was established to study the interaction of natural ligands and HLA-DR17 molecules in detail. Truncation and substitution analysis showed that a minimal sequence of 13 amino acids is sufficient for excellent binding. This peptide binding sequence can be further subdivided: A nanamer core peptide and two flanking residues at either end of the core peptide. The specific contact sites are located on the nanamer peptide with defined distances in relative positions 1, 4, 6 and 9. The contact sites in position P1 and P9 show different degrees of degradation, whereby the anchor residue P1 is taken (occupied) by hydrophobic/aromatic residues exclusively. The conserved residues in relative position P4 and P6 determine (modify) allele specific binding. The interaction between MHC class II molecules and class II-associated invariant chain peptides (CLIPs) was characterized extensively and compared to that of natural conventional ligands. The interaction of CLIPs can be subdivided, like the interaction of natural ligands, into a sequence specific and a non-specific contribution. Our data provide compelling evidence that CLIP peptides bind into the binding groove of class II molecules, analog to antigenic peptides.