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Frasch WD, Bukhari ZA, Yanagisawa S. F1FO ATP synthase molecular motor mechanisms. Front Microbiol 2022; 13:965620. [PMID: 36081786 PMCID: PMC9447477 DOI: 10.3389/fmicb.2022.965620] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The F-ATP synthase, consisting of F1 and FO motors connected by a central rotor and the stators, is the enzyme responsible for synthesizing the majority of ATP in all organisms. The F1 (αβ)3 ring stator contains three catalytic sites. Single-molecule F1 rotation studies revealed that ATP hydrolysis at each catalytic site (0°) precedes a power-stroke that rotates subunit-γ 120° with angular velocities that vary with rotational position. Catalytic site conformations vary relative to subunit-γ position (βE, empty; βD, ADP bound; βT, ATP-bound). During a power stroke, βE binds ATP (0°–60°) and βD releases ADP (60°–120°). Årrhenius analysis of the power stroke revealed that elastic energy powers rotation via unwinding the γ-subunit coiled-coil. Energy from ATP binding at 34° closes βE upon subunit-γ to drive rotation to 120° and forcing the subunit-γ to exchange its tether from βE to βD, which changes catalytic site conformations. In F1FO, the membrane-bound FO complex contains a ring of c-subunits that is attached to subunit-γ. This c-ring rotates relative to the subunit-a stator in response to transmembrane proton flow driven by a pH gradient, which drives subunit-γ rotation in the opposite direction to force ATP synthesis in F1. Single-molecule studies of F1FO embedded in lipid bilayer nanodisks showed that the c-ring transiently stopped F1-ATPase-driven rotation every 36° (at each c-subunit in the c10-ring of E. coli F1FO) and was able to rotate 11° in the direction of ATP synthesis. Protonation and deprotonation of the conserved carboxyl group on each c-subunit is facilitated by separate groups of subunit-a residues, which were determined to have different pKa’s. Mutations of any of any residue from either group changed both pKa values, which changed the occurrence of the 11° rotation proportionately. This supports a Grotthuss mechanism for proton translocation and indicates that proton translocation occurs during the 11° steps. This is consistent with a mechanism in which each 36° of rotation the c-ring during ATP synthesis involves a proton translocation-dependent 11° rotation of the c-ring, followed by a 25° rotation driven by electrostatic interaction of the negatively charged unprotonated carboxyl group to the positively charged essential arginine in subunit-a.
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2
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Garone C, Pietra A, Nesci S. From the Structural and (Dys)Function of ATP Synthase to Deficiency in Age-Related Diseases. Life (Basel) 2022; 12:401. [PMID: 35330152 PMCID: PMC8949411 DOI: 10.3390/life12030401] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/25/2022] [Accepted: 03/08/2022] [Indexed: 12/21/2022] Open
Abstract
The ATP synthase is a mitochondrial inner membrane complex whose function is essential for cell bioenergy, being responsible for the conversion of ADP into ATP and playing a role in mitochondrial cristae morphology organization. The enzyme is composed of 18 protein subunits, 16 nuclear DNA (nDNA) encoded and two mitochondrial DNA (mtDNA) encoded, organized in two domains, FO and F1. Pathogenetic variants in genes encoding structural subunits or assembly factors are responsible for fatal human diseases. Emerging evidence also underlines the role of ATP-synthase in neurodegenerative diseases as Parkinson's, Alzheimer's, and motor neuron diseases such as Amyotrophic Lateral Sclerosis. Post-translational modification, epigenetic modulation of ATP gene expression and protein level, and the mechanism of mitochondrial transition pore have been deemed responsible for neuronal cell death in vivo and in vitro models for neurodegenerative diseases. In this review, we will explore ATP synthase assembly and function in physiological and pathological conditions by referring to the recent cryo-EM studies and by exploring human disease models.
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Affiliation(s)
- Caterina Garone
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40137 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum University of Bologna, 40137 Bologna, Italy
- UOC Neuropsichiatria dell’età Pediatrica, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40137 Bologna, Italy
| | - Andrea Pietra
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40137 Bologna, Italy;
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40137 Bologna, Italy
| | - Salvatore Nesci
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano Emilia, Italy
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3
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Algieri C, Trombetti F, Pagliarani A, Fabbri M, Nesci S. The inhibition of gadolinium ion (Gd 3+) on the mitochondrial F 1F O-ATPase is linked to the modulation of the mitochondrial permeability transition pore. Int J Biol Macromol 2021; 184:250-258. [PMID: 34126146 DOI: 10.1016/j.ijbiomac.2021.06.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/18/2022]
Abstract
The mitochondrial permeability transition pore (PTP), which drives regulated cell death when Ca2+ concentration suddenly increases in mitochondria, was related to changes in the Ca2+-activated F1FO-ATPase. The effects of the gadolinium cation (Gd3+), widely used for diagnosis and therapy, and reported as PTP blocker, were evaluated on the F1FO-ATPase activated by Mg2+ or Ca2+ and on the PTP. Gd3+ more effectively inhibits the Ca2+-activated F1FO-ATPase than the Mg2+-activated F1FO-ATPase by a mixed-type inhibition on the former and by uncompetitive mechanism on the latter. Most likely Gd3+ binding to F1, is favoured by Ca2+ insertion. The maximal inactivation rates (kinact) of pseudo-first order inactivation are similar either when the F1FO-ATPase is activated by Ca2+ or by Mg2+. The half-maximal inactivator concentrations (KI) are 2.35 ± 0.35 mM and 0.72 ± 0.11 mM, respectively. The potency of a mechanism-based inhibitor (kinact/KI) also highlights a higher inhibition efficiency of Gd3+ on the Ca2+-activated F1FO-ATPase (0.59 ± 0.09 mM-1∙s-1) than on the Mg2+-activated F1FO-ATPase (0.13 ± 0.02 mM-1∙s-1). Consistently, the PTP is desensitized in presence of Gd3+. The Gd3+ inhibition on both the mitochondrial Ca2+-activated F1FO-ATPase and the PTP strengthens the link between the PTP and the F1FO-ATPase when activated by Ca2+ and provides insights on the biological effects of Gd3+.
