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The six steps of the complete F 1-ATPase rotary catalytic cycle. Nat Commun 2021; 12:4690. [PMID: 34344897 DOI: 10.1038/s41467-021-25029-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
F1Fo ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalysis mechanism. Isolated F1-ATPase catalytic cores can hydrolyze ATP, passing through six intermediate conformational states to generate rotation of their central γ-subunit. Although previous structural studies have contributed greatly to understanding rotary catalysis in the F1-ATPase, the structure of an important conformational state (the binding-dwell) has remained elusive. Here, we exploit temperature and time-resolved cryo-electron microscopy to determine the structure of the binding- and catalytic-dwell states of Bacillus PS3 F1-ATPase. Each state shows three catalytic β-subunits in different conformations, establishing the complete set of six states taken up during the catalytic cycle and providing molecular details for both the ATP binding and hydrolysis strokes. We also identify a potential phosphate-release tunnel that indicates how ADP and phosphate binding are coordinated during synthesis. Overall these findings provide a structural basis for the entire F1-ATPase catalytic cycle.
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Nishizaka T, Masaike T, Nakane D. Insights into the mechanism of ATP-driven rotary motors from direct torque measurement. Biophys Rev 2019; 11:653-657. [PMID: 31321734 DOI: 10.1007/s12551-019-00564-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 06/20/2019] [Indexed: 11/29/2022] Open
Abstract
Motor proteins are molecular machines that convert chemical energy into mechanical work. In addition to existing studies performed on the linear motors found in eukaryotic cells, researchers in biophysics have also focused on rotary motors such as F1-ATPase. Detailed studies on the rotary F1-ATPase motor have correlated all chemical states to specific mechanical events at the single-molecule level. Recent studies showed that there exists another ATP-driven protein motor in life: the rotary machinery that rotates archaeal flagella (archaella). Rotation speed, stepwise movement, and variable directionality of the motor of Halobacterium salinarum were described in previous studies. Here we review recent experimental work discerning the molecular mechanism underlying how the archaellar motor protein FlaI drives rotation by generation of motor torque. In combination, those studies found that rotation slows as the viscous drag of markers increases, but torque remains constant at 160 pN·nm independent of rotation speed. Unexpectedly, the estimated work done in a single rotation is twice the expected energy that would come from hydrolysis of six ATP molecules in the FlaI hexamer. To reconcile the apparent contradiction, a new and general model for the mechanism of ATP-driven rotary motors is discussed.
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Affiliation(s)
- Takayuki Nishizaka
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan.
| | - Tomoko Masaike
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda City, Chiba, 278-8510, Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
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Single-molecule pull-out manipulation of the shaft of the rotary motor F 1-ATPase. Sci Rep 2019; 9:7451. [PMID: 31092848 PMCID: PMC6520343 DOI: 10.1038/s41598-019-43903-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 04/29/2019] [Indexed: 01/29/2023] Open
Abstract
F1-ATPase is a rotary motor protein in which the central γ-subunit rotates inside the cylinder made of α3β3 subunits. To investigate interactions between the γ shaft and the cylinder at the molecular scale, load was imposed on γ through a polystyrene bead by three-dimensional optical trapping in the direction along which the shaft penetrates the cylinder. Pull-out event was observed under high-load, and thus load-dependency of lifetime of the interaction was estimated. Notably, accumulated counts of lifetime were comprised of fast and slow components. Both components exponentially dropped with imposed loads, suggesting that the binding energy is compensated by the work done by optical trapping. Because the mutant, in which the half of the shaft was deleted, showed only one fast component in the bond lifetime, the slow component is likely due to the native interaction mode held by multiple interfaces.
