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Uttley M, Horne G, Tsigkinopoulou A, Del Carratore F, Hawari A, Kiezel-Tsugunova M, Kendall AC, Jones J, Messenger D, Bhogal RK, Breitling R, Nicolaou A. An adaptable in silico ensemble model of the arachidonic acid cascade. Mol Omics 2024; 20:453-468. [PMID: 38860509 PMCID: PMC11318654 DOI: 10.1039/d3mo00187c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 05/27/2024] [Indexed: 06/12/2024]
Abstract
Eicosanoids are a family of bioactive lipids, including derivatives of the ubiquitous fatty acid arachidonic acid (AA). The intimate involvement of eicosanoids in inflammation motivates the development of predictive in silico models for a systems-level exploration of disease mechanisms, drug development and replacement of animal models. Using an ensemble modelling strategy, we developed a computational model of the AA cascade. This approach allows the visualisation of plausible and thermodynamically feasible predictions, overcoming the limitations of fixed-parameter modelling. A quality scoring method was developed to quantify the accuracy of ensemble predictions relative to experimental data, measuring the overall uncertainty of the process. Monte Carlo ensemble modelling was used to quantify the prediction confidence levels. Model applicability was demonstrated using mass spectrometry mediator lipidomics to measure eicosanoids produced by HaCaT epidermal keratinocytes and 46BR.1N dermal fibroblasts, treated with stimuli (calcium ionophore A23187), (ultraviolet radiation, adenosine triphosphate) and a cyclooxygenase inhibitor (indomethacin). Experimentation and predictions were in good qualitative agreement, demonstrating the ability of the model to be adapted to cell types exhibiting differences in AA release and enzyme concentration profiles. The quantitative agreement between experimental and predicted outputs could be improved by expanding network topology to include additional reactions. Overall, our approach generated an adaptable, tuneable ensemble model of the AA cascade that can be tailored to represent different cell types and demonstrated that the integration of in silico and in vitro methods can facilitate a greater understanding of complex biological networks such as the AA cascade.
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Affiliation(s)
- Megan Uttley
- Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - Grace Horne
- Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - Areti Tsigkinopoulou
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Francesco Del Carratore
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
- Department of Biochemistry, Cell and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool, Liverpool, UK
| | - Aliah Hawari
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Magdalena Kiezel-Tsugunova
- Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - Alexandra C Kendall
- Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - Janette Jones
- Unilever R&D, Quarry Road East, Bebington, Wirral, CH63 3JW, UK
| | - David Messenger
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Ranjit Kaur Bhogal
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Anna Nicolaou
- Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
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2
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Seeger DR, Schofield B, Besch D, Golovko SA, Kotha P, Parmer M, Solaymani-Mohammadi S, Golovko MY. Exogenous oxygen is required for prostanoid induction under brain ischemia as evidence for a novel regulatory mechanism. J Lipid Res 2023; 64:100452. [PMID: 37783389 PMCID: PMC10630775 DOI: 10.1016/j.jlr.2023.100452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023] Open
Abstract
Previously, we and others reported a rapid and dramatic increase in brain prostanoids (PG), including prostaglandins, prostacyclins, and thromboxanes, under ischemia that is traditionally explained through the activation of esterified arachidonic acid (20:4n6) release by phospholipases as a substrate for cyclooxygenases (COX). However, the availability of another required COX substrate, oxygen, has not been considered in this mechanism. To address this mechanism for PG upregulation through oxygen availability, we analyzed mouse brain PG, free 20:4n6, and oxygen levels at different time points after ischemic onset using head-focused microwave irradiation (MW) to inactivate enzymes in situ before craniotomy. The oxygen half-life in the ischemic brain was 5.32 ± 0.45 s and dropped to undetectable levels within 12 s of ischemia onset, while there were no significant free 20:4n6 or PG changes at 30 s of ischemia. Furthermore, there was no significant PG increase at 2 and 10 min after ischemia onset compared to basal levels, while free 20:4n6 was increased ∼50 and ∼100 fold, respectively. However, PG increased ∼30-fold when ischemia was followed by craniotomy of nonMW tissue that provided oxygen for active enzymes. Moreover, craniotomy performed under anoxic conditions without MW did not result in PG induction, while exposure of these brains to atmospheric oxygen significantly induced PG. Our results indicate, for the first time, that oxygen availability is another important regulatory factor for PG production under ischemia. Further studies are required to investigate the physiological role of COX/PG regulation through tissue oxygen concentration.
