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Kishikawa JI, Nakanishi A, Furuta A, Kato T, Namba K, Tamakoshi M, Mitsuoka K, Yokoyama K. Mechanical inhibition of isolated V o from V/A-ATPase for proton conductance. eLife 2020; 9:56862. [PMID: 32639230 PMCID: PMC7367684 DOI: 10.7554/elife.56862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V1 domain, with proton flow through the Vo membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V1 domain, the Vo domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the Vo domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and isolated Vo at near-atomic resolution, respectively. These structures clarify how the isolated Vo domain adopts the auto-inhibited form and how the holo complex prevents formation of the inhibited Vo form.
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Affiliation(s)
- Jun-Ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Institute for Protein Research, Osaka University, Suita, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Research Center for Ultra-High Voltage Electron Microscopy, Mihogaoka, Osaka, Japan
| | - Aya Furuta
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Suita, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, Suita, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Research Center for Ultra-High Voltage Electron Microscopy, Mihogaoka, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
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Sun J, Wu Y, Liu Z, Cao D, Wang Y, Cheng C, Chen D, Wasielewski MR, Stoddart JF. Visible Light-Driven Artificial Molecular Switch Actuated by Radical–Radical and Donor–Acceptor Interactions. J Phys Chem A 2015; 119:6317-25. [DOI: 10.1021/acs.jpca.5b04570] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Junling Sun
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Yilei Wu
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
- Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208-3113, United States
| | - Zhichang Liu
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Dennis Cao
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Yuping Wang
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Chuyang Cheng
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Dongyang Chen
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
- Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208-3113, United States
| | - J. Fraser Stoddart
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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Abstract
Technical progress in laser-sources and detectors has allowed the temporal and spatial resolution of chemical reactions down to femtoseconds and Å-units. In photon-excitable systems the key to chemical kinetics, trajectories across the vibrational saddle landscape, are experimentally accessible. Simple and thus well-defined chemical compounds are preferred objects for calibrating new methodologies and carving out paradigms of chemical dynamics, as shown in several contributions to this Faraday Discussion. Aerobic life on earth is powered by solar energy, which is captured by microorganisms and plants. Oxygenic photosynthesis relies on a three billion year old molecular machinery which is as well defined as simpler chemical constructs. It has been analysed to a very high precision. The transfer of excitation between pigments in antennae proteins, of electrons between redox-cofactors in reaction centres, and the oxidation of water by a Mn4Ca-cluster are solid state reactions. ATP, the general energy currency of the cell, is synthesized by a most agile, rotary molecular machine. While the efficiency of photosynthesis competes well with photovoltaics at the time scale of nanoseconds, it is lower by an order of magnitude for crops and again lower for bio-fuels. The enormous energy demand of mankind calls for engineered (bio-mimetic or bio-inspired) solar-electric and solar-fuel devices.
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Affiliation(s)
- Wolfgang Junge
- Dept. Biology & Chemistry, University of Osnabrück, R. 35/E42 Barbarastrasse 11, 49076 Osnabrück, Germany.
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4
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Liu S, Chistol G, Bustamante C. Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. Biophys J 2014; 106:1844-58. [PMID: 24806916 DOI: 10.1016/j.bpj.2014.03.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/19/2014] [Indexed: 01/27/2023] Open
Abstract
Ring NTPases represent a large and diverse group of proteins that couple their nucleotide hydrolysis activity to a mechanical task involving force generation and some type of transport process in the cell. Because of their shape, these enzymes often operate as gates that separate distinct cellular compartments to control and regulate the passage of chemical species across them. In this manner, ions and small molecules are moved across membranes, biopolymer substrates are segregated between cells or moved into confined spaces, double-stranded nucleic acids are separated into single strands to provide access to the genetic information, and polypeptides are unfolded and processed for recycling. Here we review the recent advances in the characterization of these motors using single-molecule manipulation and detection approaches. We describe the various mechanisms by which ring motors convert chemical energy to mechanical force or torque and coordinate the activities of individual subunits that constitute the ring. We also examine how single-molecule studies have contributed to a better understanding of the structural elements involved in motor-substrate interaction, mechanochemical coupling, and intersubunit coordination. Finally, we discuss how these molecular motors tailor their operation-often through regulation by other cofactors-to suit their unique biological functions.
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Affiliation(s)
- Shixin Liu
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; California Institute for Quantitative Biosciences, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California
| | - Gheorghe Chistol
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Physics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; California Institute for Quantitative Biosciences, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Physics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Molecular and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, and Kavli Energy NanoSciences Institute, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California.
