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Pérez I, Heitkamp T, Börsch M. Mechanism of ADP-Inhibited ATP Hydrolysis in Single Proton-Pumping F oF 1-ATP Synthase Trapped in Solution. Int J Mol Sci 2023; 24:ijms24098442. [PMID: 37176150 PMCID: PMC10178918 DOI: 10.3390/ijms24098442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
FoF1-ATP synthases in mitochondria, in chloroplasts, and in most bacteria are proton-driven membrane enzymes that supply the cells with ATP made from ADP and phosphate. Different control mechanisms exist to monitor and prevent the enzymes' reverse chemical reaction of fast wasteful ATP hydrolysis, including mechanical or redox-based blockade of catalysis and ADP inhibition. In general, product inhibition is expected to slow down the mean catalytic turnover. Biochemical assays are ensemble measurements and cannot discriminate between a mechanism affecting all enzymes equally or individually. For example, all enzymes could work more slowly at a decreasing substrate/product ratio, or an increasing number of individual enzymes could be completely blocked. Here, we examined the effect of increasing amounts of ADP on ATP hydrolysis of single Escherichia coli FoF1-ATP synthases in liposomes. We observed the individual catalytic turnover of the enzymes one after another by monitoring the internal subunit rotation using single-molecule Förster resonance energy transfer (smFRET). Observation times of single FRET-labeled FoF1-ATP synthases in solution were extended up to several seconds using a confocal anti-Brownian electrokinetic trap (ABEL trap). By counting active versus inhibited enzymes, we revealed that ADP inhibition did not decrease the catalytic turnover of all FoF1-ATP synthases equally. Instead, increasing ADP in the ADP/ATP mixture reduced the number of remaining active enzymes that operated at similar catalytic rates for varying substrate/product ratios.
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Affiliation(s)
- Iván Pérez
- Single-Molecule Microscopy Group, Jena University Hospital, 07743 Jena, Germany
| | - Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, 07743 Jena, Germany
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, 07743 Jena, Germany
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2
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F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis. Int J Mol Sci 2023; 24:ijms24065417. [PMID: 36982498 PMCID: PMC10049701 DOI: 10.3390/ijms24065417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the spread of drug-resistant disease-causing strains, there is an increasing interest in F1·Fo as new targets for antimicrobial drugs, in particular, anti-tuberculosis drugs, and inhibitors of these membrane proteins are being considered in this capacity. However, the specific drug search is hampered by the complex mechanism of regulation of F1·Fo in bacteria, in particular, in mycobacteria: the enzyme efficiently synthesizes ATP, but is not capable of ATP hydrolysis. In this review, we consider the current state of the problem of “unidirectional” F1·Fo catalysis found in a wide range of bacterial F1·Fo and enzymes from other organisms, the understanding of which will be useful for developing a strategy for the search for new drugs that selectively disrupt the energy production of bacterial cells.
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3
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Krah A, Vogelaar T, de Jong SI, Claridge JK, Bond PJ, McMillan DGG. ATP binding by an F 1F o ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria. Front Mol Biosci 2023; 10:1059673. [PMID: 36923639 PMCID: PMC10010621 DOI: 10.3389/fmolb.2023.1059673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/03/2023] [Indexed: 03/03/2023] Open
Abstract
It is a conjecture that the ε subunit regulates ATP hydrolytic function of the F1Fo ATP synthase in bacteria. This has been proposed by the ε subunit taking an extended conformation, with a terminal helix probing into the central architecture of the hexameric catalytic domain, preventing ATP hydrolysis. The ε subunit takes a contracted conformation when bound to ATP, thus would not interfere with catalysis. A recent crystallographic study has disputed this; the Caldalkalibacillus thermarum TA2.A1 F1Fo ATP synthase cannot natively hydrolyse ATP, yet studies have demonstrated that the loss of the ε subunit terminal helix results in an ATP synthase capable of ATP hydrolysis, supporting ε subunit function. Analysis of sequence and crystallographic data of the C. thermarum F1Fo ATP synthase revealed two unique histidine residues. Molecular dynamics simulations suggested that the protonation state of these residues may influence ATP binding site stability. Yet these residues lie outside the ATP/Mg2+ binding site of the ε subunit. We then probed the effect of pH on the ATP binding affinity of the ε subunit from the C. thermarum F1Fo ATP synthase at various physiologically relevant pH values. We show that binding affinity changes 5.9 fold between pH 7.0, where binding is weakest, to pH 8.5 where it is strongest. Since the C. thermarum cytoplasm is pH 8.0 when it grows optimally, this correlates to the ε subunit being down due to ATP/Mg2+ affinity, and not being involved in blocking ATP hydrolysis. Here, we have experimentally correlated that the pH of the bacterial cytoplasm is of critical importance for ε subunit ATP affinity regulated by second-shell residues thus the function of the ε subunit changes with growth conditions.
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Affiliation(s)
- Alexander Krah
- Korea Institute for Advanced Study, School of Computational Sciences, Seoul, South Korea.,Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Timothy Vogelaar
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Sam I de Jong
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jolyon K Claridge
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Duncan G G McMillan
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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4
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Frasch WD, Bukhari ZA, Yanagisawa S. F1FO ATP synthase molecular motor mechanisms. Front Microbiol 2022; 13:965620. [PMID: 36081786 PMCID: PMC9447477 DOI: 10.3389/fmicb.2022.965620] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The F-ATP synthase, consisting of F1 and FO motors connected by a central rotor and the stators, is the enzyme responsible for synthesizing the majority of ATP in all organisms. The F1 (αβ)3 ring stator contains three catalytic sites. Single-molecule F1 rotation studies revealed that ATP hydrolysis at each catalytic site (0°) precedes a power-stroke that rotates subunit-γ 120° with angular velocities that vary with rotational position. Catalytic site conformations vary relative to subunit-γ position (βE, empty; βD, ADP bound; βT, ATP-bound). During a power stroke, βE binds ATP (0°–60°) and βD releases ADP (60°–120°). Årrhenius analysis of the power stroke revealed that elastic energy powers rotation via unwinding the γ-subunit coiled-coil. Energy from ATP binding at 34° closes βE upon subunit-γ to drive rotation to 120° and forcing the subunit-γ to exchange its tether from βE to βD, which changes catalytic site conformations. In F1FO, the membrane-bound FO complex contains a ring of c-subunits that is attached to subunit-γ. This c-ring rotates relative to the subunit-a stator in response to transmembrane proton flow driven by a pH gradient, which drives subunit-γ rotation in the opposite direction to force ATP synthesis in F1. Single-molecule studies of F1FO embedded in lipid bilayer nanodisks showed that the c-ring transiently stopped F1-ATPase-driven rotation every 36° (at each c-subunit in the c10-ring of E. coli F1FO) and was able to rotate 11° in the direction of ATP synthesis. Protonation and deprotonation of the conserved carboxyl group on each c-subunit is facilitated by separate groups of subunit-a residues, which were determined to have different pKa’s. Mutations of any of any residue from either group changed both pKa values, which changed the occurrence of the 11° rotation proportionately. This supports a Grotthuss mechanism for proton translocation and indicates that proton translocation occurs during the 11° steps. This is consistent with a mechanism in which each 36° of rotation the c-ring during ATP synthesis involves a proton translocation-dependent 11° rotation of the c-ring, followed by a 25° rotation driven by electrostatic interaction of the negatively charged unprotonated carboxyl group to the positively charged essential arginine in subunit-a.
