Although associations between the expression of particular HLA genes and susceptibility to specific autoimmune diseases has been known for some time, the role HLA molecules play in the autoimmune response is unclear. Through the establishment of chimeric HLA-DR/I-E transgenes, the authors examined the function of the rheumatoid arthritis (RA) susceptibility alleles HLA-DR1 (DRB1*0101) and DR4 (DRB1*0401) in presenting antigenic peptides derived from the model antigen, type II collagen (CII), and in mediating an autoimmune response. As a transgene, these chimeric DR molecules confer susceptibility to an autoimmune arthritis induced by immunization with human CII. Both the DR1 and DR4-restricted T cell responses to CII are focused on an immunodominant determinant CII(263-270). Peptide binding studies revealed that the majority of the CII-peptide binding affinity for DR1 and DR4 is controlled by the Phe at 263 and, unexpectedly, the adjacent Lys. Only these 2 CII amino acids were found to provide binding anchors. Amino acid substitutions at the remaining positions had either no effect or significantly increased the affinity of the hCII peptide. These data indicate that DR1 and DR4 bind this CII peptide in a nearly identical manner and that the primary structure of CII may dictate a different binding motif for DR1 and DR4 than has been described for other peptides. In all, these studies demonstrate that DR1 and DR4 are capable of binding peptides derived from human type II collagen (hCII) and support the hypothesis that autoimmune responses to hCII play a role in the pathogenesis of RA.