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Kinetic Mathematical Modeling of Oxidative Phosphorylation in Cardiomyocyte Mitochondria. Cells 2022; 11:cells11244020. [PMID: 36552784 PMCID: PMC9777548 DOI: 10.3390/cells11244020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OXPHOS) is an oxygen-dependent process that consumes catabolized nutrients to produce adenosine triphosphate (ATP) to drive energy-dependent biological processes such as excitation-contraction coupling in cardiomyocytes. In addition to in vivo and in vitro experiments, in silico models are valuable for investigating the underlying mechanisms of OXPHOS and predicting its consequences in both physiological and pathological conditions. Here, we compare several prominent kinetic models of OXPHOS in cardiomyocytes. We examine how their mathematical expressions were derived, how their parameters were obtained, the conditions of their experimental counterparts, and the predictions they generated. We aim to explore the general landscape of energy production mechanisms in cardiomyocytes for future in silico models.
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2
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Shichkova P, Coggan JS, Markram H, Keller D. A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. Front Mol Neurosci 2021; 14:604559. [PMID: 34858137 PMCID: PMC8631404 DOI: 10.3389/fnmol.2021.604559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/05/2021] [Indexed: 12/12/2022] Open
Abstract
Accurate molecular concentrations are essential for reliable analyses of biochemical networks and the creation of predictive models for molecular and systems biology, yet protein and metabolite concentrations used in such models are often poorly constrained or irreproducible. Challenges of using data from different sources include conflicts in nomenclature and units, as well as discrepancies in experimental procedures, data processing and implementation of the model. To obtain a consistent estimate of protein and metabolite levels, we integrated and normalized data from a large variety of sources to calculate Adjusted Molecular Concentrations. We found a high degree of reproducibility and consistency of many molecular species across brain regions and cell types, consistent with tight homeostatic regulation. We demonstrated the value of this normalization with differential protein expression analyses related to neurodegenerative diseases, brain regions and cell types. We also used the results in proof-of-concept simulations of brain energy metabolism. The standardized Brain Molecular Atlas overcomes the obstacles of missing or inconsistent data to support systems biology research and is provided as a resource for biomolecular modeling.
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Affiliation(s)
- Polina Shichkova
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland
| | - Jay S Coggan
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland
| | - Henry Markram
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland.,Laboratory of Neural Microcircuitry, Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Daniel Keller
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland
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3
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Lee JW. Mitochondrial energetics with transmembrane electrostatically localized protons: do we have a thermotrophic feature? Sci Rep 2021; 11:14575. [PMID: 34272427 PMCID: PMC8285424 DOI: 10.1038/s41598-021-93853-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/07/2021] [Indexed: 01/24/2023] Open
Abstract
Transmembrane electrostatically localized protons (TELP) theory has been recently recognized as an important addition over the classic Mitchell's chemiosmosis; thus, the proton motive force (pmf) is largely contributed from TELP near the membrane. As an extension to this theory, a novel phenomenon of mitochondrial thermotrophic function is now characterized by biophysical analyses of pmf in relation to the TELP concentrations at the liquid-membrane interface. This leads to the conclusion that the oxidative phosphorylation also utilizes environmental heat energy associated with the thermal kinetic energy (kBT) of TELP in mitochondria. The local pmf is now calculated to be in a range from 300 to 340 mV while the classic pmf (which underestimates the total pmf) is in a range from 60 to 210 mV in relation to a range of membrane potentials from 50 to 200 mV. Depending on TELP concentrations in mitochondria, this thermotrophic function raises pmf significantly by a factor of 2.6 to sixfold over the classic pmf. Therefore, mitochondria are capable of effectively utilizing the environmental heat energy with TELP for the synthesis of ATP, i.e., it can lock heat energy into the chemical form of energy for cellular functions.
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Affiliation(s)
- James Weifu Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA.
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4
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Lee JW. Energy Renewal: Isothermal Utilization of Environmental Heat Energy with Asymmetric Structures. ENTROPY (BASEL, SWITZERLAND) 2021; 23:665. [PMID: 34070431 PMCID: PMC8228076 DOI: 10.3390/e23060665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 11/18/2022]
Abstract
Through the research presented herein, it is quite clear that there are two thermodynamically distinct types (A and B) of energetic processes naturally occurring on Earth. Type A, such as glycolysis and the tricarboxylic acid cycle, apparently follows the second law well; Type B, as exemplified by the thermotrophic function with transmembrane electrostatically localized protons presented here, does not necessarily have to be constrained by the second law, owing to its special asymmetric function. This study now, for the first time, numerically shows that transmembrane electrostatic proton localization (Type-B process) represents a negative entropy event with a local protonic entropy change (ΔSL) in a range from -95 to -110 J/K∙mol. This explains the relationship between both the local protonic entropy change (ΔSL) and the mitochondrial environmental temperature (T) and the local protonic Gibbs free energy (ΔGL=TΔSL) in isothermal environmental heat utilization. The energy efficiency for the utilization of total protonic Gibbs free energy (ΔGT including ΔGL=TΔSL) in driving the synthesis of ATP is estimated to be about 60%, indicating that a significant fraction of the environmental heat energy associated with the thermal motion kinetic energy (kBT) of transmembrane electrostatically localized protons is locked into the chemical form of energy in ATP molecules. Fundamentally, it is the combination of water as a protonic conductor, and thus the formation of protonic membrane capacitor, with asymmetric structures of mitochondrial membrane and cristae that makes this amazing thermotrophic feature possible. The discovery of energy Type-B processes has inspired an invention (WO 2019/136037 A1) for energy renewal through isothermal environmental heat energy utilization with an asymmetric electron-gated function to generate electricity, which has the potential to power electronic devices forever, including mobile phones and laptops. This invention, as an innovative Type-B mimic, may have many possible industrial applications and is likely to be transformative in energy science and technologies for sustainability on Earth.
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Affiliation(s)
- James Weifu Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
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5
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Willis W, Willis E, Kuzmiak-Glancy S, Kras K, Hudgens J, Barakati N, Stern J, Mandarino L. Oxidative phosphorylation K 0.5ADP in vitro depends on substrate oxidative capacity: Insights from a luciferase-based assay to evaluate ADP kinetic parameters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148430. [PMID: 33887230 DOI: 10.1016/j.bbabio.2021.148430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022]
Abstract
The K0.5ADP of oxidative phosphorylation (OxPhos) identifies the cytosolic ADP concentration which elicits one-half the maximum OxPhos rate. This kinetic parameter is commonly measured to assess mitochondrial metabolic control sensitivity. Here we describe a luciferase-based assay to evaluate the ADP kinetic parameters of mitochondrial ATP production from OxPhos, adenylate kinase (AK), and creatine kinase (CK). The high sensitivity, reproducibility, and throughput of the microplate-based assay enabled a comprehensive kinetic assessment of all three pathways in mitochondria isolated from mouse liver, kidney, heart, and skeletal muscle. Carboxyatractyloside titrations were also performed with the assay to estimate the flux control strength of the adenine nucleotide translocase (ANT) over OxPhos in human skeletal muscle mitochondria. ANT flux control coefficients were 0.91 ± 0.07, 0.83 ± 0.06, and 0.51 ± 0.07 at ADP concentrations of 6.25, 12.5, and 25 μM, respectively, an [ADP] range which spanned the K0.5ADP. The oxidative capacity of substrate combinations added to drive OxPhos was found to dramatically influence ADP kinetics in mitochondria from several tissues. In mouse skeletal muscle ten different substrate combinations elicited a 7-fold range of OxPhos Vmax, which correlated positively (R2 = 0.963) with K0.5ADP values ranging from 2.3 ± 0.2 μM to 11.9 ± 0.6 μM. We propose that substrate-enhanced capacity to generate the protonmotive force increases the OxPhos K0.5ADP because flux control at ANT increases, thus K0.5ADP rises toward the dissociation constant, KdADP, of ADP-ANT binding. The findings are discussed in the context of top-down metabolic control analysis.
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Affiliation(s)
- Wayne Willis
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona, Tucson, AZ, United States.
| | - Elizabeth Willis
- College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Sarah Kuzmiak-Glancy
- Department of Kinesiology, University of Maryland, College Park, MD, United States
| | - Katon Kras
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States
| | - Jamie Hudgens
- College of Pharmacy, Midwestern University, Glendale, AZ, United States
| | - Neusha Barakati
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States
| | - Jennifer Stern
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona, Tucson, AZ, United States
| | - Lawrence Mandarino
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, AZ, United States; Center for Disparities in Diabetes, Obesity, and Metabolism, University of Arizona, Tucson, AZ, United States
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Galkina KV, Zyrina AN, Golyshev SA, Kashko ND, Markova OV, Sokolov SS, Severin FF, Knorre DA. Mitochondrial dynamics in yeast with repressed adenine nucleotide translocator AAC2. Eur J Cell Biol 2020; 99:151071. [PMID: 32057484 DOI: 10.1016/j.ejcb.2020.151071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/25/2022] Open
Abstract
The mitochondrial network structure dynamically adapts to cellular metabolic challenges. Mitochondrial depolarisation, particularly, induces fragmentation of the network. This fragmentation may be a result of either a direct regulation of the mitochondrial fusion machinery by transmembrane potential or an indirect effect of metabolic remodelling. Activities of ATP synthase and adenine nucleotide translocator (ANT) link the mitochondrial transmembrane potential with the cytosolic NTP/NDP ratio. Given that mitochondrial fusion requires cytosolic GTP, a decrease in the NTP/NDP ratio might also account for protonophore-induced mitochondrial fragmentation. For evaluating the contributions of direct and indirect mechanisms to mitochondrial remodelling, we assessed the morphology of the mitochondrial network in yeast cells with inhibited ANT. We showed that the repression of AAC2 (PET9), a major ANT gene in yeast, increases mitochondrial transmembrane potential. However, the mitochondrial network in this strain was fragmented. Meanwhile, AAC2 repression did not prevent mitochondrial fusion in zygotes; nor did it inhibit mitochondrial hyperfusion induced by Dnm1p inhibitor mdivi-1. These results suggest that the inhibition of ANT, rather than preventing mitochondrial fusion, facilitates mitochondrial fission. The protonophores were not able to induce additional mitochondrial fragmentation in an AAC2-repressed strain and in yeast cells with inhibited ATP synthase. Importantly, treatment with the ATP synthase inhibitor oligomycin A also induced mitochondrial fragmentation and hyperpolarization. Taken together, our data suggest that ATP/ADP translocation plays a crucial role in shaping of the mitochondrial network and exemplify that an increase in mitochondrial membrane potential does not necessarily oppose mitochondrial fragmentation.