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Affiliation(s)
- Drew R Seeger
- Department of Biomedical Sciences, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND, USA
| | - Brennon Schofield
- Department of Biomedical Sciences, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND, USA
| | - Derek Besch
- Department of Biomedical Sciences, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND, USA
| | - Svetlana A Golovko
- Department of Biomedical Sciences, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND, USA
| | - Peddanna Kotha
- Department of Biomedical Sciences, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND, USA
| | - Meredith Parmer
- Department of Biomedical Sciences, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND, USA
| | - Shahram Solaymani-Mohammadi
- Department of Biomedical Sciences, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND, USA
| | - Mikhail Y Golovko
- Department of Biomedical Sciences, School of Medicine and Health Science, University of North Dakota, Grand Forks, ND, USA.
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3
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Qiao J, Ma L, Roth J, Li Y, Liu Y. Kinetic basis for the activation of human cyclooxygenase-2 rather than cyclooxygenase-1 by nitric oxide. Org Biomol Chem 2019; 16:765-770. [PMID: 29308820 DOI: 10.1039/c7ob02992f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Numerous studies have shown that nitric oxide (NO) interacts with human cyclooxygenase (COX); however, conflicting results exist with respect to their interactions. Herein, recombinant human COX-1 and COX-2 were prepared and treated with NO donors individually under anaerobic and aerobic conditions. The S-nitrosylation detection and subsequent kinetic investigations into the arachidonic acid (AA) oxidation of COX enzymes indicate that NO S-nitrosylates both COX-1 and COX-2 in an oxygen-dependent manner, but enhances only the dioxygenase activity of COX-2. The solution viscosity, deuterium kinetic isotope effect (KIE), and oxygen-18 KIE experiments further demonstrate that NO activates COX-2 by altering the protein conformation to stimulate substrate association/product release and by accelerating the rate of hydrogen abstraction from AA by catalytic tyrosine radicals. These novel findings provide useful information for designing new drugs with less cardiotoxic effects that can block the interaction between NO and COX.
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Affiliation(s)
- Jie Qiao
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Science, Hubei University, Wuhan, Hubei 430062, China.
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4
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How Supraphysiological Oxygen Levels in Standard Cell Culture Affect Oxygen-Consuming Reactions. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:8238459. [PMID: 30363917 PMCID: PMC6186316 DOI: 10.1155/2018/8238459] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022]
Abstract
Most mammalian tissue cells experience oxygen partial pressures in vivo equivalent to 1–6% O2 (i.e., physioxia). In standard cell culture, however, headspace O2 levels are usually not actively regulated and under these conditions are ~18%. This drives hyperoxia in cell culture media that can affect a wide variety of cellular activities and may compromise the ability of in vitro models to reproduce in vivo biology. Here, we review and discuss some specific O2-consuming organelles and enzymes, including mitochondria, NADPH oxidases, the transplasma membrane redox system, nitric oxide synthases, xanthine oxidase, and monoamine oxidase with respect to their sensitivities to O2 levels. Many of these produce reactive oxygen and/or nitrogen species (ROS/RNS) as either primary end products or byproducts and are acutely sensitive to O2 levels in the range from 1% to 18%. Interestingly, many of them are also transcriptional targets of hypoxia-inducible factors (HIFs) and chronic cell growth at physioxia versus 18% O2 may alter their expression. Aquaporins, which facilitate hydrogen peroxide diffusion into and out of cells, are also regulated by HIFs, indicating that O2 levels may affect intercellular communication via hydrogen peroxide. The O2 sensitivities of these important activities emphasize the importance of maintaining physioxia in culture.
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5
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Wu G, Tsai AL. Dynamics of Radical Intermediates in Prostaglandin H Synthase-1 Cyclooxygenase Reactions is Modulated by Multiple Factors. Protein Pept Lett 2017; 23:1013-1023. [PMID: 27748183 DOI: 10.2174/0929866523666161007151812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/30/2016] [Accepted: 10/01/2016] [Indexed: 11/22/2022]
Abstract
Prostaglandin H synthase (PGHS) catalyzes the biosynthesis of PGG2 and PGH2, the precursor of all prostanoids, from arachidonic acid (AA). PGHS exhibits two enzymatic activities following a branched-chain radical mechanism: 1) a peroxidase activity (POX) that utilizes hydroperoxide through heme redox cycles to generate the critical Tyr385 tyrosyl radical for coupling both enzyme activities; 2) the cyclooxygenase (COX) activity inserting two oxygen molecules into AA to generate endoperoxide/hydroperoxide PGG2 through a series of radical intermediates. Upon the generation of Tyr385 radical, COX catalysis is initiated, with C13 pro-S hydrogen abstraction from AA by Tyr385 radical to generate arachidonyl substrate radical. Oxygen provides a large driving force for the subsequent fast steps leading to the formation of PGG2, including radical redistributions, ring formations, and rearrangements. On the other hand, if the supply of oxygen is severed, equilibrium between arachidonyl radical and tyrosyl radical(s) biases largely towards the latter. In this study, we demonstrate that such equilibrium is shifted by many factors, including temperature, chemical structures of fatty acid substrates and limited supply of oxygen. We also, for the first time, reveal that this equilibrium is significantly affected by co-substrates of POX. The presence of efficient POX co-substrates, which reduces heme to its ferric state, apparently biases the equilibrium towards arachidonyl radical. Therefore a dynamic interplay exists between the two activities of PGHS.
