Major histocompatibility (MHC) class II molecules are cell surface heterodimeric (alphabeta) glycoproteins that display processed antigens to T cell receptors (TCRs) of CD4-positive T cells. The present study describes that individual recombinant alpha and beta chains of human MHC class II molecules lacking the transmembrane region (alpha-Tm and beta-Tm) are capable of binding antigenic peptide and that these complexes of chain-peptide are recognized by TCRs to induce antigen-specific apoptosis in restricted T cells. The alpha-Tm and the beta-Tm of human HLA-DR2 (DRB5*0101) were cloned, expressed in Escherichia coli, and purified in large scale by conventional chromatographic methods. The in vitro binding of an immunodominant epitope from the myelin basic protein (MBP-(83-102)Y83) to purified DR2 alpha-Tm and DR2 beta-Tm was demonstrated with biotinylated and fluoresceinated MBP-(83-102)Y83 peptide. The specificity of the MBP-(83-102)Y83 peptide binding to both DR2 alpha-Tm and DR2 beta-Tm was demonstrated in a competitive peptide binding assay. When exposed to a transformed T cell clone (SS8T) restricted to DR2(DRB5*0101) and MBP-(84-102) peptide, complexes of DR2 alpha-Tm and DR2 beta-Tm with MBP-(83-102)Y83 peptide were able to specifically recognize TCRs as measured by the increase in gamma-interferon (gamma-IFN) cytokine. Such recognition of TCRs by soluble alpha-MBP-(83-102)Y83 and beta-MBP-(83-102)Y83 complexes led to the induction of antigen-specific apoptosis in SS8T cells as measured by double fluorescence flow cytometry and electron microscopy. These results provide the first evidence that soluble complexes of antigenic peptide and individual chains of human MHC class II molecules lacking the transmembrane region can recognize TCRs and induce antigen-specific apoptosis in T cells. Since activated CD4-positive T cells are involved in pathogenesis of various autoimmune diseases, the apoptosis triggered by individual soluble chain-peptide complexes has significant potential for eliminating autoreactive T cells.