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Updates and Original Case Studies Focused on the NMR-Linked Metabolomics Analysis of Human Oral Fluids Part I: Emerging Platforms and Perspectives. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
1H NMR-based metabolomics analysis of human saliva, other oral fluids, and/or tissue biopsies serves as a valuable technique for the exploration of metabolic processes, and when associated with ’state-of-the-art’ multivariate (MV) statistical analysis strategies, provides a powerful means of examining the identification of characteristic metabolite patterns, which may serve to differentiate between patients with oral health conditions (e.g., periodontitis, dental caries, and oral cancers) and age-matched heathy controls. This approach may also be employed to explore such discriminatory signatures in the salivary 1H NMR profiles of patients with systemic diseases, and to date, these have included diabetes, Sjörgen’s syndrome, cancers, neurological conditions such as Alzheimer’s disease, and viral infections. However, such investigations are complicated in view of quite a large number of serious inconsistencies between the different studies performed by independent research groups globally; these include differing protocols and routes for saliva sample collection (e.g., stimulated versus unstimulated samples), their timings (particularly the oral activity abstention period involved, which may range from one to 12 h or more), and methods for sample transport, storage, and preparation for NMR analysis, not to mention a very wide variety of demographic variables that may influence salivary metabolite concentrations, notably the age, gender, ethnic origin, salivary flow-rate, lifestyles, diets, and smoking status of participant donors, together with their exposure to any other possible convoluting environmental factors. In view of the explosive increase in reported salivary metabolomics investigations, in this update, we critically review a wide range of critical considerations for the successful performance of such experiments. These include the nature, composite sources, and biomolecular status of human saliva samples; the merits of these samples as media for the screening of disease biomarkers, notably their facile, unsupervised collection; and the different classes of such metabolomics investigations possible. Also encompassed is an account of the history of NMR-based salivary metabolomics; our recommended regimens for the collection, transport, and storage of saliva samples, along with their preparation for NMR analysis; frequently employed pulse sequences for the NMR analysis of these samples; the supreme resonance assignment benefits offered by homo- and heteronuclear two-dimensional NMR techniques; deliberations regarding salivary biomolecule quantification approaches employed for such studies, including the preprocessing and bucketing of multianalyte salivary NMR spectra, and the normalization, transformation, and scaling of datasets therefrom; salivary phenotype analysis, featuring the segregation of a range of different metabolites into ‘pools’ grouped according to their potential physiological sources; and lastly, future prospects afforded by the applications of LF benchtop NMR spectrometers for direct evaluations of the oral or systemic health status of patients at clinical ‘point-of-contact’ sites, e.g., dental surgeries. This commentary is then concluded with appropriate recommendations for the conduct of future salivary metabolomics studies. Also included are two original case studies featuring investigations of (1) the 1H NMR resonance line-widths of selected biomolecules and their possible dependence on biomacromolecular binding equilibria, and (2) the combined univariate (UV) and MV analysis of saliva specimens collected from a large group of healthy control participants in order to potentially delineate the possible origins of biomolecules therein, particularly host- versus oral microbiome-derived sources. In a follow-up publication, Part II of this series, we conduct censorious reviews of reported observations acquired from a diversity of salivary metabolomics investigations performed to evaluate both localized oral and non-oral diseases. Perplexing problems encountered with these again include those arising from sample collection and preparation protocols, along with 1H NMR spectral misassignments.
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Complex effects of macrolide venturicidins on bacterial F-ATPases likely contribute to their action as antibiotic adjuvants. Sci Rep 2021; 11:13631. [PMID: 34211053 PMCID: PMC8249445 DOI: 10.1038/s41598-021-93098-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial energy metabolism is now recognized as a critical factor for the efficacy of antibiotics. The F-type ATPase/ATP synthase (FOF1) is a central player in cellular bioenergetics of bacteria and eukaryotes, and its potential as a selective antibiotic target has been confirmed by the success of bedaquiline in combatting multidrug-resistant tuberculosis. Venturicidin macrolides were initially identified for their antifungal properties and were found to specifically inhibit FOF1 of eukaryotes and bacteria. Venturicidins alone are not effective antibacterials but recently were found to have adjuvant activity, potentiating the efficacy of aminoglycoside antibiotics against several species of resistant bacteria. Here we discovered more complex effects of venturicidins on the ATPase activity of FOF1 in bacterial membranes from Escherichia coli and Pseudomonas aeruginosa. Our major finding is that higher concentrations of venturicidin induce time- and ATP-dependent decoupling of F1-ATPase activity from the venturicidin-inhibited, proton-transporting FO complex. This dysregulated ATPase activity is likely to be a key factor in the depletion of cellular ATP induced by venturicidins in prior studies with P. aeruginosa and Staphylococcus aureus. Further studies of how this functional decoupling occurs could guide development of new antibiotics and/or adjuvants that target the F-type ATPase/ATP synthase.
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Milgrom YM, Duncan TM. F-ATP-ase of Escherichia coli membranes: The ubiquitous MgADP-inhibited state and the inhibited state induced by the ε-subunit's C-terminal domain are mutually exclusive. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148189. [PMID: 32194063 DOI: 10.1016/j.bbabio.2020.148189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 12/21/2022]
Abstract
ATP synthases are important energy-coupling, rotary motor enzymes in all kingdoms of life. In all F-type ATP synthases, the central rotor of the catalytic F1 complex is composed of the γ subunit and the N-terminal domain (NTD) of the ε subunit. In the enzymes of diverse bacteria, the C-terminal domain of ε (εCTD) can undergo a dramatic conformational change to trap the enzyme in a transiently inactive state. This inhibitory mechanism is absent in the mitochondrial enzyme, so the εCTD could provide a means to selectively target ATP synthases of pathogenic bacteria for antibiotic development. For Escherichia coli and other bacterial model systems, it has been difficult to dissect the relationship between ε inhibition and a MgADP-inhibited state that is ubiquitous for FOF1 from bacteria and eukaryotes. A prior study with the isolated catalytic complex from E. coli, EcF1, showed that these two modes of inhibition are mutually exclusive, but it has long been known that interactions of F1 with the membrane-embedded FO complex modulate inhibition by the εCTD. Here, we study membranes containing EcFOF1 with wild-type ε, ε lacking the full εCTD, or ε with a small deletion at the C-terminus. By using compounds with distinct activating effects on F-ATP-ase activity, we confirm that εCTD inhibition and ubiquitous MgADP inhibition are mutually exclusive for membrane-bound E. coli F-ATP-ase. We determine that most of the enzyme complexes in wild-type membranes are in the ε-inhibited state (>50%) or in the MgADP-inhibited state (30%).
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Affiliation(s)
- Yakov M Milgrom
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E Adams St, Syracuse, NY 13210, USA.
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E Adams St, Syracuse, NY 13210, USA.
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8
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Functional importance of αAsp-350 in the catalytic sites of Escherichia coli ATP synthase. Arch Biochem Biophys 2019; 672:108050. [PMID: 31330132 DOI: 10.1016/j.abb.2019.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/10/2019] [Accepted: 07/18/2019] [Indexed: 12/21/2022]
Abstract
Negatively charged residue αAsp-350 of the highly conserved VISIT-DG sequence is required for Pi binding and maintenance of the phosphate-binding subdomain in the catalytic sites of Escherichia coli F1Fo ATP synthase. αAsp-350 is situated in close proximity, 2.88 Å and 3.5 Å, to the conserved known phosphate-binding residues αR376 and βR182. αD350 is also in close proximity, 1.3 Å, to another functionally important residue αG351. Mutation of αAsp-350 to Ala, Gln, or Arg resulted in substantial loss of oxidative phosphorylation and reduction in ATPase activity by 6- to 16-fold. The loss of the acidic side chain in the form of αD350A, αD350Q, and αD350R caused loss of Pi binding. While removal of Arg in the form of αR376D resulted in the loss of Pi binding, the addition of Arg in the form of αG351R did not affect Pi binding. Our data demonstrates that αD350R helps in the proper orientation of αR376 and βR182 for Pi binding. Fluoroaluminate, fluoroscandium, and sodium azide caused almost complete inhibition of wild type enzyme and caused variable inhibition of αD350 mutant enzymes. NBD-Cl (4-chloro-7-nitrobenzo-2-oxa-1, 3-diazole) caused complete inhibition of wild type enzyme while some residual activity was left in mutant enzymes. Inhibition characteristics supported the conclusion that NBD-Cl reacts in βE (empty) catalytic sites. Phosphate protected against NBD-Cl inhibition of wild type and αG351R mutant enzymes but not inhibition of αD350A, αD350Q, αD350R, or αR376D mutant enzymes. These results demonstrate that αAsp-350 is an essential residue required for phosphate binding, through its interaction with αR376 and βR182, for normal function of phosphate binding subdomain and for transition state stabilization in ATP synthase catalytic sites.
