1
|
Sekiya M, Sakamoto Y, Futai M, Nakanishi-Matsui M. Role of α/β interface in F 1 ATPase rotational catalysis probed by inhibitors and mutations. Int J Biol Macromol 2017; 99:615-621. [DOI: 10.1016/j.ijbiomac.2017.02.089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/24/2017] [Indexed: 01/26/2023]
|
2
|
Arai HC, Yukawa A, Iwatate RJ, Kamiya M, Watanabe R, Urano Y, Noji H. Torque generation mechanism of F1-ATPase upon NTP binding. Biophys J 2015; 107:156-64. [PMID: 24988350 DOI: 10.1016/j.bpj.2014.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/01/2014] [Accepted: 05/13/2014] [Indexed: 11/29/2022] Open
Abstract
Molecular machines fueled by NTP play pivotal roles in a wide range of cellular activities. One common feature among NTP-driven molecular machines is that NTP binding is a major force-generating step among the elementary reaction steps comprising NTP hydrolysis. To understand the mechanism in detail,in this study, we conducted a single-molecule rotation assay of the ATP-driven rotary motor protein F1-ATPase using uridine triphosphate (UTP) and a base-free nucleotide (ribose triphosphate) to investigate the impact of a pyrimidine base or base depletion on kinetics and force generation. Although the binding rates of UTP and ribose triphosphate were 10(3) and 10(6) times, respectively, slower than that of ATP, they supported rotation, generating torque comparable to that generated by ATP. Affinity change of F1 to UTP coupled with rotation was determined, and the results again were comparable to those for ATP, suggesting that F1 exerts torque upon the affinity change to UTP via rotation similar to ATP-driven rotation. Thus, the adenine-ring significantly enhances the binding rate, although it is not directly involved in force generation. Taking into account the findings from another study on F1 with mutated phosphate-binding residues, it was proposed that progressive bond formation between the phosphate region and catalytic residues is responsible for the rotation-coupled change in affinity.
Collapse
Affiliation(s)
- Hidenobu C Arai
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Ayako Yukawa
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Ryu John Iwatate
- Laboratory of Chemical Biology and Molecular Imaging, School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mako Kamiya
- Laboratory of Chemical Biology and Molecular Imaging, School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Rikiya Watanabe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan; PRESTO, Japan Science and Technology Agency, Tokyo, Japan
| | - Yasuteru Urano
- Laboratory of Chemical Biology and Molecular Imaging, School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
3
|
Watanabe R, Matsukage Y, Yukawa A, Tabata KV, Noji H. Robustness of the rotary catalysis mechanism of F1-ATPase. J Biol Chem 2014; 289:19331-40. [PMID: 24876384 DOI: 10.1074/jbc.m114.569905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
F1-ATPase (F1) is the rotary motor protein fueled by ATP hydrolysis. Previous studies have suggested that three charged residues are indispensable for catalysis of F1 as follows: the P-loop lysine in the phosphate-binding loop, GXXXXGK(T/S); a glutamic acid that activates water molecules for nucleophilic attack on the γ-phosphate of ATP (general base); and an arginine directly contacting the γ-phosphate (arginine finger). These residues are well conserved among P-loop NTPases. In this study, we investigated the role of these charged residues in catalysis and torque generation by analyzing alanine-substituted mutants in the single-molecule rotation assay. Surprisingly, all mutants continuously drove rotary motion, even though the rotational velocity was at least 100,000 times slower than that of wild type. Thus, although these charged residues contribute to highly efficient catalysis, they are not indispensable to chemo-mechanical energy coupling, and the rotary catalysis mechanism of F1 is far more robust than previously thought.