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Affiliation(s)
- Cristina Algieri
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Fabiana Trombetti
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Alessandra Pagliarani
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy.
| | - Micaela Fabbri
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Salvatore Nesci
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy.
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4
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Algieri V, Algieri C, Maiuolo L, De Nino A, Pagliarani A, Tallarida MA, Trombetti F, Nesci S. 1,5-Disubstituted-1,2,3-triazoles as inhibitors of the mitochondrial Ca 2+ -activated F 1 F O -ATP(hydrol)ase and the permeability transition pore. Ann N Y Acad Sci 2020; 1485:43-55. [PMID: 32959908 DOI: 10.1111/nyas.14474] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/24/2020] [Accepted: 08/01/2020] [Indexed: 02/06/2023]
Abstract
The mitochondrial permeability transition pore (mPTP), a high-conductance channel triggered by a sudden Ca2+ concentration increase, is composed of the F1 FO -ATPase. Since mPTP opening leads to mitochondrial dysfunction, which is a feature of many diseases, a great pharmacological challenge is to find mPTP modulators. In our study, the effects of two 1,5-disubstituted 1,2,3-triazole derivatives, five-membered heterocycles with three nitrogen atoms in the ring and capable of forming secondary interactions with proteins, were investigated. Compounds 3a and 3b were selected among a wide range of structurally related compounds because of their chemical properties and effectiveness in preliminary studies. In swine heart mitochondria, both compounds inhibit Ca2+ -activated F1 FO -ATPase without affecting F-ATPase activity sustained by the natural cofactor Mg2+ . The inhibition is mutually exclusive, probably because of their shared enzyme site, and uncompetitive with respect to the ATP substrate, since they only bind to the enzyme-ATP complex. Both compounds show the same inhibition constant (K'i ), but compound 3a has a doubled inactivation rate constant compared with compound 3b. Moreover, both compounds desensitize mPTP opening without altering mitochondrial respiration. The results strengthen the link between Ca2+ -activated F1 FO -ATPase and mPTP and suggest that these inhibitors can be pharmacologically exploited to counteract mPTP-related diseases.
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Affiliation(s)
- Vincenzo Algieri
- Department of Chemistry and Chemical Technologies, University of Calabria, Cosenza, Italy
| | - Cristina Algieri
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Italy
| | - Loredana Maiuolo
- Department of Chemistry and Chemical Technologies, University of Calabria, Cosenza, Italy
| | - Antonio De Nino
- Department of Chemistry and Chemical Technologies, University of Calabria, Cosenza, Italy
| | - Alessandra Pagliarani
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Italy
| | | | - Fabiana Trombetti
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Italy
| | - Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Italy
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5
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Algieri C, Trombetti F, Pagliarani A, Ventrella V, Bernardini C, Fabbri M, Forni M, Nesci S. Mitochondrial Ca 2+ -activated F 1 F O -ATPase hydrolyzes ATP and promotes the permeability transition pore. Ann N Y Acad Sci 2019; 1457:142-157. [PMID: 31441951 DOI: 10.1111/nyas.14218] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 01/14/2023]
Abstract
The properties of the mitochondrial F1 FO -ATPase catalytic site, which can bind Mg2+ , Mn2+ , or Ca2+ and hydrolyze ATP, were explored by inhibition kinetic analyses to cast light on the Ca2+ -activated F1 FO -ATPase connection with the permeability transition pore (PTP) that initiates cascade events leading to cell death. While the natural cofactor Mg2+ activates the F1 FO -ATPase in competition with Mn2+ , Ca2+ is a noncompetitive inhibitor in the presence of Mg2+ . Selective F1 inhibitors (Is-F1 ), namely NBD-Cl, piceatannol, resveratrol, and quercetin, exerted different mechanisms (mixed and uncompetitive inhibition) on either Ca2+ - or Mg2+ -activated F1 FO -ATPase, consistent with the conclusion that the catalytic mechanism changes when Mg2+ is replaced by Ca2+ . In a partially purified F1 domain preparation, Ca2+ -activated F1 -ATPase maintained Is-F1 sensitivity, and enzyme inhibition was accompanied by the maintenance of the mitochondrial calcium retention capacity and membrane potential. The data strengthen the structural relationship between Ca2+ -activated F1 FO -ATPase and the PTP, and, in turn, on consequences, such as physiopathological cellular changes.
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Affiliation(s)
- Cristina Algieri
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Fabiana Trombetti
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | | | - Vittoria Ventrella
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Chiara Bernardini
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Micaela Fabbri
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Monica Forni
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
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6
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Biniuri Y, Shpilt Z, Albada B, Vázquez-González M, Wolff M, Hazan C, Golub E, Gelman D, Willner I. A Bis-Zn 2+ -Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer: An ATPase-Mimicking Nucleoapzyme. Chembiochem 2019; 21:53-58. [PMID: 30908871 DOI: 10.1002/cbic.201900182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Indexed: 11/09/2022]
Abstract
Catalytic nucleic acids consisting of a bis-Zn2+ -pyridyl-salen-type ([di-ZnII 3,5 bis(pyridinylimino) benzoic acid]) complex conjugated to the ATP aptamer act as ATPase-mimicking catalysts (nucleoapzymes). Direct linking of the Zn2+ complex to the 3'- or 5'-end of the aptamer (nucleoapzymes I and II) or its conjugation to the 3'- or 5'-end of the aptamer through bis-thymidine spacers (nucleoapzymes III and IV) provided a set of nucleoapzymes exhibiting variable catalytic activities. Whereas the separated bis-Zn2+ -pyridyl-salen-type catalyst and the ATP aptamer do not show any noticeable catalytic activity, the 3'-catalyst-modified nucleoapzyme (nucleoapzyme IV) and, specifically, the nucleoapzyme consisting of the catalyst linked to the 3'-position through the spacer (nucleoapzyme III) reveal enhanced catalytic features in relation to the analogous nucleoapzyme substituted at the 5'-position (kcat =4.37 and 6.88 min-1 , respectively). Evaluation of the binding properties of ATP to the different nucleoapzyme and complementary molecular dynamics simulations suggest that the distance separating the active site from the substrate linked to the aptamer binding site controls the catalytic activities of the different nucleoapzymes.