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9
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Petri J, Nakatani Y, Montgomery MG, Ferguson SA, Aragão D, Leslie AGW, Heikal A, Walker JE, Cook GM. Structure of F 1-ATPase from the obligate anaerobe Fusobacterium nucleatum. Open Biol 2019; 9:190066. [PMID: 31238823 PMCID: PMC6597759 DOI: 10.1098/rsob.190066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The crystal structure of the F1-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from the pathogenic anaerobic bacterium Fusobacterium nucleatum. The enzyme can hydrolyse ATP but is partially inhibited. The structure is similar to those of the F1-ATPases from Caldalkalibacillus thermarum, which is more strongly inhibited in ATP hydrolysis, and in Mycobacterium smegmatis, which has a very low ATP hydrolytic activity. The βE-subunits in all three enzymes are in the conventional ‘open’ state, and in the case of C. thermarum and M. smegmatis, they are occupied by an ADP and phosphate (or sulfate), but in F. nucleatum, the occupancy by ADP appears to be partial. It is likely that the hydrolytic activity of the F. nucleatum enzyme is regulated by the concentration of ADP, as in mitochondria.
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Affiliation(s)
- Jessica Petri
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand
| | - Yoshio Nakatani
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Martin G Montgomery
- 3 Medical Research Council Mitochondrial Biology Unit , Cambridge Biomedical Campus, Cambridge CB2 0XY , UK
| | - Scott A Ferguson
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand
| | - David Aragão
- 4 Australian Synchrotron , 800 Blackburn Road, Clayton, Victoria 3168 , Australia
| | - Andrew G W Leslie
- 5 Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Cambridge CB2 0QH , UK
| | - Adam Heikal
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - John E Walker
- 3 Medical Research Council Mitochondrial Biology Unit , Cambridge Biomedical Campus, Cambridge CB2 0XY , UK
| | - Gregory M Cook
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
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Lapashina AS, Feniouk BA. ADP-Inhibition of H+-F OF 1-ATP Synthase. BIOCHEMISTRY (MOSCOW) 2018; 83:1141-1160. [PMID: 30472953 DOI: 10.1134/s0006297918100012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
H+-FOF1-ATP synthase (F-ATPase, F-type ATPase, FOF1 complex) catalyzes ATP synthesis from ADP and inorganic phosphate in eubacteria, mitochondria, chloroplasts, and some archaea. ATP synthesis is powered by the transmembrane proton transport driven by the proton motive force (PMF) generated by the respiratory or photosynthetic electron transport chains. When the PMF is decreased or absent, ATP synthase catalyzes the reverse reaction, working as an ATP-dependent proton pump. The ATPase activity of the enzyme is regulated by several mechanisms, of which the most conserved is the non-competitive inhibition by the MgADP complex (ADP-inhibition). When ADP binds to the catalytic site without phosphate, the enzyme may undergo conformational changes that lock bound ADP, resulting in enzyme inactivation. PMF can induce release of inhibitory ADP and reactivate ATP synthase; the threshold PMF value required for enzyme reactivation might exceed the PMF for ATP synthesis. Moreover, membrane energization increases the catalytic site affinity to phosphate, thereby reducing the probability of ADP binding without phosphate and preventing enzyme transition to the ADP-inhibited state. Besides phosphate, oxyanions (e.g., sulfite and bicarbonate), alcohols, lauryldimethylamine oxide, and a number of other detergents can weaken ADP-inhibition and increase ATPase activity of the enzyme. In this paper, we review the data on ADP-inhibition of ATP synthases from different organisms and discuss the in vivo role of this phenomenon and its relationship with other regulatory mechanisms, such as ATPase activity inhibition by subunit ε and nucleotide binding in the noncatalytic sites of the enzyme. It should be noted that in Escherichia coli enzyme, ADP-inhibition is relatively weak and rather enhanced than prevented by phosphate.
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Affiliation(s)
- A S Lapashina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - B A Feniouk
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Lapashina AS, Prikhodko AS, Shugaeva TE, Feniouk BA. Residue 249 in subunit beta regulates ADP inhibition and its phosphate modulation in Escherichia coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:181-188. [PMID: 30528692 DOI: 10.1016/j.bbabio.2018.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/29/2022]
Abstract
ATPase activity of proton-translocating FOF1-ATP synthase (F-type ATPase or F-ATPase) is suppressed in the absence of protonmotive force by several regulatory mechanisms. The most conservative of these mechanisms found in all enzymes studied so far is allosteric inhibition of ATP hydrolysis by MgADP (ADP-inhibition). When MgADP is bound without phosphate in the catalytic site, the enzyme lapses into an inactive state with MgADP trapped. In chloroplasts and mitochondria, as well as in most bacteria, phosphate prevents MgADP inhibition. However, in Escherichia coli ATP synthase ADP-inhibition is relatively weak and phosphate does not prevent it but seems to enhance it. We found that a single amino acid residue in subunit β is responsible for these features of E. coli enzyme. Mutation βL249Q significantly enhanced ADP-inhibition in E. coli ATP synthase, increased the extent of ATP hydrolysis stimulation by sulfite, and rendered the ADP-inhibition sensitive to phosphate in the same manner as observed in FOF1 from mitochondria, chloroplasts, and most aerobic\photosynthetic bacteria.
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Affiliation(s)
- Anna S Lapashina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anastasia S Prikhodko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Tatiana E Shugaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Boris A Feniouk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia.
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12
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13
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Sielaff H, Duncan TM, Börsch M. The regulatory subunit ε in Escherichia coli F OF 1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:775-788. [PMID: 29932911 DOI: 10.1016/j.bbabio.2018.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022]
Abstract
F-type ATP synthases are extraordinary multisubunit proteins that operate as nanomotors. The Escherichia coli (E. coli) enzyme uses the proton motive force (pmf) across the bacterial plasma membrane to drive rotation of the central rotor subunits within a stator subunit complex. Through this mechanical rotation, the rotor coordinates three nucleotide binding sites that sequentially catalyze the synthesis of ATP. Moreover, the enzyme can hydrolyze ATP to turn the rotor in the opposite direction and generate pmf. The direction of net catalysis, i.e. synthesis or hydrolysis of ATP, depends on the cell's bioenergetic conditions. Different control mechanisms have been found for ATP synthases in mitochondria, chloroplasts and bacteria. This review discusses the auto-inhibitory behavior of subunit ε found in FOF1-ATP synthases of many bacteria. We focus on E. coli FOF1-ATP synthase, with insights into the regulatory mechanism of subunit ε arising from structural and biochemical studies complemented by single-molecule microscopy experiments.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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14
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Krah A, Kato-Yamada Y, Takada S. The structural basis of a high affinity ATP binding ε subunit from a bacterial ATP synthase. PLoS One 2017; 12:e0177907. [PMID: 28542497 PMCID: PMC5436830 DOI: 10.1371/journal.pone.0177907] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/04/2017] [Indexed: 01/09/2023] Open
Abstract
The ε subunit from bacterial ATP synthases functions as an ATP sensor, preventing ATPase activity when the ATP concentration in bacterial cells crosses a certain threshold. The R103A/R115A double mutant of the ε subunit from thermophilic Bacillus PS3 has been shown to bind ATP two orders of magnitude stronger than the wild type protein. We use molecular dynamics simulations and free energy calculations to derive the structural basis of the high affinity ATP binding to the R103A/R115A double mutant. Our results suggest that the double mutant is stabilized by an enhanced hydrogen-bond network and fewer repulsive contacts in the ligand binding site. The inferred structural basis of the high affinity mutant may help to design novel nucleotide sensors based on the ε subunit from bacterial ATP synthases.
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Affiliation(s)
- Alexander Krah
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan
- School of Computational Sciences, Korea Institute for Advanced Study, Dongdaemun-gu, Seoul, Republic of Korea
- * E-mail:
| | - Yasuyuki Kato-Yamada
- Department of Life Science, College of Science, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan
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15
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On the ATP binding site of the ε subunit from bacterial F-type ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:332-40. [PMID: 26780667 DOI: 10.1016/j.bbabio.2016.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/11/2015] [Accepted: 01/14/2016] [Indexed: 11/20/2022]
Abstract
F-type ATP synthases are reversible machinery that not only synthesize adenosine triphosphate (ATP) using an electrochemical gradient across the membrane, but also can hydrolyze ATP to pump ions under certain conditions. To prevent wasteful ATP hydrolysis, subunit ε in bacterial ATP synthases changes its conformation from the non-inhibitory down- to the inhibitory up-state at a low cellular ATP concentration. Recently, a crystal structure of the ε subunit in complex with ATP was solved in a non-biologically relevant dimeric form. Here, to derive the functional ATP binding site motif, we carried out molecular dynamics simulations and free energy calculations. Our results suggest that the ATP binding site markedly differs from the experimental resolved one; we observe a reorientation of several residues, which bind to ATP in the crystal structure. In addition we find that an Mg(2+) ion is coordinated by ATP, replacing interactions of the second chain in the crystal structure. Thus we demonstrate more generally the influence of crystallization effects on ligand binding sites and their respective binding modes. Furthermore, we propose a role for two highly conserved residues to control the ATP binding/unbinding event, which have not been considered before. Additionally our results provide the basis for the rational development of new biosensors based on subunit ε, as shown previously for novel sensors measuring the ATP concentration in cells.
