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Gu S, Fu L, Wang J, Sun X, Wang X, Lou J, Zhao M, Wang C, Zhang Q. MtDNA Copy Number in Oral Epithelial Cells Serves as a Potential Biomarker of Mitochondrial Damage by Neonicotinoid Exposure: A Cross-Sectional Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15816-15824. [PMID: 37819077 DOI: 10.1021/acs.est.3c03835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
As the mitochondrial DNA copy number (mtDNAcn) has been reported to be a biomarker for mtDNA damage in honeybees when exposed to sublethal neonicotinoids, the feasibility of using human mitochondria as a predictor upon neonicotinoid exposure remains elusive. This study investigated the association between the urinary neonicotinoid and the relative mtDNAcn (RmtDNAcn) of oral epithelial cells collected in a cross-sectional study with repeated measurements over 6 weeks. The molecular mechanism underlying neonicotinoid-caused mitochondrial damage was also examined by in vitro assay. Herein, the average integrated urinary neonicotinoid (IMIRPF) concentration ranged from 8.01 to 13.70 μg/L (specific gravity-adjusted) during the sampling period. Concomitantly, with an increase in the urinary IMIRPF, the RmtDNAcn significantly increased from 1.20 (low group) to 1.93 (high group), indicating potential dose-dependent mitochondrial damage. Furthermore, the linear regression analysis confirmed the significant correlation between the IMIRPF and RmtDNAcn. Results from in vitro assays demonstrated that neonicotinoid exposure led to the inhibition of the genes encoding mitochondrial oxidative phosphorylation (OXPHOS) complexes I and III (e.g., ND2, ND6, CytB, and CYC1), accompanied by increased reactive oxygen species production in SH-SY5Y cells. Conjointly, neonicotinoid exposure led to mitochondrial dysfunction and a resulting increase in the RmtDNAcn, which may serve as a plausible biomarker in humans.
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Affiliation(s)
- Sijia Gu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Lili Fu
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China
| | - Jing Wang
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China
| | - Xiaohui Sun
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China
| | - Ximing Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Jianlin Lou
- School of Medicine, and The First Affiliated Hospital, Huzhou University, Huzhou, Zhejiang 313000, China
| | - Meirong Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Cui Wang
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Quan Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
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2
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Sadri S, Tomar N, Yang C, Audi SH, Cowley AW, Dash RK. Effects of ROS pathway inhibitors and NADH and FADH 2 linked substrates on mitochondrial bioenergetics and ROS emission in the heart and kidney cortex and outer medulla. Arch Biochem Biophys 2023; 744:109690. [PMID: 37429534 PMCID: PMC10528392 DOI: 10.1016/j.abb.2023.109690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Mitochondria are major sources of reactive oxygen species (ROS), which play important roles in both physiological and pathological processes. However, the specific contributions of different ROS production and scavenging components in the mitochondria of metabolically active tissues such as heart and kidney cortex and outer medulla (OM) are not well understood. Therefore, the goal of this study was to determine contributions of different ROS production and scavenging components and provide detailed comparisons of mitochondrial respiration, bioenergetics, ROS emission between the heart and kidney cortex and OM using tissues obtained from the same Sprague-Dawley rat under identical conditions and perturbations. Specifically, data were obtained using both NADH-linked substrate pyruvate + malate and FADH2-linked substrate succinate followed by additions of inhibitors of different components of the electron transport chain (ETC) and oxidative phosphorylation (OxPhos) and other ROS production and scavenging systems. Currently, there is limited data available for the mitochondria of kidney cortex and OM, the two major energy-consuming tissues in the body only next to the heart, and scarce quantitative information on the interplay between mitochondrial ROS production and scavenging systems in the three tissues. The findings from this study demonstrate significant differences in mitochondrial respiratory and bioenergetic functions and ROS emission among the three tissues. The results quantify the rates of ROS production from different complexes of the ETC, identify the complexes responsible for variations in mitochondrial membrane depolarization and regulations of ROS production, and quantify the contributions of ROS scavenging enzymes towards overall mitochondrial ROS emission. These findings advance our fundamental knowledge of tissue-specific and substrate-dependent mitochondrial respiratory and bioenergetic functions and ROS emission. This is important given the critical role that excess ROS production, oxidative stress, and mitochondrial dysfunction in the heart and kidney cortex and OM play in the pathogenesis of cardiovascular and renal diseases, including salt-sensitive hypertension.