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Affiliation(s)
- Yonatan Biniuri
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Zohar Shpilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands
| | | | - Mariusz Wolff
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Carina Hazan
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Eyal Golub
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Dimitri Gelman
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
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7
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Abstract
Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein's scaffold. Can motifs such as P-loops confer function in a simpler context? We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop's key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif.
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8
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Nesci S, Trombetti F, Ventrella V, Pagliarani A. From the Ca 2+-activated F 1F O-ATPase to the mitochondrial permeability transition pore: an overview. Biochimie 2018; 152:85-93. [PMID: 29964086 DOI: 10.1016/j.biochi.2018.06.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023]
Abstract
Based on recent advances on the Ca2+-activated F1FO-ATPase features, a novel multistep mechanism involving the mitochondrial F1FO complex in the formation and opening of the still enigmatic mitochondrial permeability transition pore (MPTP), is proposed. MPTP opening makes the inner mitochondrial membrane (IMM) permeable to ions and solutes and, through cascade events, addresses cell fate to death. Since MPTP forms when matrix Ca2+ concentration rises and ATP is hydrolyzed by the F1FO-ATPase, conformational changes, triggered by Ca2+ insertion in F1, may be transmitted to FO and locally modify the IMM curvature. These events would cause F1FO-ATPase dimer dissociation and MPTP opening.
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Affiliation(s)
- Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy
| | - Fabiana Trombetti
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy
| | - Vittoria Ventrella
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy
| | - Alessandra Pagliarani
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy.
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9
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Nesci S, Trombetti F, Ventrella V, Pirini M, Pagliarani A. Kinetic properties of the mitochondrial F 1 F O -ATPase activity elicited by Ca 2+ in replacement of Mg 2+. Biochimie 2017; 140:73-81. [DOI: 10.1016/j.biochi.2017.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/22/2017] [Indexed: 12/24/2022]
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Bernardi P, Rasola A, Forte M, Lippe G. The Mitochondrial Permeability Transition Pore: Channel Formation by F-ATP Synthase, Integration in Signal Transduction, and Role in Pathophysiology. Physiol Rev 2015; 95:1111-55. [PMID: 26269524 DOI: 10.1152/physrev.00001.2015] [Citation(s) in RCA: 420] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The mitochondrial permeability transition (PT) is a permeability increase of the inner mitochondrial membrane mediated by a channel, the permeability transition pore (PTP). After a brief historical introduction, we cover the key regulatory features of the PTP and provide a critical assessment of putative protein components that have been tested by genetic analysis. The discovery that under conditions of oxidative stress the F-ATP synthases of mammals, yeast, and Drosophila can be turned into Ca(2+)-dependent channels, whose electrophysiological properties match those of the corresponding PTPs, opens new perspectives to the field. We discuss structural and functional features of F-ATP synthases that may provide clues to its transition from an energy-conserving into an energy-dissipating device as well as recent advances on signal transduction to the PTP and on its role in cellular pathophysiology.
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Affiliation(s)
- Paolo Bernardi
- Department of Biomedical Sciences and Consiglio Nazionale delle Ricerche Neuroscience Institute, University of Padova, Padova, Italy; Vollum Institute, Oregon Health and Sciences University, Portland, Oregon; and Department of Food Science, University of Udine, Udine, Italy
| | - Andrea Rasola
- Department of Biomedical Sciences and Consiglio Nazionale delle Ricerche Neuroscience Institute, University of Padova, Padova, Italy; Vollum Institute, Oregon Health and Sciences University, Portland, Oregon; and Department of Food Science, University of Udine, Udine, Italy
| | - Michael Forte
- Department of Biomedical Sciences and Consiglio Nazionale delle Ricerche Neuroscience Institute, University of Padova, Padova, Italy; Vollum Institute, Oregon Health and Sciences University, Portland, Oregon; and Department of Food Science, University of Udine, Udine, Italy
| | - Giovanna Lippe
- Department of Biomedical Sciences and Consiglio Nazionale delle Ricerche Neuroscience Institute, University of Padova, Padova, Italy; Vollum Institute, Oregon Health and Sciences University, Portland, Oregon; and Department of Food Science, University of Udine, Udine, Italy
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11
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Bernardi P, Di Lisa F, Fogolari F, Lippe G. From ATP to PTP and Back: A Dual Function for the Mitochondrial ATP Synthase. Circ Res 2015; 116:1850-62. [PMID: 25999424 DOI: 10.1161/circresaha.115.306557] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondria not only play a fundamental role in heart physiology but are also key effectors of dysfunction and death. This dual role assumes a new meaning after recent advances on the nature and regulation of the permeability transition pore, an inner membrane channel whose opening requires matrix Ca(2+) and is modulated by many effectors including reactive oxygen species, matrix cyclophilin D, Pi (inorganic phosphate), and matrix pH. The recent demonstration that the F-ATP synthase can reversibly undergo a Ca(2+)-dependent transition to form a channel that mediates the permeability transition opens new perspectives to the field. These findings demand a reassessment of the modifications of F-ATP synthase that take place in the heart under pathological conditions and of their potential role in determining the transition of F-ATP synthase from and energy-conserving into an energy-dissipating device.
