Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase
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 120ø steps during it rotation. The apparent lack of further substeps in the trajectories not on...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-08-01
|
| Series: | Frontiers in Molecular Biosciences |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1184249/full |
| _version_ | 1797756498158288896 |
|---|---|
| author | Nathan Suiter Nathan Suiter Sándor Volkán-Kacsó Sándor Volkán-Kacsó |
| author_facet | Nathan Suiter Nathan Suiter Sándor Volkán-Kacsó Sándor Volkán-Kacsó |
| author_sort | Nathan Suiter |
| collection | DOAJ |
| description | 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 120ø 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, 40o 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. |
| first_indexed | 2024-03-12T18:01:18Z |
| format | Article |
| id | doaj.art-4ff1d0827fd248b6919578b34a6923a4 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-03-12T18:01:18Z |
| publishDate | 2023-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-4ff1d0827fd248b6919578b34a6923a42023-08-02T09:49:44ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2023-08-011010.3389/fmolb.2023.11842491184249Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPaseNathan Suiter0Nathan Suiter1Sándor Volkán-Kacsó2Sándor Volkán-Kacsó3Department of Mathematics, Physics and Statistics, Azusa Pacific University, Azusa, CA, United StatesNoyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United StatesDepartment of Mathematics, Physics and Statistics, Azusa Pacific University, Azusa, CA, United StatesNoyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United StatesA 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 120ø 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, 40o 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.https://www.frontiersin.org/articles/10.3389/fmolb.2023.1184249/fullATPATP synthaseADP releasesingle-molecule trackingsingle-molecule theory |
| spellingShingle | Nathan Suiter Nathan Suiter Sándor Volkán-Kacsó Sándor Volkán-Kacsó Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase Frontiers in Molecular Biosciences ATP ATP synthase ADP release single-molecule tracking single-molecule theory |
| title | Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase |
| title_full | Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase |
| title_fullStr | Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase |
| title_full_unstemmed | Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase |
| title_short | Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase |
| title_sort | angle dependent rotation velocity consistent with adp release in bacterial f1 atpase |
| topic | ATP ATP synthase ADP release single-molecule tracking single-molecule theory |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1184249/full |
| work_keys_str_mv | AT nathansuiter angledependentrotationvelocityconsistentwithadpreleaseinbacterialf1atpase AT nathansuiter angledependentrotationvelocityconsistentwithadpreleaseinbacterialf1atpase AT sandorvolkankacso angledependentrotationvelocityconsistentwithadpreleaseinbacterialf1atpase AT sandorvolkankacso angledependentrotationvelocityconsistentwithadpreleaseinbacterialf1atpase |