Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

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.

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Item Type:	Article
Authors/Creators:	Russell Lewis, B. https://orcid.org/0000-0002-0248-6177 Uddin, M.R. Moniruzzaman, M. https://orcid.org/0000-0001-9956-6036 Kuo, K.M. Higgins, A.J. Shah, L.M.N. https://orcid.org/0000-0002-6666-6046 Sobott, F. https://orcid.org/0000-0001-9029-1865 Parks, J.M. https://orcid.org/0000-0002-3103-9333 Hammerschmid, D. https://orcid.org/0000-0002-0210-3690 Gumbart, J.C. https://orcid.org/0000-0002-1510-7842 Zgurskaya, H.I. https://orcid.org/0000-0001-8929-4727 Reading, E. https://orcid.org/0000-0001-8219-0052
Copyright, Publisher and Additional Information:	© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/ licenses/by/4.0/.
Keywords:	Escherichia coli; Bacterial Outer Membrane Proteins; Escherichia coli Proteins; Membrane Transport Proteins; Multidrug Resistance-Associated Proteins; Anti-Bacterial Agents; Biological Transport
Dates:	Published: 1 December 2023 Published (online): 18 July 2023 Accepted: 15 June 2023
Institution:	The University of Leeds
Academic Units:	The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds)
Depositing User:	Symplectic Publications
Date Deposited:	10 Aug 2023 15:03
Last Modified:	10 Aug 2023 15:03
Published Version:	https://www.nature.com/articles/s41467-023-39615-x...
Status:	Published
Publisher:	Springer
Identification Number:	10.1038/s41467-023-39615-x
Related URLs:	PubMed URL
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:202198

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Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

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