Effects of polymorphism of HLA on binding of antigenic peptides to HLA and recognition of peptides complexed with HLA by T cell receptor

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HLA-DR molecules are highly polymorphic molecules and bind antigenic peptides to present it to CD4 positive helper T cells. The particular DR alleles are thought to determine susceptibility to autoimmune diseases because the frequencies of particular DR allelse are increased in the patients group as compared with those in healthy controls. Thus DRB1 ^<**>0405 and DRB1 ^<**>0406 which differs in only four amino acid residues from DRB1 ^<**>0405 control susceptibility to rheumatoid arthritis and insulin autoimmune syndrome respectively. We have investigated the structural characteristics of antigenic peptides bound to either DRB1 ^<**>0405 or DRB1 ^<**>0406 molecules. For this aim, self peptides bound to purified DRB1 ^<**>0405 molecules were isolated and fractionated by a reversed phase HPLC.Amino acid sequences of seven independent peptides were determined and four of them were identified to be fragments of known proteins. These self peptides were synthesized and radio-iodinated, and binding of labeled peptides to DR molecules were investigated. The strongest binder among seven self peptides was identified and this peptide bound to both DRB1 ^<**>0405 and DRB1 ^<**>0406 equally. The binding inhibition assay, in which binding activity of a peptide to be tested was determined by measuring inhibitory effect of the excess amount of peptide on binding of the labeled strongest binder to DR molecule, was established. In order to determine amino acid residues important for DR binding in the strongest binder, analogue peptides having only one amino acid substitution from the original peptides were synthesized and their binding to both DRB1 ^<**>0405 and DRB1 ^<**>0406 was investigated. DR binding peptides consisted of nine to twenty amino acids were bound at three major anchorage amino acid residues of the peptide to DR molecule. These three anchorage residues were separated by two and one intervening amino acids. The first