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Milgrom YM. Characteristics of protection by MgADP and MgATP of α3β3γ subcomplex of thermophilic Bacillus PS3 βY341W-mutant F1-ATPase from inhibition by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole support a bi-site mechanism of catalysis. BIOCHEMISTRY (MOSCOW) 2012; 76:1253-61. [PMID: 22117552 DOI: 10.1134/s0006297911110071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MgADP and MgATP binding to catalytic sites of βY341W-α(3)β(3)γ subcomplex of F(1)-ATPase from thermophilic Bacillus PS3 has been assessed using their effect on the enzyme inhibition by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole (NBD-Cl). It was assumed that NBD-Cl can inhibit only when catalytic sites are empty, and inhibition is prevented if a catalytic site is occupied with a nucleotide. In the absence of an activator, MgADP and MgATP protect βY341W-α(3)β(3)γ subcomplex from inhibition by NBD-Cl by binding to two catalytic sites with an affinity of 37 µM and 12 mM, and 46 µM and 15 mM, respectively. In the presence of an activator lauryldimethylamine-N-oxide (LDAO), MgADP protects βY341W-α(3)β(3)γ subcomplex from inhibition by NBD-Cl by binding to a catalytic site with a K(d) of 12 mM. Nucleotide binding to a catalytic site with affinity in the millimolar range has not been previously revealed in the fluorescence quenching experiments with βY341W-α(3)β(3)γ subcomplex. In the presence of activators LDAO or selenite, MgATP protects βY341W-α(3)β(3)γ subcomplex from inhibition by NBD-Cl only partially, and the enzyme remains sensitive to inhibition by NBD-Cl even at MgATP concentrations that are saturating for ATPase activity. The results support a bi-site mechanism of catalysis by F(1)-ATPases.
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Affiliation(s)
- Y M Milgrom
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York 13210, USA.
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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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Modulation of nucleotide binding to the catalytic sites of thermophilic F(1)-ATPase by the epsilon subunit: implication for the role of the epsilon subunit in ATP synthesis. Biochem Biophys Res Commun 2009; 390:230-4. [PMID: 19785990 DOI: 10.1016/j.bbrc.2009.09.092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 09/23/2009] [Indexed: 11/22/2022]
Abstract
Effect of epsilon subunit on the nucleotide binding to the catalytic sites of F(1)-ATPase from the thermophilic Bacillus PS3 (TF(1)) has been tested by using alpha(3)beta(3)gamma and alpha(3)beta(3)gammaepsilon complexes of TF(1) containing betaTyr341 to Trp substitution. The nucleotide binding was assessed with fluorescence quenching of the introduced Trp. The presence of the epsilon subunit weakened ADP binding to each catalytic site, especially to the highest affinity site. This effect was also observed when GDP or IDP was used. The ratio of the affinity of the lowest to the highest nucleotide binding sites had changed two orders of magnitude by the epsilon subunit. The differences may relate to the energy required for the binding change in the ATP synthesis reaction and contribute to the efficient ATP synthesis.
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Kagawa Y, Hamamoto T, Endo H. The alpha/beta interfaces of alpha(1)beta(1), alpha(3)beta(3), and F1: domain motions and elastic energy stored during gamma rotation. J Bioenerg Biomembr 2009; 32:471-84. [PMID: 15254382 DOI: 10.1023/a:1005612923995] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
ATP synthase (F(o)F(1)) consists of F(1) (ATP-driven motor) and F(o) (H(+)-driven motor). F(1) is a complex of alpha(3)beta(3)gammadeltaepsilon subunits, and gamma is the rotating cam in alpha(3)beta(3). Thermophilic F(1) (TF(1)) is exceptional in that it can be crystallized as a beta monomer and an alpha(3)beta(3) oligomer, and it is sufficiently stable to allow alphabeta refolding and reassembly of hybrid complexes containing 1, 2, and 3 modified alpha or beta. The nucleotide-dependent open-close conversion of conformation is an inherent property of an isolated beta and energy and signals are transferred through alpha/beta interfaces. The catalytic and noncatalytic interfaces of both mitochondrial F(1) (MF(1)) and TF(1) were analyzed by an atom search within the limits of 0.40 nm across the alphabeta interfaces. Seven (plus thermophilic loop in TF(1)) contact areas are located at both the catalytic and noncatalytic interfaces on the open beta form. The number of contact areas on closed beta increased to 11 and 9, respectively, in the catalytic and noncatalytic interfaces. The interfaces in the barrel domain are immobile. The torsional elastic strain applied through the mobile areas is concentrated in hinge residues and the P-loop in beta. The notion of elastic energy in F(o)F(1) has been revised. X-ray crystallography of F(1) is a static snap shot of one state and the elastic hypotheses are still inconsistent with the structure, dyamics, and kinetics of F(o)F(1). The domain motion and elastic energy in F(o)F(1) will be elucidated by time-resolved crystallography.
