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Marshansky V. Discovery and Study of Transmembrane Rotary Ion-Translocating Nano-Motors: F-ATPase/Synthase of Mitochondria/Bacteria and V-ATPase of Eukaryotic Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:702-719. [PMID: 36171652 DOI: 10.1134/s000629792208003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
This review discusses the history of discovery and study of the operation of the two rotary ion-translocating ATPase nano-motors: (i) F-ATPase/synthase (holocomplex F1FO) of mitochondria/bacteria and (ii) eukaryotic V-ATPase (holocomplex V1VO). Vacuolar adenosine triphosphatase (V-ATPase) is a transmembrane multisubunit complex found in all eukaryotes from yeast to humans. It is structurally and functionally similar to the F-ATPase/synthase of mitochondria/bacteria and the A-ATPase/synthase of archaebacteria, which indicates a common evolutionary origin of the rotary ion-translocating nano-motors built into cell membranes and invented by Nature billions of years ago. Previously we have published several reviews on this topic with appropriate citations of our original research. This review is focused on the historical analysis of the discovery and study of transmembrane rotary ion-translocating ATPase nano-motors functioning in bacteria, eukaryotic cells and mitochondria of animals.
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Sharma S, Oot RA, Wilkens S. MgATP hydrolysis destabilizes the interaction between subunit H and yeast V 1-ATPase, highlighting H's role in V-ATPase regulation by reversible disassembly. J Biol Chem 2018; 293:10718-10730. [PMID: 29754144 DOI: 10.1074/jbc.ra118.002951] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/22/2018] [Indexed: 01/01/2023] Open
Abstract
Vacuolar H+-ATPases (V-ATPases; V1Vo-ATPases) are rotary-motor proton pumps that acidify intracellular compartments and, in some tissues, the extracellular space. V-ATPase is regulated by reversible disassembly into autoinhibited V1-ATPase and Vo proton channel sectors. An important player in V-ATPase regulation is subunit H, which binds at the interface of V1 and Vo H is required for MgATPase activity in holo-V-ATPase but also for stabilizing the MgADP-inhibited state in membrane-detached V1 However, how H fulfills these two functions is poorly understood. To characterize the H-V1 interaction and its role in reversible disassembly, we determined binding affinities of full-length H and its N-terminal domain (HNT) for an isolated heterodimer of subunits E and G (EG), the N-terminal domain of subunit a (aNT), and V1 lacking subunit H (V1ΔH). Using isothermal titration calorimetry (ITC) and biolayer interferometry (BLI), we show that HNT binds EG with moderate affinity, that full-length H binds aNT weakly, and that both H and HNT bind V1ΔH with high affinity. We also found that only one molecule of HNT binds V1ΔH with high affinity, suggesting conformational asymmetry of the three EG heterodimers in V1ΔH. Moreover, MgATP hydrolysis-driven conformational changes in V1 destabilized the interaction of H or HNT with V1ΔH, suggesting an interplay between MgADP inhibition and subunit H. Our observation that H binding is affected by MgATP hydrolysis in V1 points to H's role in the mechanism of reversible disassembly.
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Affiliation(s)
- Stuti Sharma
- From the Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210
| | - Rebecca A Oot
- From the Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210
| | - Stephan Wilkens
- From the Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210
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Oot RA, Couoh-Cardel S, Sharma S, Stam NJ, Wilkens S. Breaking up and making up: The secret life of the vacuolar H + -ATPase. Protein Sci 2017; 26:896-909. [PMID: 28247968 DOI: 10.1002/pro.3147] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 02/21/2017] [Indexed: 01/24/2023]
Abstract
The vacuolar ATPase (V-ATPase; V1 Vo -ATPase) is a large multisubunit proton pump found in the endomembrane system of all eukaryotic cells where it acidifies the lumen of subcellular organelles including lysosomes, endosomes, the Golgi apparatus, and clathrin-coated vesicles. V-ATPase function is essential for pH and ion homeostasis, protein trafficking, endocytosis, mechanistic target of rapamycin (mTOR), and Notch signaling, as well as hormone secretion and neurotransmitter release. V-ATPase can also be found in the plasma membrane of polarized animal cells where its proton pumping function is involved in bone remodeling, urine acidification, and sperm maturation. Aberrant (hypo or hyper) activity has been associated with numerous human diseases and the V-ATPase has therefore been recognized as a potential drug target. Recent progress with moderate to high-resolution structure determination by cryo electron microscopy and X-ray crystallography together with sophisticated single-molecule and biochemical experiments have provided a detailed picture of the structure and unique mode of regulation of the V-ATPase. This review summarizes the recent advances, focusing on the structural and biophysical aspects of the field.
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Affiliation(s)
- Rebecca A Oot
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
| | - Sergio Couoh-Cardel
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
| | - Stuti Sharma
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
| | - Nicholas J Stam
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
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Stam NJ, Wilkens S. Structure of the Lipid Nanodisc-reconstituted Vacuolar ATPase Proton Channel: DEFINITION OF THE INTERACTION OF ROTOR AND STATOR AND IMPLICATIONS FOR ENZYME REGULATION BY REVERSIBLE DISSOCIATION. J Biol Chem 2016; 292:1749-1761. [PMID: 27965356 DOI: 10.1074/jbc.m116.766790] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/11/2016] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic vacuolar H+-ATPase (V-ATPase) is a multisubunit enzyme complex that acidifies subcellular organelles and the extracellular space. V-ATPase consists of soluble V1-ATPase and membrane-integral Vo proton channel sectors. To investigate the mechanism of V-ATPase regulation by reversible disassembly, we recently determined a cryo-EM reconstruction of yeast Vo The structure indicated that, when V1 is released from Vo, the N-terminal cytoplasmic domain of subunit a (aNT) changes conformation to bind rotor subunit d However, insufficient resolution precluded a precise definition of the aNT-d interface. Here we reconstituted Vo into lipid nanodiscs for single-particle EM. 3D reconstructions calculated at ∼15-Å resolution revealed two sites of contact between aNT and d that are mediated by highly conserved charged residues. Alanine mutagenesis of some of these residues disrupted the aNT-d interaction, as shown by isothermal titration calorimetry and gel filtration of recombinant subunits. A recent cryo-EM study of holo V-ATPase revealed three major conformations corresponding to three rotational states of the central rotor of the enzyme. Comparison of the three V-ATPase conformations with the structure of nanodisc-bound Vo revealed that Vo is halted in rotational state 3. Combined with our prior work that showed autoinhibited V1-ATPase to be arrested in state 2, we propose a model in which the conformational mismatch between free V1 and Vo functions to prevent unintended reassembly of holo V-ATPase when activity is not needed.
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Affiliation(s)
- Nicholas J Stam
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Stephan Wilkens
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210.
