Interactions between a subset of substrate side chains and AAA+ motor pore loops determine grip during protein unfolding
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
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
- Axel T Brunger, Stanford University, United States
Version history
- Received: March 13, 2019
- Accepted: June 27, 2019
- Accepted Manuscript published: June 28, 2019 (version 1)
- 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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