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16
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Abstract
The F1F0-ATP synthase (EC 3.6.1.34) is a remarkable enzyme that functions as a rotary motor. It is found in the inner membranes of Escherichia coli and is responsible for the synthesis of ATP in response to an electrochemical proton gradient. Under some conditions, the enzyme functions reversibly and uses the energy of ATP hydrolysis to generate the gradient. The ATP synthase is composed of eight different polypeptide subunits in a stoichiometry of α3β3γδεab2c10. Traditionally they were divided into two physically separable units: an F1 that catalyzes ATP hydrolysis (α3β3γδε) and a membrane-bound F0 sector that transports protons (ab2c10). In terms of rotary function, the subunits can be divided into rotor subunits (γεc10) and stator subunits (α3β3δab2). The stator subunits include six nucleotide binding sites, three catalytic and three noncatalytic, formed primarily by the β and α subunits, respectively. The stator also includes a peripheral stalk composed of δ and b subunits, and part of the proton channel in subunit a. Among the rotor subunits, the c subunits form a ring in the membrane, and interact with subunit a to form the proton channel. Subunits γ and ε bind to the c-ring subunits, and also communicate with the catalytic sites through interactions with α and β subunits. The eight subunits are expressed from a single operon, and posttranscriptional processing and translational regulation ensure that the polypeptides are made at the proper stoichiometry. Recent studies, including those of other species, have elucidated many structural and rotary properties of this enzyme.
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17
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Linking structural features from mitochondrial and bacterial F-type ATP synthases to their distinct mechanisms of ATPase inhibition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:94-102. [DOI: 10.1016/j.pbiomolbio.2015.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 01/11/2023]
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18
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Kinetic and hysteretic behavior of ATP hydrolysis of the highly stable dimeric ATP synthase of Polytomella sp. Arch Biochem Biophys 2015; 575:30-7. [PMID: 25843420 DOI: 10.1016/j.abb.2015.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/20/2015] [Accepted: 03/21/2015] [Indexed: 11/21/2022]
Abstract
The F1FO-ATP synthase of the colorless alga Polytomella sp. exhibits a robust peripheral arm constituted by nine atypical subunits only present in chlorophycean algae. The isolated dimeric enzyme exhibits a latent ATP hydrolytic activity which can be activated by some detergents. To date, the kinetic behavior of the algal ATPase has not been studied. Here we show that while the soluble F1 sector exhibits Michaelis-Menten kinetics, the dimer exhibits a more complex behavior. The kinetic parameters (Vmax and Km) were obtained for both the F1 sector and the dimeric enzyme as isolated or activated by detergent, and this activation was also seen on the enzyme reconstituted in liposomes. Unlike other ATP synthases, the algal dimer hydrolyzes ATP on a wide range of pH and temperature. The enzyme was inhibited by oligomycin, DCCD and Mg-ADP, although oligomycin induced a peculiar inhibition pattern that can be attributed to structural differences in the algal subunit-c. The hydrolytic activity was temperature-dependent and exhibited activation energy of 4 kcal/mol. The enzyme also exhibited a hysteretic behavior with a lag phase strongly dependent on temperature but not on pH, that may be related to a possible regulatory role in vivo.
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19
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Effects of an ATP analogue, adenosine 5'-[α-thio]-triphosphate, on F1-ATPase rotary catalysis, torque generation, and inhibited intermediated formation. Biochem Biophys Res Commun 2015; 458:515-519. [PMID: 25681765 DOI: 10.1016/j.bbrc.2015.01.146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 01/30/2015] [Indexed: 01/03/2023]
Abstract
F1-ATPase (F1), an important rotary motor protein, converts the chemical energy of ATP hydrolysis into mechanical energy using rotary motion with extremely high efficiency. The energy-conversion mechanism for this molecular motor has been extensively clarified by previous studies, which indicate that the interactions between the catalytic residues and the β- and γ-phosphates of ATP are indispensable for efficient catalysis and torque generation. However, the role of α-phosphate is largely unknown. In this study, we observed the rotation of F1 fuelled with an ATP analogue, adenosine 5'-[α-thio]-triphosphate (ATPαS), in which the oxygen has been substituted with a sulfur ion to perturb the α-phosphate/F1 interactions. In doing so, we have revealed that ATPαS does not appear to have any impact on the kinetic properties of the motor or on torque generation compared to ATP. On the other hand, F1 was observed to lapse into the ADP-inhibited intermediate states when in the presence of ATPαS more severely than in the presence of ATP, suggesting that the α-phosphate group of ATP contributes to the avoidance of ADP-inhibited intermediate formation.
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20
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Malyan AN. Noncatalytic nucleotide binding sites: properties and mechanism of involvement in ATP synthase activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1512-23. [PMID: 24490737 DOI: 10.1134/s0006297913130099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
ATP synthases (FoF1-ATPases) of chloroplasts, mitochondria, and bacteria catalyze ATP synthesis or hydrolysis coupled with the transmembrane transfer of protons or sodium ions. Their activity is regulated through their reversible inactivation resulting from a decreased transmembrane potential difference. The inactivation is believed to conserve ATP previously synthesized under conditions of sufficient energy supply against unproductive hydrolysis. This review is focused on the mechanism of nucleotide-dependent regulation of the ATP synthase activity where the so-called noncatalytic nucleotide binding sites are involved. Properties of these sites varying upon free enzyme transition to its membrane-bound form, their dependence on membrane energization, and putative mechanisms of noncatalytic site-mediated regulation of the ATP synthase activity are discussed.
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Affiliation(s)
- A N Malyan
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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21
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Suzuki T, Tanaka K, Wakabayashi C, Saita EI, Yoshida M. Chemomechanical coupling of human mitochondrial F1-ATPase motor. Nat Chem Biol 2014; 10:930-6. [PMID: 25242551 DOI: 10.1038/nchembio.1635] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 08/08/2014] [Indexed: 11/09/2022]
Abstract
The rotary motor enzyme F1-ATPase (F1) is a catalytic subcomplex of FoF1-ATP synthase that produces most of the ATP in respiring cells. Chemomechanical coupling has been studied extensively for bacterial F1 but very little for mitochondrial F1. Here we report ATP-driven rotation of human mitochondrial F1. A rotor-shaft γ-subunit in the stator α3β3 ring rotates 120° per ATP with three catalytic steps: ATP binding to one β-subunit at 0°, inorganic phosphate (Pi) release from another β-subunit at 65° and ATP hydrolysis on the third β-subunit at 90°. Rotation is often interrupted at 90° by persistent ADP binding and is stalled at 65° by a specific inhibitor azide. A mitochondrial endogenous inhibitor for FoF1-ATP synthase, IF1, blocks rotation at 90°. These features differ from those of bacterial F1, in which both ATP hydrolysis and Pi release occur at around 80°, demonstrating that chemomechanical coupling angles of the γ-subunit are tuned during evolution.