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5
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ATP synthase: the right size base model for nanomotors in nanomedicine. ScientificWorldJournal 2014; 2014:567398. [PMID: 24605056 PMCID: PMC3925597 DOI: 10.1155/2014/567398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/05/2013] [Indexed: 11/17/2022] Open
Abstract
Nanomedicine results from nanotechnology where molecular scale minute precise nanomotors can be used to treat disease conditions. Many such biological nanomotors are found and operate in living systems which could be used for therapeutic purposes. The question is how to build nanomachines that are compatible with living systems and can safely operate inside the body? Here we propose that it is of paramount importance to have a workable base model for the development of nanomotors in nanomedicine usage. The base model must placate not only the basic requirements of size, number, and speed but also must have the provisions of molecular modulations. Universal occurrence and catalytic site molecular modulation capabilities are of vital importance for being a perfect base model. In this review we will provide a detailed discussion on ATP synthase as one of the most suitable base models in the development of nanomotors. We will also describe how the capabilities of molecular modulation can improve catalytic and motor function of the enzyme to generate a catalytically improved and controllable ATP synthase which in turn will help in building a superior nanomotor. For comparison, several other biological nanomotors will be described as well as their applications for nanotechnology.
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Shah NB, Hutcheon ML, Haarer BK, Duncan TM. F1-ATPase of Escherichia coli: the ε- inhibited state forms after ATP hydrolysis, is distinct from the ADP-inhibited state, and responds dynamically to catalytic site ligands. J Biol Chem 2013; 288:9383-95. [PMID: 23400782 DOI: 10.1074/jbc.m113.451583] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
F1-ATPase is the catalytic complex of rotary nanomotor ATP synthases. Bacterial ATP synthases can be autoinhibited by the C-terminal domain of subunit ε, which partially inserts into the enzyme's central rotor cavity to block functional subunit rotation. Using a kinetic, optical assay of F1·ε binding and dissociation, we show that formation of the extended, inhibitory conformation of ε (εX) initiates after ATP hydrolysis at the catalytic dwell step. Prehydrolysis conditions prevent formation of the εX state, and post-hydrolysis conditions stabilize it. We also show that ε inhibition and ADP inhibition are distinct, competing processes that can follow the catalytic dwell. We show that the N-terminal domain of ε is responsible for initial binding to F1 and provides most of the binding energy. Without the C-terminal domain, partial inhibition by the ε N-terminal domain is due to enhanced ADP inhibition. The rapid effects of catalytic site ligands on conformational changes of F1-bound ε suggest dynamic conformational and rotational mobility in F1 that is paused near the catalytic dwell position.
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Affiliation(s)
- Naman B Shah
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
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7
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Iino R, Noji H. Intersubunit coordination and cooperativity in ring-shaped NTPases. Curr Opin Struct Biol 2013; 23:229-34. [PMID: 23395511 DOI: 10.1016/j.sbi.2013.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/27/2012] [Accepted: 01/17/2013] [Indexed: 01/28/2023]
Abstract
Ring-shaped nucleoside triphosphatases (ring NTPases) are biological molecular machines powered by energy from NTP hydrolysis and are responsible for various cellular activities. These ring NTPases translocate their substrates or rotate their own subunits to/in the hole of the ring. Coordination and cooperativity among subunits in the oligomer ring is a topic of debate focused on understanding the operation mechanism of these protein machines. With the help of X-ray crystallographic structural analysis and optical microscopic single-molecules studies, distinct models, including stochastic, concerted, and rotary catalysis have been proposed. Here, we discuss these models and introduce high-speed atomic force microscopy as a new potent tool for verification of the model, with our recent example of the rotary catalysis of the stator ring of F1-adenosine triphosphatase.
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Affiliation(s)
- Ryota Iino
- Department of Applied Chemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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8
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Iino R, Noji H. Operation mechanism of F(o) F(1)-adenosine triphosphate synthase revealed by its structure and dynamics. IUBMB Life 2013; 65:238-46. [PMID: 23341301 DOI: 10.1002/iub.1120] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 11/26/2012] [Indexed: 11/11/2022]
Abstract
F(o) F(1) -Adenosine triphosphate (ATP) synthase, a complex of two rotary motor proteins, reversibly converts the electrochemical potential of protons across the cell membrane into phosphate transfer potential of ATP to provide the energy currency of the cell. The water-soluble motor is F(1) -ATPase, which possesses ATP synthesis/hydrolysis catalytic sites. Isolated F(1) hydrolyses ATP to rotate the rotary shaft against the stator ring. The membrane-embedded motor is F(o) , which is driven by proton flow down the proton electrochemical potential. In the F(o) F(1) complex, the direction of mechanical rotation, the chemical reaction, and the proton transport are determined by the relative amplitudes between the Gibbs free energy of the ATP hydrolysis reaction and the electrochemical potential of protons across the membrane. Therefore, F(o) F(1) -ATP synthase is a highly efficient molecular device in which the chemical, mechanical, and potential energies are tightly and reversibly converted. In this critical review, we summarize our latest knowledge about the operation mechanism of this sophisticated nanomachine, revealed by its structure and dynamics.
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Affiliation(s)
- Ryota Iino
- Department of Applied Chemistry, University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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