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

Nathan Suiter; Sándor Volkán-Kacsó

doi:10.3389/fmolb.2023.1184249

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

Front Mol Biosci. 2023 Aug 2:10:1184249. doi: 10.3389/fmolb.2023.1184249. eCollection 2023.

Authors

Nathan Suiter^{1

2}, Sándor Volkán-Kacsó^{1

2}

Affiliations

¹ Department of Mathematics, Physics and Statistics, Azusa Pacific University, Azusa, CA, United States.
² Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United States.

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 $\sim 10 μ$ s), suggesting thereby a common mechanism for removing a nucleotide release bottleneck in the rotary mechanism.

Keywords: ADP release; ATP; ATP synthase; single-molecule theory; single-molecule tracking.

Grants and funding

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