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Affiliation(s)
- Toshiharu Suzuki
- 1] Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan. [2] ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation (JST), Miraikan, Koto-ku, Tokyo, Japan. [3] Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
| | - Kazumi Tanaka
- 1] ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation (JST), Miraikan, Koto-ku, Tokyo, Japan. [2] Department of Molecular Bioscience, Kyoto-Sangyo University, Kamigamomotoyama, Kyoto, Japan
| | - Chiaki Wakabayashi
- ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation (JST), Miraikan, Koto-ku, Tokyo, Japan
| | - Ei-ichiro Saita
- 1] ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation (JST), Miraikan, Koto-ku, Tokyo, Japan. [2] Department of Molecular Bioscience, Kyoto-Sangyo University, Kamigamomotoyama, Kyoto, Japan
| | - Masasuke Yoshida
- 1] Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan. [2] ATP Synthesis Regulation Project, International Research Project (ICORP), Japan Science and Technology Corporation (JST), Miraikan, Koto-ku, Tokyo, Japan. [3] Department of Molecular Bioscience, Kyoto-Sangyo University, Kamigamomotoyama, Kyoto, Japan
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22
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Watanabe R, Noji H. Timing of inorganic phosphate release modulates the catalytic activity of ATP-driven rotary motor protein. Nat Commun 2014; 5:3486. [PMID: 24686317 PMCID: PMC3988807 DOI: 10.1038/ncomms4486] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 02/21/2014] [Indexed: 12/04/2022] Open
Abstract
F1-ATPase is a rotary motor protein driven by ATP hydrolysis. The rotary motion of F1-ATPase is tightly coupled to catalysis, in which the catalytic sites strictly obey the reaction sequences at the resolution of elementary reaction steps. This fine coordination of the reaction scheme is thought to be important to achieve extremely high chemomechanical coupling efficiency and reversibility, which is the prominent feature of F1-ATPase among molecular motor proteins. In this study, we intentionally change the reaction scheme by using single-molecule manipulation, and we examine the resulting effect on the rotary motion of F1-ATPase. When the sequence of the products released, that is, ADP and inorganic phosphate, is switched, we find that F1 frequently stops rotating for a long time, which corresponds to inactivation of catalysis. This inactive state presents MgADP inhibition, and thus, we find that an improper reaction sequence of F1-ATPase catalysis induces MgADP inhibition. The F1-ATPase is a motor protein which exhibits rotary motion as a result of catalytic hydrolysis of ATP. Here, the authors investigate how the sequence of this reaction influences molecular rotation, showing that premature product release can result in protein inactivation.
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Affiliation(s)
- Rikiya Watanabe
- 1] Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan [2] PRESTO, JST, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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23
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ε subunit of Bacillus subtilis F1-ATPase relieves MgADP inhibition. PLoS One 2013; 8:e73888. [PMID: 23967352 PMCID: PMC3742539 DOI: 10.1371/journal.pone.0073888] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/23/2013] [Indexed: 11/19/2022] Open
Abstract
MgADP inhibition, which is considered as a part of the regulatory system of ATP synthase, is a well-known process common to all F1-ATPases, a soluble component of ATP synthase. The entrapment of inhibitory MgADP at catalytic sites terminates catalysis. Regulation by the ε subunit is a common mechanism among F1-ATPases from bacteria and plants. The relationship between these two forms of regulatory mechanisms is obscure because it is difficult to distinguish which is active at a particular moment. Here, using F1-ATPase from Bacillus subtilis (BF1), which is strongly affected by MgADP inhibition, we can distinguish MgADP inhibition from regulation by the ε subunit. The ε subunit did not inhibit but activated BF1. We conclude that the ε subunit relieves BF1 from MgADP inhibition.
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24
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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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25
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An alternative role of FoF1-ATP synthase in Escherichia coli: synthesis of thiamine triphosphate. Sci Rep 2013; 3:1071. [PMID: 23323214 PMCID: PMC3545222 DOI: 10.1038/srep01071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 12/21/2012] [Indexed: 11/19/2022] Open
Abstract
In E. coli, thiamine triphosphate (ThTP), a putative signaling molecule, transiently accumulates in response to amino acid starvation. This accumulation requires the presence of an energy substrate yielding pyruvate. Here we show that in intact bacteria ThTP is synthesized from free thiamine diphosphate (ThDP) and Pi, the reaction being energized by the proton-motive force (Δp) generated by the respiratory chain. ThTP production is suppressed in strains carrying mutations in F1 or a deletion of the atp operon. Transformation with a plasmid encoding the whole atp operon fully restored ThTP production, highlighting the requirement for FoF1-ATP synthase in ThTP synthesis. Our results show that, under specific conditions of nutritional downshift, FoF1-ATP synthase catalyzes the synthesis of ThTP, rather than ATP, through a highly regulated process requiring pyruvate oxidation. Moreover, this chemiosmotic mechanism for ThTP production is conserved from E. coli to mammalian brain mitochondria.
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26
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Bilyard T, Nakanishi-Matsui M, Steel BC, Pilizota T, Nord AL, Hosokawa H, Futai M, Berry RM. High-resolution single-molecule characterization of the enzymatic states in Escherichia coli F1-ATPase. Philos Trans R Soc Lond B Biol Sci 2012; 368:20120023. [PMID: 23267177 DOI: 10.1098/rstb.2012.0023] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rotary motor F(1)-ATPase from the thermophilic Bacillus PS3 (TF(1)) is one of the best-studied of all molecular machines. F(1)-ATPase is the part of the enzyme F(1)F(O)-ATP synthase that is responsible for generating most of the ATP in living cells. Single-molecule experiments have provided a detailed understanding of how ATP hydrolysis and synthesis are coupled to internal rotation within the motor. In this work, we present evidence that mesophilic F(1)-ATPase from Escherichia coli (EF(1)) is governed by the same mechanism as TF(1) under laboratory conditions. Using optical microscopy to measure rotation of a variety of marker particles attached to the γ-subunit of single surface-bound EF(1) molecules, we characterized the ATP-binding, catalytic and inhibited states of EF(1). We also show that the ATP-binding and catalytic states are separated by 35±3°. At room temperature, chemical processes occur faster in EF(1) than in TF(1), and we present a methodology to compensate for artefacts that occur when the enzymatic rates are comparable to the experimental temporal resolution. Furthermore, we show that the molecule-to-molecule variation observed at high ATP concentration in our single-molecule assays can be accounted for by variation in the orientation of the rotating markers.
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Affiliation(s)
- Thomas Bilyard
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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27
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The regulatory C-terminal domain of subunit ε of F₀F₁ ATP synthase is dispensable for growth and survival of Escherichia coli. J Bacteriol 2011; 193:2046-52. [PMID: 21335453 DOI: 10.1128/jb.01422-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The C-terminal domain of subunit ε of the bacterial F₀F₁ ATP synthase is reported to be an intrinsic inhibitor of ATP synthesis/hydrolysis activity in vitro, preventing wasteful hydrolysis of ATP under low-energy conditions. Mutants defective in this regulatory domain exhibited no significant difference in growth rate, molar growth yield, membrane potential, or intracellular ATP concentration under a wide range of growth conditions and stressors compared to wild-type cells, suggesting this inhibitory domain is dispensable for growth and survival of Escherichia coli.
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28
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Bulygin VV, Milgrom YM. Probes of inhibition of Escherichia coli F(1)-ATPase by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole in the presence of MgADP and MgATP support a bi-site mechanism of ATP hydrolysis by the enzyme. BIOCHEMISTRY (MOSCOW) 2010; 75:327-35. [PMID: 20370611 DOI: 10.1134/s0006297910030090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Binding of MgADP and MgATP to Escherichia coli F(1)-ATPase (EcF(1)) has been assessed by their effects on extent of the enzyme inhibition by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole (NBD-Cl). MgADP at low concentrations (K(d) 1.3 microM) promotes the inhibition, whereas at higher concentrations (K(d) 0.7 mM) EcF(1) is protected from inhibition. The mutant betaY331W-EcF(1) requires much higher MgADP, K(d) of about 10 mM, for protection. Such MgADP binding was not revealed by fluorescence quenching measurements. MgATP partially protects EcF(1) from inactivation by NBD-Cl, but the enzyme remains sensitive to NBD-Cl in the presence of MgATP at concentrations as high as 10 mM. The activating anion selenite in the absence of MgATP partially protects EcF(1) from inhibition by NBD-Cl. A complete protection of EcF(1) from inhibition by NBD-Cl has been observed in the presence of both MgATP and selenite. The results support a bi-site catalytic mechanism for MgATP hydrolysis by F(1)-ATPases and suggest that stimulation of the enzyme activity by activating anions is due to the anion binding to a catalytic site that remains unoccupied at saturating substrate concentration.
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Affiliation(s)
- V V Bulygin
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA
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29
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Bulygin VV, Milgrom YM. A bi-site mechanism for Escherichia coli F1-ATPase accounts for the observed positive catalytic cooperativity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1016-23. [PMID: 19269272 DOI: 10.1016/j.bbabio.2009.02.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 02/23/2009] [Accepted: 02/26/2009] [Indexed: 11/20/2022]
Abstract
Nucleotide binding to nucleotide-depleted F(1)-ATPase from Escherichia coli (EcF(1)) during MgATP hydrolysis in the presence of excess epsilon subunit has been studied using a combination of centrifugal filtration and column-centrifugation methods. The results show that nucleotide-binding properties of catalytic sites on EcF(1) are affected by the state of occupancy of noncatalytic sites. The ATP-concentration dependence of catalytic-site occupancy during MgATP hydrolysis demonstrates that a bi-site mechanism is responsible for the positive catalytic cooperativity observed during multi-site catalysis by EcF(1). The results suggest that a bi-site mechanism is a general feature of F(1) catalysis.