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Affiliation(s)
- Y Kagawa
- Department of Biochemistry, Jichi Medical School, Minamikawachi, Tochigi, 329-0498, Graduate School, Women's University of Nutrition, Sakado, Saitama 350-0288, Japan.
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Allison WS, Ren H, Dou C. Inhibitory Mg-ADP-fluoroaluminate complexes bound to catalytic sites of F(1)-ATPases: are they ground-state or transition-state analogs? J Bioenerg Biomembr 2009; 32:531-8. [PMID: 15254389 DOI: 10.1023/a:1005677310791] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Schemes are proposed for coupling sequential opening and closing the three catalytic sites of F(1) to rotation of the gamma subunit during ATP synthesis and hydrolysis catalyzed by the F(o)F(1)-ATP synthase. A prominent feature of the proposed mechanisms is that the transition state during ATP synthesis is formed when a catalytic site is in the process of closing and that the transition state during ATP hydrolysis is formed when a catalytic site is in the process of opening. The unusual kinetics of formation of Mg-ADP-fluoroaluminate complexes in one or two catalytic sites of nucleotide-depleted MF(1) and wild-type and mutant alpha(3)beta(3)gamma subcomplexes of TF(1) are also reviewed. From these considerations, it is concluded that Mg-ADP-fluoroaluminate complexes formed at catalytic sites of isolated F(1)-ATPases or F(1) in membrane-bound F(o)F(1) are ground-state analogs.
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Affiliation(s)
- W S Allison
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0506, USA
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Characterization of a novel bacterial arginine kinase from Desulfotalea psychrophila. Comp Biochem Physiol B Biochem Mol Biol 2008; 150:312-9. [PMID: 18499493 DOI: 10.1016/j.cbpb.2008.03.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 03/30/2008] [Accepted: 03/31/2008] [Indexed: 11/22/2022]
Abstract
Phosphagen kinases are found throughout the animal kingdom and catalyze the transfer of a high-energy gamma phosphoryl-group from ATP to a guanidino group on a suitable acceptor molecule such as creatine or arginine. Recent genome sequencing efforts in several proteobacteria, including Desulfotalea psychrophila LSv54, Myxococcus xanthus, Sulfurovum sp. NBC37-1, and Moritella sp. PE36 have revealed what appears to be a phosphagen kinase homolog present in their genomes. Based on sequence comparisons these putative homologs bear a strong resemblance to arginine kinases found in many invertebrates and some protozoa. We describe here a biochemical characterization of one of these homologs from D. psychrophila expressed in E. coli that confirms its ability to reversibly catalyze phosphoryl transfer from ATP to arginine. A phylogenetic analysis suggests that these bacteria homologs are not widely distributed in proteobacteria species. They appear more related to protozoan arginine kinases than to similar proteins seen in some Gram-positive bacteria that share key catalytic residues but encode protein tyrosine kinases. This raises the possibility of horizontal gene transfer as a likely origin of the bacterial arginine kinases.