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5
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D'Alessandro M, Turina P, Melandri BA, Dunn SD. Modulation of coupling in the Escherichia coli ATP synthase by ADP and P i: Role of the ε subunit C-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:34-44. [PMID: 27751906 DOI: 10.1016/j.bbabio.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 08/06/2016] [Accepted: 10/13/2016] [Indexed: 01/28/2023]
Abstract
The ε-subunit of ATP-synthase is an endogenous inhibitor of the hydrolysis activity of the complex and its α-helical C-terminal domain (εCTD) undergoes drastic changes among at least two different conformations. Even though this domain is not essential for ATP synthesis activity, there is evidence for its involvement in the coupling mechanism of the pump. Recently, it was proposed that coupling of the ATP synthase can vary as a function of ADP and Pi concentration. In the present work, we have explored the possible role of the εCTD in this ADP- and Pi-dependent coupling, by examining an εCTD-lacking mutant of Escherichia coli. We show that the loss of Pi-dependent coupling can be observed also in the εCTD-less mutant, but the effects of Pi on both proton pumping and ATP hydrolysis were much weaker in the mutant than in the wild-type. We also show that the εCTD strongly influences the binding of ADP to a very tight binding site (half-maximal effect≈1nM); binding at this site induces higher coupling in EFOF1 and increases responses to Pi. It is proposed that one physiological role of the εCTD is to regulate the kinetics and affinity of ADP/Pi binding, promoting ADP/Pi-dependent coupling.
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Affiliation(s)
- M D'Alessandro
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - P Turina
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.
| | - B A Melandri
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - S D Dunn
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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Couoh-Cardel S, Hsueh YC, Wilkens S, Movileanu L. Yeast V-ATPase Proteolipid Ring Acts as a Large-conductance Transmembrane Protein Pore. Sci Rep 2016; 6:24774. [PMID: 27098228 PMCID: PMC4838861 DOI: 10.1038/srep24774] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/04/2016] [Indexed: 12/12/2022] Open
Abstract
The vacuolar H+ -ATPase (V-ATPase) is a rotary motor enzyme that acidifies intracellular organelles and the extracellular milieu in some tissues. Besides its canonical proton-pumping function, V-ATPase’s membrane sector, Vo, has been implicated in non-canonical functions including membrane fusion and neurotransmitter release. Here, we report purification and biophysical characterization of yeast V-ATPase c subunit ring (c-ring) using electron microscopy and single-molecule electrophysiology. We find that yeast c-ring forms dimers mediated by the c subunits’ cytoplasmic loops. Electrophysiology measurements of the c-ring reconstituted into a planar lipid bilayer revealed a large unitary conductance of ~8.3 nS. Thus, the data support a role of V-ATPase c-ring in membrane fusion and neuronal communication.
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Affiliation(s)
- Sergio Couoh-Cardel
- Department of Biochemistry &Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
| | - Yi-Ching Hsueh
- Department of Physics, Syracuse University, 201 Physics Bldg., Syracuse, New York 13244-1130, USA
| | - Stephan Wilkens
- Department of Biochemistry &Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Bldg., Syracuse, New York 13244-1130, USA.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA.,The Syracuse Biomaterials Institute, Syracuse University, 318 Bowne Hall, Syracuse, New York 13244-1200, USA
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Couoh-Cardel S, Milgrom E, Wilkens S. Affinity Purification and Structural Features of the Yeast Vacuolar ATPase Vo Membrane Sector. J Biol Chem 2015; 290:27959-71. [PMID: 26416888 DOI: 10.1074/jbc.m115.662494] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/27/2022] Open
Abstract
The membrane sector (Vo) of the proton pumping vacuolar ATPase (V-ATPase, V1Vo-ATPase) from Saccharomyces cerevisiae was purified to homogeneity, and its structure was characterized by EM of single molecules and two-dimensional crystals. Projection images of negatively stained Vo two-dimensional crystals showed a ring-like structure with a large asymmetric mass at the periphery of the ring. A cryo-EM reconstruction of Vo from single-particle images showed subunits a and d in close contact on the cytoplasmic side of the proton channel. A comparison of three-dimensional reconstructions of free Vo and Vo as part of holo V1Vo revealed that the cytoplasmic N-terminal domain of subunit a (aNT) must undergo a large conformational change upon enzyme disassembly or (re)assembly from Vo, V1, and subunit C. Isothermal titration calorimetry using recombinant subunit d and aNT revealed that the two proteins bind each other with a Kd of ~5 μm. Treatment of the purified Vo sector with 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] resulted in selective release of subunit d, allowing purification of a VoΔd complex. Passive proton translocation assays revealed that both Vo and VoΔd are impermeable to protons. We speculate that the structural change in subunit a upon release of V1 from Vo during reversible enzyme dissociation plays a role in blocking passive proton translocation across free Vo and that the interaction between aNT and d seen in free Vo functions to stabilize the Vo sector for efficient reassembly of V1Vo.
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Affiliation(s)
- Sergio Couoh-Cardel
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Elena Milgrom
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Stephan Wilkens
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
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Bisetto E, Comelli M, Salzano AM, Picotti P, Scaloni A, Lippe G, Mavelli I. Proteomic analysis of F1F0-ATP synthase super-assembly in mitochondria of cardiomyoblasts undergoing differentiation to the cardiac lineage. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:807-16. [PMID: 23587863 DOI: 10.1016/j.bbabio.2013.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/28/2013] [Accepted: 04/05/2013] [Indexed: 02/06/2023]
Abstract
Mitochondria are essential organelles with multiple functions, especially in energy metabolism. An increasing number of data highlighted their role for cellular differentiation processes. We investigated differences in ATP synthase supra-molecular organization occurring in H9c2 cardiomyoblasts in the course of cardiac-like differentiation, along with ATP synthase biogenesis and maturation of mitochondrial cristae morphology. Using BN-PAGE analysis combined with one-step mild detergent extraction from mitochondria, a significant increase in dimer/monomer ratio was observed, indicating a distinct rise in the stability of the enzyme super-assembly. Remarkably, sub-stoichiometric mean values for ATP synthase subunit e were determined in both parental and cardiac-like H9c2 by an MS-based quantitative proteomics approach. This indicates a similar high proportion of complex molecules lacking subunit e in both cell types, and suggests a minor contribution of this component in the observed changes. 2D BN-PAGE/immunoblotting analysis and MS/MS analysis on single BN-PAGE band showed that the amount of inhibitor protein IF1 bound within the ATP synthase complexes increased in cardiac-like H9c2 and appeared greater in the dimer. In concomitance, a consistent improvement of enzyme activity, measured as both ATP synthesis and ATP hydrolysis rate, was observed, despite the increase of bound IF1 evocative of a greater inhibitory effect on the enzyme ATPase activity. The results suggest i) a role for IF1 in promoting dimer stabilization and super-assembly in H9c2 with physiological IF1 expression levels, likely unveiled by the fact that the contacts through accessory subunit e appear to be partially destabilized, ii) a link between dimer stabilization and enzyme activation.
