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Páli T, Feniouk B, Wilkens S. Editorial: Functions, working mechanisms, and regulation of rotary ATPases and Ductin proteins. Front Mol Biosci 2024; 11:1399421. [PMID: 38606286 PMCID: PMC11007226 DOI: 10.3389/fmolb.2024.1399421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Affiliation(s)
- Tibor Páli
- Institute of Biophysics, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Boris Feniouk
- A.N. Belozersky Institute, Lomonosov Moscow State University, Moscow, Russia
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
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Burton-Smith RN, Song C, Ueno H, Murata T, Iino R, Murata K. Six states of Enterococcus hirae V-type ATPase reveals non-uniform rotor rotation during turnover. Commun Biol 2023; 6:755. [PMID: 37507515 PMCID: PMC10382590 DOI: 10.1038/s42003-023-05110-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The vacuolar-type ATPase from Enterococcus hirae (EhV-ATPase) is a thus-far unique adaptation of V-ATPases, as it performs Na+ transport and demonstrates an off-axis rotor assembly. Recent single molecule studies of the isolated V1 domain have indicated that there are subpauses within the three major states of the pseudo three-fold symmetric rotary enzyme. However, there was no structural evidence for these. Herein we activate the EhV-ATPase complex with ATP and identified multiple structures consisting of a total of six states of this complex by using cryo-electron microscopy. The orientations of the rotor complex during turnover, especially in the intermediates, are not as perfectly uniform as expected. The densities in the nucleotide binding pockets in the V1 domain indicate the different catalytic conditions for the six conformations. The off-axis rotor and its' interactions with the stator a-subunit during rotation suggests that this non-uniform rotor rotation is performed through the entire complex.
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Affiliation(s)
- Raymond N Burton-Smith
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Chihong Song
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage-Ku, Chiba, 263-8522, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institute for Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
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Nakano A, Kishikawa JI, Mitsuoka K, Yokoyama K. Mechanism of ATP hydrolysis dependent rotation of bacterial ATP synthase. Nat Commun 2023; 14:4090. [PMID: 37429854 DOI: 10.1038/s41467-023-39742-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
F1 domain of ATP synthase is a rotary ATPase complex in which rotation of central γ-subunit proceeds in 120° steps against a surrounding α3β3 fueled by ATP hydrolysis. How the ATP hydrolysis reactions occurring in three catalytic αβ dimers are coupled to mechanical rotation is a key outstanding question. Here we describe catalytic intermediates of the F1 domain in FoF1 synthase from Bacillus PS3 sp. during ATP mediated rotation captured using cryo-EM. The structures reveal that three catalytic events and the first 80° rotation occur simultaneously in F1 domain when nucleotides are bound at all the three catalytic αβ dimers. The remaining 40° rotation of the complete 120° step is driven by completion of ATP hydrolysis at αDβD, and proceeds through three sub-steps (83°, 91°, 101°, and 120°) with three associated conformational intermediates. All sub-steps except for one between 91° and 101° associated with phosphate release, occur independently of the chemical cycle, suggesting that the 40° rotation is largely driven by release of intramolecular strain accumulated by the 80° rotation. Together with our previous results, these findings provide the molecular basis of ATP driven rotation of ATP synthases.
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Affiliation(s)
- Atsuki Nakano
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Jun-Ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan.
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4
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Wu JZ, Zeziulia M, Kwon W, Jentsch TJ, Grinstein S, Freeman SA. ClC-7 drives intraphagosomal chloride accumulation to support hydrolase activity and phagosome resolution. J Cell Biol 2023; 222:e202208155. [PMID: 37010469 PMCID: PMC10072274 DOI: 10.1083/jcb.202208155] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/22/2023] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Degradative organelles contain enzymes that function optimally at the acidic pH generated by the V-ATPase. The resulting transmembrane H+ gradient also energizes the secondary transport of several solutes, including Cl-. We report that Cl- influx, driven by the 2Cl-/H+ exchanger ClC-7, is necessary for the resolution of phagolysosomes formed by macrophages. Cl- transported via ClC-7 had been proposed to provide the counterions required for electrogenic H+ pumping. However, we found that deletion of ClC-7 had a negligible effect on phagosomal acidification. Instead, luminal Cl- was found to be required for activation of a wide range of phagosomal hydrolases including proteases, nucleases, and glycosidases. These findings argue that the primary role of ClC-7 is the accumulation of (phago)lysosomal Cl- and that the V-ATPases not only optimize the activity of degradative hydrolases by lowering the pH but, importantly, also play an indirect role in their activation by providing the driving force for accumulation of luminal Cl- that stimulates hydrolase activity allosterically.