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Sugawa M, Masaike T, Mikami N, Yamaguchi S, Shibata K, Saito K, Fujii F, Toyoshima YY, Nishizaka T, Yajima J. Circular orientation fluorescence emitter imaging (COFEI) of rotational motion of motor proteins. Biochem Biophys Res Commun 2018; 504:709-714. [PMID: 30213631 DOI: 10.1016/j.bbrc.2018.08.178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Single-molecule fluorescence polarization technique has been utilized to detect structural changes in biomolecules and intermolecular interactions. Here we developed a single-molecule fluorescence polarization measurement system, named circular orientation fluorescence emitter imaging (COFEI), in which a ring pattern of an acquired fluorescent image (COFEI image) represents an orientation of a polarization and a polarization factor. Rotation and pattern change of the COFEI image allow us to find changes in the polarization by eye and further values of the parameters of a polarization are determined by simple image analysis with high accuracy. We validated its potential applications of COFEI by three assays: 1) Detection of stepwise rotation of F1-ATPase via single quantum nanorod attached to the rotary shaft γ; 2) Visualization of binding of fluorescent ATP analog to the catalytic subunit in F1-ATPase; and 3) Association and dissociation of one head of dimeric kinesin-1 on the microtubule during its processive movement through single bifunctional fluorescent probes attached to the head. These results indicate that the COFEI provides us the advantages of the user-friendly measurement system and persuasive data presentations.
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Affiliation(s)
- Mitsuhiro Sugawa
- Graduate School of Arts & Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Tomoko Masaike
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda City, Chiba, 278-8510, Japan
| | - Nagisa Mikami
- Department of Physics, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Shin Yamaguchi
- Graduate School of Arts & Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Keitaro Shibata
- Graduate School of Arts & Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Kei Saito
- Graduate School of Arts & Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Fumihiko Fujii
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoko Y Toyoshima
- Graduate School of Arts & Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Takayuki Nishizaka
- Department of Physics, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Junichiro Yajima
- Graduate School of Arts & Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
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F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements. Proc Natl Acad Sci U S A 2016; 113:E2916-24. [PMID: 27166420 DOI: 10.1073/pnas.1524720113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite extensive studies, the structural basis for the mechanochemical coupling in the rotary molecular motor F1-ATPase (F1) is still incomplete. We performed single-molecule FRET measurements to monitor conformational changes in the stator ring-α3β3, while simultaneously monitoring rotations of the central shaft-γ. In the ATP waiting dwell, two of three β-subunits simultaneously adopt low FRET nonclosed forms. By contrast, in the catalytic intermediate dwell, two β-subunits are simultaneously in a high FRET closed form. These differences allow us to assign crystal structures directly to both major dwell states, thus resolving a long-standing issue and establishing a firm connection between F1 structure and the rotation angle of the motor. Remarkably, a structure of F1 in an ε-inhibited state is consistent with the unique FRET signature of the ATP waiting dwell, while most crystal structures capture the structure in the catalytic dwell. Principal component analysis of the available crystal structures further clarifies the five-step conformational transitions of the αβ-dimer in the ATPase cycle, highlighting the two dominant modes: the opening/closing motions of β and the loosening/tightening motions at the αβ-interface. These results provide a new view of tripartite coupling among chemical reactions, stator conformations, and rotary angles in F1-ATPase.
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Abstract
Among the bacteria that glide on substrate surfaces, Mycoplasma mobile is one of the fastest, exhibiting smooth movement with a speed of 2.0-4.5 μm⋅s(-1) with a cycle of attachment to and detachment from sialylated oligosaccharides. To study the gliding mechanism at the molecular level, we applied an assay with a fluorescently labeled and membrane-permeabilized ghost model, and investigated the motility by high precision colocalization microscopy. Under conditions designed to reduce the number of motor interactions on a randomly oriented substrate, ghosts took unitary 70-nm steps in the direction of gliding. Although it remains possible that the stepping behavior is produced by multiple interactions, our data suggest that these steps are produced by a unitary gliding machine that need not move between sites arranged on a cytoskeletal lattice.
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Stewart AG, Laming EM, Sobti M, Stock D. Rotary ATPases--dynamic molecular machines. Curr Opin Struct Biol 2013; 25:40-8. [PMID: 24878343 DOI: 10.1016/j.sbi.2013.11.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/20/2013] [Accepted: 11/26/2013] [Indexed: 01/14/2023]
Abstract
Recent work has provided the detailed overall architecture and subunit composition of three subtypes of rotary ATPases. Composite models of F-type, V-type and A-type ATPases have been constructed by fitting high-resolution X-ray structures of individual components into electron microscopy derived envelopes of the intact enzymes. Electron cryo-tomography has provided new insights into the supra-molecular arrangement of eukaryotic ATP synthases within mitochondria. An inherent flexibility in rotary ATPases observed by different techniques suggests greater dynamics during operation than previously envisioned. The concerted movement of subunits within the complex might provide means of regulation and information transfer between distant parts of rotary ATPases thereby fine tuning these molecular machines to their cellular environment, while optimizing their efficiency.
