Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein

  1. Kayla A Jara
  2. Nikolaus M Loening
  3. Patrick N Reardon
  4. Zhen Yu
  5. Prajna Woonnimani
  6. Coban Brooks
  7. Cat H Vesely
  8. Elisar J Barbar  Is a corresponding author
  1. Oregon State University, United States
  2. Lewis and Clark College, United States

Abstract

As the only major retrograde transporter along microtubules, cytoplasmic dynein plays crucial roles in the intracellular transport of organelles and other cargoes. Central to the function of this motor protein complex is dynein intermediate chain (IC), which binds the three dimeric dynein light chains at multivalent sites, and dynactin p150Glued and nuclear distribution protein (NudE) at overlapping sites of its intrinsically disordered N-terminal domain. The disorder in IC has hindered cryo-electron microscopy and X-ray crystallography studies of its structure and interactions. Here we use a suite of biophysical methods to reveal how multivalent binding of the three light chains regulate IC interactions with p150Glued and NudE. Using IC from Chaetomium thermophilum, a tractable species to interrogate IC interactions, we identify a significant reduction in binding affinity of IC to p150Glued and a loss of binding to NudE for constructs containing the entire N-terminal domain as well as for full-length constructs when compared to the tight binding observed with short IC constructs. We attribute this difference to autoinhibition caused by long-range intramolecular interactions between the N-terminal single α-helix of IC, the common site for p150Glued and NudE binding, and residues closer to the end of the N-terminal domain. Reconstitution of IC subcomplexes demonstrate that autoinhibition is differentially regulated by light chains binding, underscoring their importance both in assembly and organization of IC, and in selection between multiple binding partners at the same site.

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Author details

  1. Kayla A Jara

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0406-2957
  2. Nikolaus M Loening

    Department of Chemistry, Lewis and Clark College, Portland, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5074-6906
  3. Patrick N Reardon

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Zhen Yu

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Prajna Woonnimani

    Department of Microbiology, Oregon State University, Corvallis, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Coban Brooks

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Cat H Vesely

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Elisar J Barbar

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
    For correspondence
    Elisar.Barbar@oregonstate.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4892-5259

Funding

National Science Foundation (1617019)

  • Elisar J Barbar

National Science Foundation (2003557)

  • Nikolaus M Loening

National Institute of Biological Resources (1S10OD018518)

  • Elisar J Barbar

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

Reviewing Editor

  1. Lewis E Kay, University of Toronto, Canada

Publication history

  1. Received: May 12, 2022
  2. Accepted: November 21, 2022
  3. Accepted Manuscript published: November 23, 2022 (version 1)

Copyright

© 2022, Jara 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. Kayla A Jara
  2. Nikolaus M Loening
  3. Patrick N Reardon
  4. Zhen Yu
  5. Prajna Woonnimani
  6. Coban Brooks
  7. Cat H Vesely
  8. Elisar J Barbar
(2022)
Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein
eLife 11:e80217.
https://doi.org/10.7554/eLife.80217
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