The accessibility of fluorescently labeled (antigenic) peptides bound to the detergent-solubilized mouse MHC class II protein IE d has been studied by fluorescence techniques. Based on the efficiency of fluorescence quenching by the aqueous quenchers iodide and TEMPOL, different degrees of accessibility of the peptide-attached fluorescein moiety are distinguished in the lEd-bound state, which depend on the nature of the peptide and on the site of attachment. These different extents of sequestration from the aqueous phase are reflected in the fluorescence properties of the corresponding NBD-labeled peptides bound to IE d. The results provide information on the topology of class II bound peptides.