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Affiliation(s)
- Shima Sadri
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Namrata Tomar
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Chun Yang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Said H Audi
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Department of Biomedical Engineering, Marquette University, Milwaukee, WI, 53223, USA
| | - Allen W Cowley
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Cardiovascular Research Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Ranjan K Dash
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Cardiovascular Research Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Department of Biomedical Engineering, Marquette University, Milwaukee, WI, 53223, USA.
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3
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Sadri S, Zhang X, Audi SH, Cowley Jr. AW, Dash RK. Computational Modeling of Substrate-Dependent Mitochondrial Respiration and Bioenergetics in the Heart and Kidney Cortex and Outer Medulla. FUNCTION 2023; 4:zqad038. [PMID: 37575476 PMCID: PMC10413947 DOI: 10.1093/function/zqad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Integrated computational modeling provides a mechanistic and quantitative framework to characterize alterations in mitochondrial respiration and bioenergetics in response to different metabolic substrates in-silico. These alterations play critical roles in the pathogenesis of diseases affecting metabolically active organs such as heart and kidney. Therefore, the present study aimed to develop and validate thermodynamically constrained integrated computational models of mitochondrial respiration and bioenergetics in the heart and kidney cortex and outer medulla (OM). The models incorporated the kinetics of major biochemical reactions and transport processes as well as regulatory mechanisms in the mitochondria of these tissues. Intrinsic model parameters such as Michaelis-Menten constants were fixed at previously estimated values, while extrinsic model parameters such as maximal reaction and transport velocities were estimated separately for each tissue. This was achieved by fitting the model solutions to our recently published respirometry data measured in isolated rat heart and kidney cortex and OM mitochondria utilizing various NADH- and FADH2-linked metabolic substrates. The models were validated by predicting additional respirometry and bioenergetics data, which were not used for estimating the extrinsic model parameters. The models were able to predict tissue-specific and substrate-dependent mitochondrial emergent metabolic system properties such as redox states, enzyme and transporter fluxes, metabolite concentrations, membrane potential, and respiratory control index under diverse physiological and pathological conditions. The models were also able to quantitatively characterize differential regulations of NADH- and FADH2-linked metabolic pathways, which contribute differently toward regulations of oxidative phosphorylation and ATP synthesis in the heart and kidney cortex and OM mitochondria.
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Affiliation(s)
- Shima Sadri
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiao Zhang
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Said H Audi
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Marquette University, Milwaukee, WI 53223, USA
| | - Allen W Cowley Jr.
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cardiovascular Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ranjan K Dash
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Marquette University, Milwaukee, WI 53223, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cardiovascular Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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4
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The evolution of the human mitochondrial bc1 complex- adaptation for reduced rate of superoxide production? J Bioenerg Biomembr 2023; 55:15-31. [PMID: 36737563 DOI: 10.1007/s10863-023-09957-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
The mitochondrial bc1 complex is a major source of mitochondrial superoxide. While bc1-generated superoxide plays a beneficial signaling role, excess production of superoxide lead to aging and degenerative diseases. The catalytic core of bc1 comprises three peptides -cytochrome b, Fe-S protein, and cytochrome c1. All three core peptides exhibit accelerated evolution in anthropoid primates. It has been suggested that the evolution of cytochrome b in anthropoids was driven by a pressure to reduce the production of superoxide. In humans, the bc1 core peptides exhibit anthropoid-specific substitutions that are clustered near functionally critical sites that may affect the production of superoxide. Here we compare the high-resolution structures of bovine, mouse, sheep and human bc1 to identify structural changes that are associated with human-specific substitutions. Several cytochrome b substitutions in humans alter its interactions with other subunits. Most significantly, there is a cluster of seven substitutions, in cytochrome b, the Fe-S protein, and cytochrome c1 that affect the interactions between these proteins at the tether arm of the Fe-S protein and may alter the rate of ubiquinone oxidation and the rate of superoxide production. Another cluster of substitutions near heme bH and the ubiquinone reduction site, Qi, may affect the rate of ubiquinone reduction and thus alter the rate of superoxide production. These results are compatible with the hypothesis that cytochrome b in humans (and other anthropoid primates) evolve to reduce the rate of production of superoxide thus enabling the exceptional longevity and exceptional cognitive ability of humans.