Collapse
Affiliation(s)
- Rikiya Watanabe
- From the Department of Applied Chemistry, University of Tokyo, PRESTO, Japan Science and Technology Agency, Bunkyo-ku, Tokyo 113-8656, and
| | - Yuki Matsukage
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Ayako Yukawa
- From the Department of Applied Chemistry, University of Tokyo
| | - Kazuhito V Tabata
- From the Department of Applied Chemistry, University of Tokyo, PRESTO, Japan Science and Technology Agency, Bunkyo-ku, Tokyo 113-8656, and
| | - Hiroyuki Noji
- From the Department of Applied Chemistry, University of Tokyo,
| |
Collapse
|
4
|
Biased Brownian stepping rotation of FoF1-ATP synthase driven by proton motive force. Nat Commun 2013; 4:1631. [PMID: 23535652 DOI: 10.1038/ncomms2631] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 02/21/2013] [Indexed: 11/08/2022] Open
Abstract
FoF1-ATP synthase (FoF1) produces most of the ATP in cells, uniquely, by converting the proton motive force (pmf) into ATP production via mechanical rotation of the inner rotor complex. Technical difficulties have hampered direct investigation of pmf-driven rotation, which are crucial to elucidating the chemomechanical coupling mechanism of FoF1. Here we develop a novel supported membrane system for direct observation of the rotation of FoF1 driven by pmf that was formed by photolysis of caged protons. Upon photolysis, FoF1 initiated rotation in the opposite direction to that of the ATP-driven rotation. The step size of pmf-driven rotation was 120°, suggesting that the kinetic bottleneck is a catalytic event on F1 with threefold symmetry. The reaction equilibrium was slightly biased to ATP synthesis like under physiological conditions, and FoF1 showed highly stochastic behaviour, frequently making a 120° backward step. This new experimental system would be applicable to single-molecule study of other membrane proteins.
Collapse
|
5
|
Roles of the beta subunit hinge domain in ATP synthase F(1) sector: hydrophobic network formed by introduced betaPhe174 inhibits subunit rotation. Biochem Biophys Res Commun 2010; 395:173-7. [PMID: 20331967 DOI: 10.1016/j.bbrc.2010.03.127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 03/19/2010] [Indexed: 11/23/2022]
Abstract
The ATP synthase beta subunit hinge domain (betaPhe148 approximately betaGly186, P-loop/alpha-helixB/loop/beta-sheet4, Escherichia coli residue numbering) dramatically changes in conformation upon nucleotide binding. We previously reported that F(1) with the betaSer174 to Phe mutation in the domain lowered the gamma subunit rotation speed, and thus decreased the ATPase activity [M. Nakanishi-Matsui, S. Kashiwagi, T. Ubukata, A. Iwamoto-Kihara, Y. Wada, M. Futai, Rotational catalysis of Escherichia coli ATP synthase F(1) sector. Stochastic fluctuation and a key domain of the beta subunit, J. Biol. Chem. 282 (2007) 20698-20704.]. Homology modeling indicates that the amino acid replacement induces a hydrophobic network, in which the betaMet159, betaIle163, and betaAla167 residues of the beta subunit are involved together with the mutant betaPhe174. The network is expected to stabilize the conformation of beta(DP) (nucleotide-bound form of the beta subunit), resulting in increased activation energy for transition to beta(E) (empty beta subunit). The modeling further predicts that replacement of betaMet159 with Ala or Ile weakens the hydrophobic network. As expected, these two mutations experimentally suppressed the ATPase activities as well as subunit rotation of betaS174F. Furthermore, the rotation rate decreased with the increase of the strength in the hydrophobic network. These results indicate that the smooth conformational change of the beta subunit hinge domain is pertinent for the rotational catalysis.
Collapse
|
6
|
Zheng W. Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase. Proteins 2009; 76:747-62. [PMID: 19280602 DOI: 10.1002/prot.22386] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
F(1) ATPase, a rotary motor comprised of a central stalk (gamma subunit) enclosed by three alpha and beta subunits alternately arranged in a hexamer, features highly cooperative binding and hydrolysis of ATP. Despite steady progress in biophysical, biochemical, and computational studies of this fascinating motor, the structural basis for cooperative ATPase involving its three catalytic sites remains not fully understood. To illuminate this key mechanistic puzzle, we have employed a coarse-grained elastic network model to probe the allosteric couplings underlying the cyclic conformational transition in F(1) ATPase at a residue level of detail. We will elucidate how ATP binding and product (ADP and phosphate) release at two catalytic sites are coupled with the rotation of gamma subunit via various domain motions in alpha(3)beta(3) hexamer (including intrasubunit hinge-bending motions in beta subunits and intersubunit rigid-body rotations between adjacent alpha and beta subunits). To this end, we have used a normal-mode-based correlation analysis to quantify the allosteric couplings of these domain motions to local motions at catalytic sites and the rotation of gamma subunit. We have then identified key amino acid residues involved in the above couplings, some of which have been validated against past studies of mutated and gamma-truncated F(1) ATPase. Our finding strongly supports a binding change mechanism where ATP binding to the empty catalytic site triggers a series of intra- and intersubunit domain motions leading to ATP hydrolysis and product release at the other two closed catalytic sites.