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Affiliation(s)
- Kseniia V Galkina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory 1-73, Moscow, 119991, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia
| | - Anna N Zyrina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia
| | - Sergey A Golyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia
| | - Nataliia D Kashko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory 1-73, Moscow, 119991, Russia
| | - Olga V Markova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia
| | - Svyatoslav S Sokolov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia
| | - Fedor F Severin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow, 119991, Russia; Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
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7
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van Hameren G, Campbell G, Deck M, Berthelot J, Gautier B, Quintana P, Chrast R, Tricaud N. In vivo real-time dynamics of ATP and ROS production in axonal mitochondria show decoupling in mouse models of peripheral neuropathies. Acta Neuropathol Commun 2019; 7:86. [PMID: 31186069 PMCID: PMC6558672 DOI: 10.1186/s40478-019-0740-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/16/2019] [Indexed: 12/31/2022] Open
Abstract
Mitochondria are critical for the function and maintenance of myelinated axons notably through Adenosine triphosphate (ATP) production. A direct by-product of this ATP production is reactive oxygen species (ROS), which are highly deleterious for neurons. While ATP shortage and ROS levels increase are involved in several neurodegenerative diseases, it is still unclear whether the real-time dynamics of both ATP and ROS production in axonal mitochondria are altered by axonal or demyelinating neuropathies. To answer this question, we imaged and quantified mitochondrial ATP and hydrogen peroxide (H2O2) in resting or stimulated peripheral nerve myelinated axons in vivo, using genetically-encoded fluorescent probes, two-photon time-lapse and CARS imaging. We found that ATP and H2O2 productions are intrinsically higher in nodes of Ranvier even in resting conditions. Axonal firing increased both ATP and H2O2 productions but with different dynamics: ROS production peaked shortly and transiently after the stimulation while ATP production increased gradually for a longer period of time. In neuropathic MFN2R94Q mice, mimicking Charcot-Marie-Tooth 2A disease, defective mitochondria failed to upregulate ATP production following axonal activity. However, elevated H2O2 production was largely sustained. Finally, inducing demyelination with lysophosphatidylcholine resulted in a reduced level of ATP while H2O2 level soared. Taken together, our results suggest that ATP and ROS productions are decoupled under neuropathic conditions, which may compromise axonal function and integrity.
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Affiliation(s)
- Gerben van Hameren
- Institut des Neurosciences de Montpellier, INSERM U1051, Université de Montpellier, 34091, Montpellier, France.
| | - Graham Campbell
- Institut des Neurosciences de Montpellier, INSERM U1051, Université de Montpellier, 34091, Montpellier, France
| | - Marie Deck
- Institut des Neurosciences de Montpellier, INSERM U1051, Université de Montpellier, 34091, Montpellier, France
| | - Jade Berthelot
- Institut des Neurosciences de Montpellier, INSERM U1051, Université de Montpellier, 34091, Montpellier, France
| | - Benoit Gautier
- Institut des Neurosciences de Montpellier, INSERM U1051, Université de Montpellier, 34091, Montpellier, France
| | - Patrice Quintana
- Institut des Neurosciences de Montpellier, INSERM U1051, Université de Montpellier, 34091, Montpellier, France
| | - Roman Chrast
- Department of Neuroscience, Karolinska Institutet, 171 77, Stockholm, Sweden
- Department of Clinical Neuroscience, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Nicolas Tricaud
- Institut des Neurosciences de Montpellier, INSERM U1051, Université de Montpellier, 34091, Montpellier, France.
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8
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Haumann J, Camara AKS, Gadicherla AK, Navarro CD, Boelens AD, Blomeyer CA, Dash RK, Boswell MR, Kwok WM, Stowe DF. Slow Ca 2+ Efflux by Ca 2+/H + Exchange in Cardiac Mitochondria Is Modulated by Ca 2+ Re-uptake via MCU, Extra-Mitochondrial pH, and H + Pumping by F OF 1-ATPase. Front Physiol 2019; 9:1914. [PMID: 30804812 PMCID: PMC6378946 DOI: 10.3389/fphys.2018.01914] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/18/2018] [Indexed: 02/04/2023] Open
Abstract
Mitochondrial (m) Ca2+ influx is largely dependent on membrane potential (ΔΨm), whereas mCa2+ efflux occurs primarily via Ca2+ ion exchangers. We probed the kinetics of Ca2+/H+ exchange (CHEm) in guinea pig cardiac muscle mitochondria. We tested if net mCa2+ flux is altered during a matrix inward H+ leak that is dependent on matrix H+ pumping by ATPm hydrolysis at complex V (FOF1-ATPase). We measured [Ca2+]m, extra-mitochondrial (e) [Ca2+]e, ΔΨm, pHm, pHe, NADH, respiration, ADP/ATP ratios, and total [ATP]m in the presence or absence of protonophore dinitrophenol (DNP), mitochondrial uniporter (MCU) blocker Ru360, and complex V blocker oligomycin (OMN). We proposed that net slow influx/efflux of Ca2+ after adding DNP and CaCl2 is dependent on whether the ΔpHm gradient is/is not maintained by reciprocal outward H+ pumping by complex V. We found that adding CaCl2 enhanced DNP-induced increases in respiration and decreases in ΔΨm while [ATP]m decreased, ΔpHm gradient was maintained, and [Ca2+]m continued to increase slowly, indicating net mCa2+ influx via MCU. In contrast, with complex V blocked by OMN, adding DNP and CaCl2 caused larger declines in ΔΨm as well as a slow fall in pHm to near pHe while [Ca2+]m continued to decrease slowly, indicating net mCa2+ efflux in exchange for H+ influx (CHEm) until the ΔpHm gradient was abolished. The kinetics of slow mCa2+ efflux with slow H+ influx via CHEm was also observed at pHe 6.9 vs. 7.6 by the slow fall in pHm until ΔpHm was abolished; if Ca2+ reuptake via the MCU was also blocked, mCa2+ efflux via CHEm became more evident. Of the two components of the proton electrochemical gradient, our results indicate that CHEm activity is driven largely by the ΔpHm chemical gradient with H+ leak, while mCa2+ entry via MCU depends largely on the charge gradient ΔΨm. A fall in ΔΨm with excess mCa2+ loading can occur during cardiac cell stress. Cardiac cell injury due to mCa2+ overload may be reduced by temporarily inhibiting FOF1-ATPase from pumping H+ due to ΔΨm depolarization. This action would prevent additional slow mCa2+ loading via MCU and permit activation of CHEm to mediate efflux of mCa2+. HIGHLIGHTSWe examined how slow mitochondrial (m) Ca2+ efflux via Ca2+/H+ exchange (CHEm) is triggered by matrix acidity after a rapid increase in [Ca2+]m by adding CaCl2 in the presence of dinitrophenol (DNP) to permit H+ influx, and oligomycin (OMN) to block H+ pumping via FOF1-ATP synthase/ase (complex V). Declines in ΔΨm and pHm after DNP and added CaCl2 were larger when complex V was blocked. [Ca2+]m slowly increased despite a fall in ΔΨm but maintained pHm when H+ pumping by complex V was permitted. [Ca2+]m slowly decreased and external [Ca2+]e increased with declines in both ΔΨm and pHm when complex V was blocked. ATPm hydrolysis supports a falling pHm and redox state and promotes a slow increase in [Ca2+]m. After rapid Ca2+ influx due to a bolus of CaCl2, slow mCa2+ efflux by CHEm occurs directly if pHe is low.
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Affiliation(s)
- Johan Haumann
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Amadou K S Camara
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States.,Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ashish K Gadicherla
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Christopher D Navarro
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Age D Boelens
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Christoph A Blomeyer
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ranjan K Dash
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, United States
| | - Michael R Boswell
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Wai-Meng Kwok
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States.,Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - David F Stowe
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States.,Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, United States.,Research Service, Veterans Affairs Medical Center, Milwaukee, WI, United States
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9
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Willis WT, Miranda-Grandjean D, Hudgens J, Willis EA, Finlayson J, De Filippis EA, Zapata Bustos R, Langlais PR, Mielke C, Mandarino LJ. Dominant and sensitive control of oxidative flux by the ATP-ADP carrier in human skeletal muscle mitochondria: Effect of lysine acetylation. Arch Biochem Biophys 2018; 647:93-103. [PMID: 29653079 DOI: 10.1016/j.abb.2018.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/29/2018] [Accepted: 04/08/2018] [Indexed: 02/01/2023]
Abstract
The adenine nucleotide translocase (ANT) of the mitochondrial inner membrane exchanges ADP for ATP. Mitochondria were isolated from human vastus lateralis muscle (n = 9). Carboxyatractyloside titration of O2 consumption rate (Jo) at clamped [ADP] of 21 μM gave ANT abundance of 0.97 ± 0.14 nmol ANT/mg and a flux control coefficient of 82% ± 6%. Flux control fell to 1% ± 1% at saturating (2 mM) [ADP]. The KmADP for Jo was 32.4 ± 1.8 μM. In terms of the free (-3) ADP anion this KmADP was 12.0 ± 0.7 μM. A novel luciferase-based assay for ATP production gave KmADP of 13.1 ± 1.9 μM in the absence of ATP competition. The free anion KmADP in this case was 2.0 ± 0.3 μM. Targeted proteomic analyses showed significant acetylation of ANT Lysine23 and that ANT1 was the most abundant isoform. Acetylation of Lysine23 correlated positively with KmADP, r = 0.74, P = 0.022. The findings underscore the central role played by ANT in the control of oxidative phosphorylation, particularly at the energy phosphate levels associated with low ATP demand. As predicted by molecular dynamic modeling, ANT Lysine23 acetylation decreased the apparent affinity of ADP for ANT binding.