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Affiliation(s)
- Paolo Bernardi
- From the Department of Biomedical Sciences, University of Padova, Italy (P.B., F.D.L.); and Department of Medical and Biological Sciences (F.F) and Department of Food Science (G.L.), University of Udine, Udine, Italy.
| | - Fabio Di Lisa
- From the Department of Biomedical Sciences, University of Padova, Italy (P.B., F.D.L.); and Department of Medical and Biological Sciences (F.F) and Department of Food Science (G.L.), University of Udine, Udine, Italy
| | - Federico Fogolari
- From the Department of Biomedical Sciences, University of Padova, Italy (P.B., F.D.L.); and Department of Medical and Biological Sciences (F.F) and Department of Food Science (G.L.), University of Udine, Udine, Italy
| | - Giovanna Lippe
- From the Department of Biomedical Sciences, University of Padova, Italy (P.B., F.D.L.); and Department of Medical and Biological Sciences (F.F) and Department of Food Science (G.L.), University of Udine, Udine, Italy
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12
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Ahmad Z, Winjobi M, Kabir MA. Significance of αThr-349 in the catalytic sites of Escherichia coli ATP synthase. Biochemistry 2014; 53:7376-85. [PMID: 25375895 PMCID: PMC4255642 DOI: 10.1021/bi5013063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
This
paper describes the role of α-subunit VISIT-DG sequence
residue αThr-349 in the catalytic sites of Escherichia
coli F1Fo ATP synthase. X-ray structures
show the highly conserved αThr-349 in the proximity (2.68 Å)
of the conserved phosphate binding residue βR182 in the phosphate
binding subdomain. αT349A, -D, -Q, and -R mutations caused 90–100-fold
losses of oxidative phosphorylation and reduced ATPase activity of
F1Fo in membranes. Double mutation αT349R/βR182A
was able to partially compensate for the absence of known phosphate
binding residue βR182. Azide, fluoroaluminate, and fluoroscandium
caused insignificant inhibition of αT349A, -D, and -Q mutants,
slight inhibition of the αT349R mutant, partial inhibition of
the αT349R/βR182A double mutant, and complete inhibition
of the wild type. Whereas NBD-Cl (7-chloro-4-nitrobenzo-2-oxa-1,3-diazole)
inhibited wild-type ATPase and its αT349A, -D, -R, and -Q mutants
essentially completely, βR182A ATPase and double mutant αT349A/βR182A
were inhibited partially. Inhibition characteristics supported the
conclusion that NBD-Cl reacts in βE (empty) catalytic sites,
as shown previously by X-ray structure analysis. Phosphate protected
against NBD-Cl inhibition in the wild type, αT349R, and double
mutant αT349R/βR182A but not in αT349A, αT349D,
or αT349Q. The results demonstrate that αThr-349 is a
supplementary residue involved in phosphate binding and transition
state stabilization in ATP synthase catalytic sites through its interaction
with βR182.
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Affiliation(s)
- Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences , Kirksville, Missouri 63501, United States
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13
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Bojovschi A, Liu MS, Sadus RJ. Mg²⁺ coordinating dynamics in Mg:ATP fueled motor proteins. J Chem Phys 2014; 140:115102. [PMID: 24655204 DOI: 10.1063/1.4867898] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The coordination of Mg(2+) with the triphosphate group of adenosine triphosphate (ATP) in motor proteins is investigated using data mining and molecular dynamics. The possible coordination structures available from crystal data for actin, myosin, RNA polymerase, DNA polymerase, DNA helicase, and F1-ATPase are verified and investigated further by molecular dynamics. Coordination states are evaluated using structural analysis and quantified by radial distribution functions, coordination numbers, and pair interaction energy calculations. The results reveal a diverse range of both transitory and stable coordination arrangements between Mg(2+) and ATP. The two most stable coordinating states occur when Mg(2+) coordinates two or three oxygens from the triphosphate group of ATP. Evidence for five-site coordination is also reported involving water in addition to the triphosphate group. The stable states correspond to a pair interaction energy of either ∼-2750 kJ/mol or -3500 kJ/mol. The role of water molecules in the hydration shell surrounding Mg(2+) is also reported.
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Affiliation(s)
- A Bojovschi
- Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
| | - Ming S Liu
- Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
| | - Richard J Sadus
- Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
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14
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ATP synthase: the right size base model for nanomotors in nanomedicine. ScientificWorldJournal 2014; 2014:567398. [PMID: 24605056 PMCID: PMC3925597 DOI: 10.1155/2014/567398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/05/2013] [Indexed: 11/17/2022] Open
Abstract
Nanomedicine results from nanotechnology where molecular scale minute precise nanomotors can be used to treat disease conditions. Many such biological nanomotors are found and operate in living systems which could be used for therapeutic purposes. The question is how to build nanomachines that are compatible with living systems and can safely operate inside the body? Here we propose that it is of paramount importance to have a workable base model for the development of nanomotors in nanomedicine usage. The base model must placate not only the basic requirements of size, number, and speed but also must have the provisions of molecular modulations. Universal occurrence and catalytic site molecular modulation capabilities are of vital importance for being a perfect base model. In this review we will provide a detailed discussion on ATP synthase as one of the most suitable base models in the development of nanomotors. We will also describe how the capabilities of molecular modulation can improve catalytic and motor function of the enzyme to generate a catalytically improved and controllable ATP synthase which in turn will help in building a superior nanomotor. For comparison, several other biological nanomotors will be described as well as their applications for nanotechnology.