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Affiliation(s)
- Elena Bisetto
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
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Parsons LS, Wilkens S. Probing subunit-subunit interactions in the yeast vacuolar ATPase by peptide arrays. PLoS One 2012; 7:e46960. [PMID: 23071676 PMCID: PMC3470569 DOI: 10.1371/journal.pone.0046960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 09/07/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Vacuolar (H(+))-ATPase (V-ATPase; V(1)V(o)-ATPase) is a large multisubunit enzyme complex found in the endomembrane system of all eukaryotic cells where its proton pumping action serves to acidify subcellular organelles. In the plasma membrane of certain specialized tissues, V-ATPase functions to pump protons from the cytoplasm into the extracellular space. The activity of the V-ATPase is regulated by a reversible dissociation mechanism that involves breaking and re-forming of protein-protein interactions in the V(1)-ATPase - V(o)-proton channel interface. The mechanism responsible for regulated V-ATPase dissociation is poorly understood, largely due to a lack of detailed knowledge of the molecular interactions that are responsible for the structural and functional link between the soluble ATPase and membrane bound proton channel domains. METHODOLOGY/PRINCIPAL FINDINGS To gain insight into where some of the stator subunits of the V-ATPase associate with each other, we have developed peptide arrays from the primary sequences of V-ATPase subunits. By probing the peptide arrays with individually expressed V-ATPase subunits, we have identified several key interactions involving stator subunits E, G, C, H and the N-terminal domain of the membrane bound a subunit. CONCLUSIONS The subunit-peptide interactions identified from the peptide arrays complement low resolution structural models of the eukaryotic vacuolar ATPase obtained from transmission electron microscopy. The subunit-subunit interaction data are discussed in context of our current model of reversible enzyme dissociation.
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Affiliation(s)
- Lee S. Parsons
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, United States of America
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Toro EJ, Ostrov DA, Wronski TJ, Holliday LS. Rational identification of enoxacin as a novel V-ATPase-directed osteoclast inhibitor. Curr Protein Pept Sci 2012; 13:180-91. [PMID: 22044158 PMCID: PMC3409362 DOI: 10.2174/138920312800493151] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 11/22/2022]
Abstract
Binding between vacuolar H+-ATPases (V-ATPases) and microfilaments is mediated by an actin binding domain in the B-subunit. Both isoforms of mammalian B-subunit bind microfilaments with high affinity. A similar actin-binding activity has been demonstrated in the B-subunit of yeast. A conserved “profilin-like” domain in the B-subunit mediates this actin-binding activity, named due to its sequence and structural similarity to an actin-binding surface of the canonical actin binding protein profilin. Subtle mutations in the “profilin-like” domain eliminate actin binding activity without disrupting the ability of the altered protein to associate with the other subunits of V-ATPase to form a functional proton pump. Analysis of these mutated B-subunits suggests that the actin-binding activity is not required for the “housekeeping” functions of V-ATPases, but is important for certain specialized roles. In osteoclasts, the actin-binding activity is required for transport of V-ATPases to the plasma membrane, a prerequisite for bone resorption. A virtual screen led to the identification of enoxacin as a small molecule that bound to the actin-binding surface of the B2-subunit and competitively inhibited B2-subunit and actin interaction. Enoxacin disrupted osteoclastic bone resorption in vitro, but did not affect osteoblast formation or mineralization. Recently, enoxacin was identified as an inhibitor of the virulence of Candidaalbicans and more importantly of cancer growth and metastasis. Efforts are underway to determine the mechanisms by which enoxacin and other small molecule inhibitors of B2 and microfilament binding interaction selectively block bone resorption, the virulence of Candida, cancer growth, and metastasis.
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Affiliation(s)
- Edgardo J Toro
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, FL 32610, USA
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Gerle C. Stabilization of Fo/Vo/Ao by a radial electric field. Biophysics (Nagoya-shi) 2011; 7:99-104. [PMID: 27857597 PMCID: PMC5036770 DOI: 10.2142/biophysics.7.99] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 09/26/2011] [Indexed: 12/01/2022] Open
Abstract
The membrane domain of rotary ATPases (Fo/Vo/Ao) contains a membrane-embedded rotor ring which rotates against an adjacent cation channel-forming subunit during catalysis. The mechanism that allows stabilization of the highly mobile and yet tightly connected domains during operation while not impeding rotation is unknown. Remarkably, all known ATPase rotor rings are filled by lipids. In the crystal structure of the rotor ring of a V-ATPase from Enterococcus hirae the ring filling lipids form a proper membrane that is lower with respect to the embedding membrane surrounding both subunits. I propose first, that a vertical shift between lumenal lipids and embedding outside membrane is a general feature of rotor rings and second that it leads to a radial potential fall-off between rotor ring and cation channel, creating attractive forces that impact rotor-stator interaction in Fo/Vo/Ao during rotation.
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Affiliation(s)
- Christoph Gerle
- Career Path Promotion Unit for Young Life Scientists, Kyoto University, Bldg. E, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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12
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Mnatsakanyan N, Kemboi SK, Salas J, Weber J. The beta subunit loop that couples catalysis and rotation in ATP synthase has a critical length. J Biol Chem 2011; 286:29788-96. [PMID: 21705326 PMCID: PMC3191020 DOI: 10.1074/jbc.m111.254730] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/06/2011] [Indexed: 11/06/2022] Open
Abstract
ATP synthase uses a unique rotational mechanism to convert chemical energy into mechanical energy and back into chemical energy. The helix-turn-helix structure in the C-terminal domain of the β subunit containing the conserved DELSEED motif, termed "DELSEED-loop," was suggested to be involved in coupling between catalysis and rotation. If this is indeed the role of the loop, it must have a critical length, the minimum length required to sustain its function. Here, the critical length of the DELSEED-loop was determined by functional analysis of mutants of Bacillus PS3 ATP synthase that had 7-14 amino acids within the loop deleted. A 10 residue deletion lost the ability to catalyze ATP synthesis, but was still an active ATPase. Deletion of 14 residues abolished any enzymatic activity. Modeling indicated that in both deletion mutants the DELSEED-loop was shortened by ∼10 Å; fluorescence resonance energy transfer experiments confirmed the modeling results. This appears to define the minimum length for DELSEED-loop required for coupling of catalysis and rotation. In addition, we could demonstrate that the loss of high-affinity binding to the catalytic site(s) that had been observed previously in two deletion mutants with 3-4 residues removed was not due to the loss of negative charged residues of the DELSEED motif in these mutants. An AALSAAA mutant in which all negative charges of the DELSEED motif were removed showed a normal pattern for MgATP binding to the catalytic sites, with a clearly present high-affinity site.
