Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly

Anthony J. Hazel; Narges Abdali; Inga V. Leus; Jerry M. Parks; Jeremy C. Smith; Helen I. Zgurskaya; James C. Gumbart

doi:10.1021/acsinfecdis.9b00273

Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly

Anthony J. Hazel, Narges Abdali, Inga V. Leus, Jerry M. Parks, Jeremy C. Smith, Helen I. Zgurskaya, James C. Gumbart

Molecular Biophysics

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB-TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC. We determined a three-dimensional potential of mean force (PMF) for AcrA, which displays two main conformational basins representing assembly competent and incompetent states. Corresponding experiments show that stabilizing mutations at an interdomain interface shift the dynamic equilibrium between these states to the incompetent one, disrupting pump assembly and function and resensitizing bacteria to existing antibiotics. The modulation of AcrA dynamics through pharmacological intervention therefore presents a promising route for the development of new antibiotics.

Original language	English
Pages (from-to)	1926-1935
Number of pages	10
Journal	ACS Infectious Diseases
Volume	5
Issue number	11
DOIs	https://doi.org/10.1021/acsinfecdis.9b00273
State	Published - Nov 8 2019

Funding

This work was supported by National Institutes of Health grants R01-AI052293 to H.I.Z. and R01-GM123169 to J.C.G. An award of computer time was provided by the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. Additional computational resources were provided via the Extreme Science and Engineering Discovery Environment (XSEDE; allocation TG-MCB130173) which is supported by NSF grant number OCI-1053575.*%blankline%**%blankline%* This work was supported by National Institutes of Health grants R01-AI052293 to H.I.Z. and R01-GM123169 to J.C.G. An award of computer time was provided by the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. Additional computational resources were provided via the Extreme Science and Engineering Discovery Environment (XSEDE; allocation TG-MCB130173), which is supported by NSF grant number OCI-1053575.

Funders	Funder number
National Science Foundation	OCI-1053575
National Institutes of Health	R01-GM123169
U.S. Department of Energy	DE-AC05-00OR22725, TG-MCB130173
National Institute of Allergy and Infectious Diseases	R01AI052293
Office of Science

Keywords

Gram-negative bacteria
antibiotic resistance
efflux pump
free-energy calculations
molecular dynamics simulations

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10.1021/acsinfecdis.9b00273

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title = "Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly",

abstract = "Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB-TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC. We determined a three-dimensional potential of mean force (PMF) for AcrA, which displays two main conformational basins representing assembly competent and incompetent states. Corresponding experiments show that stabilizing mutations at an interdomain interface shift the dynamic equilibrium between these states to the incompetent one, disrupting pump assembly and function and resensitizing bacteria to existing antibiotics. The modulation of AcrA dynamics through pharmacological intervention therefore presents a promising route for the development of new antibiotics.",

keywords = "Gram-negative bacteria, antibiotic resistance, efflux pump, free-energy calculations, molecular dynamics simulations",

author = "Hazel, {Anthony J.} and Narges Abdali and Leus, {Inga V.} and Parks, {Jerry M.} and Smith, {Jeremy C.} and Zgurskaya, {Helen I.} and Gumbart, {James C.}",

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AB - Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB-TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC. We determined a three-dimensional potential of mean force (PMF) for AcrA, which displays two main conformational basins representing assembly competent and incompetent states. Corresponding experiments show that stabilizing mutations at an interdomain interface shift the dynamic equilibrium between these states to the incompetent one, disrupting pump assembly and function and resensitizing bacteria to existing antibiotics. The modulation of AcrA dynamics through pharmacological intervention therefore presents a promising route for the development of new antibiotics.

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Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly

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