Collapse
Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, New York 14260, USA.
| |
Collapse
|
7
|
Sekiya M, Nakamoto RK, Al-Shawi MK, Nakanishi-Matsui M, Futai M. Temperature dependence of single molecule rotation of the Escherichia coli ATP synthase F1 sector reveals the importance of gamma-beta subunit interactions in the catalytic dwell. J Biol Chem 2009; 284:22401-22410. [PMID: 19502237 DOI: 10.1074/jbc.m109.009019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The temperature-dependent rotation of F1-ATPase gamma subunit was observed in V(max) conditions at low viscous drag using a 60-nm gold bead (Nakanishi-Matsui, M., Kashiwagi, S., Hosokawa, H., Cipriano, D. J., Dunn, S. D., Wada, Y., and Futai, M. (2006) J. Biol. Chem. 281, 4126-4131). The Arrhenius slopes of the speed of the individual 120 degrees steps and reciprocal of the pause length between rotation steps were very similar, indicating a flat energy pathway followed by the rotationally coupled catalytic cycle. In contrast, the Arrhenius slope of the reciprocal pause length of the gammaM23K mutant F1 was significantly increased, whereas that of the rotation rate was similar to wild type. The effects of the rotor gammaM23K substitution and the counteracting effects of betaE381D mutation in the interacting stator subunits demonstrate that the rotor-stator interactions play critical roles in the utilization of stored elastic energy. The gammaM23K enzyme must overcome an abrupt activation energy barrier, forcing it onto a less favored pathway that results in uncoupling catalysis from rotation.
Collapse
Affiliation(s)
- Mizuki Sekiya
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, and Futai Special Laboratory, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Marwan K Al-Shawi
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Mayumi Nakanishi-Matsui
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, and Futai Special Laboratory, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Masamitsu Futai
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, and Futai Special Laboratory, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| |
Collapse
|
8
|
Nakanishi-Matsui M, Futai M. Stochastic rotational catalysis of proton pumping F-ATPase. Philos Trans R Soc Lond B Biol Sci 2008; 363:2135-42. [PMID: 18339602 DOI: 10.1098/rstb.2008.2266] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
F-ATPases synthesize ATP from ADP and phosphate coupled with an electrochemical proton gradient in bacterial or mitochondrial membranes and can hydrolyse ATP to form the gradient. F-ATPases consist of a catalytic F1 and proton channel F0 formed from the alpha3beta3gammadelta and ab2c10 subunit complexes, respectively. The rotation of gammaepsilonc10 couples catalyses and proton transport. Consistent with the threefold symmetry of the alpha3beta3 catalytic hexamer, 120 degrees stepped revolution has been observed, each step being divided into two substeps. The ATP-dependent revolution exhibited stochastic fluctuation and was driven by conformation transmission of the beta subunit (phosphate-binding P-loop/alpha-helix B/loop/beta-sheet4). Recent results regarding mechanically driven ATP synthesis finally proved the role of rotation in energy coupling.