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Ahmad Z, Ahmad M, Okafor F, Jones J, Abunameh A, Cheniya RP, Kady IO. Effect of structural modulation of polyphenolic compounds on the inhibition of Escherichia coli ATP synthase. Int J Biol Macromol 2012; 50:476-86. [PMID: 22285988 PMCID: PMC4303583 DOI: 10.1016/j.ijbiomac.2012.01.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 11/23/2022]
Abstract
In this paper we present the inhibitory effect of a variety of structurally modulated/modified polyphenolic compounds on purified F(1) or membrane bound F(1)F(o)Escherichia coli ATP synthase. Structural modulation of polyphenols with two phenolic rings inhibited ATP synthase essentially completely; one or three ringed polyphenols individually or fused together inhibited partially. We found that the position of hydroxyl and nitro groups plays critical role in the degree of binding and inhibition of ATPase activity. The extended positioning of hydroxyl groups on imino diphenolic compounds diminished the inhibition and abridged position enhanced the inhibition potency. This was contrary to the effect by simple single ringed phenolic compounds where extended positioning of hydroxyl group was found to be effective for inhibition. Also, introduction of nitro group augmented the inhibition on molar scale in comparison to the inhibition by resveratrol but addition of phosphate group did not. Similarly, aromatic diol or triol with rigid or planar ring structure and no free rotation poorly inhibited the ATPase activity. The inhibition was identical in both F(1)F(o) membrane preparations as well as in isolated purified F(1) and was reversible in all cases. Growth assays suggested that modulated compounds used in this study inhibited F(1)-ATPase as well as ATP synthesis nearly equally.
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Affiliation(s)
- Zulfiqar Ahmad
- Department of Biological and Environmental Sciences, Box 610, Alabama A&M University, Normal, AL 35762, USA.
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16
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Blum DJ, Ko YH, Pedersen PL. Mitochondrial ATP Synthase Catalytic Mechanism: A Novel Visual Comparative Structural Approach Emphasizes Pivotal Roles for Mg2+ and P-Loop Residues in Making ATP. Biochemistry 2012; 51:1532-46. [DOI: 10.1021/bi201595v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David J. Blum
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, 725
North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Young H. Ko
- Cancer Cure Med, LLC, 300 Redland Court, Suite 212, Owings Mills, Maryland
21117, United States
| | - Peter L. Pedersen
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, 725
North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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17
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Ahmad Z, Okafor F, Laughlin TF. Role of Charged Residues in the Catalytic Sites of Escherichia coli ATP Synthase. JOURNAL OF AMINO ACIDS 2011; 2011:785741. [PMID: 22312470 PMCID: PMC3268026 DOI: 10.4061/2011/785741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/21/2011] [Indexed: 11/21/2022]
Abstract
Here we describe the role of charged amino acids at the catalytic sites of Escherichia coli ATP synthase. There are four positively charged and four negatively charged residues in the vicinity of of E. coli ATP synthase catalytic sites. Positive charges are contributed by three arginine and one lysine, while negative charges are contributed by two aspartic acid and two glutamic acid residues. Replacement of arginine with a neutral amino acid has been shown to abrogate phosphate binding, while restoration of phosphate binding has been accomplished by insertion of arginine at the same or a nearby location. The number and position of positive charges plays a critical role in the proper and efficient binding of phosphate. However, a cluster of many positive charges inhibits phosphate binding. Moreover, the presence of negatively charged residues seems a requisite for the proper orientation and functioning of positively charged residues in the catalytic sites. This implies that electrostatic interactions between amino acids are an important constituent of initial phosphate binding in the catalytic sites. Significant loss of function in growth and ATPase activity assays in mutants generated through charge modulations has demonstrated that precise location and stereochemical interactions are of paramount importance.
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Affiliation(s)
- Zulfiqar Ahmad
- Department of Biology, Alabama A&M University, P.O. Box 610, Normal, AL 35762, USA
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18
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Priest C, Prives C, Poyurovsky MV. Deconstructing nucleotide binding activity of the Mdm2 RING domain. Nucleic Acids Res 2010; 38:7587-98. [PMID: 20671028 PMCID: PMC2995081 DOI: 10.1093/nar/gkq669] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Mdm2, a central negative regulator of the p53 tumor suppressor, possesses a Really Interesting New Gene (RING) domain within its C-terminus. In addition to E3 ubiquitin ligase activity, the Mdm2 RING preferentially binds adenine base nucleotides, and such binding leads to a conformational change in the Mdm2 C-terminus. Here, we present further biochemical analysis of the nucleotide–Mdm2 interaction. We have found that MdmX, an Mdm2 family member with high sequence homology, binds adenine nucleotides with similar affinity and specificity as Mdm2, suggesting that residues involved in nucleotide binding may be conserved between the two proteins and adenosine triphosphate (ATP) binding may have similar functional consequences for both Mdm family members. By generating and testing a series of proteins with deletions and substitution mutations within the Mdm2 RING, we mapped the specific adenine nucleotide binding region of Mdm2 to residues 429–484, encompassing the minimal RING domain. Using a series of ATP derivatives, we demonstrate that phosphate coordination by the Mdm2 P-loop contributes to, but is not primarily responsible for, ATP binding. Additionally, we have identified the 2′ and 3′ hydroxyls of the ribose and the C6 amino group of the adenine base moiety as being essential for binding.
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Affiliation(s)
- Christina Priest
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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19
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Chinnam N, Dadi PK, Sabri SA, Ahmad M, Kabir MA, Ahmad Z. Dietary bioflavonoids inhibit Escherichia coli ATP synthase in a differential manner. Int J Biol Macromol 2010; 46:478-86. [PMID: 20346967 DOI: 10.1016/j.ijbiomac.2010.03.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 03/16/2010] [Accepted: 03/17/2010] [Indexed: 12/11/2022]
Abstract
The aim of this study was to determine if the dietary benefits of bioflavonoids are linked to the inhibition of ATP synthase. We studied the inhibitory effect of 17 bioflavonoid compounds on purified F1 or membrane bound F1Fo E. coli ATP synthase. We found that the extent of inhibition by bioflavonoid compounds was variable. Morin, silymarin, baicalein, silibinin, rimantadin, amantidin, or, epicatechin resulted in complete inhibition. The most potent inhibitors on molar scale were morin (IC50 approximately 0.07 mM)>silymarin (IC50 approximately 0.11 mM)>baicalein (IC50 approximately 0.29 mM)>silibinin (IC50 approximately 0.34 mM)>rimantadin (IC50 approximately 2.0 mM)>amantidin (IC50 approximately 2.5 mM)>epicatechin (IC50 approximately 4.0 mM). Inhibition by hesperidin, chrysin, kaempferol, diosmin, apigenin, genistein, or rutin was partial in the range of 40-60% and inhibition by galangin, daidzein, or luteolin was insignificant. The main skeleton, size, shape, geometry, and position of functional groups on inhibitors played important role in the effective inhibition of ATP synthase. In all cases inhibition was found fully reversible and identical in both F1Fo membrane preparations and isolated purified F1. ATPase and growth assays suggested that the bioflavonoid compounds used in this study inhibited F1-ATPase as well as ATP synthesis nearly equally, which signifies a link between the beneficial effects of dietary bioflavonoids and their inhibitory action on ATP synthase.