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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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6
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Chenna S, Koopman WJH, Prehn JHM, Connolly NMC. Mechanisms and mathematical modelling of ROS production by the mitochondrial electron transport chain. Am J Physiol Cell Physiol 2022; 323:C69-C83. [PMID: 35613354 DOI: 10.1152/ajpcell.00455.2021] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Reactive oxygen species (ROS) are recognised both as damaging molecules and intracellular signalling entities. In addition to its role in ATP generation, the mitochondrial electron transport chain (ETC) constitutes a relevant source of mitochondrial ROS, in particular during pathological conditions. Mitochondrial ROS homeostasis depends on species- and site-dependent ROS production, their bioreactivity, diffusion, and scavenging. However, our quantitative understanding of mitochondrial ROS homeostasis has thus far been hampered by technical limitations, including lack of truly site- and/or ROS-specific reporter molecules. In this context, the use of computational models is of great value to complement and interpret empirical data, as well as to predict variables that are difficult to assess experimentally. During the last decades, various mechanistic models of ETC-mediated ROS production have been developed. Although these often-complex models have generated novel insights, their parameterisation, analysis, and integration with other computational models is not straightforward. In contrast, phenomenological (sometimes termed "minimal") models use a relatively small set of equations to describe empirical relationship(s) between ROS-related and other parameters, and generally aim to explore system behaviour and generate hypotheses for experimental validation. In this review, we first discuss ETC-linked ROS homeostasis and introduce various detailed mechanistic models. Next, we present how bioenergetic parameters (e.g. NADH/NAD+ ratio, mitochondrial membrane potential) relate to site-specific ROS production within the ETC and how these relationships can be used to design minimal models of ROS homeostasis. Finally, we illustrate how minimal models have been applied to explore pathophysiological aspects of ROS.
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Affiliation(s)
- Sandeep Chenna
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Werner J H Koopman
- Department of Pediatrics, Amalia Children's Hospital, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Disorders (RCMM), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Jochen H M Prehn
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.,SFI FutureNeuro Research Centre, Dublin, Ireland
| | - Niamh M C Connolly
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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7
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Manoj KM, Gideon DA, Parashar A. What is the Role of Lipid Membrane-embedded Quinones in Mitochondria and Chloroplasts? Chemiosmotic Q-cycle versus Murburn Reaction Perspective. Cell Biochem Biophys 2020; 79:3-10. [PMID: 32989571 DOI: 10.1007/s12013-020-00945-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2020] [Indexed: 01/23/2023]
Abstract
Quinones are found in the lipid membranes of prokaryotes like E. coli and cyanobacteria, and are also abundant in eukaryotic mitochondria and chloroplasts. They are intricately involved in the reaction mechanism of redox phosphorylations. In the Mitchellian chemiosmotic school of thought, membrane-lodged quinones are perceived as highly mobile conveyors of two-electron equivalents from the first leg of Electron Transport Chain (ETC) to the 'second pit-stop' of Cytochrome bc1 or b6f complex (CBC), where they undergo a regenerative 'Q-cycle'. In Manoj's murburn mechanism, the membrane-lodged quinones are perceived as relatively slow-moving one- or two- electron donors/acceptors, enabling charge separation and the CBC resets a one-electron paradigm via 'turbo logic'. Herein, we compare various purviews of the two mechanistic schools with respect to: constraints in mobility, protons' availability, binding of quinones with proteins, structural features of the protein complexes, energetics of reaction, overall reaction logic, etc. From various perspectives, the murburn mechanism appeals as a viable alternative explanation well-rooted in thermodynamics/kinetics and one which lends adequate structure-function correlations for the roles of quinones, lipid membrane and associated proteins.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2 (PO), Palakkad, Kerala, 679122, India.
| | - Daniel Andrew Gideon
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2 (PO), Palakkad, Kerala, 679122, India
| | - Abhinav Parashar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, 522213, India.
