skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Switch loop flexibility affects substrate transport of the AcrB efflux pump

Abstract

The functionally important switch-loop of the trimeric multidrug transporter AcrB separates the access and deep drug binding pockets in every protomer. This loop, comprising 11 amino acid residues, has been shown to be crucial for substrate transport, as drugs have to travel past the loop to reach the deep binding pocket and from there are transported outside the cell via the connected AcrA and TolC channels. It contains four symmetrically arranged glycine residues suggesting that flexibility is a key feature for pump activity. Upon combinatorial substitution of these glycine residues to proline, functional and structural asymmetry was observed. Proline substitutions on the PC1 proximal side completely abolished transport and reduced backbone flexibility of the switch loop, which adopted a conformation restricting the pathway towards the deep binding pocket. Here, two phenylalanine residues located adjacent to the substitution sensitive glycine residues play a role in blocking the pathway upon rigidification of the loop, since the removal of the phenyl rings from the rigid loop restores drug transport activity.

Authors:
 [1]; ORCiD logo [2];  [3];  [4]; ORCiD logo [2];  [1]
  1. Goethe Univ. Frankfurt, Frankfurt am Main (Germany)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Goethe Univ. Frankfurt, Frankfurt am Main (Germany); Engelhard Arzneimittel GmbH & Co. KG, Niederdorfelden (Germany)
  4. Middle Tennessee State Univ., Murfreesboro, TN (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1402663
Alternate Identifier(s):
OSTI ID: 1549482
Report Number(s):
LA-UR-17-28721
Journal ID: ISSN 0022-2836; TRN: US1703120
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Molecular Biology
Additional Journal Information:
Journal Volume: 429; Journal Issue: 24; Journal ID: ISSN 0022-2836
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Biological Science

Citation Formats

Muller, Reinke T., Travers, Timothy, Cha, Hi-jea, Phillips, Joshua L., Gnanakaran, Sandrasegaram, and Pos, Klaas M.. Switch loop flexibility affects substrate transport of the AcrB efflux pump. United States: N. p., 2017. Web. https://doi.org/10.1016/j.jmb.2017.09.018.
Muller, Reinke T., Travers, Timothy, Cha, Hi-jea, Phillips, Joshua L., Gnanakaran, Sandrasegaram, & Pos, Klaas M.. Switch loop flexibility affects substrate transport of the AcrB efflux pump. United States. https://doi.org/10.1016/j.jmb.2017.09.018
Muller, Reinke T., Travers, Timothy, Cha, Hi-jea, Phillips, Joshua L., Gnanakaran, Sandrasegaram, and Pos, Klaas M.. Thu . "Switch loop flexibility affects substrate transport of the AcrB efflux pump". United States. https://doi.org/10.1016/j.jmb.2017.09.018. https://www.osti.gov/servlets/purl/1402663.
@article{osti_1402663,
title = {Switch loop flexibility affects substrate transport of the AcrB efflux pump},
author = {Muller, Reinke T. and Travers, Timothy and Cha, Hi-jea and Phillips, Joshua L. and Gnanakaran, Sandrasegaram and Pos, Klaas M.},
abstractNote = {The functionally important switch-loop of the trimeric multidrug transporter AcrB separates the access and deep drug binding pockets in every protomer. This loop, comprising 11 amino acid residues, has been shown to be crucial for substrate transport, as drugs have to travel past the loop to reach the deep binding pocket and from there are transported outside the cell via the connected AcrA and TolC channels. It contains four symmetrically arranged glycine residues suggesting that flexibility is a key feature for pump activity. Upon combinatorial substitution of these glycine residues to proline, functional and structural asymmetry was observed. Proline substitutions on the PC1 proximal side completely abolished transport and reduced backbone flexibility of the switch loop, which adopted a conformation restricting the pathway towards the deep binding pocket. Here, two phenylalanine residues located adjacent to the substitution sensitive glycine residues play a role in blocking the pathway upon rigidification of the loop, since the removal of the phenyl rings from the rigid loop restores drug transport activity.},
doi = {10.1016/j.jmb.2017.09.018},
journal = {Journal of Molecular Biology},
number = 24,
volume = 429,
place = {United States},
year = {2017},
month = {10}
}

Journal Article:

Citation Metrics:
Cited by: 2 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Structural basis of RND-type multidrug exporters
journal, April 2015

  • Yamaguchi, Akihito; Nakashima, Ryosuke; Sakurai, Keisuke
  • Frontiers in Microbiology, Vol. 6
  • DOI: 10.3389/fmicb.2015.00327