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Bulygin VV, Milgrom YM. Studies of nucleotide binding to the catalytic sites of Escherichia coli betaY331W-F1-ATPase using fluorescence quenching. Proc Natl Acad Sci U S A 2007; 104:4327-31. [PMID: 17360523 PMCID: PMC1838601 DOI: 10.1073/pnas.0700078104] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Indexed: 11/18/2022] Open
Abstract
Most studies of nucleotide binding to catalytic sites of Escherichia coli betaY331W-F(1)-ATPase by the quenching of the betaY331W fluorescence have been conducted in the presence of approximately 20 mM sulfate. We find that, in the absence of sulfate, the nucleotide concentration dependence of fluorescence quenching induced by ADP, ATP, and MgADP is biphasic, revealing two classes of binding sites, each contributing about equally to the overall extent of quenching. For the high-affinity catalytic site, the K(d) values for MgADP, ADP, and ATP equal 10, 43, and 185 nM, respectively. For the second class of sites, the K(d) values for these ligands are approximately 1,000x larger at 8.1, 37, and 200 microM, respectively. The presence of sulfate or phosphate during assay results in a marked increase in the apparent K(d) values for the high-affinity catalytic site. The results show, contrary to earlier reports, that Mg(2+) is not required for expression of different affinities for a nucleotide by the three catalytic sites. In addition, they demonstrate that the fluorescence of the introduced tryptophans is nearly completely quenched when only two sites bind nucleotide. Binding of ADP to the third site with a K(d) near mM gives little fluorescence change. Many previous results of fluorescence quenching of introduced tryptophans appear to require reinterpretation. Our findings support a bi-site catalytic mechanism for F(1)-ATPase.
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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
| | - Yakov M. Milgrom
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, NY 13210
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Nishizaka T, Mizutani K, Masaike T. Single-molecule observation of rotation of F1-ATPase through microbeads. Methods Mol Biol 2007; 392:171-81. [PMID: 17951718 DOI: 10.1007/978-1-59745-490-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
F(o)F(1)-ATP synthase catalyzes the synthesis of ATP using proton-motive force across a membrane. When isolated, the F1 sector, composed of five polypeptide chains with a stoichiometry of alpha(3)beta(3)gammadeltaepsilon, solely hydrolyzes ATP into ADP and phosphate, and is thus called F(1)-ATPase. Rotation of a shaft domain in F(o)F(1)-ATP synthase has been hypothesized by Paul Boyer, and ultimately was confirmed by direct observation as rotation of the gamma-subunit in an isolated alpha(3)beta(3)gamma subcomplex. Unitary turnover of ATP induces 120 degrees steps, consistent with the configuration of three catalytic sites arranged 120 degrees apart around gamma. We have shown the relationships between chemical and mechanical events by imaging individual F(1) molecules under an optical microscope. A new scheme emerges: as soon as a catalytic site binds ATP, the gamma-subunit always turns the same face (interaction surface) to the beta hosting that site; approximately 80 degrees rotation is driven by ATP binding; approximately 40 degrees rotation is induced by completion of hydrolysis [and/or phosphate release] in the site that bound ATP one step earlier.
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Sakaki N, Shimo-Kon R, Adachi K, Itoh H, Furuike S, Muneyuki E, Yoshida M, Kinosita K. One rotary mechanism for F1-ATPase over ATP concentrations from millimolar down to nanomolar. Biophys J 2004; 88:2047-56. [PMID: 15626703 PMCID: PMC1305257 DOI: 10.1529/biophysj.104.054668] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
F(1)-ATPase is a rotary molecular motor in which the central gamma-subunit rotates inside a cylinder made of alpha(3)beta(3)-subunits. The rotation is driven by ATP hydrolysis in three catalytic sites on the beta-subunits. How many of the three catalytic sites are filled with a nucleotide during the course of rotation is an important yet unsettled question. Here we inquire whether F(1) rotates at extremely low ATP concentrations where the site occupancy is expected to be low. We observed under an optical microscope rotation of individual F(1) molecules that carried a bead duplex on the gamma-subunit. Time-averaged rotation rate was proportional to the ATP concentration down to 200 pM, giving an apparent rate constant for ATP binding of 2 x 10(7) M(-1)s(-1). A similar rate constant characterized bulk ATP hydrolysis in solution, which obeyed a simple Michaelis-Menten scheme between 6 mM and 60 nM ATP. F(1) produced the same torque of approximately 40 pN.nm at 2 mM, 60 nM, and 2 nM ATP. These results point to one rotary mechanism governing the entire range of nanomolar to millimolar ATP, although a switchover between two mechanisms cannot be dismissed. Below 1 nM ATP, we observed less regular rotations, indicative of the appearance of another reaction scheme.