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Affiliation(s)
- Vladimir V Bulygin
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA
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30
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Proton Translocation and ATP Synthesis by the FoF1-ATPase of Purple Bacteria. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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York J, Spetzler D, Hornung T, Ishmukhametov R, Martin J, Frasch WD. Abundance of Escherichia coli F1-ATPase molecules observed to rotate via single-molecule microscopy with gold nanorod probes. J Bioenerg Biomembr 2007; 39:435-9. [DOI: 10.1007/s10863-007-9114-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Regulatory mechanisms of proton-translocating F(O)F (1)-ATP synthase. Results Probl Cell Differ 2007; 45:279-308. [PMID: 18026702 DOI: 10.1007/400_2007_043] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
H(+)-F(O)F(1)-ATP synthase catalyzes synthesis of ATP from ADP and inorganic phosphate using the energy of transmembrane electrochemical potential difference of proton (deltamu(H)(+). The enzyme can also generate this potential difference by working as an ATP-driven proton pump. Several regulatory mechanisms are known to suppress the ATPase activity of F(O)F(1): 1. Non-competitive inhibition by MgADP, a feature shared by F(O)F(1) from bacteria, chloroplasts and mitochondria 2. Inhibition by subunit epsilon in chloroplast and bacterial enzyme 3. Inhibition upon oxidation of two cysteines in subunit gamma in chloroplast F(O)F(1) 4. Inhibition by an additional regulatory protein (IF(1)) in mitochondrial enzyme In this review we summarize the information available on these regulatory mechanisms and discuss possible interplay between them.
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33
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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.
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Affiliation(s)
- Mayumi Nakanishi-Matsui
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation, Tokyo 141-0021, Japan
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34
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Bowler MW, Montgomery MG, Leslie AGW, Walker JE. Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 A resolution. J Biol Chem 2007; 282:14238-42. [PMID: 17350959 DOI: 10.1074/jbc.m700203200] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of bovine F(1)-ATPase, crystallized in the presence of AMP-PNP and ADP, but in the absence of azide, has been determined at 1.9A resolution. This structure has been compared with the previously described structure of bovine F(1)-ATPase determined at 1.95A resolution with crystals grown under the same conditions but in the presence of azide. The two structures are extremely similar, but they differ in the nucleotides that are bound to the catalytic site in the beta(DP)-subunit. In the present structure, the nucleotide binding sites in the beta(DP)- and beta(TP)-subunits are both occupied by AMP-PNP, whereas in the earlier structure, the beta(TP) site was occupied by AMP-PNP and the beta(DP) site by ADP, where its binding is enhanced by a bound azide ion. Also, the conformation of the side chain of the catalytically important residue, alphaArg-373 differs in the beta(DP)- and beta(TP)-subunits. Thus, the structure with bound azide represents the ADP inhibited state of the enzyme, and the new structure represents a ground state intermediate in the active catalytic cycle of ATP hydrolysis.
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Affiliation(s)
- Matthew W Bowler
- The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge, UK
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Berger G, Girault G, Zimmermann JL. USE OF HPLC FOR THE STUDY OF ADP BINDING TO CHLOROPLAST ATPase. II. ITS EFFECT ON ENZYMATIC ACTIVITY. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-100100441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- G. Berger
- a CEA Saclay , Section de Bioenergetique, Gif sur Yvette Cedex, F-91191, France
| | - G. Girault
- a CEA Saclay , Section de Bioenergetique, Gif sur Yvette Cedex, F-91191, France
| | - J. L. Zimmermann
- a CEA Saclay , Section de Bioenergetique, Gif sur Yvette Cedex, F-91191, France
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36
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Zharova TV, Vinogradov AD. Energy-linked binding of Pi is required for continuous steady-state proton-translocating ATP hydrolysis catalyzed by F0.F1 ATP synthase. Biochemistry 2007; 45:14552-8. [PMID: 17128994 DOI: 10.1021/bi061520v] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of medium Pi (half-maximal concentration of 20 microM at pH 8.0) was found to be required for the prevention of the rapid decline in the rate of proton-motive force (pmf)-induced ATP hydrolysis by Fo.F1 ATP synthase in coupled vesicles derived from Paracoccus denitrificans. The initial rate of the reaction was independent of Pi. The apparent affinity of Pi for its "ATPase-protecting" site was strongly decreased with partial uncoupling of the vesicles. Pi did not reactivate ATPase when added after complete time-dependent deactivation during the enzyme turnover. Arsenate and sulfate, which was shown to compete with Pi when Fo.F1 catalyzed oxidative phosphorylation, substituted for Pi as the protectors of ATPase against the turnover-dependent deactivation. Under conditions where the enzyme turnover was not permitted (no ATP was present), Pi was not required for the pmf-induced activation of ATPase, whereas the presence of medium Pi (or sulfate) delayed the spontaneous deactivation of the enzyme which was induced by the membrane de-energization. The data are interpreted to suggest that coupled and uncoupled ATP hydrolysis catalyzed by Fo.F1 ATP synthases proceeds via different intermediates. Pi dissociates after ADP if the coupling membrane is energized (no E.ADP intermediate exists). Pi dissociates before ADP during uncoupled ATP hydrolysis, leaving the E.ADP intermediate which is transformed into the inactive ADP(Mg2+)-inhibited form of the enzyme (latent ATPase).
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Affiliation(s)
- Tatyana V Zharova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119992, Russian Federation
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37
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Feniouk BA, Suzuki T, Yoshida M. Regulatory interplay between proton motive force, ADP, phosphate, and subunit epsilon in bacterial ATP synthase. J Biol Chem 2006; 282:764-72. [PMID: 17092944 DOI: 10.1074/jbc.m606321200] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP synthase couples transmembrane proton transport, driven by the proton motive force (pmf), to the synthesis of ATP from ADP and inorganic phosphate (P(i)). In certain bacteria, the reaction is reversed and the enzyme generates pmf, working as a proton-pumping ATPase. The ATPase activity of bacterial enzymes is prone to inhibition by both ADP and the C-terminal domain of subunit epsilon. We studied the effects of ADP, P(i), pmf, and the C-terminal domain of subunit epsilon on the ATPase activity of thermophilic Bacillus PS3 and Escherichia coli ATP synthases. We found that pmf relieved ADP inhibition during steady-state ATP hydrolysis, but only in the presence of P(i). The C-terminal domain of subunit epsilon in the Bacillus PS3 enzyme enhanced ADP inhibition by counteracting the effects of pmf. It appears that these features allow the enzyme to promptly respond to changes in the ATP:ADP ratio and in pmf levels in order to avoid potentially wasteful ATP hydrolysis in vivo.
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Affiliation(s)
- Boris A Feniouk
- ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation, Midori-ku, Yokohama 226-0026, Japan
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38
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Malyan AN. Light-dependent incorporation of adenine nucleotide into noncatalytic sites of chloroplast ATP synthase. BIOCHEMISTRY (MOSCOW) 2006; 70:1245-50. [PMID: 16336184 DOI: 10.1007/s10541-005-0254-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding of ADP and ATP to noncatalytic sites of dithiothreitol-modified chloroplast ATP synthase was studied. Selective binding of nucleotides to noncatalytic sites was provided by preliminary light incubation of thylakoid membranes with [14C]ADP followed by its dissociation from catalytic sites during dark ATP hydrolysis stimulated by bisulfite ions ("cold chase"). Incorporation of labeled nucleotides increased with increasing light intensity. Concentration-dependent equilibrium between free and bound nucleotides was achieved within 2-10 min with the following characteristic parameters: the maximal value of nucleotide incorporation was 1.5 nmol/mg of chlorophyll, and the dissociation constant was 1.5 microM. The dependence of nucleotide incorporation on Mg2+ concentration was slight and changed insignificantly upon substituting Ca2+ for Mg2+. Dissociation of nucleotide from noncatalytic sites was illumination-dependent. The dissociation kinetics suggested the existence of at least two nucleotide-binding sites with different dissociation rate constants.
