Lipid-mediated mechanism of drug extrusion by a heterodimeric ABC exporter

Multi-drug transport by ATP binding cassette (ABC) exporters entails a mechanism to modulate drug affinity across the transport cycle. Here, we combine cryo-EM and molecular dynamics (MD) simulations to illuminate a model of how lipid competition drives substrate translocation by ABC exporters. Cryo-EM structures of the ABC transporter BmrCD in drug-loaded inward-facing (IF) and outward-facing (OF) conformations in lipid nanodiscs reveal structural mechanism of alternating access, drug-transporter interactions, and the scale of drug movement. Remarkably, the structures uncovered lipid molecules bound to the transporter vestibule along with the drugs. MD trajectories from the IF structure show that these lipid molecules stimulate drug disorder and translocation towards the vestibule apex. Similarly, lipid molecules, poised at the OF vestibule entrance, enter the vestibule and weaken drug-transporter interactions facilitating drug release. Our results complete a near-atomic model of BmrCD conformational cycle and advance a general mechanism of lipid-driven drug transport by ABC exporters.