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Affiliation(s)
- Nagababu Chinnam
- Department of Biological Sciences, Box 70703, East Tennessee State University, Johnson City, TN 37614, USA
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20
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Laughlin TF, Ahmad Z. Inhibition of Escherichia coli ATP synthase by amphibian antimicrobial peptides. Int J Biol Macromol 2010; 46:367-74. [PMID: 20100509 DOI: 10.1016/j.ijbiomac.2010.01.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 01/18/2010] [Accepted: 01/18/2010] [Indexed: 11/30/2022]
Abstract
Previously melittin, the alpha-helical basic honey bee venom peptide, was shown to inhibit F(1)-ATPase by binding at the beta-subunit DELSEED motif of F(1)F(o)-ATP synthase. Herein, we present the inhibitory effects of the basic alpha-helical amphibian antimicrobial peptides, ascaphin-8, aurein 2.2, aurein 2.3, carein 1.8, carein 1.9, citropin 1.1, dermaseptin, maculatin 1.1, maganin II, MRP, or XT-7, on purified F(1) and membrane bound F(1)F(0)Escherichia coli ATP synthase. We found that the extent of inhibition by amphibian peptides is variable. Whereas MRP-amide inhibited ATPase essentially completely (approximately 96% inhibition), carein 1.8 did not inhibit at all (0% inhibition). Inhibition by other peptides was partial with a range of approximately 13-70%. MRP-amide was also the most potent inhibitor on molar scale (IC(50) approximately 3.25 microM). Presence of an amide group at the c-terminal of peptides was found to be critical in exerting potent inhibition of ATP synthase ( approximately 20-40% additional inhibition). Inhibition was fully reversible and found to be identical in both F(1)F(0) membrane preparations as well as in isolated purified F(1). Interestingly, growth of E. coli was abrogated in the presence of ascaphin-8, aurein 2.2, aurein 2.3, citropin 1.1, dermaseptin, magainin II-amide, MRP, MRP-amide, melittin, or melittin-amide but was unaffected in the presence of carein 1.8, carein 1.9, maculatin 1.1, magainin II, or XT-7. Hence inhibition of F(1)-ATPase and E. coli cell growth by amphibian antimicrobial peptides suggests that their antimicrobial/anticancer properties are in part linked to their actions on ATP synthase.
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Affiliation(s)
- Thomas F Laughlin
- Department of Biological Sciences, Box 70703, East Tennessee State University, Johnson City, TN 37614, USA
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21
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Inhibition of ATPase activity of Escherichia coli ATP synthase by polyphenols. Int J Biol Macromol 2009; 45:72-9. [PMID: 19375450 DOI: 10.1016/j.ijbiomac.2009.04.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Revised: 04/07/2009] [Accepted: 04/08/2009] [Indexed: 01/09/2023]
Abstract
We have studied the inhibitory effect of five polyphenols namely, resveratrol, piceatannol, quercetin, quercetrin, and quercetin-3-beta-D glucoside on Escherichia coli ATP synthase. Recently published X-ray crystal structures of bovine mitochondrial ATP synthase inhibited by resveratrol, piceatannol, and quercetin, suggest that these compounds bind in a hydrophobic pocket between the gamma-subunit C-terminal tip and the hydrophobic inside of the surrounding annulus in a region critical for rotation of the gamma-subunit. Herein, we show that resveratrol, piceatannol, quercetin, quercetrin, or quercetin-3-beta-d glucoside all inhibit E. coli ATP synthase but to different degrees. Whereas piceatannol inhibited ATPase essentially completely ( approximately 0 residual activity), inhibition by other compounds was partial with approximately 20% residual activity by quercetin, approximately 50% residual activity by quercetin-3-beta-D glucoside, and approximately 60% residual activity by quercetrin or resveratrol. Piceatannol was the most potent inhibitor (IC(50) approximately 14 microM) followed by quercetin (IC(50) approximately 33 microM), quercetin-3-beta-D glucoside (IC(50) approximately 71 microM), resveratrol (IC(50) approximately 94 microM), quercitrin (IC(50) approximately 120 microM). Inhibition was identical in both F(1)F(o) membrane preparations as well as in isolated purified F(1). In all cases inhibition was reversible. Interestingly, resveratrol and piceatannol inhibited both ATPase and ATP synthesis whereas quercetin, quercetrin or quercetin-3-beta-d glucoside inhibited only ATPase activity and not ATP synthesis.