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8
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Markevich NI, Galimova MH, Markevich LN. Hysteresis and bistability in the succinate-CoQ reductase activity and reactive oxygen species production in the mitochondrial respiratory complex II. Redox Biol 2020; 37:101630. [PMID: 32747163 PMCID: PMC7767736 DOI: 10.1016/j.redox.2020.101630] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/14/2020] [Accepted: 06/28/2020] [Indexed: 11/25/2022] Open
Abstract
The mitochondrial respiratory Complex II (CII) is one of key enzymes of cell energy metabolism, linking the tricarboxylic acid (TCA) cycle and the electron transport chain (ETC). CII reversibly oxidizes succinate to fumarate in the TCA cycle and transfers the electrons, produced by this reaction to the membrane quinone pool, providing ubiquinol QH2 to ETC. CII is also known as a generator of reactive oxygen species (ROS). It was shown experimentally that succinate can serve as not only a substrate in the forward succinate-quinone oxidoreductase (SQR) direction, but also an enzyme activator. Molecular and kinetic mechanisms of this property of CII are still unclear. In order to account for activation of CII by succinate in the forward SQR direction, we developed and analyzed a computational mechanistic model of electron transfer and ROS formation in CII. It was found that re-binding of succinate to the unoccupied dicarboxylate binding site when FAD is reduced with subsequent oxidation of FADH2 creates a positive feedback loop in the succinate oxidation. The model predicts that this positive feedback can result in hysteresis and bistable switches in SQR activity and ROS production in CII. This requires that the rate constant of re-binding of succinate has to be higher than the rate constant of the initial succinate binding to the active center when FAD is oxidized. Hysteresis and bistability in the SQR activity and ROS production in CII can play an important physiological role. In the presence of hysteresis with two stable branches with high and low SQR activity, high SQR activity is maintained even with a very strong drop in the succinate concentration, which may be necessary in the process of cell functioning in stressful situations. For the same reason, a high stationary rate of ROS production in CII can be maintained at low succinate concentrations. Computational model of electron flows in the respiratory Complex II was developed. The Complex II model predicts a positive feedback loop in the succinate oxidation. Complex II can operate as a bistable switch between two alternative stable states. ROS production in Complex II may have a hysteretic behaviour.
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Affiliation(s)
- Nikolay I Markevich
- Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Moscow region, 142290, Russian Federation.
| | - Miliausha H Galimova
- Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Moscow region, 142290, Russian Federation
| | - Lubov N Markevich
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russian Federation
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9
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Takeuchi A, Matsuoka S. Integration of mitochondrial energetics in heart with mathematical modelling. J Physiol 2020; 598:1443-1457. [DOI: 10.1113/jp276817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/23/2020] [Indexed: 11/08/2022] Open
Affiliation(s)
- Ayako Takeuchi
- Department of Integrative and Systems PhysiologyFaculty of Medical Sciencesand Life Science Innovation CenterUniversity of Fukui Fukui 910‐1193 Japan
| | - Satoshi Matsuoka
- Department of Integrative and Systems PhysiologyFaculty of Medical Sciencesand Life Science Innovation CenterUniversity of Fukui Fukui 910‐1193 Japan
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10
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Mazat JP, Devin A, Ransac S. Modelling mitochondrial ROS production by the respiratory chain. Cell Mol Life Sci 2020; 77:455-465. [PMID: 31748915 PMCID: PMC11104992 DOI: 10.1007/s00018-019-03381-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022]
Abstract
ROS (superoxide and oxygen peroxide in this paper) play a dual role as signalling molecules and strong oxidizing agents leading to oxidative stress. Their production mainly occurs in mitochondria although they may have other locations (such as NADPH oxidase in particular cell types). Mitochondrial ROS production depends in an interweaving way upon many factors such as the membrane potential, the cell type and the respiratory substrates. Moreover, it is experimentally difficult to quantitatively assess the contribution of each potential site in the respiratory chain. To overcome these difficulties, mathematical models have been developed with different degrees of complexity in order to analyse different physiological questions ranging from a simple reproduction/simulation of experimental results to a detailed model of the possible mechanisms leading to ROS production. Here, we analyse experimental results concerning ROS production including results still under discussion. We then critically review the three models of ROS production in the whole respiratory chain available in the literature and propose some direction for future modelling work.
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Affiliation(s)
- Jean-Pierre Mazat
- UMR 5095, IBGC CNRS, 1 Rue Camille Saint-Saëns 33077, Bordeaux Cedex, France.