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Affiliation(s)
- Nelli Mnatsakanyan
- From the Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Silas K. Kemboi
- From the Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Jasmin Salas
- From the Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Joachim Weber
- From the Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
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13
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Couoh-Cardel SJ, Uribe-Carvajal S, Wilkens S, García-Trejo JJ. Structure of dimeric F1F0-ATP synthase. J Biol Chem 2010; 285:36447-55. [PMID: 20833715 DOI: 10.1074/jbc.m110.144907] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The structure of the dimeric ATP synthase from yeast mitochondria was analyzed by transmission electron microscopy and single particle image analysis. In addition to the previously reported side views of the dimer, top view and intermediate projections served to resolve the arrangement of the rotary c(10) ring and the other stator subunits at the F(0)-F(0) dimeric interface. A three-dimensional reconstruction of the complex was calculated from a data set of 9960 molecular images at a resolution of 27 Å. The structural model of the dimeric ATP synthase shows the two monomers arranged at an angle of ∼45°, consistent with our earlier analysis of the ATP synthase from bovine heart mitochondria (Minauro-Sanmiguel, F., Wilkens, S., and Garcia, J. J. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 12356-12358). In the ATP synthase dimer, the two peripheral stalks are located near the F(1)-F(1) interface but are turned away from each other so that they are not in contact. Based on the three-dimensional reconstruction, a model of how dimeric ATP synthase assembles to form the higher order oligomeric structures that are required for mitochondrial cristae biogenesis is discussed.
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Affiliation(s)
- Sergio J Couoh-Cardel
- Department of Biology, Chemistry Faculty, National Autonomous University of Mexico, Mexico City 04510, Mexico
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14
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D'Alessandro M, Turina P, Melandri BA. Quantitative evaluation of the intrinsic uncoupling modulated by ADP and P(i) in the reconstituted ATP synthase of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:130-43. [PMID: 20800570 DOI: 10.1016/j.bbabio.2010.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 08/17/2010] [Accepted: 08/18/2010] [Indexed: 11/18/2022]
Abstract
The ATP synthase from Escherichia coli was isolated and reconstituted into liposomes. The ATP hydrolysis by these proteoliposomes was coupled to proton pumping, and the ensuing inner volume acidification was measured by the fluorescent probe 9-amino-6-chloro-2-methoxyacridine (ACMA). The ACMA response was calibrated by acid-base transitions, and converted into internal pH values. The rates of internal acidification and of ATP hydrolysis were measured in parallel, as a function of P(i) or ADP concentration. Increasing P(i) monotonically inhibited the hydrolysis rate with a half-maximal effect at 510μM, whereas it stimulated the acidification rate up to 100-200μM, inhibiting it only at higher concentrations. The ADP concentration in the assay, due both to contaminant ADP in ATP and to the hydrolysis reaction, was progressively decreased by means of increasing pyruvate kinase activities. Decreasing ADP stimulated the hydrolysis rate, whereas it inhibited the internal acidification rate. The quantitative analysis showed that the relative number of translocated protons per hydrolyzed ATP, i.e. the relative coupling ratio, depended on the concentrations of P(i) and ADP with apparent K(d) values of 220μM and 27nM respectively. At the smallest ADP concentrations reached, and in the absence of P(i), the coupling ratio dropped down to 15% relative to the value observed at the highest ADP and P(i) concentrations tested. In addition, the data indicate the presence of two ADP and P(i) binding sites, of which only the highest affinity one is related to changes in the coupling ratio.
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Affiliation(s)
- Manuela D'Alessandro
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
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15
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Parra KJ, Osgood MP, Pappas DL. A research-based laboratory course designed to strengthen the research-teaching nexus. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2010; 38:172-179. [PMID: 21567820 DOI: 10.1002/bmb.20358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We describe a 10-week laboratory course of guided research experiments thematically linked by topic, which had an ultimate goal of strengthening the undergraduate research-teaching nexus. This undergraduate laboratory course is a direct extension of faculty research interests. From DNA isolation, characterization, and mutagenesis, to protein expression and structural analysis, the research protocols were adapted to suit the weekly 3-hour biochemistry course. The experiments described are flexible and hypothesis driven, allowing original research to be conducted. Students gain practice in some of the most common techniques used in biochemistry and molecular biology, including minipreps and DNA spectrophometric analysis, DNA restriction digestion and agarose gel electrophoresis, PCR mutagenesis, DNA sequencing analyses, E. coli transformations, whole cell protein extractions, SDS-PAGE, immunoblots, molecular modeling, and bioinformatics. The studies that begun in the classroom were continued in the research laboratory by undergraduate students, and eventually, the results were published in peer reviewed research articles. This research-educational program effectively integrated basic research endeavors into the undergraduate curriculum. It proved to be synergistic by nature: research stimulated teaching and teaching supported research. In our experience, this is an effective mechanism to conduct productive research while satisfying teaching duties in undergraduate institutions, where scholarly research is expected but teaching is the primary mission.
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Affiliation(s)
- Karlett J Parra
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131.
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16
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Johnson RM, Allen C, Melman SD, Waller A, Young SM, Sklar LA, Parra KJ. Identification of inhibitors of vacuolar proton-translocating ATPase pumps in yeast by high-throughput screening flow cytometry. Anal Biochem 2009; 398:203-11. [PMID: 20018164 DOI: 10.1016/j.ab.2009.12.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 09/22/2009] [Accepted: 12/10/2009] [Indexed: 11/28/2022]
Abstract
Fluorescence intensity of the pH-sensitive carboxyfluorescein derivative 2,7-bis(2-carboxyethyl)-5(6)-carboxyfluorescein (BCECF) was monitored by high-throughput flow cytometry in living yeast cells. We measured fluorescence intensity of BCECF trapped in yeast vacuoles, acidic compartments equivalent to lysosomes where vacuolar proton-translocating ATPases (V-ATPases) are abundant. Because V-ATPases maintain a low pH in the vacuolar lumen, V-ATPase inhibition by concanamycin A alkalinized the vacuole and increased BCECF fluorescence. Likewise, V-ATPase-deficient mutant cells had greater fluorescence intensity than wild-type cells. Thus, we detected an increase of fluorescence intensity after short- and long-term inhibition of V-ATPase function. We used yeast cells loaded with BCECF to screen a small chemical library of structurally diverse compounds to identify V-ATPase inhibitors. One compound, disulfiram, enhanced BCECF fluorescence intensity (although to a degree beyond that anticipated for pH changes alone in the mutant cells). Once confirmed by dose-response assays (EC(50)=26 microM), we verified V-ATPase inhibition by disulfiram in secondary assays that measured ATP hydrolysis in vacuolar membranes. The inhibitory action of disulfiram against V-ATPase pumps revealed a novel effect previously unknown for this compound. Because V-ATPases are highly conserved, new inhibitors identified could be used as research and therapeutic tools in cancer, viral infections, and other diseases where V-ATPases are involved.