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22
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Li W, Brudecki LE, Senior AE, Ahmad Z. Role of {alpha}-subunit VISIT-DG sequence residues Ser-347 and Gly-351 in the catalytic sites of Escherichia coli ATP synthase. J Biol Chem 2009; 284:10747-54. [PMID: 19240022 DOI: 10.1074/jbc.m809209200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This paper describes the role of alpha-subunit VISIT-DG sequence residues alphaSer-347 and alphaGly-351 in catalytic sites of Escherichia coli F(1)F(o) ATP synthase. X-ray structures show the very highly conserved alpha-subunit VISIT-DG sequence in close proximity to the conserved phosphate-binding residues alphaArg-376, betaArg-182, betaLys-155, and betaArg-246 in the phosphate-binding subdomain. Mutations alphaS347Q and alphaG351Q caused loss of oxidative phosphorylation and reduced ATPase activity of F(1)F(o) in membranes by 100- and 150-fold, respectively, whereas alphaS347A mutation showed only a 13-fold loss of activity and also retained some oxidative phosphorylation activity. The ATPase of alphaS347Q mutant was not inhibited, and the alphaS347A mutant was slightly inhibited by MgADP-azide, MgADP-fluoroaluminate, or MgADP-fluoroscandium, in contrast to wild type and alphaG351Q mutant. Whereas 7-chloro-4-nitrobenzo-2-oxa-1, 3-diazole (NBD-Cl) inhibited wild type and alphaG351Q mutant ATPase essentially completely, ATPase in alphaS347A or alphaS347Q mutant was inhibited maximally by approximately 80-90%, although reaction still occurred at residue betaTyr-297, proximal to the alpha-subunit VISIT-DG sequence, near the phosphate-binding pocket. Inhibition characteristics supported the conclusion that NBD-Cl reacts inbetaE (empty) catalytic sites, as shown previously by x-ray structure analysis. Phosphate protected against NBD-Cl inhibition in wild type and alphaG351Q mutant but not in alphaS347Q or alphaS347A mutant. The results demonstrate that alphaSer-347 is an additional residue involved in phosphate-binding and transition state stabilization in ATP synthase catalytic sites. In contrast, alphaGly-351, although strongly conserved and clearly important for function, appears not to play a direct role.
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Affiliation(s)
- Wenzong Li
- Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee 37614, USA
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23
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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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24
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Brudecki LE, Grindstaff JJ, Ahmad Z. Role of alphaPhe-291 residue in the phosphate-binding subdomain of catalytic sites of Escherichia coli ATP synthase. Arch Biochem Biophys 2008; 471:168-75. [PMID: 18242162 DOI: 10.1016/j.abb.2008.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2007] [Revised: 01/15/2008] [Accepted: 01/17/2008] [Indexed: 11/28/2022]
Abstract
The role of alphaPhe-291 residue in phosphate binding by Escherichia coli F1F0-ATP synthase was examined. X-ray structures of bovine mitochondrial enzyme suggest that this residue resides in close proximity to the conserved betaR246 residue. Herein, we show that mutations alphaF291D and alphaF291E in E. coli reduce the ATPase activity of F1F0 membranes by 350-fold. Yet, significant oxidative phosphorylation activity is retained. In contrast to wild-type, ATPase activities of mutants were not inhibited by MgADP-azide, MgADP-fluoroaluminate, or MgADP-fluoroscandium. Whereas, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) inhibited wild-type ATPase essentially completely, ATPase in mutants was inhibited maximally by approximately 75%, although reaction still occurred at residue betaTyr-297, proximal to alphaPhe-291 in the phosphate-binding pocket. Inhibition characteristics supported the conclusion that NBD-Cl reacts in betaE (empty) catalytic sites, as shown previously by X-ray structure analysis. Phosphate protected against NBD-Cl inhibition in wild-type but not in mutants. In addition, our data suggest that the interaction of alphaPhe-291 with phosphate during ATP hydrolysis or synthesis may be distinct.
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Affiliation(s)
- Laura E Brudecki
- Department of Biological Sciences, Box 70703, East Tennessee State University, Johnson City, TN 37614, USA
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25
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Barriuso-Iglesias M, Barreiro C, Flechoso F, Martín JF. Transcriptional analysis of the F0F1 ATPase operon of Corynebacterium glutamicum ATCC 13032 reveals strong induction by alkaline pH. MICROBIOLOGY-SGM 2006; 152:11-21. [PMID: 16385111 DOI: 10.1099/mic.0.28383-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Corynebacterium glutamicum, a soil Gram-positive bacterium used for industrial amino acid production, was found to grow optimally at pH 7.0-9.0 when incubated in 5 litre fermenters under pH-controlled conditions. The highest biomass was accumulated at pH 9.0. Growth still occurred at pH 9.5 but at a reduced rate. The expression of the pH-regulated F0 F1 ATPase operon (containing the eight genes atpBEFHAGDC) was induced at alkaline pH. A 7.5 kb transcript, corresponding to the eight-gene operon, was optimally expressed at pH 9.0. The same occurred with a 1.2 kb transcript corresponding to the atpB gene. RT-PCR studies confirmed the alkaline pH induction of the F0 F1 operon and the existence of the atpI gene. The atpI gene, located upstream of the F0 F1 operon, was expressed at a lower level than the polycistronic 7.5 kb mRNA, from a separate promoter (P-atp1). Expression of the major promoter of the F0 F1 operon, designated P-atp2, and the P-atp1 promoter was quantified by coupling them to the pET2 promoter-probe vector. Both P-atp1 and P-atp2 were functional in C. glutamicum and Escherichia coli. Primer extension analysis identified one transcription start point inside each of the two promoter regions. The P-atp1 promoter fitted the consensus sequence of promoters recognized by the vegetative sigma factor of C. glutamicum, whereas the -35 and -10 boxes of P-atp2 fitted the consensus sequence for sigma(H)-recognized Mycobacterium tuberculosis promoters C(C)/(G)GG(A)/(G)AC 17-22 nt (C)/(G)GTT(C)/(G), known to be involved in expression of heat-shock and other stress-response genes. These results suggest that the F0 F1 operon is highly expressed at alkaline pH, probably using a sigma (H) RNA polymerase.