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Affiliation(s)
- W T Willis
- University of Arizona, College of Medicine, Department of Medicine, 1501 N. Campbell Avenue, P.O. Box 245099, Tucson, AZ 85724-5099, USA.
| | - D Miranda-Grandjean
- Mayo Clinic, Division of Endocrinology, East Shea Boulevard and 134th Street, Scottsdale, AZ 85259, USA.
| | - J Hudgens
- Mayo Clinic, Division of Endocrinology, East Shea Boulevard and 134th Street, Scottsdale, AZ 85259, USA.
| | - E A Willis
- Mayo Clinic, Division of Endocrinology, East Shea Boulevard and 134th Street, Scottsdale, AZ 85259, USA.
| | - J Finlayson
- University of Arizona, College of Medicine, Department of Medicine, 1501 N. Campbell Avenue, P.O. Box 245099, Tucson, AZ 85724-5099, USA.
| | - E A De Filippis
- Mayo Clinic, Division of Endocrinology, East Shea Boulevard and 134th Street, Scottsdale, AZ 85259, USA.
| | - R Zapata Bustos
- University of Arizona, College of Medicine, Department of Medicine, 1501 N. Campbell Avenue, P.O. Box 245099, Tucson, AZ 85724-5099, USA.
| | - P R Langlais
- University of Arizona, College of Medicine, Department of Medicine, 1501 N. Campbell Avenue, P.O. Box 245099, Tucson, AZ 85724-5099, USA.
| | - C Mielke
- Mayo Clinic, Division of Endocrinology, East Shea Boulevard and 134th Street, Scottsdale, AZ 85259, USA.
| | - L J Mandarino
- University of Arizona, College of Medicine, Department of Medicine, 1501 N. Campbell Avenue, P.O. Box 245099, Tucson, AZ 85724-5099, USA.
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10
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Komlódi T, Tretter L. Methylene blue stimulates substrate-level phosphorylation catalysed by succinyl-CoA ligase in the citric acid cycle. Neuropharmacology 2017; 123:287-298. [PMID: 28495375 DOI: 10.1016/j.neuropharm.2017.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 10/19/2022]
Abstract
Methylene blue (MB), a potential neuroprotective agent, is efficient in various neurodegenerative disease models. Beneficial effects of MB have been attributed to improvements in mitochondrial functions. Substrate-level phosphorylation (SLP) results in the production of ATP independent from the ATP synthase (ATP-ase). In energetically compromised mitochondria, ATP produced by SLP can prevent the reversal of the adenine nucleotide translocase and thus the hydrolysis of glycolytic ATP. The aim of the present study was to investigate the effect of MB on mitochondrial SLP catalysed by succinyl-CoA ligase. Measurements were carried out on isolated guinea pig cortical mitochondria respiring on α-ketoglutarate, glutamate, malate or succinate. The mitochondrial functions and parameters like ATP synthesis, oxygen consumption, membrane potential, and NAD(P)H level were followed online, in parallel with the redox state of MB. SLP-mediated ATP synthesis was measured in the presence of inhibitors for ATP-ase and adenylate kinase. In the presence of the ATP-ase inhibitor oligomycin MB stimulated respiration with all of the respiratory substrates. However, the rate of ATP synthesis increased only with substrates α-ketoglutarate and glutamate (forming succinyl-CoA). MB efficiently stimulated SLP and restored the membrane potential in mitochondria also with the combined inhibition of Complex I and ATP synthase. ATP formed by SLP alleviated the energetic insufficiency generated by the lack of oxidative phosphorylation. Thus, the MB-mediated stimulation of SLP might be important in maintaining the energetic competence of mitochondria and in preventing the mitochondrial hydrolysis of glycolytic ATP. The mitochondrial effects of MB are explained by the ability to accept electrons from reducing equivalents and transfer them to cytochrome c bypassing the respiratory Complexes I and III.
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Affiliation(s)
- T Komlódi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto St., Budapest, 1094, Hungary
| | - L Tretter
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto St., Budapest, 1094, Hungary.
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11
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Goltsov A, Tashkandi G, Langdon SP, Harrison DJ, Bown JL. Kinetic modelling of in vitro data of PI3K, mTOR1, PTEN enzymes and on-target inhibitors Rapamycin, BEZ235, and LY294002. Eur J Pharm Sci 2017; 97:170-181. [PMID: 27832967 DOI: 10.1016/j.ejps.2016.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/28/2016] [Accepted: 11/06/2016] [Indexed: 10/20/2022]
Abstract
The phosphatidylinositide 3-kinases (PI3K) and mammalian target of rapamycin-1 (mTOR1) are two key targets for anti-cancer therapy. Predicting the response of the PI3K/AKT/mTOR1 signalling pathway to targeted therapy is made difficult because of network complexities. Systems biology models can help explore those complexities but the value of such models is dependent on accurate parameterisation. Motivated by a need to increase accuracy in kinetic parameter estimation, and therefore the predictive power of the model, we present a framework to integrate kinetic data from enzyme assays into a unified enzyme kinetic model. We present exemplar kinetic models of PI3K and mTOR1, calibrated on in vitro enzyme data and founded on Michaelis-Menten (MM) approximation. We describe the effects of an allosteric mTOR1 inhibitor (Rapamycin) and ATP-competitive inhibitors (BEZ235 and LY294002) that show dual inhibition of mTOR1 and PI3K. We also model the kinetics of phosphatase and tensin homolog (PTEN), which modulates sensitivity of the PI3K/AKT/mTOR1 pathway to these drugs. Model validation with independent data sets allows investigation of enzyme function and drug dose dependencies in a wide range of experimental conditions. Modelling of the mTOR1 kinetics showed that Rapamycin has an IC50 independent of ATP concentration and that it is a selective inhibitor of mTOR1 substrates S6K1 and 4EBP1: it retains 40% of mTOR1 activity relative to 4EBP1 phosphorylation and inhibits completely S6K1 activity. For the dual ATP-competitive inhibitors of mTOR1 and PI3K, LY294002 and BEZ235, we derived the dependence of the IC50 on ATP concentration that allows prediction of the IC50 at different ATP concentrations in enzyme and cellular assays. Comparison of drug effectiveness in enzyme and cellular assays showed that some features of these drugs arise from signalling modulation beyond the on-target action and MM approximation and require a systems-level consideration of the whole PI3K/PTEN/AKT/mTOR1 network in order to understand mechanisms of drug sensitivity and resistance in different cancer cell lines. We suggest that using these models in a systems biology investigation of the PI3K/AKT/mTOR1 signalling in cancer cells can bridge the gap between direct drug target action and the therapeutic response to these drugs and their combinations.
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Affiliation(s)
- Alexey Goltsov
- School of Science, Engineering and Technology, University of Abertay, Dundee, UK.
| | - Ghassan Tashkandi
- Division of Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Simon P Langdon
- Division of Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | | | - James L Bown
- School of Science, Engineering and Technology, University of Abertay, Dundee, UK; School of Arts, Media and Computer Games, University of Abertay, Dundee, UK.
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12
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Shokolenko IN, Alexeyev MF. Mitochondrial transcription in mammalian cells. Front Biosci (Landmark Ed) 2017; 22:835-853. [PMID: 27814650 DOI: 10.2741/4520] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
As a consequence of recent discoveries of intimate involvement of mitochondria with key cellular processes, there has been a resurgence of interest in all aspects of mitochondrial biology, including the intricate mechanisms of mitochondrial DNA maintenance and expression. Despite four decades of research, there remains a lot to be learned about the processes that enable transcription of genetic information from mitochondrial DNA to RNA, as well as their regulation. These processes are vitally important, as evidenced by the lethality of inactivating the central components of mitochondrial transcription machinery. Here, we review the current understanding of mitochondrial transcription and its regulation in mammalian cells. We also discuss key theories in the field and highlight controversial subjects and future directions as we see them.