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Affiliation(s)
- Rebecca M Johnson
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, USA
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17
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Gayen S, Balakrishna AM, Grüber G. NMR solution structure of the N-terminal domain of subunit E (E1–52) of A1AO ATP synthase from Methanocaldococcus jannaschii. J Bioenerg Biomembr 2009; 41:343-8. [DOI: 10.1007/s10863-009-9237-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 08/20/2009] [Indexed: 12/01/2022]
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18
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Interaction of the Thermoplasma acidophilum A1A0-ATP synthase peripheral stalk with the catalytic domain. FEBS Lett 2009; 583:3121-6. [PMID: 19720061 DOI: 10.1016/j.febslet.2009.08.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 08/25/2009] [Indexed: 11/23/2022]
Abstract
The peripheral stalk of the archaeal ATP synthase (A1A0)-ATP synthase is formed by the heterodimeric EH complex and is part of the stator domain, which counteracts the torque of rotational catalysis. Here we used nuclear magnetic resonance spectroscopy to probe the interaction of the C-terminal domain of the EH heterodimer (E(CT1)H(CT)) with the N-terminal 23 residues of the B subunit (B(NT)). The data show a specific interaction of B(NT) peptide with 26 residues of the E(CT1)H(CT) domain, thereby providing a molecular picture of how the peripheral stalk is anchored to the A3B3 catalytic domain in A1A0.
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19
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Mnatsakanyan N, Hook JA, Quisenberry L, Weber J. ATP synthase with its gamma subunit reduced to the N-terminal helix can still catalyze ATP synthesis. J Biol Chem 2009; 284:26519-25. [PMID: 19636076 DOI: 10.1074/jbc.m109.030528] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP synthase uses a unique rotary mechanism to couple ATP synthesis and hydrolysis to transmembrane proton translocation. As part of the synthesis mechanism, the torque of the rotor has to be converted into conformational rearrangements of the catalytic binding sites on the stator to allow synthesis and release of ATP. The gamma subunit of the rotor, which plays a central role in the energy conversion, consists of two long helices inside the central cavity of the stator cylinder plus a globular portion outside the cylinder. Here, we show that the N-terminal helix alone is able to fulfill the function of full-length gamma in ATP synthesis as long as it connects to the rest of the rotor. This connection can occur via the epsilon subunit. No direct contact between gamma and the c ring seems to be required. In addition, the results indicate that the epsilon subunit of the rotor exists in two different conformations during ATP synthesis and ATP hydrolysis.
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Affiliation(s)
- Nelli Mnatsakanyan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
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20
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Kish-Trier E, Wilkens S. Domain architecture of the stator complex of the A1A0-ATP synthase from Thermoplasma acidophilum. J Biol Chem 2009; 284:12031-40. [PMID: 19234304 PMCID: PMC2673272 DOI: 10.1074/jbc.m808962200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 02/18/2009] [Indexed: 12/22/2022] Open
Abstract
A key structural element in the ion translocating F-, A-, and V-ATPases is the peripheral stalk, an assembly of two polypeptides that provides a structural link between the ATPase and ion channel domains. Previously, we have characterized the peripheral stalk forming subunits E and H of the A-ATPase from Thermoplasma acidophilum and demonstrated that the two polypeptides interact to form a stable heterodimer with 1:1 stoichiometry (Kish-Trier, E., Briere, L. K., Dunn, S. D., and Wilkens, S. (2008) J. Mol. Biol. 375, 673-685). To define the domain architecture of the A-ATPase peripheral stalk, we have now generated truncated versions of the E and H subunits and analyzed their ability to bind each other. The data show that the N termini of the subunits form an alpha-helical coiled-coil, approximately 80 residues in length, whereas the C-terminal residues interact to form a globular domain containingalpha- and beta-structure. We find that the isolated C-terminal domain of the E subunit exists as a dimer in solution, consistent with a recent crystal structure of the related Pyrococcus horikoshii A-ATPase E subunit (Lokanath, N. K., Matsuura, Y., Kuroishi, C., Takahashi, N., and Kunishima, N. (2007) J. Mol. Biol. 366, 933-944). However, upon the addition of a peptide comprising the C-terminal 21 residues of the H subunit (or full-length H subunit), dimeric E subunit C-terminal domain dissociates to form a 1:1 heterodimer. NMR spectroscopy was used to show that H subunit C-terminal peptide binds to E subunit C-terminal domain via the terminal alpha-helices, with little involvement of the beta-sheet region. Based on these data, we propose a structural model of the A-ATPase peripheral stalk.
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Affiliation(s)
- Erik Kish-Trier
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
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21
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Guillot TS, Miller GW. Protective actions of the vesicular monoamine transporter 2 (VMAT2) in monoaminergic neurons. Mol Neurobiol 2009; 39:149-70. [PMID: 19259829 DOI: 10.1007/s12035-009-8059-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 02/18/2009] [Indexed: 12/13/2022]
Abstract
Vesicular monoamine transporters (VMATs) are responsible for the packaging of neurotransmitters such as dopamine, serotonin, norepinephrine, and epinephrine into synaptic vesicles. These proteins evolved from precursors in the major facilitator superfamily of transporters and are among the members of the toxin extruding antiporter family. While the primary function of VMATs is to sequester neurotransmitters within vesicles, they can also translocate toxicants away from cytosolic sites of action. In the case of dopamine, this dual role of VMAT2 is combined-dopamine is more readily oxidized in the cytosol where it can cause oxidative stress so packaging into vesicles serves two purposes: neurotransmission and neuroprotection. Furthermore, the deleterious effects of exogenous toxicants on dopamine neurons, such as MPTP, can be attenuated by VMAT2 activity. The active metabolite of MPTP can be kept within vesicles and prevented from disrupting mitochondrial function thereby sparing the dopamine neuron. The highly addictive drug methamphetamine is also neurotoxic to dopamine neurons by using dopamine itself to destroy the axon terminals. Methamphetamine interferes with vesicular sequestration and increases the production of dopamine, escalating the amount in the cytosol and leading to oxidative damage of terminal components. Vesicular transport seems to resist this process by sequestering much of the excess dopamine, which is illustrated by the enhanced methamphetamine neurotoxicity in VMAT2-deficient mice. It is increasingly evident that VMAT2 provides neuroprotection from both endogenous and exogenous toxicants and that while VMAT2 has been adapted by eukaryotes for synaptic transmission, it is derived from phylogenetically ancient proteins that originally evolved for the purpose of cellular protection.