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Affiliation(s)
- Naoyoshi Sakaki
- Department of Functional Molecular Science, The Graduate University for Advanced Studies, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan
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Abstract
F1-ATPase is a rotary motor made of a single protein molecule. Its rotation is driven by free energy obtained by ATP hydrolysis. In vivo, another motor, Fo, presumably rotates the F1 motor in the reverse direction, reversing also the chemical reaction in F1 to let it synthesize ATP. Here we attempt to answer two related questions, How is free energy obtained by ATP hydrolysis converted to the mechanical work of rotation, and how is mechanical work done on F1 converted to free energy to produce ATP? After summarizing single-molecule observations of F1 rotation, we introduce a toy model and discuss its free-energy diagrams to possibly answer the above questions. We also discuss the efficiency of molecular motors in general.
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Affiliation(s)
- Kazuhiko Kinosita
- Center for Integrative Bioscience, Okazaki National Research Institutes, Higashiyama 5-1, Myodaiji, Okazaki 444-8585, Japan.
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Nishizaka T, Oiwa K, Noji H, Kimura S, Muneyuki E, Yoshida M, Kinosita K. Chemomechanical coupling in F1-ATPase revealed by simultaneous observation of nucleotide kinetics and rotation. Nat Struct Mol Biol 2004; 11:142-8. [PMID: 14730353 DOI: 10.1038/nsmb721] [Citation(s) in RCA: 213] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2003] [Accepted: 11/13/2003] [Indexed: 11/09/2022]
Abstract
F(1)-ATPase is a rotary molecular motor in which unidirectional rotation of the central gamma subunit is powered by ATP hydrolysis in three catalytic sites arranged 120 degrees apart around gamma. To study how hydrolysis reactions produce mechanical rotation, we observed rotation under an optical microscope to see which of the three sites bound and released a fluorescent ATP analog. Assuming that the analog mimics authentic ATP, the following scheme emerges: (i) in the ATP-waiting state, one site, dictated by the orientation of gamma, is empty, whereas the other two bind a nucleotide; (ii) ATP binding to the empty site drives an approximately 80 degrees rotation of gamma; (iii) this triggers a reaction(s), hydrolysis and/or phosphate release, but not ADP release in the site that bound ATP one step earlier; (iv) completion of this reaction induces further approximately 40 degrees rotation.
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Affiliation(s)
- Takayuki Nishizaka
- Kansai Advanced Research Center, Protein Biophysics Group, Iwaoka 588-2, Nishi-ku, Kobe 651-2492, Japan.
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Ono S, Hara KY, Hirao J, Matsui T, Noji H, Yoshida M, Muneyuki E. Origin of apparent negative cooperativity of F(1)-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1607:35-44. [PMID: 14556911 DOI: 10.1016/j.bbabio.2003.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In order to get insight into the origin of apparent negative cooperativity observed for F(1)-ATPase, we compared ATPase activity and ATPMg binding of mutant subcomplexes of thermophilic F(1)-ATPase, alpha((W463F)3)beta((Y341W)3)gamma and alpha((K175A/T176A/W463F)3)beta((Y341W)3)gamma. For alpha((W463F)3)beta((Y341W)3)gamma, apparent K(m)'s of ATPase kinetics (4.0 and 233 microM) did not agree with apparent K(m)'s deduced from fluorescence quenching of the introduced tryptophan residue (on the order of nM, 0.016 and 13 microM). On the other hand, in case of alpha((K175A/T176A/W463F)3)beta((Y341W)3)gamma, which lacks noncatalytic nucleotide binding sites, the apparent K(m) of ATPase activity (10 microM) roughly agreed with the highest K(m) of fluorescence measurements (27 microM). The results indicate that in case of alpha((W463F)3)beta((Y341W)3)gamma, the activating effect of ATP binding to noncatalytic sites dominates overall ATPase kinetics and the highest apparent K(m) of ATPase activity does not represent the ATP binding to a catalytic site. In case of alpha((K175A/T176A/W463F)3)beta((Y341W)3)gamma, the K(m) of ATPase activity reflects the ATP binding to a catalytic site due to the lack of noncatalytic sites. The Eadie-Hofstee plot of ATPase reaction by alpha((K175A/T176A/W463F)3)beta((Y341W)3)gamma was rather linear compared with that of alpha((W463F)3)beta((Y341W)3)gamma, if not perfectly straight, indicating that the apparent negative cooperativity observed for wild-type F(1)-ATPase is due to the ATP binding to catalytic sites and noncatalytic sites. Thus, the frequently observed K(m)'s of 100-300 microM and 1-30 microM range for wild-type F(1)-ATPase correspond to ATP binding to a noncatalytic site and catalytic site, respectively.