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Affiliation(s)
- Inna N Shokolenko
- University of South Alabama, Patt Capps Covey College of Allied Health Professions, Biomedical Sciences Department, 5721 USA Drive N, HAHN 4021, Mobile, AL 36688-0002, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, 5851 USA Dr. North, MSB3074, Mobile, AL 36688, USA,
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13
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Gerencser AA, Mookerjee SA, Jastroch M, Brand MD. Measurement of the Absolute Magnitude and Time Courses of Mitochondrial Membrane Potential in Primary and Clonal Pancreatic Beta-Cells. PLoS One 2016; 11:e0159199. [PMID: 27404273 PMCID: PMC4942067 DOI: 10.1371/journal.pone.0159199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/28/2016] [Indexed: 12/22/2022] Open
Abstract
The aim of this study was to simplify, improve and validate quantitative measurement of the mitochondrial membrane potential (ΔψM) in pancreatic β-cells. This built on our previously introduced calculation of the absolute magnitude of ΔψM in intact cells, using time-lapse imaging of the non-quench mode fluorescence of tetramethylrhodamine methyl ester and a bis-oxonol plasma membrane potential (ΔψP) indicator. ΔψM is a central mediator of glucose-stimulated insulin secretion in pancreatic β-cells. ΔψM is at the crossroads of cellular energy production and demand, therefore precise assay of its magnitude is a valuable tool to study how these processes interplay in insulin secretion. Dispersed islet cell cultures allowed cell type-specific, single-cell observations of cell-to-cell heterogeneity of ΔψM and ΔψP. Glucose addition caused hyperpolarization of ΔψM and depolarization of ΔψP. The hyperpolarization was a monophasic step increase, even in cells where the ΔψP depolarization was biphasic. The biphasic response of ΔψP was associated with a larger hyperpolarization of ΔψM than the monophasic response. Analysis of the relationships between ΔψP and ΔψM revealed that primary dispersed β-cells responded to glucose heterogeneously, driven by variable activation of energy metabolism. Sensitivity analysis of the calibration was consistent with β-cells having substantial cell-to-cell variations in amounts of mitochondria, and this was predicted not to impair the accuracy of determinations of relative changes in ΔψM and ΔψP. Finally, we demonstrate a significant problem with using an alternative ΔψM probe, rhodamine 123. In glucose-stimulated and oligomycin-inhibited β-cells the principles of the rhodamine 123 assay were breached, resulting in misleading conclusions.
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Affiliation(s)
- Akos A. Gerencser
- Buck Institute for Research on Aging, Novato, California, United States of America
- Image Analyst Software, Novato, California, United States of America
| | - Shona A. Mookerjee
- Buck Institute for Research on Aging, Novato, California, United States of America
- Touro University California College of Pharmacy, Vallejo, California, United States of America
| | - Martin Jastroch
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Martin D. Brand
- Buck Institute for Research on Aging, Novato, California, United States of America
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14
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Succinate, an intermediate in metabolism, signal transduction, ROS, hypoxia, and tumorigenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1086-1101. [PMID: 26971832 DOI: 10.1016/j.bbabio.2016.03.012] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/06/2016] [Accepted: 03/07/2016] [Indexed: 12/31/2022]
Abstract
Succinate is an important metabolite at the cross-road of several metabolic pathways, also involved in the formation and elimination of reactive oxygen species. However, it is becoming increasingly apparent that its realm extends to epigenetics, tumorigenesis, signal transduction, endo- and paracrine modulation and inflammation. Here we review the pathways encompassing succinate as a metabolite or a signal and how these may interact in normal and pathological conditions.(1).
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15
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Chinopoulos C, Kiss G, Kawamata H, Starkov AA. Measurement of ADP-ATP exchange in relation to mitochondrial transmembrane potential and oxygen consumption. Methods Enzymol 2015; 542:333-48. [PMID: 24862274 DOI: 10.1016/b978-0-12-416618-9.00017-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have previously described a fluorometric method to measure ADP-ATP exchange rates in mitochondria of permeabilized cells, in which several enzymes that consume substantial amounts of ATP and other competing reactions interconverting adenine nucleotides are present. This method relies on recording changes in free extramitochondrial Mg(2+) with the Mg(2+)-sensitive fluorescent indicator Magnesium Green (MgGr)™, exploiting the differential affinity of ADP and ATP for Mg(2+). In particular, cells are permeabilized with digitonin in the presence of BeF3(-) and Na3VO4, inhibiting all ATP- and ADP-utilizing reactions but mitochondrial exchange of ATP with ADP catalyzed by the adenine nucleotide translocase. The rate of ATP appearing in the medium upon the addition of ADP to energized mitochondria is then calculated from the rate of change in free extramitochondrial Mg(2+) using standard binding equations. Here, we describe a variant of this method involving an improved calibration step. This step minimizes errors that may be introduced during the conversion of the MgGr™ signal into free extramitochondrial [Mg(2+)] and ATP. Furthermore, we describe an approach for combining this methodology with the measurement of mitochondrial membrane potential and oxygen consumption in the same sample. The method described herein is useful for the study of malignant cells, which are known to thrive in hypoxic environments and to harbor mitochondria with profound functional alterations.
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Affiliation(s)
| | - Gergely Kiss
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
| | - Hibiki Kawamata
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, USA
| | - Anatoly A Starkov
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, USA
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16
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Lengert N, Drossel B. In silico analysis of exercise intolerance in myalgic encephalomyelitis/chronic fatigue syndrome. Biophys Chem 2015; 202:21-31. [PMID: 25899994 DOI: 10.1016/j.bpc.2015.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/26/2015] [Accepted: 03/28/2015] [Indexed: 11/16/2022]
Abstract
Post-exertional malaise is commonly observed in patients with myalgic encephalomyelitis/chronic fatigue syndrome, but its mechanism is not yet well understood. A reduced capacity for mitochondrial ATP synthesis is associated with the pathogenesis of CFS and is suspected to be a major contribution to exercise intolerance in CFS patients. To demonstrate the connection between a reduced mitochondrial capacity and exercise intolerance, we present a model which simulates metabolite dynamics in skeletal muscles during exercise and recovery. CFS simulations exhibit critically low levels of ATP, where an increased rate of cell death would be expected. To stabilize the energy supply at low ATP concentrations the total adenine nucleotide pool is reduced substantially causing a prolonged recovery time even without consideration of other factors, such as immunological dysregulations and oxidative stress. Repeated exercises worsen this situation considerably. Furthermore, CFS simulations exhibited an increased acidosis and lactate accumulation consistent with experimental observations.
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Affiliation(s)
- Nicor Lengert
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany.
| | - Barbara Drossel
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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17
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Dimovasili C, Aschner M, Plaitakis A, Zaganas I. Differential interaction of hGDH1 and hGDH2 with manganese: Implications for metabolism and toxicity. Neurochem Int 2015; 88:60-5. [PMID: 25837286 DOI: 10.1016/j.neuint.2015.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/13/2015] [Indexed: 10/23/2022]
Abstract
Manganese (Mn) is an essential trace element that serves as co-factor for many important mammalian enzymes. In humans, the importance of this cation is highlighted by the fact that low levels of Mn cause developmental and metabolic abnormalities and, on the other hand, chronic exposure to excessive amounts of Mn is characterized by neurotoxicity, possibly mediated by perturbation of astrocytic mitochondrial energy metabolism. Here we sought to study the effect of Mn on the two human glutamate dehydrogenases (hGDH1 and hGDH2, respectively), key mitochondrial enzymes involved in numerous cellular processes, including mitochondrial metabolism, glutamate homeostasis and neurotransmission, and cell signaling. Our studies showed that, compared to magnesium (Mg) and calcium (Ca), Mn exerted a significant inhibitory effect on both human isoenzymes with hGDH2 being more sensitive than hGDH1, especially under conditions of low ADP levels. Specifically, in the presence of 0.25 mM ADP, the Mn IC50 was 1.14 ± 0.02 mM and 1.54 ± 0.08 mM for hGDH2 and for hGDH1, respectively (p = 0.0001). Increasing Mn levels potentiated this differential effect, with 3 mM Mn inhibiting hGDH2 by 96.5% and hGDH1 by 70.2%. At 1 mM ADP, the Mn IC50 was 1.84 ± 0.02 mM and 2.04 ± 0.07 mM (p = 0.01) for hGDH2 and hGDH1, respectively, with 3 mM Mn inhibiting hGDH2 by 93.6% and hGDH1 by 70.9%. These results were due to the sigmoidal inhibitory curve of Mn that was more pronounced for hGDH2 than for hGDH1. Indeed, at 0.25 mM, the Hill coefficient value was higher for hGDH2 (3.42 ± 0.20) than for hGDH1 (1.94 ± 0.25; p = 0.0002) indicating that interaction of Mn with hGDH2 was substantially more co-operative than for hGDH1. These findings, showing an enhanced sensitivity of the hGDH2 isoenzyme to Mn, especially at low ADP levels, might be of pathophysiological relevance under conditions of Mn neurotoxicity.
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Affiliation(s)
- Christina Dimovasili
- Neurology Laboratory, School of Health Sciences, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andreas Plaitakis
- Neurology Laboratory, School of Health Sciences, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Ioannis Zaganas
- Neurology Laboratory, School of Health Sciences, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece.
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18
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Spahn S, Brandt K, Müller V. A low phosphorylation potential in the acetogen Acetobacterium woodii reflects its lifestyle at the thermodynamic edge of life. Arch Microbiol 2015; 197:745-51. [PMID: 25820826 DOI: 10.1007/s00203-015-1107-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/04/2015] [Accepted: 03/17/2015] [Indexed: 11/26/2022]
Abstract
The anaerobic, acetogenic bacterium Acetobacterium woodii grows on hydrogen and carbon dioxide and uses the Wood-Ljungdahl pathway to fix carbon but also to synthesize ATP. The free energy change of acetogenesis from H2 + CO2 allows for synthesis of only a fraction of an ATP under environmental conditions, and A. woodii is clearly a paradigm for microbial life under extreme energy limitation. However, it was unknown how much energy is required to make ATP under these conditions. In the present study, we determined the phosphorylation potential in cells metabolizing three different acetogenic substrates. It accounts to 37.9 ± 1.3 kJ/mol ATP during acetogenesis from fructose, 32.1 ± 0.3 kJ/mol ATP during acetogenesis from H2 + CO2 and 30.2 ± 0.9 kJ/mol ATP during acetogenesis from CO, the lowest phosphorylation potential ever described. The physiological consequences in terms of energy conservation under extreme energy limitation are discussed.