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Affiliation(s)
- Thomas S Guillot
- Center for Neurodegenerative Disease, Emory University, Atlanta, GA, USA
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22
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Mnatsakanyan N, Krishnakumar AM, Suzuki T, Weber J. The role of the betaDELSEED-loop of ATP synthase. J Biol Chem 2009; 284:11336-45. [PMID: 19246448 DOI: 10.1074/jbc.m900374200] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP synthase uses a unique rotational mechanism to convert chemical energy into mechanical energy and back into chemical energy. The helix-turn-helix motif, termed "DELSEED-loop," in the C-terminal domain of the beta subunit was suggested to be involved in coupling between catalysis and rotation. Here, the role of the DELSEED-loop was investigated by functional analysis of mutants of Bacillus PS3 ATP synthase that had 3-7 amino acids within the loop deleted. All mutants were able to catalyze ATP hydrolysis, some at rates several times higher than the wild-type enzyme. In most cases ATP hydrolysis in membrane vesicles generated a transmembrane proton gradient, indicating that hydrolysis occurred via the normal rotational mechanism. Except for two mutants that showed low activity and low abundance in the membrane preparations, the deletion mutants were able to catalyze ATP synthesis. In general, the mutants seemed less well coupled than the wild-type enzyme, to a varying degree. Arrhenius analysis demonstrated that in the mutants fewer bonds had to be rearranged during the rate-limiting catalytic step; the extent of this effect was dependent on the size of the deletion. The results support the idea of a significant involvement of the DELSEED-loop in mechanochemical coupling in ATP synthase. In addition, for two deletion mutants it was possible to prepare an alpha(3)beta(3)gamma subcomplex and measure nucleotide binding to the catalytic sites. Interestingly, both mutants showed a severely reduced affinity for MgATP at the high affinity site.
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Affiliation(s)
- Nelli Mnatsakanyan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
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23
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Zhang Z, Zheng Y, Mazon H, Milgrom E, Kitagawa N, Kish-Trier E, Heck AJR, Kane PM, Wilkens S. Structure of the yeast vacuolar ATPase. J Biol Chem 2008; 283:35983-95. [PMID: 18955482 PMCID: PMC2602884 DOI: 10.1074/jbc.m805345200] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 10/15/2008] [Indexed: 01/01/2023] Open
Abstract
The subunit architecture of the yeast vacuolar ATPase (V-ATPase) was analyzed by single particle transmission electron microscopy and electrospray ionization (ESI) tandem mass spectrometry. A three-dimensional model of the intact V-ATPase was calculated from two-dimensional projections of the complex at a resolution of 25 angstroms. Images of yeast V-ATPase decorated with monoclonal antibodies against subunits A, E, and G position subunit A within the pseudo-hexagonal arrangement in the V1, the N terminus of subunit G in the V1-V0 interface, and the C terminus of subunit E at the top of the V1 domain. ESI tandem mass spectrometry of yeast V1-ATPase showed that subunits E and G are most easily lost in collision-induced dissociation, consistent with a peripheral location of the subunits. An atomic model of the yeast V-ATPase was generated by fitting of the available x-ray crystal structures into the electron microscopy-derived electron density map. The resulting atomic model of the yeast vacuolar ATPase serves as a framework to help understand the role the peripheral stalk subunits are playing in the regulation of the ATP hydrolysis driven proton pumping activity of the vacuolar ATPase.
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Affiliation(s)
- Zhenyu Zhang
- Department of Biochemistry, University of California, Riverside, California 92521, USA
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24
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D'Alessandro M, Turina P, Melandri BA. Intrinsic uncoupling in the ATP synthase of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1518-27. [PMID: 18952048 DOI: 10.1016/j.bbabio.2008.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/23/2008] [Accepted: 09/23/2008] [Indexed: 11/25/2022]
Abstract
The ATP hydrolysis activity and proton pumping of the ATP synthase of Escherichia coli in isolated native membranes have been measured and compared as a function of ADP and Pi concentration. The ATP hydrolysis activity was inhibited by Pi with an half-maximal effect at 140 microM, which increased progressively up in the millimolar range when the ADP concentration was progressively decreased by increasing amounts of an ADP trap. In addition, the relative extent of this inhibition decreased with decreasing ADP. The half-maximal inhibition by ADP was found in the submicromolar range, and the extent of inhibition was enhanced by the presence of Pi. The parallel measurement of ATP hydrolysis activity and proton pumping indicated that, while the rate of ATP hydrolysis was decreased as a function of either ligand, the rate of proton pumping increased. The latter showed a biphasic response to the concentration of Pi, in which an inhibition followed the initial stimulation. Similarly as previously found for the ATP synthase from Rhodobacter caspulatus [P. Turina, D. Giovannini, F. Gubellini, B.A. Melandri, Physiological ligands ADP and Pi modulate the degree of intrinsic coupling in the ATP synthase of the photosynthetic bacterium Rhodobacter capsulatus, Biochemistry 43 (2004) 11126-11134], these data indicate that the E. coli ATP synthase can operate at different degrees of energetic coupling between hydrolysis and proton transport, which are modulated by ADP and Pi.
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Affiliation(s)
- Manuela D'Alessandro
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
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25
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Shu YG, Lai PY. Systematic Kinetics Study of FoF1-ATPase: Analytic Results and Comparison with Experiments. J Phys Chem B 2008; 112:13453-9. [DOI: 10.1021/jp8052696] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yao-Gen Shu
- Department of Physics, Graduate Institute of Biophysics and Center for Complex Systems, National Central University, Chung-Li, Taiwan 320, R. O. C., and Institute of Theoretical Physics, The Chinese Academy of Sciences, P.O. Box 2735, Beijing 100080, China
| | - Pik-Yin Lai
- Department of Physics, Graduate Institute of Biophysics and Center for Complex Systems, National Central University, Chung-Li, Taiwan 320, R. O. C., and Institute of Theoretical Physics, The Chinese Academy of Sciences, P.O. Box 2735, Beijing 100080, China
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26
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Probing the functional tolerance of the b subunit of Escherichia coli ATP synthase for sequence manipulation through a chimera approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:583-91. [DOI: 10.1016/j.bbabio.2008.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/05/2008] [Accepted: 03/07/2008] [Indexed: 11/19/2022]
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27
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Mao HZ, Abraham CG, Krishnakumar AM, Weber J. A functionally important hydrogen-bonding network at the betaDP/alphaDP interface of ATP synthase. J Biol Chem 2008; 283:24781-8. [PMID: 18579516 DOI: 10.1074/jbc.m804142200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP synthase uses a unique rotary mechanism to couple ATP synthesis and hydrolysis to transmembrane proton translocation. The F1 subcomplex has three catalytic nucleotide binding sites, one on each beta subunit, at the interface to the adjacent alpha subunit. In the x-ray structure of F1 (Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628), the three catalytic beta/alpha interfaces differ in the extent of inter-subunit interactions between the C termini of the beta and alpha subunits. At the closed betaDP/alphaDP interface, a hydrogen-bonding network is formed between both subunits, which is absent at the more open betaTP/alphaTP interface and at the wide open betaE/alphaE interface. The hydrogen-bonding network reaches from betaL328 (Escherichia coli numbering) and betaQ441 via alphaQ399, betaR398, and alphaE402 to betaR394, and ends in a cation/pi interaction between betaR394 and alphaF406. Using mutational analysis in E. coli ATP synthase, the functional importance of the betaDP/alphaDP hydrogen-bonding network is demonstrated. Its elimination results in a severely impaired enzyme but has no pronounced effect on the binding affinities of the catalytic sites. A possible role for the hydrogen-bonding network in coupling of ATP synthesis/hydrolysis and rotation will be discussed.