- Université de Bordeaux, 146 Rue Léo-Saignat, 33076, Bordeaux Cedex, France.
| | - Anne Devin
- UMR 5095, IBGC CNRS, 1 Rue Camille Saint-Saëns 33077, Bordeaux Cedex, France
| | - Stéphane Ransac
- UMR 5095, IBGC CNRS, 1 Rue Camille Saint-Saëns 33077, Bordeaux Cedex, France
- Université de Bordeaux, 146 Rue Léo-Saignat, 33076, Bordeaux Cedex, France
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11
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Singharoy A, Maffeo C, Delgado-Magnero KH, Swainsbury DJK, Sener M, Kleinekathöfer U, Vant JW, Nguyen J, Hitchcock A, Isralewitz B, Teo I, Chandler DE, Stone JE, Phillips JC, Pogorelov TV, Mallus MI, Chipot C, Luthey-Schulten Z, Tieleman DP, Hunter CN, Tajkhorshid E, Aksimentiev A, Schulten K. Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell 2019; 179:1098-1111.e23. [PMID: 31730852 PMCID: PMC7075482 DOI: 10.1016/j.cell.2019.10.021] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/04/2019] [Accepted: 10/21/2019] [Indexed: 01/01/2023]
Abstract
We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local curvature to tune photoexcitation of pigments. Brownian dynamics of small molecules within the chromatophore probe the mechanisms of directional charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore's structural integrity and robust energy conversion. Parallels are drawn with the more universal mitochondrial bioenergetic machinery, from whence molecular-scale insights into the mechanism of cellular aging are inferred. Together, our integrative method and spectroscopic experiments pave the way to first-principles modeling of whole living cells.
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Affiliation(s)
- Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA.
| | - Christopher Maffeo
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karelia H Delgado-Magnero
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Melih Sener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - John W Vant
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Barry Isralewitz
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ivan Teo
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Danielle E Chandler
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - John E Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - James C Phillips
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taras V Pogorelov
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - M Ilaria Mallus
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Christophe Chipot
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Laboratoire International Associé CNRS-UIUC, UMR 7019, Université de Lorraine, 54506 Vandœuvre-lès-Nancy, France
| | - Zaida Luthey-Schulten
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Departments of Biochemistry, Chemistry, Bioengineering, and Pharmacology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Aleksei Aksimentiev
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Klaus Schulten
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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12
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Analysis of a Functional Dimer Model of Ubiquinol Cytochrome c Oxidoreductase. Biophys J 2017; 113:1599-1612. [PMID: 28978450 PMCID: PMC5627346 DOI: 10.1016/j.bpj.2017.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 11/21/2022] Open
Abstract
Ubiquinol cytochrome c oxidoreductase (bc1 complex) serves as an important electron junction in many respiratory systems. It funnels electrons coming from NADH and ubiquinol to cytochrome c, but it is also capable of producing significant amounts of the free radical superoxide. In situ and in other experimental systems, the enzyme exists as a dimer. But until recently, it was believed to operate as a functional monomer. Here we show that a functional dimer model is capable of explaining both kinetic and superoxide production rate data. The model consists of six electronic states characterized by the number of electrons deposited on the complex. It is fully reversible and strictly adheres to the thermodynamics governing the reactions. A total of nine independent data sets were used to parameterize the model. To explain the data with a consistent set of parameters, it was necessary to incorporate intramonomer Coulombic effects between hemes bL and bH and intermonomer Coulombic effects between bL hemes. The fitted repulsion energies fall within the theoretical range of electrostatic calculations. In addition, model analysis demonstrates that the Q pool is mostly oxidized under normal physiological operation but can switch to a more reduced state when reverse electron transport conditions are in place.