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Affiliation(s)
- Sebastian Spahn
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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19
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Bonora M, Wieckowski MR, Chinopoulos C, Kepp O, Kroemer G, Galluzzi L, Pinton P. Molecular mechanisms of cell death: central implication of ATP synthase in mitochondrial permeability transition. Oncogene 2015; 34:1475-86. [PMID: 24727893 DOI: 10.1038/onc.2014.96] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 02/20/2014] [Accepted: 02/27/2014] [Indexed: 12/14/2022]
Abstract
The term mitochondrial permeability transition (MPT) is commonly used to indicate an abrupt increase in the permeability of the inner mitochondrial membrane to low molecular weight solutes. Widespread MPT has catastrophic consequences for the cell, de facto marking the boundary between cellular life and death. MPT results indeed in the structural and functional collapse of mitochondria, an event that commits cells to suicide via regulated necrosis or apoptosis. MPT has a central role in the etiology of both acute and chronic diseases characterized by the loss of post-mitotic cells. Moreover, cancer cells are often relatively insensitive to the induction of MPT, underlying their increased resistance to potentially lethal cues. Thus, intense efforts have been dedicated not only at the understanding of MPT in mechanistic terms, but also at the development of pharmacological MPT modulators. In this setting, multiple mitochondrial and extramitochondrial proteins have been suspected to critically regulate the MPT. So far, however, only peptidylprolyl isomerase F (best known as cyclophilin D) appears to constitute a key component of the so-called permeability transition pore complex (PTPC), the supramolecular entity that is believed to mediate MPT. Here, after reviewing the structural and functional features of the PTPC, we summarize recent findings suggesting that another of its core components is represented by the c subunit of mitochondrial ATP synthase.
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Affiliation(s)
- M Bonora
- Section of Pathology, Oncology and Experimental Biology, Laboratory for Technologies of Advanced Therapies (LTTA), Department of Morphology, Surgery and Experimental Medicine, Interdisciplinary Centre for the Study of Inflammation (ICSI), University of Ferrara, Ferrara, Italy
| | - M R Wieckowski
- Department of Biochemistry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - C Chinopoulos
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
| | - O Kepp
- 1] Equipe 11 labelisée par la Ligue Nationale contre le cancer, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France [2] Université Paris Descartes/Paris 5, Sorbonne Paris Cité, Paris, France [3] Metabolomics and Cell Biology platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - G Kroemer
- 1] Equipe 11 labelisée par la Ligue Nationale contre le cancer, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France [2] Université Paris Descartes/Paris 5, Sorbonne Paris Cité, Paris, France [3] Metabolomics and Cell Biology platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France [4] Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - L Galluzzi
- 1] Equipe 11 labelisée par la Ligue Nationale contre le cancer, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France [2] Université Paris Descartes/Paris 5, Sorbonne Paris Cité, Paris, France [3] Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - P Pinton
- Section of Pathology, Oncology and Experimental Biology, Laboratory for Technologies of Advanced Therapies (LTTA), Department of Morphology, Surgery and Experimental Medicine, Interdisciplinary Centre for the Study of Inflammation (ICSI), University of Ferrara, Ferrara, Italy
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20
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Mielke C, Lefort N, McLean C, Cordova JM, Langlais PR, Bordner AJ, Te JA, Ozkan SB, Willis WT, Mandarino LJ. Adenine nucleotide translocase is acetylated in vivo in human muscle: Modeling predicts a decreased ADP affinity and altered control of oxidative phosphorylation. Biochemistry 2014; 53:3817-29. [PMID: 24884163 PMCID: PMC4067143 DOI: 10.1021/bi401651e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Proteomics techniques have revealed that lysine acetylation is abundant in mitochondrial proteins. This study was undertaken (1) to determine the relationship between mitochondrial protein acetylation and insulin sensitivity in human skeletal muscle, identifying key acetylated proteins, and (2) to use molecular modeling techniques to understand the functional consequences of acetylation of adenine nucleotide translocase 1 (ANT1), which we found to be abundantly acetylated. Eight lean and eight obese nondiabetic subjects had euglycemic clamps and muscle biopsies for isolation of mitochondrial proteins and proteomics analysis. A number of acetylated mitochondrial proteins were identified in muscle biopsies. Overall, acetylation of mitochondrial proteins was correlated with insulin action (r = 0.60; P < 0.05). Of the acetylated proteins, ANT1, which catalyzes ADP-ATP exchange across the inner mitochondrial membrane, was acetylated at lysines 10, 23, and 92. The extent of acetylation of lysine 23 decreased following exercise, depending on insulin sensitivity. Molecular dynamics modeling and ensemble docking simulations predicted the ADP binding site of ANT1 to be a pocket of positively charged residues, including lysine 23. Calculated ADP-ANT1 binding affinities were physiologically relevant and predicted substantial reductions in affinity upon acetylation of lysine 23. Insertion of these derived binding affinities as parameters into a complete mathematical description of ANT1 kinetics predicted marked reductions in adenine nucleotide flux resulting from acetylation of lysine 23. Therefore, acetylation of ANT1 could have dramatic physiological effects on ADP-ATP exchange. Dysregulation of acetylation of mitochondrial proteins such as ANT1 therefore could be related to changes in mitochondrial function that are associated with insulin resistance.
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Affiliation(s)
- Clinton Mielke
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Natalie Lefort
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Carrie
G. McLean
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Jeanine M. Cordova
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Paul R. Langlais
- Division of Endocrinology, Mayo Clinic
in Arizona, Scottsdale, Arizona 85259, United
States
| | - Andrew J. Bordner
- Division of Endocrinology, Mayo Clinic
in Arizona, Scottsdale, Arizona 85259, United
States
| | - Jerez A. Te
- Division of Endocrinology, Mayo Clinic
in Arizona, Scottsdale, Arizona 85259, United
States
| | - S. Banu Ozkan
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Wayne T. Willis
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
| | - Lawrence J. Mandarino
- Center for Metabolic and Vascular
Biology, Arizona State University, Tempe, Arizona 85004, United States
- Division of Endocrinology, Mayo Clinic
in Arizona, Scottsdale, Arizona 85259, United
States
- Department of Medicine, Mayo
Clinic in Arizona, Scottsdale, Arizona 85259, United States
- Mayo Clinic in Arizona, 13400 E.
Shea Blvd., Scottsdale, AZ 85259. E-mail: . Phone: (480) 965-8365. Fax: (480) 965-6899
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21
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Valsecchi F, Konrad C, Manfredi G. Role of soluble adenylyl cyclase in mitochondria. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2555-60. [PMID: 24907564 DOI: 10.1016/j.bbadis.2014.05.035] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/19/2014] [Accepted: 05/28/2014] [Indexed: 11/25/2022]
Abstract
The soluble adenylyl cyclase (sAC) catalyzes the conversion of ATP into cyclic AMP (cAMP). Recent studies have shed new light on the role of sAC localized in mitochondria and its product cAMP, which drives mitochondrial protein phosphorylation and regulation of the oxidative phosphorylation system and other metabolic enzymes, presumably through the activation of intra-mitochondrial PKA. In this review article, we summarize recent findings on mitochondrial sAC activation by bicarbonate (HCO(3)(-)) and calcium (Ca²⁺) and the effects on mitochondrial metabolism. We also discuss putative mechanisms whereby sAC-mediated mitochondrial protein phosphorylation regulates mitochondrial metabolism. This article is part of a Special Issue entitled: The role of soluble adenylyl cyclase in health and disease.
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Affiliation(s)
- Federica Valsecchi
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Csaba Konrad
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Giovanni Manfredi
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY 10065, USA.
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22
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Abstract
Any bilayer lipid membrane can support a membrane voltage. The combination of optical perturbation and optical readout of membrane voltage opens the door to studies of electrophysiology in a huge variety of systems previously inaccessible to electrode-based measurements. Yet, the application of optogenetic electrophysiology requires careful reconsideration of the fundamentals of bioelectricity. Rules of thumb appropriate for neuroscience and cardiology may not apply in systems with dramatically different sizes, lipid compositions, charge carriers, or protein machinery. Optogenetic tools are not electrodes; thus, optical and electrode-based measurements have different quirks. Here we review the fundamental aspects of bioelectricity with the aim of laying a conceptual framework for all-optical electrophysiology.
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Affiliation(s)
- Adam E Cohen
- Department of Chemistry and Chemical Biology and
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23
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Silverstein TP. An exploration of how the thermodynamic efficiency of bioenergetic membrane systems varies with c-subunit stoichiometry of F₁F₀ ATP synthases. J Bioenerg Biomembr 2014; 46:229-41. [PMID: 24706236 DOI: 10.1007/s10863-014-9547-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
Abstract
Recently the F0 portion of the bovine mitochondrial F1F0-ATP synthase was shown to contain eight 'c' subunits (n = 8). This surprised many in the field, as previously, the only other mitochondrial F0 (for yeast) was shown to have ten 'c' subunits. The metabolic implications of 'c' subunit copy number explored in this paper lead to several surprising conclusions: (1) Aerobically respiring E. coli (n = 10) and animal mitochondria (n = 8) both have very high F1F0 thermodynamic efficiencies of ≈90% under typical conditions, whereas efficiency is only ≈65% for chloroplasts (n = 14). Reasons for this difference, including the importance of transmembrane potential (∆Ψ) as a rotational catalyst, as opposed to an energy source, are discussed. (2) Maximum theoretical P/O ratios in animal mitochondria (n = 8) are calculated to be 2.73 ATP/NADH and 1.64 ATP/FADH2, yielding 34.5 ATP/glucose (assuming NADH import via the malate/aspartate shuttle). The experimentally measured values of 2.44 (±0.15), 1.47 (±0.13), and 31.3 (±1.5), respectively, are only about 10% lower, suggesting very little energy depletion via transmembrane proton leakage. (3) Finally, the thermodynamic efficiency of oxidative phosphorylation is not lower than that of substrate level phosphorylation, as previously believed. The overall thermodynamic efficiencies of oxidative phosphorylation, glycolysis, and the citric acid cycle are ≈80% in all three processes.