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Affiliation(s)
- Sakurako Ono
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, 226-8503 Yokohama, Japan
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Shimabukuro K, Yasuda R, Muneyuki E, Hara KY, Kinosita K, Yoshida M. Catalysis and rotation of F1 motor: cleavage of ATP at the catalytic site occurs in 1 ms before 40 degree substep rotation. Proc Natl Acad Sci U S A 2003; 100:14731-6. [PMID: 14657340 PMCID: PMC299784 DOI: 10.1073/pnas.2434983100] [Citation(s) in RCA: 212] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
F1, a water-soluble portion of FoF1-ATP synthase, is an ATP hydrolysis-driven rotary motor. The central gamma-subunit rotates in the alpha 3 beta 3 cylinder by repeating the following four stages of rotation: ATP-binding dwell, rapid 80 degrees substep rotation, interim dwell, and rapid 40 degrees substep rotation. At least two 1-ms catalytic events occur in the interim dwell, but it is still unclear which steps in the ATPase cycle, except for ATP binding, correspond to these events. To discover which steps, we analyzed rotations of F1 subcomplex (alpha 3 beta 3 gamma) from thermophilic Bacillus PS3 under conditions where cleavage of ATP at the catalytic site is decelerated: hydrolysis of ATP by the catalytic-site mutant F1 and hydrolysis of a slowly hydrolyzable substrate ATP gamma S (adenosine 5'-[gamma-thio]triphosphate) by wild-type F1. In both cases, interim dwells were extended as expected from bulk phase kinetics, confirming that cleavage of ATP takes place during the interim dwell. Furthermore, the results of ATP gamma S hydrolysis by the mutant F1 ensure that cleavage of ATP most likely corresponds to one of the two 1-ms events and not some other faster undetected event. Thus, cleavage of ATP on F1 occurs in 1 ms during the interim dwell, and we call this interim dwell catalytic dwell.
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Affiliation(s)
- Katsuya Shimabukuro
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
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Abstract
Topical questions in ATP synthase research are: (1) how do protons cause subunit rotation and how does rotation generate ATP synthesis from ADP+Pi? (2) How does hydrolysis of ATP generate subunit rotation and how does rotation bring about uphill transport of protons? The finding that ATP synthase is not just an enzyme but rather a unique nanomotor is attracting a diverse group of researchers keen to find answers. Here we review the most recent work on rapidly developing areas within the field and present proposals for enzymatic and mechanoenzymatic mechanisms.
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Affiliation(s)
- Joachim Weber
- Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, Rochester, NY 14642, USA
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Ariga T, Masaike T, Noji H, Yoshida M. Stepping rotation of F(1)-ATPase with one, two, or three altered catalytic sites that bind ATP only slowly. J Biol Chem 2002; 277:24870-4. [PMID: 11964408 DOI: 10.1074/jbc.m202582200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
F(1)-ATPase is an ATP hydrolysis-driven motor in which the gamma subunit rotates in the stator cylinder alpha(3)beta(3). To know the coordination of three catalytic beta subunits during catalysis, hybrid F(1)-ATPases, each containing one, two, or three "slow" mutant beta subunits that bind ATP very slowly, were prepared, and the rotations were observed with a single molecule level. Each hybrid made one, two, or three steps per 360 degrees revolution, respectively, at 5 microm ATP where the wild-type enzyme rotated continuously without step under the same observing conditions. The observed dwell times of the steps are explained by the slow binding rate of ATP. Except for the steps, properties of rotation, such as the torque forces exerted during rotary movement, were not significantly changed from those of the wild-type enzyme. Thus, it appears that the presence of the slow beta subunit(s) does not seriously affect other normal beta subunit(s) in the same F(1)-ATPase molecule and that the order of sequential catalytic events is faithfully maintained even when ATP binding to one or two of the catalytic sites is retarded.
