Probing the accessibility of peptide in an MHC class II protein--foreign peptide complex

The peptide antigen OVA323-339 forms a highly stable complex with the I-Ad molecule which when reconstituted into lipid bilayers can stimulate the release of interleukin 2 (IL-2) by specific T cell hybrids. To probe the accessibility of various regions of the peptide in the I-Ad binding site, six analogues of OVA323-339, each with a unique site for fluorescein labeling, were synthesized. OVA peptides modified with fluorescein at the N terminus position 323 and at the epsilon-amino group of lysines at positions 328, 329, 330, 331 and 336 all bind to the I-Ad molecule. These substitutions include four amino acids previously identified as representing a structural motif common to MHC binding peptides. The fluorescein hapten on each analogue was fully accessible to quenching by anti-fluorescein antibody after binding of the peptide to the MHC class II protein, indicating that these regions of the peptide are exposed in the MHC binding site. These data suggest that the MHC class II peptide binding site is remarkably permissive with respect to tolerating bulky substitutions in the peptide antigen. The data further suggest that either the central region (328-331) of the peptide OVA323-339 is oriented in MHC class II binding site such that all of its side chains are exposed, or that the binding of the peptide is conformationally flexible allowing reorientation of the bulky substituent to the outside of the binding site in each case studied.