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Affiliation(s)
- Jing Ze Wu
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Mariia Zeziulia
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie and Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
- Graduate Program of the Freie Universität Berlin, Berlin, Germany
| | - Whijin Kwon
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada
| | - Thomas J. Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie and Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité University Medicine Berlin, Berlin, Germany
| | - Sergio Grinstein
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Spencer A. Freeman
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
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Sebők-Nagy K, Blastyák A, Juhász G, Páli T. Reversible binding of divalent cations to Ductin protein assemblies-A putative new regulatory mechanism of membrane traffic processes. Front Mol Biosci 2023; 10:1195010. [PMID: 37228584 PMCID: PMC10203432 DOI: 10.3389/fmolb.2023.1195010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Ductins are a family of homologous and structurally similar membrane proteins with 2 or 4 trans-membrane alpha-helices. The active forms of the Ductins are membranous ring- or star-shaped oligomeric assemblies and they provide various pore, channel, gap-junction functions, assist in membrane fusion processes and also serve as the rotor c-ring domain of V-and F-ATPases. All functions of the Ductins have been reported to be sensitive to the presence of certain divalent metal cations (Me2+), most frequently Cu2+ or Ca2+ ions, for most of the better known members of the family, and the mechanism of this effect is not yet known. Given that we have earlier found a prominent Me2+ binding site in a well-characterised Ductin protein, we hypothesise that certain divalent cations can structurally modulate the various functions of Ductin assemblies via affecting their stability by reversible non-covalent binding to them. A fine control of the stability of the assembly ranging from separated monomers through a loosely/weakly to tightly/strongly assembled ring might render precise regulation of Ductin functions possible. The putative role of direct binding of Me2+ to the c-ring subunit of active ATP hydrolase in autophagy and the mechanism of Ca2+-dependent formation of the mitochondrial permeability transition pore are also discussed.
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Affiliation(s)
- Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - András Blastyák
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Gábor Juhász
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
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Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K. Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding. J Biol Chem 2023; 299:102884. [PMID: 36626983 PMCID: PMC9971907 DOI: 10.1016/j.jbc.2023.102884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with FoF1 ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo-electron microscopy during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions. However, further characterization is needed to understand the transition from the ground state to the steady state. Here, we identified the cryo-electron microscopy structures of V/A-ATPase corresponding to short-lived initial intermediates during the activation of the ground state structure by time-resolving snapshot analysis. These intermediate structures provide insights into how the ground-state structure changes to the active, steady state through the sequential binding of ATP to its three catalytic sites. All the intermediate structures of V/A-ATPase adopt the same asymmetric structure, whereas the three catalytic dimers adopt different conformations. This is significantly different from the initial activation process of FoF1, where the overall structure of the F1 domain changes during the transition from a pseudo-symmetric to a canonical asymmetric structure (PNAS NEXUS, pgac116, 2022). In conclusion, our findings provide dynamical information that will enhance the future prospects for studying the initial activation processes of the enzymes, which have unknown intermediate structures in their functional pathway.
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Affiliation(s)
- Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan,Institute for Protein Research, Osaka University, Osaka Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan.