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24
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The Odyssey of a Young Gene: Structure–Function Studies in Human Glutamate Dehydrogenases Reveal Evolutionary-Acquired Complex Allosteric Regulation Mechanisms. Neurochem Res 2014; 39:471-86. [DOI: 10.1007/s11064-014-1251-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/24/2014] [Accepted: 01/29/2014] [Indexed: 01/13/2023]
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25
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Kiss G, Konrad C, Pour-Ghaz I, Mansour JJ, Németh B, Starkov AA, Adam-Vizi V, Chinopoulos C. Mitochondrial diaphorases as NAD⁺ donors to segments of the citric acid cycle that support substrate-level phosphorylation yielding ATP during respiratory inhibition. FASEB J 2014; 28:1682-97. [PMID: 24391134 DOI: 10.1096/fj.13-243030] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Substrate-level phosphorylation mediated by succinyl-CoA ligase in the mitochondrial matrix produces high-energy phosphates in the absence of oxidative phosphorylation. Furthermore, when the electron transport chain is dysfunctional, provision of succinyl-CoA by the α-ketoglutarate dehydrogenase complex (KGDHC) is crucial for maintaining the function of succinyl-CoA ligase yielding ATP, preventing the adenine nucleotide translocase from reversing. We addressed the source of the NAD(+) supply for KGDHC under anoxic conditions and inhibition of complex I. Using pharmacologic tools and specific substrates and by examining tissues from pigeon liver exhibiting no diaphorase activity, we showed that mitochondrial diaphorases in the mouse liver contribute up to 81% to the NAD(+) pool during respiratory inhibition. Under these conditions, KGDHC's function, essential for the provision of succinyl-CoA to succinyl-CoA ligase, is supported by NAD(+) derived from diaphorases. Through this process, diaphorases contribute to the maintenance of substrate-level phosphorylation during respiratory inhibition, which is manifested in the forward operation of adenine nucleotide translocase. Finally, we show that reoxidation of the reducible substrates for the diaphorases is mediated by complex III of the respiratory chain.
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Affiliation(s)
- Gergely Kiss
- 1Department of Medical Biochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest 1094, Hungary.
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Tso SC, Qi X, Gui WJ, Wu CY, Chuang JL, Wernstedt-Asterholm I, Morlock LK, Owens KR, Scherer PE, Williams NS, Tambar UK, Wynn RM, Chuang DT. Structure-guided development of specific pyruvate dehydrogenase kinase inhibitors targeting the ATP-binding pocket. J Biol Chem 2013; 289:4432-43. [PMID: 24356970 DOI: 10.1074/jbc.m113.533885] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyruvate dehydrogenase kinase isoforms (PDKs 1-4) negatively regulate activity of the mitochondrial pyruvate dehydrogenase complex by reversible phosphorylation. PDK isoforms are up-regulated in obesity, diabetes, heart failure, and cancer and are potential therapeutic targets for these important human diseases. Here, we employed a structure-guided design to convert a known Hsp90 inhibitor to a series of highly specific PDK inhibitors, based on structural conservation in the ATP-binding pocket. The key step involved the substitution of a carbonyl group in the parent compound with a sulfonyl in the PDK inhibitors. The final compound of this series, 2-[(2,4-dihydroxyphenyl)sulfonyl]isoindoline-4,6-diol, designated PS10, inhibits all four PDK isoforms with IC50 = 0.8 μM for PDK2. The administration of PS10 (70 mg/kg) to diet-induced obese mice significantly augments pyruvate dehydrogenase complex activity with reduced phosphorylation in different tissues. Prolonged PS10 treatments result in improved glucose tolerance and notably lessened hepatic steatosis in the mouse model. The results support the pharmacological approach of targeting PDK to control both glucose and fat levels in obesity and type 2 diabetes.
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ADP protects cardiac mitochondria under severe oxidative stress. PLoS One 2013; 8:e83214. [PMID: 24349464 PMCID: PMC3862761 DOI: 10.1371/journal.pone.0083214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/31/2013] [Indexed: 12/31/2022] Open
Abstract
ADP is not only a key substrate for ATP generation, but also a potent inhibitor of mitochondrial permeability transition pore (mPTP). In this study, we assessed how oxidative stress affects the potency of ADP as an mPTP inhibitor and whether its reduction of reactive oxygen species (ROS) production might be involved. We determined quantitatively the effects of ADP on mitochondrial Ca(2+) retention capacity (CRC) until the induction of mPTP in normal and stressed isolated cardiac mitochondria. We used two models of chronic oxidative stress (old and diabetic mice) and two models of acute oxidative stress (ischemia reperfusion (IR) and tert-butyl hydroperoxide (t-BH)). In control mitochondria, the CRC was 344 ± 32 nmol/mg protein. 500 μmol/L ADP increased CRC to 774 ± 65 nmol/mg protein. This effect of ADP seemed to relate to its concentration as 50 μmol/L had a significantly smaller effect. Also, oligomycin, which inhibits the conversion of ADP to ATP by F0F1ATPase, significantly increased the effect of 50 μmol/L ADP. Chronic oxidative stress did not affect CRC or the effect of 500 μmol/L ADP. After IR or t-BH exposure, CRC was drastically reduced to 1 ± 0.2 and 32 ± 4 nmol/mg protein, respectively. Surprisingly, ADP increased the CRC to 447 ± 105 and 514 ± 103 nmol/mg protein in IR and t-BH, respectively. Thus, it increased CRC by the same amount as in control. In control mitochondria, ADP decreased both substrate and Ca(2+)-induced increase of ROS. However, in t-BH mitochondria the effect of ADP on ROS was relatively small. We conclude that ADP potently restores CRC capacity in severely stressed mitochondria. This effect is most likely not related to a reduction in ROS production. As the effect of ADP relates to its concentration, increased ADP as occurs in the pathophysiological situation may protect mitochondrial integrity and function.
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Zaganas I, Pajęcka K, Wendel Nielsen C, Schousboe A, Waagepetersen HS, Plaitakis A. The effect of pH and ADP on ammonia affinity for human glutamate dehydrogenases. Metab Brain Dis 2013; 28:127-31. [PMID: 23420347 DOI: 10.1007/s11011-013-9382-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/23/2013] [Indexed: 11/26/2022]
Abstract
Glutamate dehydrogenase (GDH) uses ammonia to reversibly convert α-ketoglutarate to glutamate using NADP(H) and NAD(H) as cofactors. While GDH in most mammals is encoded by a single GLUD1 gene, humans and other primates have acquired a GLUD2 gene with distinct tissue expression profile. The two human isoenzymes (hGDH1 and hGDH2), though highly homologous, differ markedly in their regulatory properties. Here we obtained hGDH1 and hGDH2 in recombinant form and studied their Km for ammonia in the presence of 1.0 mM ADP. The analyses showed that lowering the pH of the buffer (from 8.0 to 7.0) increased the Km for ammonia substantially (hGDH1: from 12.8 ± 1.4 mM to 57.5 ± 1.6 mM; hGDH2: from 14.7 ± 1.6 mM to 62.2 ± 1.7 mM), thus essentially precluding reductive amination. Moreover, lowering the ADP concentration to 0.1 mM not only increased the K0.5 [NH4 (+)] of hGDH2, but also introduced a positive cooperative binding phenomenon in this isoenzyme. Hence, intra-mitochondrial acidification, as occurring in astrocytes during glutamatergic transmission should favor the oxidative deamination of glutamate. Similar considerations apply to the handling of glutamate by the proximal convoluted tubules of the kidney during systemic acidosis. The reverse could apply for conditions of local or systemic hyperammonemia or alkalosis.
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Affiliation(s)
- Ioannis Zaganas
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece.
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29
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Kiss G, Konrad C, Doczi J, Starkov AA, Kawamata H, Manfredi G, Zhang SF, Gibson GE, Beal MF, Adam-Vizi V, Chinopoulos C. The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix substrate-level phosphorylation. FASEB J 2013; 27:2392-406. [PMID: 23475850 DOI: 10.1096/fj.12-220202] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A decline in α-ketoglutarate dehydrogenase complex (KGDHC) activity has been associated with neurodegeneration. Provision of succinyl-CoA by KGDHC is essential for generation of matrix ATP (or GTP) by substrate-level phosphorylation catalyzed by succinyl-CoA ligase. Here, we demonstrate ATP consumption in respiration-impaired isolated and in situ neuronal somal mitochondria from transgenic mice with a deficiency of either dihydrolipoyl succinyltransferase (DLST) or dihydrolipoyl dehydrogenase (DLD) that exhibit a 20-48% decrease in KGDHC activity. Import of ATP into the mitochondrial matrix of transgenic mice was attributed to a shift in the reversal potential of the adenine nucleotide translocase toward more negative values due to diminished matrix substrate-level phosphorylation, which causes the translocase to reverse prematurely. Immunoreactivity of all three subunits of succinyl-CoA ligase and maximal enzymatic activity were unaffected in transgenic mice as compared to wild-type littermates. Therefore, decreased matrix substrate-level phosphorylation was due to diminished provision of succinyl-CoA. These results were corroborated further by the finding that mitochondria from wild-type mice respiring on substrates supporting substrate-level phosphorylation exhibited ~30% higher ADP-ATP exchange rates compared to those obtained from DLST(+/-) or DLD(+/-) littermates. We propose that KGDHC-associated pathologies are a consequence of the inability of respiration-impaired mitochondria to rely on "in-house" mitochondrial ATP reserves.
