Conformational and dynamical plasticity in substrate-binding proteins underlies selective transport in ABC importers

  1. Marijn de Boer
  2. Giorgos Gkouridis
  3. Ruslan Vietrov
  4. Stephanie L Begg
  5. Gea K Schuurman-Wolters
  6. Florence Husada
  7. Nikolaos Eleftheriadis
  8. Bert Poolman  Is a corresponding author
  9. Christopher A McDevitt  Is a corresponding author
  10. Thorben Cordes  Is a corresponding author
  1. University of Groningen, Netherlands
  2. KU Leuven, Belgium
  3. University of Melbourne, Australia
  4. Ludwig Maximilians-Universität München, Germany

Abstract

Substrate-binding proteins (SBPs) are associated with ATP-binding cassette importers and switch from an open to a closed conformation upon substrate binding, providing specificity for transport. We investigated the effect of substrates on the conformational dynamics of six SBPs and the impact on transport. Using single-molecule FRET, we reveal an unrecognized diversity of plasticity in SBPs. We show that a unique closed SBP conformation does not exist for transported substrates. Instead, SBPs sample a range of conformations that activate transport. Certain non-transported ligands leave the structure largely unaltered or trigger a conformation distinct from that of transported substrates. Intriguingly, in some cases similar SBP conformations are formed by both transported and non-transported ligands. In this case, the inability for transport arises from slow opening of the SBP or the selectivity provided by the translocator. Our results reveal the complex interplay between ligand-SBP interactions, SBP conformational dynamics and substrate transport.

Data availability

Data generated or analysed during this study are included in the manuscript and supporting files. Source data files are available for smFRET histogrammes, representative smFRET time-traces and smFRET dwell-time histogrammes as shown in the manuscript. Primer sequences for created protein mutants are included.

Article and author information

Author details

  1. Marijn de Boer

    Molecular Microscopy Research Group, University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  2. Giorgos Gkouridis

    Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  3. Ruslan Vietrov

    Department of Biochemistry, University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  4. Stephanie L Begg

    Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
    Competing interests
    The authors declare that no competing interests exist.
  5. Gea K Schuurman-Wolters

    Department of Biochemistry, University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  6. Florence Husada

    Molecular Microscopy Research Group, University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  7. Nikolaos Eleftheriadis

    Molecular Microscopy Research Group, University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  8. Bert Poolman

    Department of Biochemistry, University of Groningen, Groningen, Netherlands
    For correspondence
    b.poolman@rug.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1455-531X
  9. Christopher A McDevitt

    Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
    For correspondence
    christopher.mcdevitt@unimelb.edu.au
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1596-4841
  10. Thorben Cordes

    Faculty of Biology, Ludwig Maximilians-Universität München, Planegg Martinsried, Germany
    For correspondence
    cordes@bio.lmu.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8598-5499

Funding

European Commission (638536)

  • Thorben Cordes

European Molecular Biology Organization (ALF 47-2012)

  • Giorgos Gkouridis

Deutsche Forschungsgemeinschaft (GRK2062/1 (C03))

  • Thorben Cordes

Deutsche Forschungsgemeinschaft (SFB863 (A13))

  • Thorben Cordes

National Health and Medical Research Council (1080784)

  • Christopher A McDevitt

National Health and Medical Research Council (1122582)

  • Christopher A McDevitt

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (722.012.012)

  • Giorgos Gkouridis

European Commission (670578)

  • Bert Poolman

Australian Research Council (DP170102102)

  • Christopher A McDevitt

Australian Research Council (FT170100006)

  • Christopher A McDevitt

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Baron Chanda, University of Wisconsin-Madison, United States

Version history

  1. Received: December 21, 2018
  2. Accepted: March 22, 2019
  3. Accepted Manuscript published: March 22, 2019 (version 1)
  4. Version of Record published: April 5, 2019 (version 2)

Copyright

© 2019, de Boer et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Marijn de Boer
  2. Giorgos Gkouridis
  3. Ruslan Vietrov
  4. Stephanie L Begg
  5. Gea K Schuurman-Wolters
  6. Florence Husada
  7. Nikolaos Eleftheriadis
  8. Bert Poolman
  9. Christopher A McDevitt
  10. Thorben Cordes
(2019)
Conformational and dynamical plasticity in substrate-binding proteins underlies selective transport in ABC importers
eLife 8:e44652.
https://doi.org/10.7554/eLife.44652

Share this article

https://doi.org/10.7554/eLife.44652

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