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Amphipol-Trapped ExbB–ExbD Membrane Protein Complex from Escherichia coli: A Biochemical and Structural Case Study

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Abstract

Nutrient import across Gram-negative bacteria’s outer membrane is powered by the proton-motive force, delivered by the cytoplasmic membrane protein complex ExbB–ExbD–TonB. Having purified the ExbB4–ExbD2 complex in the detergent dodecyl maltoside, we substituted amphipol A8-35 for detergent, forming a water-soluble membrane protein/amphipol complex. Properties of the ExbB4–ExbD2 complex in detergent or in amphipols were compared by gel electrophoresis, size exclusion chromatography, asymmetric flow field-flow fractionation, thermal stability assays, and electron microscopy. Bound detergent and fluorescently labeled amphipol were assayed quantitatively by 1D NMR and analytical ultracentrifugation, respectively. The structural arrangement of ExbB4–ExbD2 was examined by EM, small-angle X-ray scattering, and small-angle neutron scattering using a deuterated amphipol. The amphipol-trapped ExbB4–ExbD2 complex is slightly larger than its detergent-solubilized counterpart. We also investigated a different oligomeric form of the two proteins, ExbB6–ExbD4, and propose a structural arrangement of its transmembrane α-helical domains.

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Acknowledgments

Particular thanks are due to F. Giusti (UMR 7099, Paris) for synthesizing the deuterated and the fluorescent amphipols used in this project. This work was supported by an operating grant to J.W.C. from the Canadian Institutes of Health Research (CIHR reference number 200709MOP-178048-BMA-CFAA-11449). The Groupe d’étude des protéines membranaires (GÉPROM), supported by the Fonds de la recherche en santé du Québec (FRSQ), awarded a Projet Novateur to J.W.C. A.S. was awarded fellowships from the CREATE program, Cellular Dynamics of Macromolecular Complexes, Natural Sciences and Engineering Research Council (NSERC) of Canada; from GÉPROM; and from the F.C. Harrison and the Rozanis Funds, Department of Microbiology and Immunology, McGill University. Work in UMR 7099 was supported by the French Centre National de la Recherche Scientifique (CNRS), by Université Paris-7 Denis Diderot, and by grant “DYNAMO”, ANR-11-LABX-0011-01, from the French “Initiative d’Excellence” program. Canada Foundation for Innovation provided infrastructure for the Facility for Electron Microscope Research, McGill University; www.medicine.mcgill.ca/femr/home.html. We appreciate support from Isabelle Rouiller for EM studies. Tara Sprules, manager of the Quebec/Eastern Canada High Field NMR Facility,www.nmrlab.mcgill.ca, guided NMR experiments to quantitate detergent. Research at the Bio-SANS (Center for Structural Molecular Biology) was supported by the U.S. Department of Energy’s Office of Biological and Environmental Research. Research at Oak Ridge National Laboratory’s High Flux Isotope Reactor was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy. Use of the National Synchrotron Light Source, Brookhaven National Laboratory, was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886. We appreciate the access to AF4 equipment in the laboratory of Françoise Winnik at the Université de Montréal. This work was facilitated by computing resources from CLUMEQ, under Compute/Calcul Canada. We appreciate laboratory support from Nathalie Croteau and suggestions on the manuscript by J. A. Kashul.

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Authors and Affiliations

  1. Department of Microbiology and Immunology, McGill University, Montreal, H3A 2B4, QC, Canada

    Aleksandr Sverzhinsky, Jacqueline W. Chung & James W. Coulton

  2. Center for Structural Molecular Biology and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Shuo Qian

  3. Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY, 11973, USA

    Lin Yang & Marc Allaire

  4. Membrane Protein Laboratory, Diamond Light Source, Didcot, OX11 0DE, UK

    Isabel Moraes

  5. Research Complex at Harwell Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK

    Isabel Moraes

  6. Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK

    Isabel Moraes

  7. Faculté de Pharmacie and Département de Chimie, Université de Montréal, Montreal, H3C 3J7, QC, Canada

    Dewang Ma

  8. Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, Paris, France

    Manuela Zoonens & Jean-Luc Popot

  9. CNRS/Université Paris 7, Institut de Biologie Physico-Chimique (FRC 550), Paris, France

    Manuela Zoonens & Jean-Luc Popot

  10. Microbiome and Disease Tolerance Centre, 3775 University Street, Montreal, QC, H3A 2B4, Canada

    James W. Coulton

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  1. Aleksandr Sverzhinsky
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  2. Shuo Qian
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  3. Lin Yang
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  4. Marc Allaire
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  5. Isabel Moraes
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  6. Dewang Ma
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  7. Jacqueline W. Chung
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  8. Manuela Zoonens
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  9. Jean-Luc Popot
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  10. James W. Coulton
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Correspondence to James W. Coulton.

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Sverzhinsky, A., Qian, S., Yang, L. et al. Amphipol-Trapped ExbB–ExbD Membrane Protein Complex from Escherichia coli: A Biochemical and Structural Case Study. J Membrane Biol 247, 1005–1018 (2014). https://doi.org/10.1007/s00232-014-9678-4

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