Structural intermediates observed only in intact Escherichia coli indicate a mechanism for TonB-dependent transport

  1. Thushani D Nilaweera
  2. David A Nyenhuis
  3. David S Cafiso  Is a corresponding author
  1. University of Virginia, United States


Outer membrane TonB-dependent transporters facilitate the uptake of trace nutrients and carbohydrates in Gram negative bacteria and are essential for pathogenic bacteria and the health of the microbiome. Despite this, their mechanism of transport is still unknown. Here, pulse EPR measurements were made in intact cells on the Escherichia coli vitamin B12 transporter, BtuB. Substrate binding was found to alter the C-terminal region of the core and shift an extracellular substrate binding loop 2 nm towards the periplasm; moreover, this structural transition is regulated by an ionic lock that is broken upon binding of the inner membrane protein TonB. Significantly, this structural transition is not observed when BtuB is reconstituted into phospholipid bilayers. These measurements suggest an alternative to existing models of transport, and they demonstrate the importance of studying outer membrane proteins in their native environment.

Data availability

Raw unprocessed DEER data are available in a compressed folder called "SourceData". The Pymol session file used to produce Fig. 6b is included as a supplementary file.

Article and author information

Author details

  1. Thushani D Nilaweera

    Genetics and Biochemistry Branch, University of Virginia, Charlottesville, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. David A Nyenhuis

    Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. David S Cafiso

    Chemistry, University of Virginia, Charlottesville, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3813-8721


Office of Extramural Research, National Institutes of Health (NIGMS GM035215)

  • David S Cafiso

Office of Extramural Research, National Institutes of Health (NIGMS S10OD025149)

  • David S Cafiso

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

Reviewing Editor

  1. Janice L Robertson, Washington University in St Louis, United States

Version history

  1. Preprint posted: March 18, 2021 (view preprint)
  2. Received: March 18, 2021
  3. Accepted: July 11, 2021
  4. Accepted Manuscript published: July 12, 2021 (version 1)
  5. Accepted Manuscript updated: July 13, 2021 (version 2)
  6. Accepted Manuscript updated: July 30, 2021 (version 3)
  7. Version of Record published: August 5, 2021 (version 4)


© 2021, Nilaweera 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. Thushani D Nilaweera
  2. David A Nyenhuis
  3. David S Cafiso
Structural intermediates observed only in intact Escherichia coli indicate a mechanism for TonB-dependent transport
eLife 10:e68548.

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