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13
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Vinnakota KC, Bazil JN, Van den Bergh F, Wiseman RW, Beard DA. Feedback Regulation and Time Hierarchy of Oxidative Phosphorylation in Cardiac Mitochondria. Biophys J 2016; 110:972-80. [PMID: 26910434 DOI: 10.1016/j.bpj.2016.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 12/27/2015] [Accepted: 01/04/2016] [Indexed: 11/18/2022] Open
Abstract
To determine how oxidative ATP synthesis is regulated in the heart, the responses of cardiac mitochondria oxidizing pyruvate to alterations in [ATP], [ADP], and inorganic phosphate ([Pi]) were characterized over a range of steady-state levels of extramitochondrial [ATP], [ADP], and [Pi]. Evolution of the steady states of the measured variables with the flux of respiration shows that: (1) a higher phosphorylation potential is achieved by mitochondria at higher [Pi] for a given flux of respiration; (2) the time hierarchy of oxidative phosphorylation is given by phosphorylation subsystem, electron transport chain, and substrate dehydrogenation subsystems listed in increasing order of their response times; (3) the matrix ATP hydrolysis mass action ratio [ADP] × [Pi]/[ATP] provides feedback to the substrate dehydrogenation flux over the entire range of respiratory flux examined in this study; and finally, (4) contrary to previous models of regulation of oxidative phosphorylation, [Pi] does not modulate the activity of complex III.
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Affiliation(s)
- Kalyan C Vinnakota
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan.
| | - Jason N Bazil
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Françoise Van den Bergh
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Robert W Wiseman
- Department of Physiology, Michigan State University, East Lansing, Michigan
| | - Daniel A Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
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14
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Bazil JN, Beard DA, Vinnakota KC. Catalytic Coupling of Oxidative Phosphorylation, ATP Demand, and Reactive Oxygen Species Generation. Biophys J 2016; 110:962-71. [PMID: 26910433 DOI: 10.1016/j.bpj.2015.09.036] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/03/2015] [Accepted: 09/25/2015] [Indexed: 01/13/2023] Open
Abstract
Competing models of mitochondrial energy metabolism in the heart are highly disputed. In addition, the mechanisms of reactive oxygen species (ROS) production and scavenging are not well understood. To deepen our understanding of these processes, a computer model was developed to integrate the biophysical processes of oxidative phosphorylation and ROS generation. The model was calibrated with experimental data obtained from isolated rat heart mitochondria subjected to physiological conditions and workloads. Model simulations show that changes in the quinone pool redox state are responsible for the apparent inorganic phosphate activation of complex III. Model simulations predict that complex III is responsible for more ROS production during physiological working conditions relative to complex I. However, this relationship is reversed under pathological conditions. Finally, model analysis reveals how a highly reduced quinone pool caused by elevated levels of succinate is likely responsible for the burst of ROS seen during reperfusion after ischemia.
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Affiliation(s)
- Jason N Bazil
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Daniel A Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan.
| | - Kalyan C Vinnakota
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
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15
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Moxley MA, Beard DA, Bazil JN. Global Kinetic Analysis of Mammalian E3 Reveals pH-dependent NAD+/NADH Regulation, Physiological Kinetic Reversibility, and Catalytic Optimum. J Biol Chem 2015; 291:2712-30. [PMID: 26644471 DOI: 10.1074/jbc.m115.676619] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 12/11/2022] Open
Abstract
Mammalian E3 is an essential mitochondrial enzyme responsible for catalyzing the terminal reaction in the oxidative catabolism of several metabolites. E3 is a key regulator of metabolic fuel selection as a component of the pyruvate dehydrogenase complex (PDHc). E3 regulates PDHc activity by altering the affinity of pyruvate dehydrogenase kinase, an inhibitor of the enzyme complex, through changes in reduction and acetylation state of lipoamide moieties set by the NAD(+)/NADH ratio. Thus, an accurate kinetic model of E3 is needed to predict overall mammalian PDHc activity. Here, we have combined numerous literature data sets and new equilibrium spectroscopic experiments with a multitude of independently collected forward and reverse steady-state kinetic assays using pig heart E3. The latter kinetic assays demonstrate a pH-dependent transition of NAD(+) activation to inhibition, shown here, to our knowledge, for the first time in a single consistent data set. Experimental data were analyzed to yield a thermodynamically constrained four-redox-state model of E3 that simulates pH-dependent activation/inhibition and active site redox states for various conditions. The developed model was used to determine substrate/product conditions that give maximal E3 rates and show that, due to non-Michaelis-Menten behavior, the maximal flux is different compared with the classically defined kcat.