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Affiliation(s)
- Alastair G Stewart
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia.
| | - Elise M Laming
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
| | - Meghna Sobti
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
| | - Daniela Stock
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
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Flexibility within the rotor and stators of the vacuolar H+-ATPase. PLoS One 2013; 8:e82207. [PMID: 24312643 PMCID: PMC3846802 DOI: 10.1371/journal.pone.0082207] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/21/2013] [Indexed: 11/19/2022] Open
Abstract
The V-ATPase is a membrane-bound protein complex which pumps protons across the membrane to generate a large proton motive force through the coupling of an ATP-driven 3-stroke rotary motor (V1) to a multistroke proton pump (Vo). This is done with near 100% efficiency, which is achieved in part by flexibility within the central rotor axle and stator connections, allowing the system to flex to minimise the free energy loss of conformational changes during catalysis. We have used electron microscopy to reveal distinctive bending along the V-ATPase complex, leading to angular displacement of the V1 domain relative to the Vo domain to a maximum of ~30°. This has been complemented by elastic network normal mode analysis that shows both flexing and twisting with the compliance being located in the rotor axle, stator filaments, or both. This study provides direct evidence of flexibility within the V-ATPase and by implication in related rotary ATPases, a feature predicted to be important for regulation and their high energetic efficiencies.
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Stewart AG, Sobti M, Harvey RP, Stock D. Rotary ATPases: models, machine elements and technical specifications. BIOARCHITECTURE 2013; 3:2-12. [PMID: 23369889 PMCID: PMC3639240 DOI: 10.4161/bioa.23301] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Rotary ATPases are molecular rotary motors involved in biological energy conversion. They either synthesize or hydrolyze the universal biological energy carrier adenosine triphosphate. Recent work has elucidated the general architecture and subunit compositions of all three sub-types of rotary ATPases. Composite models of the intact F-, V- and A-type ATPases have been constructed by fitting high-resolution X-ray structures of individual subunits or sub-complexes into low-resolution electron densities of the intact enzymes derived from electron cryo-microscopy. Electron cryo-tomography has provided new insights into the supra-molecular arrangement of eukaryotic ATP synthases within mitochondria and mass-spectrometry has started to identify specifically bound lipids presumed to be essential for function. Taken together these molecular snapshots show that nano-scale rotary engines have much in common with basic design principles of man made machines from the function of individual “machine elements” to the requirement of the right “fuel” and “oil” for different types of motors.
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Affiliation(s)
- Alastair G Stewart
- The Victor Chang Cardiac Research Institute, Faculty of Medicine, The University of New South Wales, Sydney, NSW, Australia
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Stewart AG, Lee LK, Donohoe M, Chaston JJ, Stock D. The dynamic stator stalk of rotary ATPases. Nat Commun 2012; 3:687. [PMID: 22353718 PMCID: PMC3293630 DOI: 10.1038/ncomms1693] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/19/2012] [Indexed: 11/09/2022] Open
Abstract
Rotary ATPases couple ATP hydrolysis/synthesis with proton translocation across biological membranes and so are central components of the biological energy conversion machinery. Their peripheral stalks are essential components that counteract torque generated by rotation of the central stalk during ATP synthesis or hydrolysis. Here we present a 2.25-Å resolution crystal structure of the peripheral stalk from Thermus thermophilus A-type ATPase/synthase. We identify bending and twisting motions inherent within the structure that accommodate and complement a radial wobbling of the ATPase headgroup as it progresses through its catalytic cycles, while still retaining azimuthal stiffness necessary to counteract rotation of the central stalk. The conformational freedom of the peripheral stalk is dictated by its unusual right-handed coiled-coil architecture, which is in principle conserved across all rotary ATPases. In context of the intact enzyme, the dynamics of the peripheral stalks provides a potential mechanism for cooperativity between distant parts of rotary ATPases. The peripheral stalks of rotary ATPases counteract torque generated by rotation of the central stalk during ATP synthesis or hydrolysis. Stewart et al. report the crystal structure of an A-type ATPase/synthase peripheral stalk and identify bending and twisting motions that permit the radial wobbling of the headgroup.
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Affiliation(s)
- Alastair G Stewart
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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