The human multidrug resistance P-glycoprotein (P-gp 1 ; ABCB1) uses ATP to transport a wide variety of structurally unrelated compounds of different sizes from the cell. The physiological function of P-gp is unknown. It is present in relatively higher levels in some organs such as the intestine, kidney, and blood-brain/testes barrier and therefore may function to protect the organism from toxins in the diet and the environment (1-3). Its relatively high expression in these organs can affect the therapeutic efficacy of oral drugs, whereas overexpression of P-gp in some tumor cells can complicate cancer chemotherapy regimens (4, 5).P-gp is a member of the ATP-binding cassette family of transporters (6). Its 1280 amino acids are arranged as two homologous halves with 43% amino acid identity. A linker region of ϳ60 amino acids connects the two halves of the protein (7). Each half has six transmembrane (TM) segments and a hydrophilic domain containing an ATP-binding site (8, 9). The protein functions as a monomer (10). Each half of P-gp has basal ATPase activity, but drug-stimulated ATPase activity or conferral of drug resistance requires the presence of both halves of the protein (11, 12). Both halves do not have to be covalently linked for function (11). Both nucleotide-binding domains (NBDs) are essential for activity (13)(14)(15), and the two ATP molecules likely interact at the interface of the Walker A site in one NBD and the LSGGQ consensus site in the other NBD (16). Drug substrates that stimulate or inhibit ATPase activity cause these sequences to come closer or to move farther apart, respectively (17).The TM segments likely interact with drug substrates in the lipid bilayer (18 -20). Studies on P-gp deletion mutants show that the transmembrane domains (TMDs) alone can bind drug substrates (12). Drug substrates bind at distinct regions in a common drug-binding pocket that is formed by the interface between the TMDs of both halves of P-gp (21-25). Disulfide cross-linking studies and labeling of cysteine mutants with thiol-reactive drug substrates indicate that the two halves are arranged in a "head-to-tail" arrangement (26), with TM4 -6 of TMD1 (the N-terminal TMD containing TM1-6) and TM9 -12 of TMD2 (the C-terminal TMD containing TM7-12) forming the drug-binding pocket (25,27). Drug binding involves an induced fit mechanism (28), and only binding in some orientations can allow for conformational changes to induce ATP hydrolysis (29,30). Therefore, knowledge about the packing of the TM segments between the two halves of P-gp is important for understanding the mechanism of P-gp.The drug-binding pocket is "funnel-shaped," narrow at the cytoplasmic side and wider at the extracellular end (27). We recently showed that the homologous halves of P-gp are in close contact at the cytoplasmic ends of TM5 and TM8 (31). We predicted the presence of another contact point between TM2 or TM3 with TM11 in the two halves of P-gp for the formation of the funnel-shaped drug-binding pocket. In this study, we used cysteine-scann...