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Yokoyama K. Rotary mechanism of V/A-ATPases-how is ATP hydrolysis converted into a mechanical step rotation in rotary ATPases? Front Mol Biosci 2023; 10:1176114. [PMID: 37168257 PMCID: PMC10166205 DOI: 10.3389/fmolb.2023.1176114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023] Open
Abstract
V/A-ATPase is a rotary molecular motor protein that produces ATP through the rotation of its central rotor. The soluble part of this protein, the V1 domain, rotates upon ATP hydrolysis. However, the mechanism by which ATP hydrolysis in the V1 domain couples with the mechanical rotation of the rotor is still unclear. Cryo-EM snapshot analysis of V/A-ATPase indicated that three independent and simultaneous catalytic events occurred at the three catalytic dimers (ABopen, ABsemi, and ABclosed), leading to a 120° rotation of the central rotor. Besides the closing motion caused by ATP bound to ABopen, the hydrolysis of ATP bound to ABsemi drives the 120° step. Our recent time-resolved cryo-EM snapshot analysis provides further evidence for this model. This review aimed to provide a comprehensive overview of the structure and function of V/A-ATPase from a thermophilic bacterium, one of the most well-studied rotary ATPases to date.
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Ohkubo T, Shiina T, Kawaguchi K, Sasaki D, Inamasu R, Yang Y, Li Z, Taninaka K, Sakaguchi M, Fujimura S, Sekiguchi H, Kuramochi M, Arai T, Tsuda S, Sasaki YC, Mio K. Visualizing Intramolecular Dynamics of Membrane Proteins. Int J Mol Sci 2022; 23:ijms232314539. [PMID: 36498865 PMCID: PMC9736139 DOI: 10.3390/ijms232314539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis. Recently, improvements in detectors and image analysis technology have made it possible to use single-molecule determination methods using X-rays and electron beams, such as diffracted X-ray tracking (DXT), X-ray free electron laser (XFEL) imaging, and cryo-electron microscopy (cryo-EM). High-speed atomic force microscopy (HS-AFM) is a scanning probe microscope that can capture the structural dynamics of biomolecules in real time at the single-molecule level. Time-resolved techniques also facilitate an understanding of real-time intramolecular processes during chemical reactions. In this review, recent advances in membrane protein dynamics visualization techniques were presented.
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Affiliation(s)
- Tatsunari Ohkubo
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takaaki Shiina
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
| | - Kayoko Kawaguchi
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
| | - Daisuke Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Rena Inamasu
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Yue Yang
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Zhuoqi Li
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Keizaburo Taninaka
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Masaki Sakaguchi
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Shoko Fujimura
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Hiroshi Sekiguchi
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5198, Japan
| | - Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Tatsuya Arai
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Sakae Tsuda
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
| | - Yuji C. Sasaki
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5198, Japan
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Correspondence:
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Direct observation of stepping rotation of V-ATPase reveals rigid component in coupling between V o and V 1 motors. Proc Natl Acad Sci U S A 2022; 119:e2210204119. [PMID: 36215468 PMCID: PMC9586324 DOI: 10.1073/pnas.2210204119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
V-ATPases are ion pumps consisting of two rotary motor proteins, Vo and V1, that actively transport ions across the cell membrane using the chemical energy of ATP. To understand how V-ATPases transduce the energy in the presence of a structural symmetry mismatch between Vo and V1, we simultaneously visualized the rotational pauses and forward and backward steps of Vo and V1 coupled with ion transport and ATP hydrolysis reactions, respectively. Our results suggest that V-ATPases with multiple peripheral stalks are more rigidly coupled than F-ATPases that have only one peripheral stalk and work as ATP synthases. Our high-speed/high-precision single-molecule imaging of rotary ATPases in action will pave the way for a comprehensive understanding of their energy transduction mechanisms. V-ATPases are rotary motor proteins that convert the chemical energy of ATP into the electrochemical potential of ions across cell membranes. V-ATPases consist of two rotary motors, Vo and V1, and Enterococcus hirae V-ATPase (EhVoV1) actively transports Na+ in Vo (EhVo) by using torque generated by ATP hydrolysis in V1 (EhV1). Here, we observed ATP-driven stepping rotation of detergent-solubilized EhVoV1 wild-type, aE634A, and BR350K mutants under various Na+ and ATP concentrations ([Na+] and [ATP], respectively) by using a 40-nm gold nanoparticle as a low-load probe. When [Na+] was low and [ATP] was high, under the condition that only Na+ binding to EhVo is rate limiting, wild-type and aE634A exhibited 10 pausing positions reflecting 10-fold symmetry of the EhVo rotor and almost no backward steps. Duration time before the forward steps was inversely proportional to [Na+], confirming that Na+ binding triggers the steps. When both [ATP] and [Na+] were low, under the condition that both Na+ and ATP bindings are rate limiting, aE634A exhibited 13 pausing positions reflecting 10- and 3-fold symmetries of EhVo and EhV1, respectively. The distribution of duration time before the forward step was fitted well by the sum of two exponential decay functions with distinct time constants. Furthermore, occasional backward steps smaller than 36° were observed. Small backward steps were also observed during three long ATP cleavage pauses of BR350K. These results indicate that EhVo and EhV1 do not share pausing positions, Na+ and ATP bindings occur at different angles, and the coupling between EhVo and EhV1 has a rigid component.