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Affiliation(s)
- Mónica Barriuso-Iglesias
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real 1, 24006 León, Spain
| | - Carlos Barreiro
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real 1, 24006 León, Spain
| | - Fabio Flechoso
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real 1, 24006 León, Spain
| | - Juan F Martín
- University of León, Facultad de Ciencias Biológicas y Ambientales, Campus de Vegazana s/n, 24071 León, Spain
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Av. Real 1, 24006 León, Spain
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26
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Greene MD, Frasch WD. Interactions among gamma R268, gamma Q269, and the beta subunit catch loop of Escherichia coli F1-ATPase are important for catalytic activity. J Biol Chem 2003; 278:51594-8. [PMID: 14532272 DOI: 10.1074/jbc.m309948200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Removal of the ability to form a salt bridge or hydrogen bonds between the beta subunit catch loop (beta Y297-D305) and the gamma subunit of Escherichia coli F1Fo-ATP synthase significantly altered the ability of the enzyme to hydrolyze ATP and the bacteria to grow via oxidative phosphorylation. Residues beta T304, beta D305, beta D302, gamma Q269, and gamma R268 were found to be very important for ATP hydrolysis catalyzed by soluble F1-ATPase, and the latter four residues were also very important for oxidative phosphorylation. The greatest effects on catalytic activity were observed by the substitution of side chains that contribute to the shortest and/or multiple H-bonds as well as the salt bridge. Residue beta D305 would not tolerate substitution with Val or Ser and had extremely low activity as beta D305E, suggesting that this residue is particularly important for synthesis and hydrolysis activity. These results provide evidence that tight winding of the gamma subunit coiled-coil is important to the rate-limiting step in ATP hydrolysis and are consistent with an escapement mechanism for ATP synthesis in which alpha beta gamma intersubunit interactions provide a means to make substrate binding a prerequisite of proton gradient-driven gamma subunit rotation.
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Affiliation(s)
- Matthew D Greene
- Center for the Study of Early Events in Photosynthesis, School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
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27
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Hicks DB, Wang Z, Wei Y, Kent R, Guffanti AA, Banciu H, Bechhofer DH, Krulwich TA. A tenth atp gene and the conserved atpI gene of a Bacillus atp operon have a role in Mg2+ uptake. Proc Natl Acad Sci U S A 2003; 100:10213-8. [PMID: 12917488 PMCID: PMC193541 DOI: 10.1073/pnas.1832982100] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2003] [Indexed: 11/18/2022] Open
Abstract
The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein of unknown function. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI. Most Bacillus species, and some other bacteria, possess atpZ homologues. AtpZ is predicted to be a membrane protein with a hairpin topology, and was detected by Western analyses. Deletion of atpZ, atpI, or atpZI from B. pseudofirmus OF4 led to a requirement for a greatly increased concentration of Mg2+ for growth at pH 7.5. Either atpZ, atpI, or atpZI complemented the similar phenotype of a triple mutant of Salmonella typhimurium (MM281), which is deficient in Mg2+ uptake. atpZ and atpI, separately and together, increased the Mg2+-sensitive 45Ca2+ uptake by vesicles of an Escherichia coli mutant that is defective in Ca2+ and Na+ efflux. We hypothesize that AtpZ and AtpI, as homooligomers, and perhaps as heterooligomers, are Mg2+ transporter, Ca2+ transporter, or channel proteins. Such proteins could provide Mg2+, which is required by ATP synthase, and also support charge compensation, when the enzyme is functioning in the hydrolytic direction; e.g., during cytoplasmic pH regulation.
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Affiliation(s)
- David B Hicks
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY 10029, USA
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28
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Abstract
Using molecular dynamics, we study the unbinding of ATP in F(1)-ATPase from its tight binding state to its weak binding state. The calculations are made feasible through use of interpolated atomic structures from Wang and Oster [Nature 1998, 396: 279-282]. These structures are applied to atoms distant from the catalytic site. The forces from these distant atoms gradually drive a large primary region through a series of sixteen equilibrated steps that trace the hinge bending conformational change in the beta-subunit that drives rotation of gamma-subunit. As the rotation progresses, we find a sequential weakening and breaking of the hydrogen bonds between the ATP molecule and the alpha- and beta-subunits of the ATPase. This finding agrees with the "binding-zipper" model [Oster and Wang, BIOCHIM: Biophys. Acta 2000, 1458: 482-510.] In this model, the progressive formation of the hydrogen bonds is the energy source driving the rotation of the gamma-shaft during hydrolysis. Conversely, the corresponding sequential breaking of these bonds is driven by rotation of the shaft during ATP synthesis. Our results for the energetics during rotation suggest that the nucleotide's coordination with Mg(2+) during binding and release is necessary to account for the observed high efficiency of the motor.
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Affiliation(s)
- Iris Antes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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29
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Lippe G, Di Pancrazio F, Contessi S, Bortolotti N, Polizio F, Mavelli I. The nucleotide-independent Fe(III)-binding site is located on β subunit of the mitochondrial F1-ATPase. Biochem Biophys Res Commun 2002; 297:587-92. [PMID: 12270135 DOI: 10.1016/s0006-291x(02)02220-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Upon separation of a crude preparation of beta subunit ("beta fraction") from mitochondrial F(1)-ATPase containing one equivalent of Fe(III) in the nucleotide-independent site (1Fe(III)-loaded MF(1)), Fe(III) is almost completely recovered. CD spectra show that "beta fraction" maintains the structural changes induced by Fe(III) in the whole enzyme. In accordance, EPR reveals that the Fe(III) site geometry is conserved in "beta fraction." Moreover, the EPR spectra of 1Fe(III)-loaded MF(1) and its "beta fraction" undergo similar changes of the line-shape upon Pi binding at the catalytic site, indicating that the Pi and Fe(III) are proximal on beta. Highly purified beta in nucleotide-free form binds 1mol of Fe(III)/mol of protein. MF(1) "freezed" by inhibitors with two beta in closed conformation and one beta in open or half-closed conformation binds 1mol of Fe(III)/mol of enzyme. Therefore, the Fe(III) site location in the unique beta subunit not adopting the closed conformation is proposed.
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Affiliation(s)
- G Lippe
- Department of Biomedical Sciences and Technologies, University of Udine, P.le Kolbe 4, 33100 Udine, Italy.
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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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