Purified human class II major histocompatibility antigen HLA-DR1 was subjected to high-performance gel filtration with fluorescence detection to investigate simultaneous binding of two classes of peptides: the N-terminally fluoresceinated allopeptides fluorescein isothiocyanate (FITC)-conjugated and , derived from the third hypervariable region of the I8 chain of DR1 and DR3, respectively, and the DR1-associated selfpeptide SP3, carrying the fluorophor 7-amino-4-methylcoumarin-3-acetic acid (AMCA) at the N terminus. By analyzing the dimer-associated fluorescence signals, we measured an interpeptide energy transfer AMCA -FITC that proved to be peptide-specific: it did not occur after replacement of the allopeptide by the DR1-restricted peptide IM-(18-29) from influenza matrix protein, whereas it was restored by SP3, due to the high homology of SP3 and allopeptide. Transfer analyses with truncated AMCA-SP3 and AMCA-IM-(18-29) are consistent with Leu-3 being a common anchor residue of both peptides that allows an interaction with the hydrophobic specifity pocket around Ala-37 of the a, domain. This interaction is mirrored by the intrinsic fluorescence of neighboring Trp-43: we found the protein-peptide transfer Trp(DR1) -+ AMCA with AMCA-SP3 but with none of the allopeptides. Since each energy transfer affords close proximity of two fluorophors, the following picture emerges: self-or foreign peptides bind to the DR1 binding cleft by occupation of previously described specificity pockets. Simultaneously, allopeptides of the third hypervariable region or homologous peptides may occupy a cryptic binding site by displacing the p81-helix that normally lines the binding groove. Thus, the described complexes raise additional possibilities for the molecular basis of auto-or alloreactivity.Major histocompatibility complex (MHC) class II antigens are polymorphic peptide receptors that are loaded with peptides in post-Golgi compartments of an antigen-presenting cell (1). The resulting class II MHC-peptide complexes are of great immunological relevance, since their appearance on the surface of an antigen-presenting cell leads to up-or down-regulation of certain CD4+ T-helper cells that are crucial for self-nonself discrimination (2, 3). Class II molecules bear a single peptide-binding site deduced from sequence homologies and far-reaching functional analogies with crystallographically analyzed human class I antigens (4). Thereafter, both subunits contribute four N-terminal strands of a P-pleated sheet and a laterally overlying a-helical structure forming one-half of the proposed binding groove, respectively (5). The tertiary structure of these domains seems to be highly dependent on the existence of an appropriate peptide, as shown with mouse class II molecules (6): intact MHC-self-peptide complexes migrate as compact conformers (52-56 kDa), whereas heat or acid release of peptides results in slowly migrating floppy conformers (62-67 kDa) in SDS gels. Most recently, McConnell and coworkers (7) have succeeded in showin...