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Courbon GM, Rubinstein JL. CryoEM Reveals the Complexity and Diversity of ATP Synthases. Front Microbiol 2022; 13:864006. [PMID: 35783400 PMCID: PMC9244403 DOI: 10.3389/fmicb.2022.864006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/30/2022] [Indexed: 11/14/2022] Open
Abstract
During respiration, adenosine triphosphate (ATP) synthases harness the electrochemical proton motive force (PMF) generated by the electron transport chain (ETC) to synthesize ATP. These macromolecular machines operate by a remarkable rotary catalytic mechanism that couples transmembrane proton translocation to rotation of a rotor subcomplex, and rotation to ATP synthesis. Initially, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cross-linking were the only ways to gain insights into the three-dimensional (3D) structures of ATP synthases and, in particular, provided ground-breaking insights into the soluble parts of the complex that explained the catalytic mechanism by which rotation is coupled to ATP synthesis. In contrast, early electron microscopy was limited to studying the overall shape of the assembly. However, advances in electron cryomicroscopy (cryoEM) have allowed determination of high-resolution structures, including the membrane regions of ATP synthases. These studies revealed the high-resolution structures of the remaining ATP synthase subunits and showed how these subunits work together in the intact macromolecular machine. CryoEM continues to uncover the diversity of ATP synthase structures across species and has begun to show how ATP synthases can be targeted by therapies to treat human diseases.
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Affiliation(s)
- Gautier M. Courbon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON, Canada
- *Correspondence: John L. Rubinstein
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Noji H, Ueno H. How Does F1-ATPase Generate Torque?: Analysis From Cryo-Electron Microscopy and Rotational Catalysis of Thermophilic F1. Front Microbiol 2022; 13:904084. [PMID: 35602057 PMCID: PMC9120768 DOI: 10.3389/fmicb.2022.904084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
The F1-ATPase is a rotary motor fueled by ATP hydrolysis. Its rotational dynamics have been well characterized using single-molecule rotation assays. While F1-ATPases from various species have been studied using rotation assays, the standard model for single-molecule studies has been the F1-ATPase from thermophilic Bacillus sp. PS3, named TF1. Single-molecule studies of TF1 have revealed fundamental features of the F1-ATPase, such as the principal stoichiometry of chemo-mechanical coupling (hydrolysis of 3 ATP per turn), torque (approximately 40 pN·nm), and work per hydrolysis reaction (80 pN·nm = 48 kJ/mol), which is nearly equivalent to the free energy of ATP hydrolysis. Rotation assays have also revealed that TF1 exhibits two stable conformational states during turn: a binding dwell state and a catalytic dwell state. Although many structures of F1 have been reported, most of them represent the catalytic dwell state or its related states, and the structure of the binding dwell state remained unknown. A recent cryo-EM study on TF1 revealed the structure of the binding dwell state, providing insights into how F1 generates torque coupled to ATP hydrolysis. In this review, we discuss the torque generation mechanism of F1 based on the structure of the binding dwell state and single-molecule studies.
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12
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Hibino K. Participation in 44th Indian Biophysical Society Meeting. Biophys Physicobiol 2022; 19:e190033. [PMID: 36349323 PMCID: PMC9592566 DOI: 10.2142/biophysico.bppb-v19.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Kayo Hibino
- Laboratory of Genome Dynamics, National Institute of Genetics, ROIS
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