Molecular mechanism underlying ABC exporter gating: a computational study

Abstract

ATP-binding cassette (ABC) exporters are a class of molecular machines that transport substrates out of biological membranes by gating movements leading to transitions between outward-facing (OF) and inward-facing (IF) conformational states. Despite significant advances in structural and functional studies, the molecular mechanism underlying conformational gating in ABC exporters is not completely understood. A complete elucidation of the state transitions during the transport cycle is beyond the capability of the all-atom molecular dynamics (MD) method because of the limited time scale of MD. In the present work, a coarse-grained molecular dynamics (CG-MD) method with an improved sampling strategy is performed for the bacterial ABC exporter MsbA. The resultant potential of the mean force (PMF) along the center-of-mass (COM) distances, <i>d</i>₁ and <i>d</i>₂, between the two opposing subunits of the internal and external gates, respectively, are obtained, delicately showing the details of the <inline-formula><tex-math id="M1">\begin{document}$ {\rm{OF}}\to {\rm{IF}} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="JUSTC-2022-0134_M1.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="JUSTC-2022-0134_M1.png"/></alternatives></inline-formula> transition occurring via an occluded (OC) state, in which the internal and external gates are both closed. The OC state has an important role in the unidirectionality of the transport function of ABC exporters. Our CG-MD simulations dynamically show that upon NBD dissociation, the opening of the internal gate occurs in a highly cooperative manner with the closure of the external gate. Based on our PMF calculations and CG-MD simulations in this paper, we proposed a mechanistic model that is significantly different from those recently published in the literature, shedding light on the molecular mechanism by which the ABC exporter executes conformational gating for substrate translocation.