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Published August 2, 2023 | Version Published
Journal Article Open

Angle-dependent rotation velocity consistent with ADP release in bacterial F₁-ATPase

Creators

  • 1. ROR icon Azusa Pacific University
  • 2. ROR icon California Institute of Technology

Abstract

A model-based method is used to extract a short-lived state in the rotation kinetics of the F₁-ATPase of a bacterial species, Paracoccus denitrificans (PdF1). Imaged as a single molecule, PdF1 takes large 120^ø steps during it rotation. The apparent lack of further substeps in the trajectories not only renders the rotation of PdF1 unlike that of other F-ATPases, but also hinders the establishment of its mechano-chemical kinetic scheme. We addressed these challenges using the angular velocity extracted from the single-molecule trajectories and compare it with its theoretically calculated counterpart. The theory-experiment comparison indicate the presence of a 20μs lifetime state, 40^o after ATP binding. We identify a kinetic cycle in which this state is a three-nucleotide occupancy state prior to ADP release from another site. A similar state was also reported in our earlier study of the Thermophilic bacillus F₁-ATPase (lifetime ∼10μs), suggesting thereby a common mechanism for removing a nucleotide release bottleneck in the rotary mechanism.

Copyright and License

© 2023 Suiter and Volkán-Kacsó. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Acknowledgement

We thank Hiroyuki Noji and Mariel Zarco-Zavala for providing the single-molecule rotation data used in this analysis. The authors greatly benefited from the support and advice of R. A. Marcus and fruitful discussions with R. A. Matute.

Funding

This work was supported by the Office of the Naval Research and the President's Scholarship Enhancement Grant at Azusa Pacific University.

Contributions

NS analyzed data, wrote manuscript; SK analyzed data, performed theoretical calculations, wrote manuscript. All authors contributed to the article and approved the submitted version.

Data Availability

The data analyzed in this study is subject to the following licenses/restrictions: Data analyzed are a curtesy of the H. Noji lab (U. Tokyo). Requests to access these datasets should be directed to Sandor Volkan-Kacso, svk@caltech.edu.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Files

DataSheet1_Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase.pdf

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Additional details

Identifiers

PMCID
PMC10433373

Funding

Office of Naval Research
Azusa Pacific University