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Affiliation(s)
- Gang Wu
- Division of Hematology, Department of Internal Medicine, the University of Texas Health Science Center at Houston - McGovern Medical School, MSB 5.290, 6431 Fannin, Houston, TX 77030, USA
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6
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Jackson WF. Arteriolar oxygen reactivity: where is the sensor and what is the mechanism of action? J Physiol 2016; 594:5055-77. [PMID: 27324312 PMCID: PMC5023707 DOI: 10.1113/jp270192] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/13/2016] [Indexed: 01/02/2023] Open
Abstract
Arterioles in the peripheral microcirculation are exquisitely sensitive to changes in PO2 in their environment: increases in PO2 cause vasoconstriction while decreases in PO2 result in vasodilatation. However, the cell type that senses O2 (the O2 sensor) and the signalling pathway that couples changes in PO2 to changes in arteriolar tone (the mechanism of action) remain unclear. Many (but not all) ex vivo studies of isolated cannulated resistance arteries and large, first-order arterioles support the hypothesis that these vessels are intrinsically sensitive to PO2 with the smooth muscle, endothelial cells, or red blood cells serving as the O2 sensor. However, in situ studies testing these hypotheses in downstream arterioles have failed to find evidence of intrinsic O2 sensitivity, and instead have supported the idea that extravascular cells sense O2 . Similarly, ex vivo studies of isolated, cannulated resistance arteries and large first-order arterioles support the hypotheses that O2 -dependent inhibition of production of vasodilator cyclooxygenase products or O2 -dependent destruction of nitric oxide mediates O2 reactivity of these upstream vessels. In contrast, most in vivo studies of downstream arterioles have disproved these hypotheses and instead have provided evidence supporting the idea that O2 -dependent production of vasoconstrictors mediates arteriolar O2 reactivity, with significant regional heterogeneity in the specific vasoconstrictor involved. Oxygen-induced vasoconstriction may serve as a protective mechanism to reduce the oxidative burden to which a tissue is exposed, a process that is superimposed on top of the local mechanisms which regulate tissue blood flow to meet a tissue's metabolic demand.
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Affiliation(s)
- William F Jackson
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA.
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7
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Ponomareva OA, Trushkin NA, Filimonov IS, Krivoshey AV, Barkhatov VI, Mitrofanov SI, Vrzheshch PV. Prostaglandin H synthase kinetics in the two-phase aqueous-micellar system. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2199-2207. [PMID: 27342373 DOI: 10.1016/j.bbamem.2016.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/28/2016] [Accepted: 06/17/2016] [Indexed: 10/21/2022]
Abstract
Reaction mixture for PGHS (prostaglandin-H-synthase) is a two-phase system including micellar hydrophobic phase and hydrophilic aqueous phase. Reagents added to the mixture are distributed between phases, thus concentrations of reagents dissolved in phases can differ significantly from their overall contents. Using dynamic light scattering we found that the hydrophobic phase produced by tween-20 consists of micelles, which radius (4-5nm) does not depend on either tween-20 overall content (0.1%-1% v/v) or arachidonic acid (AA) addition (10-1000μM) or PGHS addition (1μM). Tween-20 overall content changing from 0.1% to 2% v/v dramatically affected COX kinetic, but accounting AA distribution between phases allowed us to estimate "true" parameters, independent of the tween-20 overall content and the concentration of another substrate: KM(Ox) equals 9.8μM O2 in the aqueous phase or 0.0074bar in the gaseous phase, KM(AA) equals 5400μM AA in the phase of tween-20 micelles and 5400/PμM AA in the aqueous phase (P is the distribution ratio for the AA between the aqueous phase and the hydrophobic phase (P≫1000)). This approach allowed to evaluate PS, the distribution ratio for the AA between the hydrophobic phase and the PGHS active center (PS ~310). This coefficient indicates the AA selectivity toward the cyclooxygenase active center.
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Affiliation(s)
- Olga A Ponomareva
- International Biotechnological Center of Lomonosov Moscow State University, Russia.
| | - Nikita A Trushkin
- International Biotechnological Center of Lomonosov Moscow State University, Russia.
| | - Ivan S Filimonov
- International Biotechnological Center of Lomonosov Moscow State University, Russia.
| | - Alexandr V Krivoshey
- International Biotechnological Center of Lomonosov Moscow State University, Russia.
| | - Vladimir I Barkhatov
- International Biotechnological Center of Lomonosov Moscow State University, Russia.
| | - Sergey I Mitrofanov
- International Biotechnological Center of Lomonosov Moscow State University, Russia.
| | - Petr V Vrzheshch
- International Biotechnological Center of Lomonosov Moscow State University, Russia.
