Monoamines, such as serotonin, dopamine, and norepinephrine, are sequestered into synaptic vesicles by specific transporters (vesicular monoamine transporter-2; VMAT2) using energy from an electrochemical proton gradient across the vesicle membranes. Based on our previous studies using photoaffinitylabeling techniques in characterizing the VMAT2-specific ligands ketanserin and tetrabenazine, this study describes the synthesis and characterization of a fluorenone-based compound, iodoaminoflisopolol (IAmF), as a photoprobe to identify the substrate binding site (s) 125 I]IAmF photolabeling of recombinant VMAT2, expressed in SH-SY5Y cells with an engineered thrombin site between transmembranes 6 and 7, followed by thrombin digestion, retained photolabel in a 22-kDa fragment, indicating that iodoaminoflisopolol binds to the C-terminal half of the VMAT2 molecule. Thus, IAmF possesses a unique combination of VMAT2 substrate properties and a photoprobe and is, therefore, useful to identify the substrate binding site of the vesicular transporter.The vesicular monoamine transporter-2 (VMAT2) is the main transporter protein involved in sequestration of cytoplasmic neurotransmitters such as dopamine, serotonin, and norepinephrine into vesicles for storage and subsequent release (Henry et al., 1994;Peter et al., 1995;Erickson et al., 1996;Erickson and Varoqui, 2000) and is inhibited by reserpine, tetrabenazine (Scherman et al., 1983), and ketanserin (Darchen et al., 1988). The energy for amine transport is derived from a proton gradient generated by ATP hydrolysis. The proton gradient is coupled, by an unknown mechanism, to the transport of biogenic amines into the synaptic vesicle against a steep concentration gradient (Schuldiner, 1994;Rudnick, 1998;Schuldiner et al., 1998). Two protons are released from the storage vesicle in exchange for one substrate molecule transported to the inside of the vesicle (Kanner and Schuldiner, 1987). The rat synaptic vesicular monoamine transporter (rVMAT2) contains 515 amino acids, and a hydrophobic analysis of rat VMAT2 predicts 12 ␣-helical transmembrane segments, with a predicted large lumenal loop between TM1 and TM2 (Erickson et al., 1992).Photoaffinity labeling is an extremely useful technique that enables the direct probing of a target protein through a covalent bond between a ligand and its binding protein. Using photoprobes, previous studies from our laboratory identified the ketanserin and tetrabenazine (TBZ) binding regions of VMAT2 (Sievert and Ruoho, 1997). Analyses of the binding site peptides showed that although the ketanserin photoprobe Article, publication date, and citation information can be found at