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Affiliation(s)
- Takayuki Ariga
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8503, Japan
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Dong K, Ren H, Allison WS. The fluorescence spectrum of the introduced tryptophans in the alpha 3(beta F155W)3gamma subcomplex of the F1-ATPase from the thermophilic Bacillus PS3 cannot be used to distinguish between the number of nucleoside di- and triphosphates bound to catalytic sites. J Biol Chem 2002; 277:9540-7. [PMID: 11779852 DOI: 10.1074/jbc.m106911200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It has been reported that shifts in the fluorescence emission spectrum of the introduced tryptophans in the betaF155W mutant of Escherichia coli F(1) (bovine heart mitochondria F(1) residue number) can quantitatively distinguish between the number of catalytic sites occupied with ADP and ATP during steady-state ATP hydrolysis (Weber, J., Bowman, C., and Senior, A. E. (1996) J. Biol. Chem. 271, 18711--18718). In contrast, addition of MgADP, Mg-5'-adenylyl beta,gamma-imidophosphate (MgAMP-PNP), and MgATP in 1:1 ratios to the alpha(3)(betaF155W)(3)gamma subcomplex of thermophilic Bacillus PS3 F(1) (TF(1)) induced nearly identical blue shifts in the fluorescence emission maximum that was accompanied by quenching. Addition of 2 mm MgADP induced a slightly greater blue shift and a slight increase in intensity over those observed with 1:1 MgADP. However, addition of 2 mm MgAMP-PNP or MgATP induced a much greater blue shift and substantially enhanced fluorescence intensity over those observed in the presence of stoichiometric MgADP or MgAMP-PNP. It is clear from these results that the fluorescence spectrum of the introduced tryptophans in the betaF155W mutant of TF(1) does not respond in regular increments at any wavelength as catalytic sites are filled with nucleotides. The fluorescence spectrum observed after entrapping MgADP-fluoroaluminate complexes in two catalytic sites of the betaF155W subcomplex indicates that the fluorescence emission spectrum of the enzyme is maximally perturbed when nucleotides are bound to two catalytic sites. This finding is consistent with accumulating evidence suggesting that only two beta subunits in the alpha(3)beta(3)gamma subcomplex of TF(1) can simultaneously exist in the completely closed conformation.
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Affiliation(s)
- Ken Dong
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0601, USA
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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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Abstract
An early proposal was that for rapid ATP synthesis by the rotational ATP synthase, a specific second site must bind ADP and P(i), and for rapid ATP hydrolysis a different second site must bind ATP. Such bi-site activation was considered to occur whether or not an ADP or ATP was at a third site. In contrast, a more recent proposal is that rapid ATP hydrolysis requires that all three sites have bound ADP or ATP present. However, discovery that one second site binds ADP better than ATP, together with other data and considerations support the earlier proposal. The retention or rebinding of ADP can explain why three sites fill during hydrolysis as ATP concentration is increased although bi-site activation still prevails.
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Affiliation(s)
- Paul D Boyer
- Molecular Biology Institute, Boyer Hall, University of California, Los Angeles, CA 90095-1570, USA.
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19
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Abstract
The mechanism of action of F(1)F(0)-ATP synthase is controversial. Some favor a tri-site mechanism, where substrate must fill all three catalytic sites for activity, others a bi-site mechanism, where one of the three sites is always unoccupied. New approaches were applied to examine this question. First, ITP was used as hydrolysis substrate; lower binding affinities of ITP versus ATP enable more accurate assessment of sites occupancy. Second, distributions of all eight possible enzyme species (with zero, one, two or three sites filled) as fraction of total enzyme population at each ITP concentration were calculated, and compared with measured ITPase activity. Confirming data were obtained with ATP as substrate. Third, we performed a theoretical analysis of possible bi-site mechanisms. The results argue convincingly that bi-site hydrolysis activity is negligible, and may not even exist. Effectively, tri-site hydrolysis is the only mechanism. We argue that only tri-site hydrolysis drives subunit rotation. Theoretical analyses of possible bi-site mechanisms reveal serious flaws, not previously recognized. One is that, in bi-site catalysis, the predicted direction of subunit rotation is the same for both ATP synthesis and hydrolysis; a second is that infrequently occurring enzyme species are required.
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Affiliation(s)
- J Weber
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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