Statistical Thermodynamics for Functionally Rotating Mechanism of the Multidrug Efflux Transporter AcrB

Abstract

AcrB, a homotrimer, is the pivotal part of a multidrug efflux pump. A "functionally rotating" picture has been proposed for the drug transport by AcrB, but its mechanism remains unresolved. Here, we investigate the energetics of the whole functional rotation cycle using our theoretical methods. We find that the packing efficiency of AcrB is ununiform, and this ununiformity plays imperative roles primarily through the solvent-entropy effect. When a proton binds to or dissociates from a protomer, the packing properties of this protomer and its two interfaces are perturbed overall in the direction that the solvent translational entropy is lowered. The packing properties of the other two protomers are then reorganized with the recovery or maintenance of closely packed interfaces, so that the solvent-entropy loss can be compensated. The functional structural change by an isolated protomer would cause a seriously large free-energy increase. By forming a trimer, any free-energy increase caused by a protomer is always canceled out by the free-energy decrease brought by the other two protomers via the mechanism mentioned above. The functional structural rotation is thus accomplished using the free-energy decrease arising from the transfer of only a single proton per cycle. The similarities to F1-ATPase are also discussed.

A highly efficient hybrid method for calculating the hydration free energy of a protein

“…To overcome this drawback, we have recently proposed a hybrid where the hydration energy and entropy are calculated by the 3D‐RISM theory and by the ADIET combined with the MA, respectively. The high reliability of the hybrid in calculating the hydration entropy has been demonstrated in a variety of problems . The hybrid has an achievement that the binding free energy calculated for an RNA aptamer and a partial peptide of a prion protein is almost in perfect agreement with the experimental one .…”

“…The high reliability of the hybrid in calculating the hydration entropy has been demonstrated in a variety of problems. [42,68,71,72] The hybrid has an achievement that the binding free energy calculated for an RNA aptamer and a partial peptide of a prion protein is almost in perfect agreement with the experimental one. [73] If the 3D-RISM theory for calculating the hydration energy in the hybrid is replaced by the GBMA method proposed in the current study, the calculation will be accelerated to a drastic extent.…”

Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli

“…This finding suggested that the efflux of substrates is induced by a functional rotation mechanism [13][14][15], where each protomer can alternatively assume the above conformations in concert with the others. This hypothesis has been supported by subsequent experimental [25,26] and computational studies [27][28][29][30][31]. Additionally, the available asymmetric structures of AcrB allowed for the identification of specific substrate recognition sites: (i) the access pocket (AP), located in the vestibule region between PC1 and PC2 subdomains and open in protomers L and T [16,32]; (ii) the distal pocket [16,32], located more closely to the funnel domain and open only in the T protomer (hereafter DP T ; see Table S1 for the list of residues belonging to different regions of AcrB).…”

Hoisting-Loop in Bacterial Multidrug Exporter AcrB Is a Highly Flexible Hinge That Enables the Large Motion of the Subdomains

“…Computer simulations may shed a light on the complex mechanism of the exporter. Energy transduction might be due to the subtle changes in the TM-domain, explained by packing efficiency through the solvent-entropy effect translated to the porter domain, described by thermodynamics by computer simulations (Mishima et al, 2015 ) rather than a direct allosteric energy coupling. The structure of the AcrB trimer has often been compared to the αβ-subunits of bovine F 1 -ATPase, which also comprises similar functional access, binding and extrusion states by its monomers.…”

“…Perhaps similar to F 1 -ATPase (Abrahams et al, 1994 ), the most stable conformation is disturbed (in this case by the binding of ATP instead of a proton) and the adjacent subunits react accordingly to these changes (compensating for energy loss) (Ito and Ikeguchi, 2015 ). This may be compared to the trimer reorganization of both the TM- and the porter-domain (the functionally rotating mechanism) and the interaction of the monomers with each other within the homotrimer (the entropy loss in one monomer due to the conformational changes during the export cycle is balanced by the entropy-gain of the other two monomers), facilitated by the necessary compensation of the protonation and deprotonation of AcrB (the proton-motive-force is necessary to energize the energy-unfavorable transitions during the export cycle) (Mishima et al, 2015 ). Although computer simulations can show the thermodynamic properties of the transporter during transport, they have their limitations and more biochemical and biophysical studies need to be done in order to elucidate the remote energy coupling mechanism of RND transporters.…”