Molecular mechanisms of AcrB-mediated multidrug export

Zwama, Martijn; Yamaguchi, Akihito

doi:10.1016/j.resmic.2018.05.005

Cited by 46 publications

(47 citation statements)

References 75 publications

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“…1, and Supplementary Table 1). Where, in the L-state, drugs gain access to the proximal binding pocket (PBP) through entrance channels 1,8,18 . Upon a conformational change to the T-state, the drug is then moved towards the distal binding pocket (DBP) before being transported through the exit channel of the periplasmic domain, following a second conformational change from the T- to O-state 19,20 .…”

Section: Mainmentioning

confidence: 99%

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

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Ahdash

Fais

et al. 2020

Preprint

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Resistance-nodulation-division (RND) efflux pumps play a key role in inherent and evolved multidrug-resistance (MDR) in bacteria. AcrB is the prototypical member of the RND family and acts to recognise and export a wide range of chemically distinct molecules out of bacteria, conferring resistance to a variety of antibiotics. Although high resolution structures exist for AcrB, its conformational fluctuations and their putative role in function are largely unknown, preventing a complete mechanistic understanding of efflux and inhibition. Here, we determine these structural dynamics in the presence of AcrB substrates using hydrogen/deuterium exchange mass spectrometry, complemented by molecular modelling, drug binding and bacterial susceptibility studies. We show that the well-studied efflux pump inhibitor phenylalanine-arginine-β-naphthylamide (PAβN) potentiates antibiotic activity by restraining drug-binding pocket dynamics, rather than preventing antibiotic binding. We also reveal that a drug-binding pocket substitution discovered within an MDR clinical isolate, AcrBG288D, modifies the plasticity of the transport pathway, which could explain its altered substrate specificity. Our results provide molecular insight into drug export and inhibition of a major MDR-conferring efflux pump and the important directive role of its dynamics.

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Section: Mainmentioning

confidence: 99%

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

Reading

Ahdash

Fais

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…1c ). Where, in the L-state, drugs gain access to the proximal binding pocket (PBP) through entrance channels 1 , 8 , 18 . Upon a conformational change to the T-state, the drug is then moved towards the distal binding pocket (DBP) before being transported through the exit channel of the periplasmic domain, following a second conformational change from the T- to O-state 19 , 20 .…”

Section: Introductionmentioning

confidence: 99%

Perturbed structural dynamics underlie inhibition and altered efflux of the multidrug resistance pump AcrB

et al. 2020

View full text Add to dashboard Cite

Resistance–nodulation–division efflux pumps play a key role in inherent and evolved multidrug resistance in bacteria. AcrB, a prototypical member of this protein family, extrudes a wide range of antimicrobial agents out of bacteria. Although high-resolution structures exist for AcrB, its conformational fluctuations and their putative role in function are largely unknown. Here, we determine these structural dynamics in the presence of substrates using hydrogen/deuterium exchange mass spectrometry, complemented by molecular dynamics simulations, and bacterial susceptibility studies. We show that an efflux pump inhibitor potentiates antibiotic activity by restraining drug-binding pocket dynamics, rather than preventing antibiotic binding. We also reveal that a drug-binding pocket substitution discovered within a multidrug resistant clinical isolate modifies the plasticity of the transport pathway, which could explain its altered substrate efflux. Our results provide insight into the molecular mechanism of drug export and inhibition of a major multidrug efflux pump and the directive role of its dynamics.

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“…These structures show that substrates locate in a complex site made of two binding pockets, separated by a switch loop, which change in size depending on the state of the protein within the transport cycle (access, binding, extrusion). Although analysis of AcrB structures indicates that substrates do not bind via an induced-fit mechanism, it was proposed that the conformational plasticity of the two pockets may allow diverse modes of binding, although the molecular basis of polyspecificity remains largely unclear 9,10 .…”

mentioning

confidence: 99%

An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity

Debruycker

Hutchin

Masureel

et al. 2020

Nat Struct Mol Biol

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Multidrug efflux pumps present a challenge to the treatment of bacterial infections, making it vitally important to understand their mechanism of action. Here, we investigate the nature of substrate binding within Lactococcus lactis LmrP, a prototypical multidrug transporter of the major facilitator superfamily. We determined the crystal structure of LmrP in a ligand-bound outward-open state and observed an embedded lipid in the binding cavity of LmrP, an observation supported by native mass spectrometry analyses. Molecular dynamics simulations suggest that the anionic lipid stabilizes the observed ligand-bound structure. Mutants engineered to disrupt binding of the embedded lipid display reduced transport of some, but not all, antibiotic substrates. Our results suggest that a lipid within the binding cavity could provide a malleable hydrophobic component that allows adaptation to the presence of different substrates, helping to explain the broad specificity of this protein and possibly other multidrug transporters.

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Molecular mechanisms of AcrB-mediated multidrug export

Cited by 46 publications

References 75 publications

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

Perturbed structural dynamics underlie inhibition and altered efflux of the multidrug resistance pump AcrB

An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity

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