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Affiliation(s)
- Michael A Moxley
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109
| | - Daniel A Beard
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109
| | - Jason N Bazil
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109
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16
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Dasika SK, Vinnakota KC, Beard DA. Determination of the catalytic mechanism for mitochondrial malate dehydrogenase. Biophys J 2015; 108:408-19. [PMID: 25606688 DOI: 10.1016/j.bpj.2014.11.3467] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 10/31/2014] [Accepted: 11/10/2014] [Indexed: 11/15/2022] Open
Abstract
The kinetics of malate dehydrogenase (MDH) catalyzed oxidation/reduction of L-malate/oxaloacetate is pH-dependent due to the proton generated/taken up during the reaction. Previous kinetic studies on the mitochondrial MDH did not yield a consensus kinetic model that explains both substrate and pH dependency of the initial velocity. In this study, we propose, to our knowledge, a new kinetic mechanism to explain kinetic data acquired over a range of pH and substrate concentrations. Progress curves in the forward and reverse reaction directions were obtained under a variety of reactant concentrations to identify associated kinetic parameters. Experiments were conducted at physiologically relevant ionic strength of 0.17 M, pH ranging between 6.5 and 9.0, and at 25 °C. The developed model was built on the prior observation of proton uptake upon binding of NADH to MDH, and that the MDH-catalyzed oxidation of NADH may follow an ordered bi-bi mechanism with NADH/NAD binding to the enzyme first, followed by the binding of oxaloacetate/L-malate. This basic mechanism was expanded to account for additional ionic states to explain the pH dependency of the kinetic behavior, resulting in what we believe to be the first kinetic model explaining both substrate and pH dependency of the reaction velocity.
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Affiliation(s)
- Santosh K Dasika
- Department of Molecular and Integrated Physiology, University of Michigan, Ann Arbor, Michigan
| | - Kalyan C Vinnakota
- Department of Molecular and Integrated Physiology, University of Michigan, Ann Arbor, Michigan
| | - Daniel A Beard
- Department of Molecular and Integrated Physiology, University of Michigan, Ann Arbor, Michigan.
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17
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Markevich NI, Hoek JB. Computational modeling analysis of mitochondrial superoxide production under varying substrate conditions and upon inhibition of different segments of the electron transport chain. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1847:656-79. [PMID: 25868872 PMCID: PMC4426091 DOI: 10.1016/j.bbabio.2015.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 03/24/2015] [Accepted: 04/06/2015] [Indexed: 12/13/2022]
Abstract
A computational mechanistic model of superoxide (O2•-) formation in the mitochondrial electron transport chain (ETC) was developed to facilitate the quantitative analysis of factors controlling mitochondrial O2•- production and assist in the interpretation of experimental studies. The model takes into account all individual electron transfer reactions in Complexes I and III. The model accounts for multiple, often seemingly contradictory observations on the effects of ΔΨ and ΔpH, and for the effects of multiple substrate and inhibitor conditions, including differential effects of Complex III inhibitors antimycin A, myxothiazol and stigmatellin. Simulation results confirm that, in addition to O2•- formation in Complex III and at the flavin site of Complex I, the quinone binding site of Complex I is an additional superoxide generating site that accounts for experimental observations on O2•- production during reverse electron transfer. However, our simulation results predict that, when cytochrome c oxidase is inhibited during oxidation of succinate, ROS production at this site is eliminated and almost all superoxide in Complex I is generated by reduced FMN, even when the redox pressure for reverse electron transfer from succinate is strong. In addition, the model indicates that conflicting literature data on the kinetics of electron transfer in Complex III involving the iron-sulfur protein-cytochrome bL complex can be resolved in favor of a dissociation of the protein only after electron transfer to cytochrome bH. The model predictions can be helpful in understanding factors driving mitochondrial superoxide formation in intact cells and tissues.
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Affiliation(s)
- Nikolai I Markevich
- MitoCare Center for Mitochondrial Research, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 14290, Russia.