Collapse
|
9
|
Kashiwagi S, Iwamoto-Kihara A, Kojima M, Nonaka T, Futai M, Nakanishi-Matsui M. Effects of mutations in the beta subunit hinge domain on ATP synthase F1 sector rotation: interaction between Ser 174 and Ile 163. Biochem Biophys Res Commun 2007; 365:227-31. [PMID: 17983592 DOI: 10.1016/j.bbrc.2007.10.157] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 10/24/2007] [Indexed: 11/16/2022]
Abstract
A complex of gamma, epsilon, and c subunits rotates in ATP synthase (F(o)F(1)) coupling with proton transport. Replacement of betaSer174 by Phe in beta-sheet4 of the beta subunit (betaS174F) caused slow gamma subunit revolution of the F(1) sector, consistent with the decreased ATPase activity [M. Nakanishi-Matsui, S. Kashiwagi, T. Ubukata, A. Iwamoto-Kihara, Y. Wada, M. Futai, Rotational catalysis of Escherichia coli ATP synthase F1 sector. Stochastic fluctuation and a key domain of the beta subunit, J. Biol. Chem. 282 (2007) 20698-20704]. Modeling of the domain including beta-sheet4 and alpha-helixB predicted that the mutant betaPhe174 residue undergoes strong and weak hydrophobic interactions with betaIle163 and betaIle166, respectively. Supporting this prediction, the replacement of betaIle163 in alpha-helixB by Ala partially suppressed the betaS174F mutation: in the double mutant, the revolution speed and ATPase activity recovered to about half of the levels in the wild-type. Replacement of betaIle166 by Ala lowered the revolution speed and ATPase activity to the same levels as in betaS174F. Consistent with the weak hydrophobic interaction, betaIle166 to Ala mutation did not suppress betaS174F. Importance of the hinge domain [phosphate-binding loop (P-loop)/alpha-helixB/loop/beta-sheet4, betaPhe148-betaGly186] as to driving rotational catalysis is discussed.
Collapse
Affiliation(s)
- Sachiko Kashiwagi
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, Iwate 028-3694, Japan
| | | | | | | | | | | |
Collapse
|
10
|
Pilizota T, Bilyard T, Bai F, Futai M, Hosokawa H, Berry RM. A programmable optical angle clamp for rotary molecular motors. Biophys J 2007; 93:264-75. [PMID: 17434937 PMCID: PMC1914438 DOI: 10.1529/biophysj.106.091074] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2006] [Accepted: 03/08/2007] [Indexed: 11/18/2022] Open
Abstract
Optical tweezers are widely used for experimental investigation of linear molecular motors. The rates and force dependence of steps in the mechanochemical cycle of linear motors have been probed giving detailed insight into motor mechanisms. With similar goals in mind for rotary molecular motors we present here an optical trapping system designed as an angle clamp to study the bacterial flagellar motor and F(1)-ATPase. The trap position was controlled by a digital signal processing board and a host computer via acousto-optic deflectors, the motor position via a three-dimensional piezoelectric stage and the motor angle using a pair of polystyrene beads as a handle for the optical trap. Bead-pair angles were detected using back focal plane interferometry with a resolution of up to 1 degrees , and controlled using a feedback algorithm with a precision of up to 2 degrees and a bandwidth of up to 1.6 kHz. Details of the optical trap, algorithm, and alignment procedures are given. Preliminary data showing angular control of F(1)-ATPase and angular and speed control of the bacterial flagellar motor are presented.
Collapse
Affiliation(s)
- Teuta Pilizota
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | | |
Collapse
|
11
|
Nakanishi-Matsui M, Kashiwagi S, Ubukata T, Iwamoto-Kihara A, Wada Y, Futai M. Rotational catalysis of Escherichia coli ATP synthase F1 sector. Stochastic fluctuation and a key domain of the beta subunit. J Biol Chem 2007; 282:20698-704. [PMID: 17517893 DOI: 10.1074/jbc.m700551200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A complex of gamma, epsilon, and c subunits rotates in ATP synthase (FoF(1)) coupled with proton transport. A gold bead connected to the gamma subunit of the Escherichia coli F(1) sector exhibited stochastic rotation, confirming a previous study (Nakanishi-Matsui, M., Kashiwagi, S., Hosokawa, H., Cipriano, D. J., Dunn, S. D., Wada, Y., and Futai, M. (2006) J. Biol. Chem. 281, 4126-4131). A similar approach was taken for mutations in the beta subunit key region; consistent with its bulk phase ATPase activities, F(1) with the Ser-174 to Phe substitution (betaS174F) exhibited a slower single revolution time (time required for 360 degree revolution) and paused almost 10 times longer than the wild type at one of the three 120 degrees positions during the stepped revolution. The pause positions were probably not at the "ATP waiting" dwell but at the "ATP hydrolysis/product release" dwell, since the ATP concentration used for the assay was approximately 30-fold higher than the K(m) value for ATP. A betaGly-149 to Ala substitution in the phosphate binding P-loop suppressed the defect of betaS174F. The revertant (betaG149A/betaS174F) exhibited similar rotation to the wild type, except that it showed long pauses less frequently. Essentially the same results were obtained with the Ser-174 to Leu substitution and the corresponding revertant betaG149A/betaS174L. These results indicate that the domain between beta-sheet 4 (betaSer-174) and P-loop (betaGly-149) is important to drive rotation.
