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. 2010 Jan 29;285(5):3053-63.
doi: 10.1074/jbc.M109.056432. Epub 2009 Dec 7.

The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations

Jing-Wei Weng  1 , Kang-Nian Fan, Wen-Ning Wang
Affiliations

The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations

Jing-Wei Weng et al. J Biol Chem. .

Abstract

ATP binding cassette transporters are integral membrane proteins that use the energy released from ATP hydrolysis at the two nucleotide binding domains (NBDs) to translocate a wide variety of substrates through a channel at the two transmembrane domains (TMDs) across the cell membranes. MsbA from Gram-negative bacteria is a lipid and multidrug resistance ATP binding cassette exporter that can undergo large scale conformational changes between the outward-facing and the inward-facing conformations revealed by crystal structures in different states. Here, we use targeted molecular dynamics simulation methods to explore the atomic details of the conformational transition from the outward-facing to the inward-facing states of MsbA. The molecular dynamics trajectories revealed a clear spatiotemporal order of the conformational movements. The disruption of the nucleotide binding sites at the NBD dimer interface is the very first event that initiates the following conformational changes, verifying the assumption that the conformational conversion is triggered by ATP hydrolysis. The conserved x-loops of the NBDs were identified to participate in the interaction network that stabilizes the cytoplasmic tetrahelix bundle of the TMDs and play an important role in mediating the cross-talk between the NBD and TMD. The movement of the NBD dimer is transmitted through x-loops to break the tetrahelix bundle, inducing the packing rearrangements of the transmembrane helices at the cytoplasmic side and the periplasmic side sequentially. The packing rearrangement within each periplasmic wing of TMD that results in exposure of the substrate binding sites occurred at the end stage of the trajectory, preventing the wrong timing of the binding site accessibility.

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Figures

FIGURE 1.
FIGURE 1.
Simulation system of outward-facing (initial) (a) and inward-facing (b) conformations of MsbA exporter buried in the bilayer membrane. For clarity, only a part of the water molecules and POPC lipids (with phosphorus atoms enlarged) in the system is depicted. TM3, TM4, Walker-A, and LSGGQ motifs are highlighted in black.
FIGURE 2.
FIGURE 2.
The time table of the conformational changes of different parts of the transport system during the outward-facing to inward-facing transformation. The period of each event is represented by a straight line with the starting time and end time labeled.
FIGURE 3.
FIGURE 3.
The topview (a) and frontview (b) of NBD dimer interface are shown. Walker-A, LSGGQ motifs, and x-loop of chain A are highlighted in darker gray. The electrostatic and hydrogen-bond interaction pairs across the dimer interface are highlighted with frames. c, variation of some hydrogen bonds between NBD monomers, x-loop and IH2, or the TM helices of the tetrahelix bundle throughout the simulation time is shown. Each grid represents 5 frames (2.5 ps), and its gray level corresponds to the percentage of hydrogen bond emergence in this period (black, ≥ 60%; dark gray, 40%; gray, 20%; light gray, none). The hydrogen bond cutoffs are set by the donor-acceptor distance being less than 3.5 Å and the donor-hydrogen-acceptor angle being less than 30°. d, shown is the variation of the distance between mass center of Walker A motif and that of the LSGGQ motif along simulation time. The darker line denotes ATP-binding site1 (formed by Walker A motif in chain A and LSGGQ motif in chain B), and the lighter line denotes ATP binding sit e2 (formed by Walker A motif in chain B and LSGGQ motif in chain A).
FIGURE 4.
FIGURE 4.
a, shown is the interaction network near the tetrahelix bundle in the outward-facing structure. b, shown is a sketch map of the interaction network. The filled circles stand for residues, and the straight lines denote the hydrogen bond or electrostatic interactions between the linked residues.
FIGURE 5.
FIGURE 5.
Rearrangement of TM helices at cytoplasmic side. a and b are top views of the initial and target structures of the TMD-NBD interface. The cytoplasmic ends of TM3 together with IH1 and TM4 with IH2 are depicted with the loop and ribbon diagram. Chain B is in a darker color. The Cα atoms of Thr-121 on TM3 helix and Glu-208 on TM4 are depicted by balls at both their initial positions and target positions, respectively. These two figures were prepared using the program PyMOL. c, the variation of the distances between Cα atoms of Thr-121 and Glu-208 in either chain along the targeted MD trajectory is shown.
FIGURE 6.
FIGURE 6.
Unbending deformation of TM3 and TM4 helices. a, TM3 and TM4 helices in the overlapped initial (darker) and target (lighter) structures. The arrows indicate the moving direction of cytoplasmic ends of TM3 and TM4 during the conformational transition. Gly-141 that serves a pivot of unbending motion of TM3 is depicted as a blue ball. Variation of the Cα r.m.s.d. values of TM3 (b) and TM4 (c) helices relative to their target structures along the targeted MD trajectory is shown.
FIGURE 7.
FIGURE 7.
TM helices movement at the periplasmic side. a, shown is a top view of TM helices at 0, 374, and 500 ps along the targeted MD simulation. TM1, TM5, and TM6 of chain A are highlighted in darker gray. The side chains of hydrophobic residues on TM1 (Leu-48 and Leu-52), TM6 (Phe-288) and TM5 (Leu-263 and Leu-267) are depicted in sticks models. The Cα atoms of Leu-52 and Thr-285 residues are represented by empty circles. b, variation of the distance between the Cα atoms of Leu-52A/B and Thr-285A/B (cis) along targeted MD trajectory is shown. c, variation of the distance between the Cα atoms of Leu-52A/B and Thr-285B/A (trans) along the target MD trajectory is shown.
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