An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation
- Harvard Medical School, United States
Abstract
The ring-like ATPase complexes in the AAA+ family perform diverse cellular functions that require coordination between the conformational transitions of their individual ATPase subunits1,2. How the energy from ATP hydrolysis is captured to perform mechanical work by these coordinated movements is unknown. In this study, we developed a novel approach for delineating the nucleotide-dependent free-energy landscape (FEL) of the proteasome's heterohexameric ATPase complex based on complementary structural and kinetic measurements. We used the FEL to simulate the dynamics of the proteasome and quantitatively evaluated the predicted structural and kinetic properties. The FEL model predictions are consistent with a wide range of experimental observations in this and previous studies and suggested novel mechanistic features of the proteasomal ATPases. We find that the cooperative movements of the ATPase subunits result from the design of the ATPase hexamer entailing a unique free-energy minimum for each nucleotide-binding status. ATP hydrolysis dictates the direction of substrate translocation by triggering an energy-dissipating conformational transition of the ATPase complex.
Data availability
All data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 3,4,5. The original images for the single-molecule experiments are available on Dryad (https://doi.org/10.5061/dryad.t1g1jwt2t). The source code is available in GitHub (https://github.com/luyinghms/Proteasome-FEL-model.git)
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Single molecule images for: An empirical energy landscape reveals mechanism of proteasome in polypeptide translocationDryad Digital Repository, doi:10.5061/dryad.t1g1jwt2t.
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cryo-structures of substrate-engaged human 26s proteasome6MSE, 6MSD, 6MSG, 6MSH, 6MSK, 6MSJ, 6MSB.
Article and author information
Author details
Funding
National Institute of General Medical Sciences (GM134064-01)
- Ying Lu
Edward Mallinckrodt, Jr. Foundation
- Ying Lu
Harvard Medical School (Dean's initiative award)
- Ying Lu
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Fang 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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An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation
eLife 11:e71911.
https://doi.org/10.7554/eLife.71911
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