Collapse
Affiliation(s)
- Mayumi Nakanishi-Matsui
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation, Tokyo 141-0021, Japan
| | | | | | | | | | | |
Collapse
|
12
|
Futai M. Our research on proton pumping ATPases over three decades: their biochemistry, molecular biology and cell biology. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2007; 82:416-38. [PMID: 25792771 PMCID: PMC4338836 DOI: 10.2183/pjab.82.416] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 12/11/2006] [Indexed: 05/24/2023]
Abstract
ATP is synthesized by F-type proton-translocating ATPases (F-ATPases) coupled with an electrochemical proton gradient established by an electron transfer chain. This mechanism is ubiquitously found in mitochondria, chloroplasts and bacteria. Vacuolar-type ATPases (V-ATPases) are found in endomembrane organelles, including lysosomes, endosomes, synaptic vesicles, etc., of animal and plant cells. These two physiologically different proton pumps exhibit similarities in subunit assembly, catalysis and the coupling mechanism from chemistry to proton transport through subunit rotation. We mostly discuss our own studies on the two proton pumps over the last three decades, including ones on purification, kinetic analysis, rotational catalysis and the diverse roles of acidic luminal organelles. The diversity of organellar proton pumps and their stochastic fluctuation are the important concepts derived recently from our studies.
Collapse
Affiliation(s)
- Masamitsu Futai
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation, and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo,
Japan
| |
Collapse
|
13
|
Nakanishi-Matsui M, Kashiwagi S, Hosokawa H, Cipriano DJ, Dunn SD, Wada Y, Futai M. Stochastic high-speed rotation of Escherichia coli ATP synthase F1 sector: the epsilon subunit-sensitive rotation. J Biol Chem 2006; 281:4126-31. [PMID: 16352612 DOI: 10.1074/jbc.m510090200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gamma subunit of the ATP synthase F(1) sector rotates at the center of the alpha(3)beta(3) hexamer during ATP hydrolysis. A gold bead (40-200 nm diameter) was attached to the gamma subunit of Escherichia coli F(1), and then its ATP hydrolysis-dependent rotation was studied. The rotation speeds were variable, showing stochastic fluctuation. The high-speed rates of 40- and 60-nm beads were essentially similar: 721 and 671 rps (revolutions/s), respectively. The average rate of 60-nm beads was 381 rps, which is approximately 13-fold faster than that expected from the steady-state ATPase turnover number. These results indicate that the F(1) sector rotates much faster than expected from the bulk of ATPase activity, and that approximately 10% of the F(1) molecules are active on the millisecond time scale. Furthermore, the real ATP turnover number (number of ATP molecules converted to ADP and phosphate/s), as a single molecule, is variable during a short period. The epsilon subunit inhibited rotation and ATPase, whereas epsilon fused through its carboxyl terminus to cytochrome b(562) showed no effect. The epsilon subunit significantly increased the pausing time during rotation. Stochastic fluctuation of catalysis may be a general property of an enzyme, although its understanding requires combining studies of steady-state kinetics and single molecule observation.