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Affiliation(s)
- Gergely Kiss
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
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Tewari SG, Dash RK, Beard DA, Bazil JN. A biophysical model of the mitochondrial ATP-Mg/P(i) carrier. Biophys J 2012; 103:1616-25. [PMID: 23062354 DOI: 10.1016/j.bpj.2012.08.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 08/10/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022] Open
Abstract
Mitochondrial adenine nucleotide (AdN) content is regulated through the Ca(2+)-activated, electroneutral ATP-Mg/P(i) carrier (APC). The APC is a protein in the mitochondrial carrier super family that localizes to the inner mitochondrial membrane (IMM). It is known to modulate a number of processes that depend on mitochondrial AdN content, such as gluconeogenesis, protein synthesis, and citrulline synthesis. Despite this critical role, a kinetic model of the underlying mechanism has not been developed and validated. Here, a biophysical model of the APC is developed that is thermodynamically balanced and accurately reproduces a number of reported data sets from isolated rat liver and rat kidney mitochondria. The model is based on an ordered bi-bi mechanism for heteroexchange of ATP and P(i) and includes homoexchanges of ATP and P(i) to explain both the initial rate and time course data on ATP and P(i) transport via the APC. The model invokes seven kinetic parameters regarding the APC mechanism and three parameters related to matrix pH regulation by external P(i). These parameters are estimated based on 19 independent data curves; the estimated parameters are validated using six additional data curves. The model takes into account the effects of pH, Mg(2+), and Ca(2+) on ATP and P(i) transport via the APC, and supports the conclusion that the pH gradient across the IMM serves as the primary driving force for AdN uptake or efflux. Moreover, computer simulations demonstrate that extramatrix Ca(2+) modulates the turnover rate of the APC and not the binding affinity of ATP, as previously suggested.
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Affiliation(s)
- Shivendra G Tewari
- Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
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Konrad C, Kiss G, Torocsik B, Adam-Vizi V, Chinopoulos C. Absence of Ca2+-induced mitochondrial permeability transition but presence of bongkrekate-sensitive nucleotide exchange in C. crangon and P. serratus. PLoS One 2012; 7:e39839. [PMID: 22768139 PMCID: PMC3387235 DOI: 10.1371/journal.pone.0039839] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 05/28/2012] [Indexed: 12/22/2022] Open
Abstract
Mitochondria from the embryos of brine shrimp (Artemia franciscana) do not undergo Ca2+-induced permeability transition in the presence of a profound Ca2+ uptake capacity. Furthermore, this crustacean is the only organism known to exhibit bongkrekate-insensitive mitochondrial adenine nucleotide exchange, prompting the conjecture that refractoriness to bongkrekate and absence of Ca2+-induced permeability transition are somehow related phenomena. Here we report that mitochondria isolated from two other crustaceans, brown shrimp (Crangon crangon) and common prawn (Palaemon serratus) exhibited bongkrekate-sensitive mitochondrial adenine nucleotide transport, but lacked a Ca2+-induced permeability transition. Ca2+ uptake capacity was robust in the absence of adenine nucleotides in both crustaceans, unaffected by either bongkrekate or cyclosporin A. Transmission electron microscopy images of Ca2+-loaded mitochondria showed needle-like formations of electron-dense material strikingly similar to those observed in mitochondria from the hepatopancreas of blue crab (Callinectes sapidus) and the embryos of Artemia franciscana. Alignment analysis of the partial coding sequences of the adenine nucleotide translocase (ANT) expressed in Crangon crangon and Palaemon serratus versus the complete sequence expressed in Artemia franciscana reappraised the possibility of the 208-214 amino acid region for conferring sensitivity to bongkrekate. However, our findings suggest that the ability to undergo Ca2+-induced mitochondrial permeability transition and the sensitivity of adenine nucleotide translocase to bongkrekate are not necessarily related phenomena.
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Affiliation(s)
- Csaba Konrad
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
| | - Gergely Kiss
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
| | - Beata Torocsik
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
| | - Christos Chinopoulos
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
- * E-mail:
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Transcriptional requirements of the distal heavy-strand promoter of mtDNA. Proc Natl Acad Sci U S A 2012; 109:6508-12. [PMID: 22454497 DOI: 10.1073/pnas.1118594109] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The heavy strand of mtDNA contains two promoters with nonoverlapping functions. The role of the minor heavy-strand promoter (HSP2) is controversial, because the promoter has been difficult to activate in an in vitro system. We have isolated HSP2 by excluding its interaction with the more powerful HSP1 promoter, and we find that it is transcribed efficiently by recombinant mtRNA polymerase and mitochondrial transcription factor B2. The mitochondrial transcription factor A is not required for initiation, but it has the ability to alternatively activate and repress the HSP2 transcriptional unit depending on the ratio between mitochondrial transcription factor A and other transcription factors. The positioning of transcriptional initiation agrees with our current understanding of HSP2 activity in vivo. Serial deletion of HSP2 shows that only proximal sequences are required. Several mutations, including the disruption of a polycytosine track upstream of the HSP2 initiation site, influence transcriptional activity. Transcription from HSP2 is also observed when HeLa cell mitochondrial extract is used as the source of mitochondrial polymerase, and this transcription is maintained when HSP2 is provided in proper spacing and context to the HSP1 promoter. Studies of the linked heavy-strand promoters show that they are differentially regulated by ATP dosage. We conclude that HSP2 is transcribed and has features that allow it to regulate mitochondrial mRNA synthesis.
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Chinopoulos C. The "B space" of mitochondrial phosphorylation. J Neurosci Res 2011; 89:1897-904. [PMID: 21541983 DOI: 10.1002/jnr.22659] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/09/2011] [Accepted: 03/10/2011] [Indexed: 11/07/2022]
Abstract
It was recently shown that, in progressively depolarizing mitochondria, the F(0) -F(1) ATP synthase and the adenine nucleotide translocase (ANT) may change directionality independently from each other (Chinopoulos et al. [2010] FASEB J. 24:2405). When the membrane potentials at which these two molecular entities reverse directionality, termed reversal potential (Erev), are plotted as a function of matrix ATP/ADP ratio, an area of the plot is bracketed by the Erev_ATPase and the Erev_ANT, which we call "B space". Both reversal potentials are dynamic, in that they depend on the fluctuating values of the participating reactants; however, Erev_ATPase is almost always more negative than Erev_ANT. Here we review the conditions that define the boundaries of the "B space". Emphasis is placed on the role of matrix substrate-level phosphorylation, because during metabolic compromise this mechanism could maintain mitochondrial membrane potential and prevent the influx of cytosolic ATP destined for hydrolysis by the reversed F(0) -F(1) ATP synthase.
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Mitochondrial consumption of cytosolic ATP: not so fast. FEBS Lett 2011; 585:1255-9. [PMID: 21486564 DOI: 10.1016/j.febslet.2011.04.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 04/01/2011] [Accepted: 04/01/2011] [Indexed: 11/23/2022]
Abstract
In various pathologic circumstances depolarized mitochondria are thought to precipitate cell death by avidly consuming cytosolic ATP. However, for as long as the inner mitochondrial membrane remains intact the reversal potentials of the adenine nucleotide translocase (ANT) and that of F(0)-F(1) ATP synthase are strategically positioned so that they oppose import of cytosolic ATP into the matrix of respiration-impaired mitochondria. This arrangement also seems to protect against a hysteretic consumption of cytosolic ATP accumulating in the mitochondrial matrix, in view of the depolarization caused by inhibition of F(0)-F(1) ATP synthase by the endogenous protein IF1, yielding fast ANT reversal rates.
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Chinopoulos C, Konràd C, Kiss G, Metelkin E, Töröcsik B, Zhang SF, Starkov AA. Modulation of F0F1-ATP synthase activity by cyclophilin D regulates matrix adenine nucleotide levels. FEBS J 2011; 278:1112-25. [PMID: 21281446 PMCID: PMC3062657 DOI: 10.1111/j.1742-4658.2011.08026.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cyclophilin D was recently shown to bind to and decrease the activity of F(0)F(1)-ATP synthase in submitochondrial particles and permeabilized mitochondria [Giorgio V et al. (2009) J Biol Chem, 284, 33982-33988]. Cyclophilin D binding decreased both ATP synthesis and hydrolysis rates. In the present study, we reaffirm these findings by demonstrating that, in intact mouse liver mitochondria energized by ATP, the absence of cyclophilin D or the presence of cyclosporin A led to a decrease in the extent of uncoupler-induced depolarization. Accordingly, in substrate-energized mitochondria, an increase in F(0)F(1)-ATP synthase activity mediated by a relief of inhibition by cyclophilin D was evident in the form of slightly increased respiration rates during arsenolysis. However, the modulation of F(0)F(1)-ATP synthase by cyclophilin D did not increase the adenine nucleotide translocase (ANT)-mediated ATP efflux rate in energized mitochondria or the ATP influx rate in de-energized mitochondria. The lack of an effect of cyclophilin D on the ANT-mediated adenine nucleotide exchange rate was attributed to the ∼ 2.2-fold lower flux control coefficient of the F(0)F(1)-ATP synthase than that of ANT, as deduced from measurements of adenine nucleotide flux rates in intact mitochondria. These findings were further supported by a recent kinetic model of the mitochondrial phosphorylation system, suggesting that an ∼ 30% change in F(0)F(1)-ATP synthase activity in fully energized or fully de-energized mitochondria affects the ADP-ATP exchange rate mediated by the ANT in the range 1.38-1.7%. We conclude that, in mitochondria exhibiting intact inner membranes, the absence of cyclophilin D or the inhibition of its binding to F(0)F(1)-ATP synthase by cyclosporin A will affect only matrix adenine nucleotides levels.
