Physical Picture for Functionally Rotating Mechanism of the Multidrug Efflux Transporter AcrB

Abstract

The multidrug efflux pump of Escherichia coli is the tripartite complex consisting of the polytopic inner membrane protein AcrB, periplasmic adaptor protein AcrA, and outer membrane channel TolC. AcrB is in charge of the principal part of pumping drugs out of the cell from the inner membrane or periplasm through the TolC channel. AcrB comprises three porotomers with different conformations which are in access (A), binding (B), and extrusion (E) states along the drug transport cycle, respectively. A three-step “functionally rotating” picture has then been proposed for the transport of drugs: Each protomer exhibits a sequential structural change represented as (A, B, E)→(B, E, A)→(E, A, B)→(A, B, E) by utilizing the proton-motive force. Up to now, MD simulations have been performed extensively to elucidate the rotating mechanism. However, they are focused on particular aspects or elementary processes in the functional rotation cycle. The mechanism of the functional rotation and energetics of the whole cycle remain unresolved. Here we investigate the packing structure of AcrB in terms of the entropic effect originating from the translational displacement of water molecules or hydrocarbon groups constituting nonpolar chains of lipid molecules. The theoretical method, which consists of the integral equation theories for simple and molecular fluids combined with the morphometric approach, allows us to analyze solvation properties of the trimer as well as each protomer by accounting for the polyatomic structures in atomic details. We find that the packing in AcrB is highly asymmetric and the solvent-entropy effect is crucially important. We construct a physical picture for the mechanism of conformational rotation elucidating how each protomer achieves such a drastic conformational change using only a small free energy ∼8kBT.