Collapse
Affiliation(s)
- Mayumi Nakanishi-Matsui
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation, CREST, Japan Science and Technology Agency, Kamiosaki, Shinagawa, Tokyo
| | | | | | | | | | | | | |
Collapse
|
14
|
Hosokawa H, Nakanishi-Matsui M, Kashiwagi S, Fujii-Taira I, Hayashi K, Iwamoto-Kihara A, Wada Y, Futai M. ATP-dependent rotation of mutant ATP synthases defective in proton transport. J Biol Chem 2005; 280:23797-801. [PMID: 15849185 DOI: 10.1074/jbc.m502650200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During ATP hydrolysis, the gammaepsilon c10 complex (gamma and epsilon subunits and a c subunit ring formed from 10 monomers) of F0F1 ATPase (ATP synthase) rotates relative to the alpha3beta3delta ab2 complex, leading to proton transport through the interface between the a subunit and the c subunit ring. In this study, we replaced the two pertinent residues for proton transport, cAsp-61 and aArg-210 of the c and a subunits, respectively. The mutant enzymes exhibited lower ATPase activities than that of the wild type but exhibited ATP-dependent rotation in planar membranes, in which their original assemblies are maintained. The mutant enzymes were defective in proton transport, as shown previously. These results suggest that proton transport can be separated from rotation in ATP hydrolysis, although rotation ensures continuous proton transport by bringing the cAsp-61 and aArg-210 residues into the correct interacting positions.
Collapse
Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Futai M, Sun-Wada GH, Wada Y. Proton pumping ATPases and diverse inside-acidic compartments. YAKUGAKU ZASSHI 2004; 124:243-60. [PMID: 15118237 DOI: 10.1248/yakushi.124.243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proton-translocating ATPases are essential cellular energy converters that transduce the chemical energy of ATP hydrolysis into transmembrane proton electrochemical potential differences. The structures, catalytic mechanism, and cellular functions of three major classes of ATPases including the F-type, V-type, and P-type ATPase are discussed in this review. Physiological roles of the acidic organelles and compartments contained are also discussed.
Collapse
Affiliation(s)
- Masamitsu Futai
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki City, Osaka 567-0047, Japan.
| | | | | |
Collapse
|
16
|
Sun S, Chandler D, Dinner AR, Oster G. Elastic energy storage in beta-sheets with application to F1-ATPase. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2003; 32:676-83. [PMID: 12955360 DOI: 10.1007/s00249-003-0335-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2002] [Revised: 03/11/2003] [Accepted: 04/04/2003] [Indexed: 11/24/2022]
Abstract
We present a methodology for obtaining the elastic properties of protein motifs. We combine the use of interpolated structures (IS), molecular dynamics (MD) and collective coordinates to deduce the elastic properties of the beta-sheet in F(1) ATPase. We find that about 3.5 kcal/mol (6 k(B) T at room temperature) of elastic energy is stored in the beta-sheet as the beta-subunit undergoes its hinge bending motion, in good agreement with the finite element model of Wang and Oster [Nature (1998) 396:279-282]. The technique should be useful for beta-sheets in other proteins and aid in the construction of phenomenological models for molecular motors that are computationally prohibitive for MD alone.
Collapse
Affiliation(s)
- Sean Sun
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
| | | | | | | |
Collapse
|
17
|
Sun-Wada GH, Murata Y, Namba M, Yamamoto A, Wada Y, Futai M. Mouse proton pump ATPase C subunit isoforms (C2-a and C2-b) specifically expressed in kidney and lung. J Biol Chem 2003; 278:44843-51. [PMID: 12947086 DOI: 10.1074/jbc.m307197200] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The vacuolar-type H+-ATPases (V-ATPases) are multimeric proton pumps involved in a wide variety of physiological processes. We have identified two alternative splicing variants of C2 subunit isoforms: C2-a, a lung-specific isoform containing a 46-amino acid insertion, and C2-b, a kidney-specific isoform without the insert. Immunohistochemistry with isoform-specific antibodies revealed that V-ATPase with C2-a is localized specifically in lamellar bodies of type II alveolar cells, whereas the C2-b isoform is found in the plasma membranes of renal alpha and beta intercalated cells. Immunoprecipitation combined with immunohistological analysis revealed that C2-b together with other kidney-specific isoforms was selectively assembled to form a unique proton pump in intercalated cells. Furthermore, a chimeric yeast V-ATPase with mouse the C2-a or C2-b isoform showed a lower Km(ATP) and lower proton transport activity than that with C1 or Vma5p (yeast C subunit). These results suggest that V-ATPases with the C2-a and C2-b isoform are involved in luminal acidification of lamellar bodies and regulation of the renal acid-base balance, respectively.
