Structure based design was applied in order to define peptide binding motifs for MHC class II molecules. Three dimensional structures of bovine major histocompatibility complex DR molecules were built by homology to the crystal structure of HLA-DR1 complexed with the influenza haemagglutinin (HA) 306-318 peptide. The HA epitope was replaced with a trideca alanine peptide. The De novo design program (Ludi) based on three dimensional database fragment searching was used to suggest sidechain functionalities on the trideca alanine model peptide to complement the MHC pockets. The residues predicted by the Ludi program were translated into natural amino acids. Energy minimisation procedures were performed for these peptides, in order to obtain the values of non-bonded interaction energy between MHC and ligand as well as the internal bonded energy of the ligand. The motif peptides were synthesised and their biological activities were evaluated in a competitive MHC class II-peptide binding assay using purified bovine MHC class II DR molecules. The data obtained from the motif peptides predicted for the DR molecules from the BoLA-DRB3*0201 and BoLA-DRB3*1101 alleles clearly demonstrated their specific binding to their respective MHC molecules. The defined motif for the BoLA-DRB3*1201 allele, however did not display the same specificity in terms of binding to its respective MHC molecules. In summary, the data presented in this paper show that, it is possible to define peptide binding motifs based on the MHC structure only.

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