Assembly and operation of bacterial tripartite multidrug efflux pumps
journal, May 2015


RND Efflux Pumps: Structural Information Translated into Function and Inhibition Mechanisms
journal, December 2013

  • Ruggerone, Paolo; Murakami, Satoshi; M. Pos, Klaas
  • Current Topics in Medicinal Chemistry, Vol. 13, Issue 24
  • DOI: 10.2174/15680266113136660220

Mechanisms of RND multidrug efflux pumps
journal, May 2009

  • Nikaido, Hiroshi; Takatsuka, Yumiko
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1794, Issue 5, p. 769-781
  • DOI: 10.1016/j.bbapap.2008.10.004

Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export
journal, June 2000

  • Koronakis, Vassilis; Sharff, Andrew; Koronakis, Eva
  • Nature, Vol. 405, Issue 6789
  • DOI: 10.1038/35016007

Conformational Flexibility in the Multidrug Efflux System Protein AcrA
journal, March 2006


Crystal structure of bacterial multidrug efflux transporter AcrB
journal, October 2002

  • Murakami, Satoshi; Nakashima, Ryosuke; Yamashita, Eiki
  • Nature, Vol. 419, Issue 6907
  • DOI: 10.1038/nature01050

Crystal structures of a multidrug transporter reveal a functionally rotating mechanism
journal, August 2006

  • Murakami, Satoshi; Nakashima, Ryosuke; Yamashita, Eiki
  • Nature, Vol. 443, Issue 7108
  • DOI: 10.1038/nature05076

Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism
journal, September 2006


Drug Export Pathway of Multidrug Exporter AcrB Revealed by DARPin Inhibitors
journal, December 2006


Structure of the AcrAB–TolC multidrug efflux pump
journal, April 2014

  • Du, Dijun; Wang, Zhao; James, Nathan R.
  • Nature, Vol. 509, Issue 7501
  • DOI: 10.1038/nature13205

Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Suggests an Alternative Assembly Mode
journal, January 2015


Molecular architecture of the bacterial tripartite multidrug efflux pump focusing on the adaptor bridging model
journal, May 2015


Tripartite assembly of RND multidrug efflux pumps
journal, February 2016

  • Daury, Laetitia; Orange, François; Taveau, Jean-Christophe
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms10731

Drug transport mechanism of the AcrB efflux pump
journal, May 2009


The atp Synthase—A Splendid Molecular Machine
journal, June 1997


Switch-Loop Flexibility Affects Transport of Large Drugs by the Promiscuous AcrB Multidrug Efflux Transporter
journal, June 2014

  • Cha, Hi-jea; Müller, Reinke T.; Pos, Klaas M.
  • Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 8
  • DOI: 10.1128/AAC.02733-13

Crucial Role of Asp408 in the Proton Translocation Pathway of Multidrug Transporter AcrB: Evidence from Site-Directed Mutagenesis and Carbodiimide Labeling
journal, May 2009

  • Seeger, Markus A.; von Ballmoos, Christoph; Verrey, François
  • Biochemistry, Vol. 48, Issue 25
  • DOI: 10.1021/bi900446j

Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway
journal, October 2006

  • Su, C. -C.; Li, M.; Gu, R.
  • Journal of Bacteriology, Vol. 188, Issue 20
  • DOI: 10.1128/JB.00684-06

AcrB Trimer Stability and Efflux Activity, Insight from Mutagenesis Studies
journal, December 2011


Analysis of AcrB and AcrB/DARPin ligand complexes by LILBID MS
journal, September 2011

  • Brandstätter, Lorenz; Sokolova, Lucie; Eicher, Thomas
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1808, Issue 9
  • DOI: 10.1016/j.bbamem.2011.05.009

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket
journal, November 2011

  • Nakashima, Ryosuke; Sakurai, Keisuke; Yamasaki, Seiji
  • Nature, Vol. 480, Issue 7378, p. 565-569
  • DOI: 10.1038/nature10641

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop
journal, March 2012

  • Eicher, T.; Cha, H. -j.; Seeger, M. A.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 15
  • DOI: 10.1073/pnas.1114944109

Site-Directed Mutagenesis Reveals Putative Substrate Binding Residues in the Escherichia coli RND Efflux Pump AcrB
journal, October 2008

  • Bohnert, J. A.; Schuster, S.; Seeger, M. A.
  • Journal of Bacteriology, Vol. 190, Issue 24
  • DOI: 10.1128/JB.00912-08

Site-Directed Mutagenesis Reveals Amino Acid Residues in the Escherichia coli RND Efflux Pump AcrB That Confer Macrolide Resistance
journal, January 2009

