Interactions between a subset of substrate side chains and AAA+ motor pore loops determine grip during protein unfolding

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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.

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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.

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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.

"This ORCID iD identifies the author of this article:" 0000-0002-3668-8412
Tania A Baker

Department of Biology, Massachusetts Institute of Technology, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0737-3411
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.

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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.