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Affiliation(s)
- Hui Z Mao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
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28
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Chaudhry FA, Edwards RH, Fonnum F. Vesicular neurotransmitter transporters as targets for endogenous and exogenous toxic substances. Annu Rev Pharmacol Toxicol 2008; 48:277-301. [PMID: 17883368 DOI: 10.1146/annurev.pharmtox.46.120604.141146] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Exocytotic release of neurotransmitters requires their accumulation inside preformed secretory vesicles. Distinct vesicular transport activities translocate classical transmitters into synaptic vesicles energized by a H+ electrochemical gradient (Delta(mu(H+))), with subtle but important differences in dependence on the electrical and chemical components. The vesicular transporters also interact with toxic compounds and drugs. They mediate neuroprotection by sequestering toxic compounds as well as neurotransmitters into vesicles, reducing their concentration in the cytosol where they may have detrimental effects. Both therapeutic agents and psychostimulants interfering with vesicular transport have yielded insight into the pathogenesis of psychiatric as well as neurodegenerative diseases. Thus, specific inhibitors have helped to characterize both the physiological role and mechanism of vesicular neurotransmitter transport.
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Affiliation(s)
- Farrukh A Chaudhry
- Centre for Molecular Biology and Neuroscience, The Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.
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29
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The thermodynamic H+/ATP ratios of the H+-ATPsynthases from chloroplasts and Escherichia coli. Proc Natl Acad Sci U S A 2008; 105:3745-50. [PMID: 18316723 DOI: 10.1073/pnas.0708356105] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The H(+)/ATP ratio is an important parameter for the energy balance of all cells and for the coupling mechanism between proton transport and ATP synthesis. A straightforward interpretation of rotational catalysis predicts that the H(+)/ATP coincides with the ratio of the c-subunits to beta-subunits, implying that, for the chloroplast and Escherichia coli ATPsynthases, numbers of 4.7 and 3.3 are expected. Here, the energetics described by the chemiosmotic theory was used to determine the H(+)/ATP ratio for the two enzymes. The isolated complexes were reconstituted into liposomes, and parallel measurements were performed under identical conditions. The internal phase of the liposomes was equilibrated with the acidic medium during reconstitution, allowing to measure the internal pH with a glass electrode. An acid-base transition was carried out and the initial rates of ATP synthesis or ATP hydrolysis were measured with luciferin/luciferase as a function of DeltapH at constant Q = [ATP]/([ADP][P(i)]). From the shift of the equilibrium DeltapH as a function of Q the standard Gibbs free energy for phosphorylation, DeltaG(p)(0)'; and the H(+)/ATP ratio were determined. It resulted DeltaG(p)(0)' = 38 +/- 3 kJ.mol(-1) and H(+)/ATP = 4.0 +/- 0.2 for the chloroplast and H(+)/ATP = 4.0 +/- 0.3 for the E. coli enzyme, indicating that the thermodynamic H(+)/ATP ratio is the same for both enzymes and that it is different from the subunit stoichiometric ratio.
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30
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Chaudhry FA, Boulland JL, Jenstad M, Bredahl MKL, Edwards RH. Pharmacology of neurotransmitter transport into secretory vesicles. Handb Exp Pharmacol 2008:77-106. [PMID: 18064412 DOI: 10.1007/978-3-540-74805-2_4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Many neuropsychiatric disorders appear to involve a disturbance of chemical neurotransmission, and the mechanism of available therapeutic agents supports this impression. Postsynaptic receptors have received considerable attention as drug targets, but some of the most successful agents influence presynaptic processes, in particular neurotransmitter reuptake. The pharmacological potential of many other presynaptic elements, and in particular the machinery responsible for loading transmitter into vesicles, has received only limited attention. The similarity of vesicular transporters to bacterial drug resistance proteins and the increasing evidence for regulation of vesicle filling and recycling suggest that the pharmacological potential of vesicular transporters has been underestimated. In this review, we discuss the pharmacological effects of psychostimulants and therapeutic agents on transmitter release.
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Affiliation(s)
- Farrukh A Chaudhry
- The Biotechnology Centre of Oslo, University of Oslo, 1125, Blindern, Oslo, 0317, Norway.
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31
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Identification of the betaTP site in the x-ray structure of F1-ATPase as the high-affinity catalytic site. Proc Natl Acad Sci U S A 2007; 104:18478-83. [PMID: 18003896 DOI: 10.1073/pnas.0709322104] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATP synthase uses a unique rotary mechanism to couple ATP synthesis and hydrolysis to transmembrane proton translocation. The F(1) subcomplex has three catalytic nucleotide binding sites, one on each beta subunit, with widely differing affinities for MgATP or MgADP. During rotational catalysis, the sites switch their affinities. The affinity of each site is determined by the position of the central gamma subunit. The site with the highest nucleotide binding affinity is catalytically active. From the available x-ray structures, it is not possible to discern the high-affinity site. Using fluorescence resonance energy transfer between tryptophan residues engineered into gamma and trinitrophenyl nucleotide analogs on the catalytic sites, we were able to determine that the high-affinity site is close to the C-terminal helix of gamma, but at considerable distance from its N terminus. Thus, the beta(TP) site in the x-ray structure [Abrahams JP, Leslie AGW, Lutter R, Walker JE (1994) Nature 370:621-628] is the high-affinity site, in agreement with the prediction of Yang et al. [Yang W, Gao YQ, Cui Q, Ma J, Karplus M (2003) Proc Natl Acad Sci USA 100:874-879]. Taking into account the known direction of rotation, the findings establish the sequence of affinities through which each catalytic site cycles during MgATP hydrolysis as low --> high --> medium --> low.