  • Wehmeier, Caroline; Schuster, Sabine; Fähnrich, Eva
  • Antimicrobial Agents and Chemotherapy, Vol. 53, Issue 1
  • DOI: 10.1128/AAC.00921-08

Structures of Gate Loop Variants of the AcrB Drug Efflux Pump Bound by Erythromycin Substrate
journal, July 2016


Unidirectional peristaltic movement in multisite drug binding pockets of AcrB from molecular dynamics simulations
journal, January 2012

  • Feng, Zhiwei; Hou, Tingjun; Li, Youyong
  • Molecular BioSystems, Vol. 8, Issue 10
  • DOI: 10.1039/c2mb25184a

Structure validation by Cα geometry: ϕ,ψ and Cβ deviation
journal, January 2003

  • Lovell, Simon C.; Davis, Ian W.; Arendall, W. Bryan
  • Proteins: Structure, Function, and Bioinformatics, Vol. 50, Issue 3
  • DOI: 10.1002/prot.10286

Residue – Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term, for Simulation and Threading
journal, March 1996

  • Miyazawa, Sanzo; Jernigan, Robert L.
  • Journal of Molecular Biology, Vol. 256, Issue 3
  • DOI: 10.1006/jmbi.1996.0114

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions
journal, June 2011


Structural basis for the inhibition of bacterial multidrug exporters
journal, June 2013

  • Nakashima, Ryosuke; Sakurai, Keisuke; Yamasaki, Seiji
  • Nature, Vol. 500, Issue 7460, p. 102-106
  • DOI: 10.1038/nature12300

Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
journal, September 2014


Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives
journal, March 2016

  • Sjuts, Hanno; Vargiu, Attilio V.; Kwasny, Steven M.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 13
  • DOI: 10.1073/pnas.1602472113

NIH Image to ImageJ: 25 years of image analysis
journal, June 2012

  • Schneider, Caroline A.; Rasband, Wayne S.; Eliceiri, Kevin W.
  • Nature Methods, Vol. 9, Issue 7
  • DOI: 10.1038/nmeth.2089

NMR-Based Protein Potentials
journal, August 2010

  • Li, Da-Wei; Brüschweiler, Rafael
  • Angewandte Chemie International Edition, Vol. 49, Issue 38
  • DOI: 10.1002/anie.201001898

A smooth particle mesh Ewald method
journal, November 1995

  • Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.
  • The Journal of Chemical Physics, Vol. 103, Issue 19
  • DOI: 10.1063/1.470117

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation
journal, December 2007

  • Hess, Berk
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 1
  • DOI: 10.1021/ct700200b

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
journal, October 1992

  • Miyamoto, Shuichi; Kollman, Peter A.
  • Journal of Computational Chemistry, Vol. 13, Issue 8
  • DOI: 10.1002/jcc.540130805

Canonical sampling through velocity rescaling
journal, January 2007

  • Bussi, Giovanni; Donadio, Davide; Parrinello, Michele
  • The Journal of Chemical Physics, Vol. 126, Issue 1
  • DOI: 10.1063/1.2408420

Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

  • Parrinello, M.; Rahman, A.
  • Journal of Applied Physics, Vol. 52, Issue 12
  • DOI: 10.1063/1.328693

GROMACS: Fast, flexible, and free
journal, January 2005

  • Van Der Spoel, David; Lindahl, Erik; Hess, Berk
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20291

GROMACS 3.0: a package for molecular simulation and trajectory analysis
journal, August 2001

  • Lindahl, Erik; Hess, Berk; van der Spoel, David
  • Journal of Molecular Modeling, Vol. 7, Issue 8
  • DOI: 10.1007/s008940100045

GROMACS: A message-passing parallel molecular dynamics implementation
journal, September 1995

  • Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R.
  • Computer Physics Communications, Vol. 91, Issue 1-3
  • DOI: 10.1016/0010-4655(95)00042-E

    Works referencing / citing this record:

    AcrB: a mean, keen, drug efflux machine
    journal, September 2019

    • Kobylka, Jessica; Kuth, Miriam S.; Müller, Reinke T.
    • Annals of the New York Academy of Sciences, Vol. 1459, Issue 1
    • DOI: 10.1111/nyas.14239

    Efflux pump inhibitors of clinically relevant multidrug resistant bacteria
    journal, April 2019

    • Lamut, Andraž; Peterlin Mašič, Lucija; Kikelj, Danijel
    • Medicinal Research Reviews, Vol. 39, Issue 6
    • DOI: 10.1002/med.21591