Collapse
Affiliation(s)
- Ge-Hong Sun-Wada
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | | | | | | | | | | |
Collapse
|
18
|
Hirata T, Iwamoto-Kihara A, Sun-Wada GH, Okajima T, Wada Y, Futai M. Subunit rotation of vacuolar-type proton pumping ATPase: relative rotation of the G and C subunits. J Biol Chem 2003; 278:23714-9. [PMID: 12670943 DOI: 10.1074/jbc.m302756200] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vacuolar-type ATPases V1V0 (V-ATPases) are found ubiquitously in the endomembrane organelles of eukaryotic cells. In this study, we genetically introduced a His tag and a biotin tag onto the c and G subunits, respectively, of Saccharomyces cerevisiae V-ATPase. Using this engineered enzyme, we observed directly the continuous counter-clockwise rotation of an actin filament attached to the G subunit when the enzyme was immobilized on a glass surface through the c subunit. V-ATPase generated essentially the same torque as the F-ATPase (ATP synthase). The rotation was inhibited by concanamycin and nitrate but not by azide. These results demonstrated that the V- and F-ATPase carry out a common rotational catalysis.
Collapse
Affiliation(s)
- Tomoyuki Hirata
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | | | | | | | | | | |
Collapse
|
19
|
Abstract
Topical questions in ATP synthase research are: (1) how do protons cause subunit rotation and how does rotation generate ATP synthesis from ADP+Pi? (2) How does hydrolysis of ATP generate subunit rotation and how does rotation bring about uphill transport of protons? The finding that ATP synthase is not just an enzyme but rather a unique nanomotor is attracting a diverse group of researchers keen to find answers. Here we review the most recent work on rapidly developing areas within the field and present proposals for enzymatic and mechanoenzymatic mechanisms.
Collapse
Affiliation(s)
- Joachim Weber
- Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | |
Collapse
|
20
|
Nishio K, Iwamoto-Kihara A, Yamamoto A, Wada Y, Futai M. Subunit rotation of ATP synthase embedded in membranes: a or beta subunit rotation relative to the c subunit ring. Proc Natl Acad Sci U S A 2002; 99:13448-52. [PMID: 12357031 PMCID: PMC129693 DOI: 10.1073/pnas.202149599] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATP synthase F(o)F(1) (alpha(3)beta(3)gammadelta epsilon ab(2)c(10-14)) couples an electrochemical proton gradient and a chemical reaction through the rotation of its subunit assembly. In this study, we engineered F(o)F(1) to examine the rotation of the catalytic F(1) beta or membrane sector F(o) a subunit when the F(o) c subunit ring was immobilized; a biotin-tag was introduced onto the beta or a subunit, and a His-tag onto the c subunit ring. Membrane fragments were obtained from Escherichia coli cells carrying the recombinant plasmid for the engineered F(o)F(1) and were immobilized on a glass surface. An actin filament connected to the beta or a subunit rotated counterclockwise on the addition of ATP, and generated essentially the same torque as one connected to the c ring of F(o)F(1) immobilized through a His-tag linked to the alpha or beta subunit. These results established that the gamma epsilon c(10-14) and alpha(3)beta(3)deltaab(2) complexes are mechanical units of the membrane-embedded enzyme involved in rotational catalysis.
Collapse
Affiliation(s)
- Kazuaki Nishio
- Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, Core Research for Evolutional Science and Technology (CREST) of the Japan Science and Technology Corporation, Osaka 567-0047, Japan
| | | | | | | | | |
Collapse
|