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32
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Kish-Trier E, Briere LAK, Dunn SD, Wilkens S. The stator complex of the A1A0-ATP synthase--structural characterization of the E and H subunits. J Mol Biol 2007; 375:673-85. [PMID: 18036615 DOI: 10.1016/j.jmb.2007.10.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2007] [Revised: 10/10/2007] [Accepted: 10/25/2007] [Indexed: 10/22/2022]
Abstract
Archaeal ATP synthase (A-ATPase) is the functional homolog to the ATP synthase found in bacteria, mitochondria and chloroplasts, but the enzyme is structurally more related to the proton-pumping vacuolar ATPase found in the endomembrane system of eukaryotes. We have cloned, overexpressed and characterized the stator-forming subunits E and H of the A-ATPase from the thermoacidophilic Archaeon, Thermoplasma acidophilum. Size exclusion chromatography, CD, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and NMR spectroscopic experiments indicate that both polypeptides have a tendency to form dimers and higher oligomers in solution. However, when expressed together or reconstituted, the two individual polypeptides interact with high affinity to form a stable heterodimer. Analyses by gel filtration chromatography and analytical ultracentrifugation show the heterodimer to have an elongated shape, and the preparation to be monodisperse. Thermal denaturation analyses by CD and differential scanning calorimetry revealed the more cooperative unfolding transitions of the heterodimer in comparison to those of the individual polypeptides. The data are consistent with the EH heterodimer forming the peripheral stalk(s) in the A-ATPase in a fashion analogous to that of the related vacuolar ATPase.
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Affiliation(s)
- Erik Kish-Trier
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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Wood KS, Dunn SD. Role of the Asymmetry of the Homodimeric b2 Stator Stalk in the Interaction with the F1 Sector of Escherichia coli ATP Synthase. J Biol Chem 2007; 282:31920-7. [PMID: 17766239 DOI: 10.1074/jbc.m706259200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The b subunit dimer in the peripheral stator stalk of Escherichia coli ATP synthase is essential for enzyme assembly and the rotational catalytic mechanism. Recent protein chemical evidence revealed the dimerization domain of b to contain a novel two-stranded right-handed coiled coil with offset helices. Here, the existence of this structure in more complete constructs of b containing the C-terminal domain, and therefore capable of binding to the peripheral F1-ATPase, was supported by the more efficient formation of intersubunit disulfide bonds between cysteine residues that are proximal only in the offset arrangement and by the greater thermal stabilities of cross-linked heterodimers trapped in the offset configuration as opposed to homodimers with the helices trapped in-register. F1-ATPase binding analyses revealed the offset heterodimers to bind F1 more tightly than in-register homodimers. Mutations near the C terminus of b were incorporated specifically into either the N-terminally or the C-terminally shifted polypeptide, bN or bC, respectively, to determine the contribution of each position to F1 binding. Deletion of the last four residues of bN substantially weakened F1 binding, whereas the effect of the deletion in bC was modest. Similarly, benzophenone maleimide introduced at the C terminus of bN, but not bC, mediated cross-linking to the delta subunit of F1. These results imply that the polypeptide in the bN position is more important for F1 binding than the one in the bC position and illustrate the significance of the asymmetry of the b dimer in the enzyme.
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Affiliation(s)
- Kristi S Wood
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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Mulkidjanian AY, Makarova KS, Galperin MY, Koonin EV. Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nat Rev Microbiol 2007; 5:892-9. [PMID: 17938630 DOI: 10.1038/nrmicro1767] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The rotary proton- and sodium-translocating ATPases are reversible molecular machines present in all cellular life forms that couple ion movement across membranes with ATP hydrolysis or synthesis. Sequence and structural comparisons of F- and V-type ATPases have revealed homology between their catalytic and membrane subunits, but not between the subunits of the central stalk that connects the catalytic and membrane components. Based on this pattern of homology, we propose that these ATPases originated from membrane protein translocases, which, themselves, evolved from RNA translocases. We suggest that in these ancestral translocases, the position of the central stalk was occupied by the translocated polymer.
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Li MD, Wang J. Neuroproteomics and its applications in research on nicotine and other drugs of abuse. Proteomics Clin Appl 2007; 1:1406-27. [PMID: 21136639 DOI: 10.1002/prca.200700321] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Indexed: 12/24/2022]
Abstract
The rapidly growing field of neuroproteomics is able to track changes in protein expression and protein modifications underlying various physiological conditions, including the neural diseases related to drug addiction. Thus, it presents great promise in characterizing protein function, biochemical pathways, and networks to understand the mechanisms underlying drug dependence. In this article, we first provide an overview of proteomics technologies and bioinformatics tools available to analyze proteomics data. Then we summarize the recent applications of proteomics to profile the protein expression pattern in animal or human brain tissues after the administration of nicotine, alcohol, amphetamine, butorphanol, cocaine, and morphine. By comparing the protein expression profiles in response to chronic nicotine exposure with those appearing in response to treatment with other drugs of abuse, we identified three biological processes that appears to be regulated by multiple drugs of abuse: energy metabolism, oxidative stress response, and protein degradation and modification. Such similarity indicates that despite the obvious differences among their chemical properties and the receptors with which they interact, different substances of abuse may cause some similar changes in cellular activities and biological processes in neurons.
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Affiliation(s)
- Ming D Li
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, USA.
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Weber J. ATP synthase--the structure of the stator stalk. Trends Biochem Sci 2007; 32:53-6. [PMID: 17208001 PMCID: PMC2570231 DOI: 10.1016/j.tibs.2006.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 11/22/2006] [Accepted: 12/20/2006] [Indexed: 11/22/2022]
Abstract
ATP synthase synthesizes ATP from ADP and inorganic phosphate using a unique rotary mechanism whereby two subcomplexes move relative to each other, powered by a proton or sodium gradient. The non-rotating parts of the machinery are held together by the "stator stalk". The recent resolution of the structure of a major portion of the stator stalk of mitochondrial ATP synthase represents an important step towards a structural model for the ATP synthase holoenzyme.
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Affiliation(s)
- Joachim Weber
- Department of Chemistry and Biochemistry, Texas Tech University, Box 41061, Lubbock, TX 79409-1061, USA.
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Del Rizzo PA, Bi Y, Dunn SD. ATP synthase b subunit dimerization domain: a right-handed coiled coil with offset helices. J Mol Biol 2006; 364:735-46. [PMID: 17028022 DOI: 10.1016/j.jmb.2006.09.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 09/06/2006] [Accepted: 09/08/2006] [Indexed: 11/29/2022]
Abstract
The dimerization domain of Escherichia coli ATP synthase b subunit forms an atypical parallel two-stranded coiled coil. Sequence analysis reveals an 11-residue abcdefghijk repeat characteristic of right-handed coiled coils, but no other naturally occurring parallel dimeric structure of this class has been identified. The arrangement of the helices was studied by their propensity to form interhelix disulfide linkages and analysis of the stability and shape of disulfide-linked dimers. Disulfides formed preferentially between cysteine residues in an a position of one helix and either of the adjacent h positions of the partner. Such heterodimers were far more stable to thermal denaturation than homodimers and, on the basis of gel-filtration chromatography studies, were similar in shape to both non-covalent dimers and dimers linked through flexible Gly(1-3)Cys C-terminal extensions. The results indicate a right-handed coiled-coil structure with intrinsic asymmetry, the two helices being offset rather than in register. A function for the right-handed coiled coil in rotational catalysis is proposed.
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Affiliation(s)
- Paul A Del Rizzo
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A 5C1
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