Atomistic Mechanism of Large-Scale Conformational Transition in a Heterodimeric ABC Exporter

ATP-binding
cassette (ABC) transporters are ATP-driven molecular
machines, in which ATP binding and hydrolysis in the nucleotide-binding
domains (NBDs) is chemomechanically coupled to large-scale, alternating
access conformational changes in the transmembrane domains (TMDs),
ultimately leading to the translocation of substrates across biological
membranes. The precise nature of the structural dynamics behind the
large-scale conformational transition as well as the coupling of NBD
and TMD motions is still unresolved. In this work, we combine all-atom
molecular dynamics (MD) simulations with electron paramagnetic resonance
(EPR) spectroscopy to unravel the atomic-level mechanism of the dynamic
conformational transitions underlying the functional working cycle
of the heterodimeric ABC exporter TM287/288. Extensive multimicrosecond
simulations in an explicit membrane/water environment show how in
response to ATP binding, TM287/288 undergoes spontaneous conformational
transitions from the inward-facing (IF) state via an occluded (Occ)
intermediate to an outward-facing (OF) state. The latter two states
have thus far not been characterized at atomic level. ATP-induced
tightening of the NBD dimer involves closing and reorientation of
the two NBD monomers concomitant with a closure of the intracellular
TMD gate, which leads to the occluded state. Subsequently, opening
at the extracellular TMD gate yields the OF conformer. The obtained
mechanism imposes NBD-TMD coupling via a tight orchestration of conformational
transitions, between both the two domains and also within the TMDs,
ensuring that the cytoplasmic and periplasmic gate regions are never
open simultaneously.