The molecular basis of ligand binding to receptors provides important insights for drug development. Here, we explore domains of the cholecystokinin (CCK) receptor that are critical for ligand binding, using a novel series of fluorescent photolabile probes, receptor proteolysis, and rapid high resolution separation of peptide fragments by capillary electrophoresis. Each probe incorporated the same fluorophore and a photolabile p-benzoylphenylalanine at the amino terminus of the pharmacophoric domain (residue 24 of CCK-33) of CCK analogues representing full agonist, partial agonist, and antagonist of this receptor. Each was used to label the CCK receptor expressed on Chinese hamster ovary-CCKR cells, with the labeled domain then released by cyanogen bromide cleavage. Capillary electrophoresis with laser-induced fluorescence detection achieved an on-capillary mass sensitivity of 1.6 attomoles (10 ؊18 mol), with an excellent signal-to-noise ratio. Each of the biologically divergent, but structurally similar probes saturably and specifically labeled the same receptor domain, consistent with conservation of "docking" determinants. This had an apparent mass of 2.9 kDa, most consistent with the first extracellular loop domain. An additional probe having its site of covalent attachment in a different region of the probe (residue 29 of CCK-33) labeled a distinct receptor fragment with differential migration on capillary electrophoresis (third extracellular loop). Identification of the specific receptor residue(s) covalently linked to the amino-terminal probes must await further fragmentation and sequence analysis.Remarkable diversity exists for structures capable of high affinity binding and activation of G protein-coupled receptors. Understanding the molecular determinants of ligand binding provides important insights that may be useful in structurebased drug design and in understanding the basic mechanisms of receptor activation. Photoaffinity labeling provides the most direct way to identify sites of contact between residues in ligands and a receptor (1); however, traditionally this involves use of large amounts of radioactivity and inefficient and timeconsuming purification procedures. In this work, we developed a simple, rapid, and efficient procedure for analyzing sites of ligand-receptor binding, and applied this to a series of structurally related ligands representing agonists, partial agonist, and antagonist of the CCK receptor.Capillary electrophoresis (CE), 1 initially performed by Jorgenson and Lukacs (2), has emerged in recent years as a versatile and powerful tool for the analysis of biological molecules, because of its unparalleled efficiency for separation, small injection volumes, and low mass detection limits (3, 4). We recently developed a CE method for the separation of peptides cleaved from hydrophobic membrane proteins, such as bacteriorhodopsin, a possible model for the study of G protein-coupled receptors (5). In the present work, we have optimized and extended this to apply to extremely sparse, w...