Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Ben Russell Lewis, Muhammad R. Uddin , Mohammad Moniruzzaman, Katie M. Kuo, Anna J. Higgins, Laila Shah, Frank Sobott, Jerry Parks, Dietmar Hammerschmid, James Gumbart, Helen I. Zgurskaya , Eamonn Reading*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)
20 Downloads (Pure)

Abstract

Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

Original languageEnglish
Article number3900
JournalNature Communications
Volume14
Issue number1
Early online date18 Jul 2023
DOIs
Publication statusE-pub ahead of print - 18 Jul 2023

Keywords

  • Antimicrobial resistance
  • efflux pump inhibitor
  • hydrogen deuterium exchange (HDX) mass spectrometry
  • Membrane proteins

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