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Affiliation(s)
- A N Malyan
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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39
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Bowler MW, Montgomery MG, Leslie AGW, Walker JE. How azide inhibits ATP hydrolysis by the F-ATPases. Proc Natl Acad Sci U S A 2006; 103:8646-9. [PMID: 16728506 PMCID: PMC1469772 DOI: 10.1073/pnas.0602915103] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding catalytic subunit, betaDP. It occupies a position between the catalytically essential amino acids, beta-Lys-162 in the P loop and the "arginine finger" residue, alpha-Arg-373, similar to the site occupied by the gamma-phosphate in the ATP-binding subunit, betaTP. Its presence in the betaDP-subunit tightens the binding of the side chains to the nucleotide, enhancing its affinity and thereby stabilizing the state with bound ADP. This mechanism of inhibition appears to be common to many other ATPases, including ABC transporters, SecA, and DNA topoisomerase IIalpha. It also explains the stimulatory effect of azide on ATP-sensitive potassium channels by enhancing the binding of ADP.
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Affiliation(s)
- Matthew W. Bowler
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Martin G. Montgomery
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Andrew G. W. Leslie
- Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - John E. Walker
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
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40
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Feniouk BA, Suzuki T, Yoshida M. The role of subunit epsilon in the catalysis and regulation of FOF1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:326-38. [PMID: 16701076 DOI: 10.1016/j.bbabio.2006.03.022] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/13/2006] [Accepted: 03/30/2006] [Indexed: 10/24/2022]
Abstract
The regulation of ATP synthase activity is complex and involves several distinct mechanisms. In bacteria and chloroplasts, subunit epsilon plays an important role in this regulation, (i) affecting the efficiency of coupling, (ii) influencing the catalytic pathway, and (iii) selectively inhibiting ATP hydrolysis activity. Several experimental studies indicate that the regulation is achieved through large conformational transitions of the alpha-helical C-terminal domain of subunit epsilon that occur in response to membrane energization, change in ATP/ADP ratio or addition of inhibitors. This review summarizes the experimental data obtained on different organisms that clarify some basic features as well as some molecular details of this regulatory mechanism. Multiple functions of subunit epsilon, its role in the difference between the catalytic pathways of ATP synthesis and hydrolysis and its influence on the inhibition of ATP hydrolysis by ADP are also discussed.
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Affiliation(s)
- Boris A Feniouk
- ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation (JST), 5800-3 Nagatsuta, Midori-ku, Yokohama 226-0026, Japan.
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41
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Malyan AN. ADP and ATP binding to noncatalytic sites of thiol-modulated chloroplast ATP synthase. PHOTOSYNTHESIS RESEARCH 2006; 88:9-18. [PMID: 16440137 DOI: 10.1007/s11120-005-9025-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 10/12/2005] [Indexed: 05/06/2023]
Abstract
A modified 'cold chase' technique was used to study tight [(14)C]ADP and [(14)C]ATP binding to noncatalytic sites of chloroplast ATP synthase (CF(0)F(1)). The binding was very low in the dark and sharply increased with light intensity. Dissociation of labeled nucleotides incorporated into noncatalytic sites of CF(0)F(1 )or CF(1) reconstituted with EDTA-treated thylakoid membranes was also found to be light-dependent. Time dependence of nucleotide dissociation is described by the first order equation with a k (d) of about 5 min(-1). The exposure of thylakoid membranes to 0.7-24.8 muM nucleotides leads to filling of up to two noncatalytic sites of CF(0)F(1). The sites differ in their specificity: one preferentially binds ADP, whereas the other - ATP. A much higher ATP/ADP ratio of nucleotides bound at noncatalytic sites of isolated CF(1) dramatically decreases upon its reconstitution with EDTA-treated thylakoid membranes. It is suggested that the decrease is caused by conformational changes in one of the alpha subunits induced by its interaction with the delta subunit and/or subunit I-II when CF(1) becomes bound to a thylakoid membrane.
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Affiliation(s)
- Alexander N Malyan
- Institute of Basic Biological Problems, Russian Academy of Sciences, 142290, Moscow Region, Russia.
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42
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Zharova TV, Vinogradov AD. Requirement of medium ADP for the steady-state hydrolysis of ATP by the proton-translocating Paracoccus denitrificans Fo.F1-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:304-10. [PMID: 16730637 DOI: 10.1016/j.bbabio.2006.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 03/03/2006] [Accepted: 03/06/2006] [Indexed: 11/22/2022]
Abstract
Fo.F1-ATP synthase in inside-out coupled vesicles derived from Paracoccus denitrificans catalyzes Pi-dependent proton-translocating ATPase reaction if exposed to prior energization that relieves ADP.Mg2+ -induced inhibition (Zharova, T.V. and Vinogradov, A.D. (2004) J. Biol. Chem.,279, 12319-12324). Here we present evidence that the presence of medium ADP is required for the steady-state energetically self-sustained coupled ATP hydrolysis. The initial rapid ATPase activity is declined to a certain level if the reaction proceeds in the presence of the ADP-consuming, ATP-regenerating system (pyruvate kinase/phosphoenol pyruvate). The rate and extent of the enzyme de-activation are inversely proportional to the steady-state ADP concentration, which is altered by various amounts of pyruvate kinase at constant ATPase level. The half-maximal rate of stationary ATP hydrolysis is reached at an ADP concentration of 8 x 10(-6) M. The kinetic scheme is proposed explaining the requirement of the reaction products (ADP and Pi), the substrates of ATP synthesis, in the medium for proton-translocating ATP hydrolysis by P. denitrificans Fo.F1-ATP synthase.
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Affiliation(s)
- Tatyana V Zharova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119992, Russian Federation
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43
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Galkin MA, Ishmukhametov RR, Vik SB. A functionally inactive, cold-stabilized form of the Escherichia coli F1Fo ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:206-14. [PMID: 16581013 PMCID: PMC1538965 DOI: 10.1016/j.bbabio.2006.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 02/15/2006] [Accepted: 02/20/2006] [Indexed: 11/16/2022]
Abstract
An unusual effect of temperature on the ATPase activity of E. coli F1Fo ATP synthase has been investigated. The rate of ATP hydrolysis by the isolated enzyme, previously kept on ice, showed a lag phase when measured at 15 degrees C, but not at 37 degrees C. A pre-incubation of the enzyme at room temperature for 5 min completely eliminated the lag phase, and resulted in a higher steady-state rate. Similar results were obtained using the isolated enzyme after incorporation into liposomes. The initial rates of ATP-dependent proton translocation, as measured by 9-amino-6-chloro-2-methoxyacridine (ACMA) fluorescence quenching, at 15 degrees C also varied according to the pre-incubation temperature. The relationship between this temperature-dependent pattern of enzyme activity, termed thermohysteresis, and pre-incubation with other agents was examined. Pre-incubation of membrane vesicles with azide and Mg2+, without exogenous ADP, resulted in almost complete inhibition of the initial rate of ATPase when assayed at 10 degrees C, but had little effect at 37 degrees C. Rates of ATP synthesis following this pre-incubation were not affected at any temperature. Azide inhibition of ATP hydrolysis by the isolated enzyme was reduced when an ATP-regenerating system was used. A gradual reactivation of azide-blocked enzyme was slowed down by the presence of phosphate in the reaction medium. The well-known Mg2+ inhibition of ATP hydrolysis was shown to be greatly enhanced at 15 degrees C relative to at 37 degrees C. The results suggest that thermohysteresis is a consequence of an inactive form of the enzyme that is stabilized by the binding of inhibitory Mg-ADP.
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Affiliation(s)
- Mikhail A Galkin
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
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44
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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.
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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
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45
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Milgrom YM, Cross RL. Rapid hydrolysis of ATP by mitochondrial F1-ATPase correlates with the filling of the second of three catalytic sites. Proc Natl Acad Sci U S A 2005; 102:13831-6. [PMID: 16172372 PMCID: PMC1236596 DOI: 10.1073/pnas.0507139102] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strong positive catalytic cooperativity is a central feature of the binding change mechanism for F1-ATPases. However, a detail of the mechanism that remains controversial is whether the kinetic enhancement derived from using substrate-binding energy at one catalytic site to promote product release from another site occurs upon the filling of the second or third of three catalytic sites on F1. To address this question, we compare the ATP concentration dependence of the rate of ATP hydrolysis by F1 from beef heart mitochondria to the ATP concentration dependence of the level of occupancy of catalytic sites during steady-state catalysis as measured by a centrifuge filtration assay. A single Km(ATP) is observed at 77 +/- 6 microM. Analysis of the nucleotide-binding data shows that half-maximal occupancy of a second catalytic site occurs at 78 +/- 18 microM ATP. We conclude that ATP binding to a second catalytic site is sufficient to support rapid rates of catalysis.
