Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB

Tam, Heng-Keat; Malviya, Viveka Nand; Foong, W.E.; Herrmann, Andrea; Malloci, Giuliano; Ruggerone, Paolo; Vargiu, Attilio Vittorio; Pos, Klaas M.

doi:10.1016/j.jmb.2019.12.025

Cited by 39 publications

(77 citation statements)

References 42 publications

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“…Our understanding of this mechanism has been reinforced by both structural and mutagenesis approaches including conditional cross-linking [ 18 , 19 , 20 ], as well as by computer simulations [ 21 , 22 ]. The sequestering of substrates/drugs by the pump can occur through a number of different pathways—known as substrate channels, that allow for capture of the cargo from the periplasmic space (channel 2 and channel 3) or from the outer leaflet of the inner membrane (channel 1 and channel 4) [ 23 , 24 , 25 ]. In the L (A) protomer, the channels 1 and 2 converge on a “proximal” drug-binding pocket (PBP), also known as the “access” pocket [ 19 , 23 , 26 ], which is separated by a “switch-loop” from the deep- or distal-binding pocket (DBP).…”

Section: Introductionmentioning

confidence: 99%

“…Channel 3, which originates from an interprotomer space known as the vestibule has been shown to bypass the PBP providing direct access to the DBP and a distinct selectivity [ 27 ]. Channel 4 was discovered very recently as the putative entry path for fusidic acid and other carboxylated antibiotics, and is directly connected to the DBP within the T protomer (from here on referred as DBP T ) [ 25 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

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Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

et al. 2020

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Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the Salmonella AcrB transporter remained unknown to-date, with much of our structural understanding coming from the Escherichia coli orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of Salmonella AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Salmonella Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of Salmonella AcrB. Together, these reveal several important differences with respect to the E. coli protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

et al. 2020

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“…However, for one of them (Khailova et al, 2015;Nazarov et al, 2017), the spectrum of action opened up as the antibiotic was being studied, from acting only toward gram-positive bacteria (Khailova et al, 2015), to acting on any bacteria, with the exception of those which had a certain AcrAB-TolC multidrug resistance pump (Nazarov et al, 2017(Nazarov et al, , 2019. The tripartite efflux system AcrAB-TolC is the main drug efflux transporter complex in Escherichia coli (Tam et al, 2020), which extrudes multiple antibiotics (erythromycin, oxacillin, ciprofloxacin, etc. ), dyes (rhodamine 6G, ethidium, acridine, etc.…”

Section: Introductionmentioning

confidence: 99%

New Functional Criterion for Evaluation of Homologous MDR Pumps

2020

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“…Being localized between PN1 and PN2, the dynamics of this loop is correlated to the significant decrease of the interface size between these two subdomains in state B. At that stage of the mechanism, the drug binding pocket must get larger in order to accommodate the drug, whatever the recognition site-out of three-exploited by the drug [10,36,44].…”

Section: Incidence Of These Subdomains On Overall Relative Motionsmentioning

confidence: 99%

“…At that stage of the mechanism, the drug binding pocket must get larger in order to accommodate the drug, whatever the recognition site-out of three-exploited by the drug. 10,36,44 Loop8, which contains T676-loop described in the literature, is the linker between PC1 and PC2. These two subdomains do not undergo conformational changes themselves (lRMSD less than the subdomains' mean displacement, Figure 2), and their tighter interactions owes to the movements of the connecting loops.…”

Section: Incidence Of These Subdomains On Overall Relative Motionsmentioning

confidence: 99%

Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB

Simsir¹,

Broutin

Mus‐Veteau³

et al. 2020

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RND family proteins are transmembrane proteins identified as large spectrum drug transporters involved in multi-drug resistance. A prototypical case in this superfamily, responsible for antibiotic resistance in selected gram negative bacteria, is AcrB. AcrB forms a trimer using the proton motive force to efflux drugs, implementing a functional rotation mechanism. Unfortunately, the size of the system (1049 amino-acid per monomer and membrane) has prevented a systematic dynamical exploration, so that the mild understanding of this coupled transport jeopardizes our ability to counter it. The large number of crystal structures of AcrB prompts studies to further our understanding of the mechanism. To this end, we present a novel strategy based on two key ingredients which are to study dynamics by exploiting information embodied in the numerous crystal structures obtained to date, and to systematically consider subdomains, their dynamics, and their interactions. Along the way, we identify the subdomains responsible for dynamic events, refine the states (A,B,E) of the functional rotation mechanism, and analyze the evolution of intramonomer and intermonomer interfaces along the functional cycle. Our analysis shows the relevance of AcrB's efflux mechanism as a template within the HAE1 family but not beyond. It also paves the way to targeted simulations exploiting the most relevant degrees of freedom at certain steps, and also to a targeting of specific interfaces to block the drug efflux. Our work shows that complex dynamics can be unveiled from static snapshots, a strategy that may be used on a variety of molecular machines of large size.

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Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB

Cited by 39 publications

References 42 publications

Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

New Functional Criterion for Evaluation of Homologous MDR Pumps

Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB

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