Atomistic Dynamics of Alternating Access Mechanism of an ABC Transporter

Hendrik Göddeke and Lars Schäfer ()
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Hendrik Göddeke: Ruhr University Bochum, Theoretical Chemistry
Lars Schäfer: Ruhr University Bochum, Theoretical Chemistry

A chapter in High Performance Computing in Science and Engineering '19, 2021, pp 117-124 from Springer

Abstract: Abstract ATP-binding cassette (ABC) transporters are ATP-driven molecular machines. ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) are coupled to large-scale conformational changes of the transmembrane domains (TMDs), which leads to the translocation of substrate molecules across biological membranes. The atomic details of the structural dynamics underlying the conformational transitions and the coupling of NBD and TMD motions remained largely terra incognita. Here, we used all-atom molecular dynamics (MD) simulations to characterize the conformational transitions underlying the working cycle of the heterodimeric ABC exporter TM287/288 from Thermotoga maritima. Multi-microsecond MD simulations reveal how ATP binding triggers a spontaneous conformational transition from the initial inward-facing (IF) conformation via an occluded (Occ) intermediate to an outward-facing (OF) conformation. ATP binding induces tightening of the NBD dimer, which involves closing and reorientation of the two NBD monomers. Simultaneous closure of the cytoplasmic (intracellular) TMD gate region leads to the Occ state. Subsequent wide opening of the periplasmic (extracellular) TMD gate yields the OF conformer. This distinct sequence of events imposes tight coupling of NBDs and TMDs and ensures that the cytoplasmic and periplasmic TMD gates are not open at the same time to both sides of the membrane.

Date: 2021
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DOI: 10.1007/978-3-030-66792-4_8

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