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Affiliation(s)
- Yakov M Milgrom
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA
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46
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Borges E, Cognato GDP, Vuaden FC, Bogo MR, Fauth MDG, Bonan CD, Dias RD. Nucleotidase activities in membrane preparations of nervous ganglia and digestive gland of the snail Helix aspersa. Comp Biochem Physiol B Biochem Mol Biol 2005; 137:297-307. [PMID: 15050517 DOI: 10.1016/j.cbpc.2003.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2003] [Revised: 11/20/2003] [Accepted: 11/21/2003] [Indexed: 11/24/2022]
Abstract
Nucleotide-metabolizing enzymes play an important role in the regulation of nucleotide levels. In the present report, we demonstrated an enzyme activity with different kinetic properties in membrane preparations of the nervous ganglia and digestive gland from Helix aspersa. ATPase and ADPase activities were dependent on Ca2+ and Mg2+ with pH optima approximately 7.2 and between 6.0 and 8.0 in digestive gland and nervous ganglia, respectively. The enzyme activities present in membrane preparations of these tissues preferentially hydrolyzed triphosphate nucleotides. In nervous ganglia, the enzyme was insensitive to the classical ATPases inhibitors. In contrast, in digestive gland, N-ethylmaleimide (NEM) produced 45% inhibition of Ca(2+)-ATP hydrolysis. Sodium azide, at 100 microM and 20 mM, inhibited Mg(2+)-ATP hydrolysis by 36% and 55% in digestive gland, respectively. The presence of nucleotide-metabolizing enzymes in these tissues may be important for the modulation of nucleotide and nucleoside levels, controlling their actions on specific purinoceptors in these species.
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Affiliation(s)
- Eliane Borges
- Departamento de Ciências Fisiológicas, Faculdade de Biociências, Laboratório de Pesquisa Bioquímica, Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga, 6681, Caixa postal 1429, 90619-900, Porto Alegre, RS, Brazil
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47
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Ahn J, Beharry S, Molday LL, Molday RS. Functional interaction between the two halves of the photoreceptor-specific ATP binding cassette protein ABCR (ABCA4). Evidence for a non-exchangeable ADP in the first nucleotide binding domain. J Biol Chem 2003; 278:39600-8. [PMID: 12888572 DOI: 10.1074/jbc.m304236200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ABCR, also known as ABCA4, is a member of the superfamily of ATP binding cassette transporters that is believed to transport retinal or retinylidene-phosphatidylethanolamine across photoreceptor disk membranes. Mutations in the ABCR gene are responsible for Stargardt macular dystrophy and related retinal dystrophies that cause severe loss in vision. ABCR consists of two tandemly arranged halves each containing a membrane spanning segment followed by a large extracellular/lumen domain, a multi-spanning membrane domain, and a nucleotide binding domain (NBD). To define the role of each NBD, we examined the nucleotide binding and ATPase activities of the N and C halves of ABCR individually and co-expressed in COS-1 cells and derived from trypsin-cleaved ABCR in disk membranes. When disk membranes or membranes from co-transfected cells were photoaffinity labeled with 8-azido-ATP and 8-azido-ADP, only the NBD2 in the C-half bound and trapped the nucleotide. Co-expressed half-molecules displayed basal and retinal-stimulated ATPase activity similar to full-length ABCR. The individually expressed N-half displayed weak 8-azido-ATP labeling and low basal ATPase activity that was not stimulated by retinal, whereas the C-half did not bind ATP and exhibited little if any ATPase activity. Purified ABCR contained one tightly bound ADP, presumably in NBD1. Our results indicate that only NBD2 of ABCR binds and hydrolyzes ATP in the presence or absence of retinal. NBD1, containing a bound ADP, associates with NBD2 to play a crucial, non-catalytic role in ABCR function.
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Affiliation(s)
- Jinhi Ahn
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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48
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Bandyopadhyay S, Ren H, Wang CS, Allison WS. The (alpha F(357)C)(3)(beta R(372)C)(3)gamma subcomplex of the F(1)-ATPase from the thermophilic Bacillus PS3 has altered ATPase activity after cross-linking alpha and beta subunits at noncatalytic site interfaces. Biochemistry 2002; 41:3226-34. [PMID: 11863461 DOI: 10.1021/bi0120291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In crystal structures of bovine MF(1), the side chains of alpha F(357) and beta R(372) are near the adenines of nucleotides bound to noncatalytic sites. To determine if during catalysis these side chains must pass through the different arrangements in which they are present in crystal structures, the catalytic properties of the (alpha F(357)C)(3)(beta R(372)C)(3)gamma subcomplex of the TF(1)-ATPase were characterized before and after cross-linking the introduced cysteines with CuCl(2). The unmodified mutant enzyme hydrolyzes MgATP at 50% the rate exhibited by wild type. Detailed comparison of the catalytic properties of the double mutant enzyme before and after cross-linking with those of the wild-type subcomplex revealed the following. Before cross-linking, the (alpha F(357)C)(3)(beta R(372)C)(3)gamma subcomplex has less tendency than wild type to release inhibitory MgADP entrapped in a catalytic site during turnover when MgATP binds to noncatalytic sites. Following cross-linking, ATPase activity is reduced 5-fold, and inhibitory MgADP entrapped in a catalytic site during turnover does not release under conditions wherein binding of ATP to noncatalytic sites of the wild-type enzyme promotes release of MgADP from the affected catalytic site. When assayed in the presence of lauryldimethylamine oxide, which prevents turnover-dependent entrapment of inhibitory MgADP in a catalytic site, ATPase activity of the cross-linked form is 47% that of the unmodified mutant enzyme. These results suggest that, during catalysis, the side chains of alpha F(357) and beta R(372) do not pass through the extremely different relative positions in which they exist at the three noncatalytic site interfaces in crystal structures.
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Affiliation(s)
- Sanjay Bandyopadhyay
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0601, USA
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49
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Senior AE, Nadanaciva S, Weber J. The molecular mechanism of ATP synthesis by F1F0-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1553:188-211. [PMID: 11997128 DOI: 10.1016/s0005-2728(02)00185-8] [Citation(s) in RCA: 292] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
ATP synthesis by oxidative phosphorylation and photophosphorylation, catalyzed by F1F0-ATP synthase, is the fundamental means of cell energy production. Earlier mutagenesis studies had gone some way to describing the mechanism. More recently, several X-ray structures at atomic resolution have pictured the catalytic sites, and real-time video recordings of subunit rotation have left no doubt of the nature of energy coupling between the transmembrane proton gradient and the catalytic sites in this extraordinary molecular motor. Nonetheless, the molecular events that are required to accomplish the chemical synthesis of ATP remain undefined. In this review we summarize current state of knowledge and present a hypothesis for the molecular mechanism of ATP synthesis.
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Affiliation(s)
- Alan E Senior
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Box 712, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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50
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Mitome N, Ono S, Suzuki T, Shimabukuro K, Muneyuki E, Yoshida M. The presence of phosphate at a catalytic site suppresses the formation of the MgADP-inhibited form of F(1)-ATPase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:53-60. [PMID: 11784298 DOI: 10.1046/j.0014-2956.2002.02623.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
F1-ATPase is inactivated by entrapment of MgADP in catalytic sites and reactivated by MgATP or P(i). Here, using a mutant alpha(3)beta(3)gamma complex of thermophilic F(1)-ATPase (alpha W463F/beta Y341W) and monitoring nucleotide binding by fluorescence quenching of an introduced tryptophan, we found that P(i) interfered with the binding of MgATP to F(1)-ATPase, but binding of MgADP was interfered with to a lesser extent. Hydrolysis of MgATP by F(1)-ATPase during the experiments did not obscure the interpretation because another mutant, which was able to bind nucleotide but not hydrolyse ATP (alpha W463F/beta E190Q/beta Y341W), also gave the same results. The half-maximal concentrations of P(i) that suppressed the MgADP-inhibited form and interfered with MgATP binding were both approximately 20 mm. It is likely that the presence of P(i) at a catalytic site shifts the equilibrium from the MgADP-inhibited form to the enzyme-MgADP-P(i) complex, an active intermediate in the catalytic cycle.
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Affiliation(s)
- Noriyo Mitome
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan
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