1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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Interactions between a subset of substrate side chains and AAA+ motor pore loops determine grip during protein unfolding

  1. Tristan A Bell  Is a corresponding author
  2. Tania A Baker
  3. Robert T Sauer  Is a corresponding author
  1. Massachusetts Institute of Technology, United States
Research Article
  • Cited 4
  • Views 1,915
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Cite this article as: eLife 2019;8:e46808 doi: 10.7554/eLife.46808

Abstract

Most AAA+ remodeling motors denature proteins by pulling on the peptide termini of folded substrates, but it is not well-understood how motors produce grip when resisting a folded domain. Here, at single amino-acid resolution, we identify the determinants of grip by measuring how substrate tail sequences alter the unfolding activity of the unfoldase-protease ClpXP. The seven amino acids abutting a stable substrate domain are key, with residues 2-6 forming a core that contributes most significantly to grip. ClpX grips large hydrophobic and aromatic side chains strongly and small, polar, or charged side chains weakly. Multiple side chains interact with pore loops synergistically to strengthen grip. In combination with recent structures, our results support a mechanism in which unfolding grip is primarily mediated by non-specific van der Waal's interactions between core side chains of the substrate tail and a subset of YVG loops at the top of the ClpX axial pore.

Data availability

All data generated during this study are included in the manuscript and supporting files as Tables 1 and 2 and Figure 2 - figure supplement 3.

Article and author information

Author details

  1. Tristan A Bell

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    tribell@mit.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3668-8412
  2. Tania A Baker

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0737-3411
  3. Robert T Sauer

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    bobsauer@MIT.EDU
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Institutes of Health (GM-101988)

  • Robert T Sauer

National Institutes of Health (5T32GM-007287)

  • Tristan A Bell

Howard Hughes Medical Institute

  • Tania A Baker

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

Reviewing Editor

  1. Axel T Brunger, Stanford University, United States

Publication history

  1. Received: March 13, 2019
  2. Accepted: June 27, 2019
  3. Accepted Manuscript published: June 28, 2019 (version 1)
  4. Version of Record published: August 2, 2019 (version 2)

Copyright

© 2019, Bell 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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