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Affiliation(s)
- Christos Chinopoulos
- Weill Medical College Cornell University, New York, NY, 10021, USA
- Department of Medical Biochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Csaba Konràd
- Department of Medical Biochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Gergely Kiss
- Department of Medical Biochemistry, Semmelweis University, Budapest, 1094, Hungary
| | | | - Beata Töröcsik
- Department of Medical Biochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Steven F. Zhang
- Weill Medical College Cornell University, New York, NY, 10021, USA
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Konràd C, Kiss G, Töröcsik B, Lábár JL, Gerencser AA, Mándi M, Adam-Vizi V, Chinopoulos C. A distinct sequence in the adenine nucleotide translocase from Artemia franciscana embryos is associated with insensitivity to bongkrekate and atypical effects of adenine nucleotides on Ca2+ uptake and sequestration. FEBS J 2011; 278:822-36. [PMID: 21205213 DOI: 10.1111/j.1742-4658.2010.08001.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mitochondria isolated from embryos of the crustacean Artemia franciscana lack the Ca(2+)-induced permeability transition pore. Although the composition of the pore described in mammalian mitochondria is unknown, the impacts of several effectors of the adenine nucleotide translocase (ANT) on pore opening are firmly established. Notably, ADP, ATP and bongkrekate delay, whereas carboxyatractyloside hastens, Ca(2+)-induced pore opening. Here, we report that adenine nucleotides decreased, whereas carboxyatractyloside increased, Ca(2+) uptake capacity in mitochondria isolated from Artemia embryos. Bongkrekate had no effect on either Ca(2+) uptake or ADP-ATP exchange rate. Transmission electron microscopy imaging of Ca(2+)-loaded Artemia mitochondria showed needle-like formations of electron-dense material in the absence of adenine nucleotides, and dot-like formations in the presence of adenine nucleotides or Mg(2+). Energy-filtered transmission electron microscopy showed the material to be rich in calcium and phosphorus. Sequencing of the Artemia mRNA coding for ANT revealed that it transcribes a protein with a stretch of amino acids in the 198-225 region with 48-56% similarity to those from other species, including the deletion of three amino acids in positions 211, 212 and 219. Mitochondria isolated from the liver of Xenopus laevis, in which the ANT shows similarity to that in Artemia except for the 198-225 amino acid region, demonstrated a Ca(2+)-induced bongkrekate-sensitive permeability transition pore, allowing the suggestion that this region of ANT may contain the binding site for bongkrekate.
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Affiliation(s)
- Csaba Konràd
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
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Chinopoulos C, Zhang SF, Thomas B, Ten V, Starkov AA. Isolation and functional assessment of mitochondria from small amounts of mouse brain tissue. Methods Mol Biol 2011; 793:311-24. [PMID: 21913109 DOI: 10.1007/978-1-61779-328-8_20] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent discoveries have brought mitochondria functions in focus of the neuroscience research community and greatly stimulated the demand for approaches to study mitochondria dysfunction in neurodegenerative diseases. Many mouse disease models have been generated, but studying mitochondria isolated from individual mouse brain regions is a challenge because of small amount of the available brain tissue. Conventional techniques for isolation and purification of mitochondria from mouse brain subregions, such as ventral midbrain, hippocampus, or striatum, require pooling brain tissue from six to nine animals for a single mitochondrial preparation. Working with pooled tissue significantly decreases the quality of data because of the time required to dissect several brains. It also greatly increases the labor intensity and the cost of experiments as several animals are required per single data point. We describe a method for isolation of brain mitochondria from mouse striata or other 7-12 mg brain samples. The method utilizes a refrigerated table-top microtube centrifuge, and produces research grade quality mitochondria in amounts sufficient for performing multiple enzymatic and functional assays, thereby eliminating the necessity for pooling mouse brain tissue. We also include a method of measuring ADP-ATP exchange rate as a function of mitochondrial membrane potential (ΔΨm) in small amounts of isolated mitochondria, adapted to a plate reader format.
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Gizzatkulov NM, Goryanin II, Metelkin EA, Mogilevskaya EA, Peskov KV, Demin OV. DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. BMC SYSTEMS BIOLOGY 2010; 4:109. [PMID: 20698988 PMCID: PMC2925829 DOI: 10.1186/1752-0509-4-109] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 08/10/2010] [Indexed: 11/21/2022]
Abstract
Background Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting. Results We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle. Conclusion DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru.
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Kawamata H, Starkov AA, Manfredi G, Chinopoulos C. A kinetic assay of mitochondrial ADP-ATP exchange rate in permeabilized cells. Anal Biochem 2010; 407:52-7. [PMID: 20691655 DOI: 10.1016/j.ab.2010.07.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 07/28/2010] [Accepted: 07/29/2010] [Indexed: 11/27/2022]
Abstract
We previously described a method to measure ADP-ATP exchange rates in isolated mitochondria by recording the changes in free extramitochondrial [Mg(2+)] reported by an Mg(2+)-sensitive fluorescent indicator, exploiting the differential affinity of ADP and ATP to Mg(2+). In the current article, we describe a modification of this method suited for following ADP-ATP exchange rates in environments with competing reactions that interconvert adenine nucleotides such as in permeabilized cells that harbor phosphorylases and kinases, ion pumps exhibiting substantial ATPase activity, and myosin ATPase activity. Here we report that the addition of BeF(3)(-) and sodium orthovanadate (Na(3)VO(4)) to medium containing digitonin-permeabilized cells inhibits all ADP-ATP-using reactions except the adenine nucleotide translocase (ANT)-mediated mitochondrial ADP-ATP exchange. An advantage of this assay is that mitochondria that may have been also permeabilized by digitonin do not contribute to ATP consumption by the exposed F(1)F(o)-ATPase due to its sensitivity to BeF(3)(-) and Na(3)VO(4). With this assay, ADP-ATP exchange rate mediated by the ANT in permeabilized cells is measured for the entire range of mitochondrial membrane potential titrated by stepwise additions of an uncoupler and expressed as a function of citrate synthase activity per total amount of protein.
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Affiliation(s)
- Hibiki Kawamata
- Weill Medical College, Cornell University, New York, NY 10065, USA
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Abstract
The ability of mitochondria to sequester and retain divalent cations in the form of precipitates consisting of organic and inorganic moieties has been known for decades. Of these cations, Ca(2+) has emerged as a major player in both signal transduction and cell death mechanisms, and, as a consequence, the importance of mitochondria in these processes was soon recognized. Early studies showed considerable effort in identifying the mechanisms of Ca(2+) sequestration, precipitation and release by uncouplers of oxidative phosphorylation; however, relatively little information was obtained, and these processes were eventually taken for granted. Here, we re-examine: (a) the thermodynamic aspects of mitochondrial Ca(2+) uptake and release, (b) the insufficiently explained effect of uncouplers in inducing mitochondrial Ca(2+) release, (c) the thermodynamic effects of exogenously added adenine nucleotides on mitochondrial Ca(2+) uptake capacity and precipitate formation, and (d) the elusive nature of the Ca(2+) -phosphate precipitates formed in the mitochondrial matrix.
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Affiliation(s)
- Christos Chinopoulos
- Department of Medical Biochemistry, Semmelweis University, Neurobiochemical Group, Hungarian Academy of Sciences, Budapest, Hungary.
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Chinopoulos C, Gerencser AA, Mandi M, Mathe K, Töröcsik B, Doczi J, Turiak L, Kiss G, Konràd C, Vajda S, Vereczki V, Oh RJ, Adam-Vizi V. Forward operation of adenine nucleotide translocase during F0F1-ATPase reversal: critical role of matrix substrate-level phosphorylation. FASEB J 2010; 24:2405-16. [PMID: 20207940 DOI: 10.1096/fj.09-149898] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In pathological conditions, F(0)F(1)-ATPase hydrolyzes ATP in an attempt to maintain mitochondrial membrane potential. Using thermodynamic assumptions and computer modeling, we established that mitochondrial membrane potential can be more negative than the reversal potential of the adenine nucleotide translocase (ANT) but more positive than that of the F(0)F(1)-ATPase. Experiments on isolated mitochondria demonstrated that, when the electron transport chain is compromised, the F(0)F(1)-ATPase reverses, and the membrane potential is maintained as long as matrix substrate-level phosphorylation is functional, without a concomitant reversal of the ANT. Consistently, no cytosolic ATP consumption was observed using plasmalemmal K(ATP) channels as cytosolic ATP biosensors in cultured neurons, in which their in situ mitochondria were compromised by respiratory chain inhibitors. This finding was further corroborated by quantitative measurements of mitochondrial membrane potential, oxygen consumption, and extracellular acidification rates, indicating nonreversal of ANT of compromised in situ neuronal and astrocytic mitochondria; and by bioluminescence ATP measurements in COS-7 cells transfected with cytosolic- or nuclear-targeted luciferases and treated with mitochondrial respiratory chain inhibitors in the presence of glycolytic plus mitochondrial vs. only mitochondrial substrates. Our findings imply the possibility of a rescue mechanism that is protecting against cytosolic/nuclear ATP depletion under pathological conditions involving impaired respiration. This mechanism comes into play when mitochondria respire on substrates that support matrix substrate-level phosphorylation.
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Affiliation(s)
- Christos Chinopoulos
- Department of Medical Biochemistry, Semmelweis University, Tuzolto St. 37-47, Room 4.521, Budapest, Hungary 1094.
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