Atomistic Movie of Substrate Transport in an ABC Exporter

ATP-binding cassette (ABC) transporters are membrane proteins that chemo-mechanically couple the binding and hydrolysis of ATP to the translocation of substrate molecules across biological membranes. Despite intensive research and impressive recent progress, the atomic-level details of substrate transport remain largely unknown, because the intrinsically highly dynamic nature of this process challenges experimental methods in terms of their temporal and spatial resolution. We have carried out unguided all-atom molecular dynamics (MD) simulations on long time scales (more than 100 microseconds in total) of the heterodimeric ABC exporter TM287/288 with bound daunorubicin or verapamil substrate. ATP binding triggers a large-scale alternating access type conformational transition from the initial inward-facing conformation to an outward-facing conformation. Interestingly, this spontaneous conformational transition leads to the complete translocation of the substrate through the transporter, including its insertion into the outer leaflet. The MD simulations thus provide a detailed atomistic picture of the substrate transport dynamics in TM287/288, with implications also for the functional mechanisms of other ABC transporters.