| | - Jan B Hoek
- MitoCare Center for Mitochondrial Research, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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18
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Moxley MA, Beard DA, Bazil JN. A pH-dependent kinetic model of dihydrolipoamide dehydrogenase from multiple organisms. Biophys J 2014; 107:2993-3007. [PMID: 25517164 PMCID: PMC4269776 DOI: 10.1016/j.bpj.2014.09.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 09/19/2014] [Accepted: 09/24/2014] [Indexed: 11/18/2022] Open
Abstract
Dihydrolipoamide dehydrogenase is a flavoenzyme that reversibly catalyzes the oxidation of reduced lipoyl substrates with the reduction of NAD(+) to NADH. In vivo, the dihydrolipoamide dehydrogenase component (E3) is associated with the pyruvate, α-ketoglutarate, and glycine dehydrogenase complexes. The pyruvate dehydrogenase (PDH) complex connects the glycolytic flux to the tricarboxylic acid cycle and is central to the regulation of primary metabolism. Regulation of PDH via regulation of the E3 component by the NAD(+)/NADH ratio represents one of the important physiological control mechanisms of PDH activity. Furthermore, previous experiments with the isolated E3 component have demonstrated the importance of pH in dictating NAD(+)/NADH ratio effects on enzymatic activity. Here, we show that a three-state mechanism that represents the major redox states of the enzyme and includes a detailed representation of the active-site chemistry constrained by both equilibrium and thermodynamic loop constraints can be used to model regulatory NAD(+)/NADH ratio and pH effects demonstrated in progress-curve and initial-velocity data sets from rat, human, Escherichia coli, and spinach enzymes. Global fitting of the model provides stable predictions to the steady-state distributions of enzyme redox states as a function of lipoamide/dihydrolipoamide, NAD(+)/NADH, and pH. These distributions were calculated using physiological NAD(+)/NADH ratios representative of the diverse organismal sources of E3 analyzed in this study. This mechanistically detailed, thermodynamically constrained, pH-dependent model of E3 provides a stable platform on which to accurately model multicomponent enzyme complexes that implement E3 from a variety of organisms.
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Affiliation(s)
- Michael A Moxley
- Department of Biochemistry, Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Daniel A Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan.
| | - Jason N Bazil
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
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19
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Bazil JN, Pannala VR, Dash RK, Beard DA. Determining the origins of superoxide and hydrogen peroxide in the mammalian NADH:ubiquinone oxidoreductase. Free Radic Biol Med 2014; 77:121-9. [PMID: 25236739 PMCID: PMC4258523 DOI: 10.1016/j.freeradbiomed.2014.08.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/21/2014] [Accepted: 08/21/2014] [Indexed: 11/26/2022]
Abstract
NADH:ubiquinone oxidoreductase (complex I) is a proton pump in the electron transport chain that can produce a significant amounts of superoxide and hydrogen peroxide. While the flavin mononucleotide (FMN) is the putative site for hydrogen peroxide generation, sites responsible for superoxide are less certain. Here, data on complex I kinetics and ROS generation are analyzed using a computational model to determine the sites responsible for superoxide. The analysis includes all the major redox centers: the FMN, iron-sulfur cluster N2, and semiquinone. Analysis reveals that the fully reduced FMN and semiquinone are the primary sources of superoxide, and the iron-sulfur cluster N2 produces none. The FMN radical only produces ROS when the quinone reductase site is blocked. Model simulations reveal that ROS generation is maximized during reverse electron transport with both the FMN and the semiquinone producing similar amounts of superoxide. In addition, the model successfully predicts the increase in ROS generation when the membrane potential is high and matrix pH is alkaline. Of the total ROS produced by complex I, the majority originates from the FMN.
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Affiliation(s)
- Jason N Bazil
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Venkat R Pannala
- Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ranjan K Dash
- Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Daniel A Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Guillaud F, Dröse S, Kowald A, Brandt U, Klipp E. Superoxide production by cytochrome bc1 complex: A mathematical model. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1643-52. [DOI: 10.1016/j.bbabio.2014.05.358] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 12/17/2022]
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21
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Kowald A, Klipp E. Mathematical models of mitochondrial aging and dynamics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 127:63-92. [PMID: 25149214 DOI: 10.1016/b978-0-12-394625-6.00003-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Research on the role of mitochondria in aging and disease is rapidly growing. Furthermore, in recent years, it also became clear that mitochondria are dynamic structures undergoing constant and rapid cycles of fusion and fission. The involvement of mitochondria in multiple complex processes makes them a prime target for mathematical and computational modeling. This review consists of two parts. In the first (Section 2), we provide a detailed introduction to the underlying concepts of mathematical modeling to help the reader who is not so familiar with these techniques to judge the requirements and results that can be obtained through modeling. In the second part (Section 3), we review existing mathematical and computational models that investigate mitochondrial dynamics and the role of mitochondria for the aging process.
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Affiliation(s)
- Axel Kowald
- Theoretical Biophysics, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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