An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation

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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 subunits^1,2. 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)

The following data sets were generated

1. Lu Y
(2021) Single molecule images for: An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation
Dryad Digital Repository, doi:10.5061/dryad.t1g1jwt2t.

https://doi.org/10.5061/dryad.t1g1jwt2t

The following previously published data sets were used

(2019) cryo-structures of substrate-engaged human 26s proteasome
6MSE, 6MSD, 6MSG, 6MSH, 6MSK, 6MSJ, 6MSB.

https://www.rcsb.org/

Article and author information

Author details

Rui Fang

Department of Systems Biology, Harvard Medical School, Boston, United States

Competing interests
The authors declare that no competing interests exist.
Jason Hon

Department of Systems Biology, Harvard Medical School, Boston, United States

Competing interests
The authors declare that no competing interests exist.
Mengying Zhou

Department of Systems Biology, Harvard Medical School, Boston, United States

Competing interests
The authors declare that no competing interests exist.
Ying Lu

Department of Systems Biology, Harvard Medical School, Boston, United States

For correspondence
ying_lu@hms.harvard.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3516-7735

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

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.