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8
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Liu Y, Roth JP. A Revised Mechanism for Human Cyclooxygenase-2. J Biol Chem 2016; 291:948-58. [PMID: 26565028 PMCID: PMC4705412 DOI: 10.1074/jbc.m115.668038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/10/2015] [Indexed: 11/06/2022] Open
Abstract
The mechanism of ω-6 polyunsaturated fatty acid oxidation by wild-type cyclooxygenase 2 and the Y334F variant, lacking a conserved hydrogen bond to the catalytic tyrosyl radical/tyrosine, was examined for the first time under physiologically relevant conditions. The enzymes show apparent bimolecular rate constants and deuterium kinetic isotope effects that increase in proportion to co-substrate concentrations before converging to limiting values. The trends exclude multiple dioxygenase mechanisms as well as the proposal that initial hydrogen atom abstraction from the fatty acid is the first irreversible step in catalysis. Temperature dependent kinetic studies reinforce the novel finding that hydrogen transfer from the reduced catalytic tyrosine to a terminal peroxyl radical is the first irreversible step that controls regio- and stereospecific product formation.
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Affiliation(s)
- Yi Liu
- From the Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Justine P Roth
- From the Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
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9
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Audran G, Brémond P, Marque SR, Siri D, Santelli M. Energetics of the biosynthesis of prostanes from arachidonate. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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10
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Kinetic Isotope Effect of Prostaglandin H Synthase Exhibits Inverted Temperature Dependence. Catalysts 2014. [DOI: 10.3390/catal4020174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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11
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Liu Y, Mukherjee A, Nahumi N, Ozbil M, Brown D, Angeles-Boza AM, Dooley DM, Prabhakar R, Roth JP. Experimental and Computational Evidence of Metal-O2 Activation and Rate-Limiting Proton-Coupled Electron Transfer in a Copper Amine Oxidase. J Phys Chem B 2012; 117:218-29. [DOI: 10.1021/jp3121484] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yi Liu
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Nadav Nahumi
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Doreen Brown
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - David M. Dooley
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
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12
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Goswami SK, Das DK. Oxygen Sensing, Cardiac Ischemia, HIF-1α and Some Emerging Concepts. Curr Cardiol Rev 2011; 6:265-73. [PMID: 22043202 PMCID: PMC3083807 DOI: 10.2174/157340310793566136] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 09/03/2010] [Accepted: 09/15/2010] [Indexed: 11/22/2022] Open
Abstract
Oxygen plays a critical role in the perpetuation and propagation of almost all forms of life. The primary site of cellular oxygen consumption is the mitochondrial electron transport chain and in addition, oxygen is also used as a substrate for various enzymes involved in cellular homeostasis. Although our knowledge of the biochemistry and physiology of oxygen transport is century old, recent development of sophisticated tools of biophysical chemistry revealed that tissue oxygenation and oxygen sensing is a highly evolved process, especially in mammals. Perturbation of normal oxygen supply is associated with diseases like tumorigenesis, myocardial infarction and stroke. Available information suggests that when tissue oxygen supply is limited, mitochondria emanate signals involving reactive oxygen species generation which in turn stabilizes oxygen sensing transcription factor HIF-1. Upon stabilization, HIF-1 elicits necessary genetic response to cope with the diminished oxygen level. In view of such critical role of HIF-1 in cellular oxygen sensing, recently there has been a heightened interest in understanding the biology of HIF-1 in the context of cardiovascular system. The following review describes some of the recent advances in this regard.
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Affiliation(s)
- Shyamal K Goswami
- Cardiovascular Research Center, University of Connecticut School of Medicine, Farmington, Connecticut, CT 06030- 1110, USA
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13
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Smith WL, Urade Y, Jakobsson PJ. Enzymes of the cyclooxygenase pathways of prostanoid biosynthesis. Chem Rev 2011; 111:5821-65. [PMID: 21942677 PMCID: PMC3285496 DOI: 10.1021/cr2002992] [Citation(s) in RCA: 346] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- William L Smith
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, 5301 MSRB III, Ann Arbor, Michigan 48109-5606, USA.
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14
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Danish HH, Doncheva IS, Roth JP. Hydrogen tunneling steps in cyclooxygenase-2 catalysis. J Am Chem Soc 2011; 133:15846-9. [PMID: 21902213 DOI: 10.1021/ja2059523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclooxygenases-1 and -2 are tyrosyl radical (Y·)-utilizing hemoproteins responsible for the biosynthesis of lipid-derived autocoids. COX-2, in particular, is a primary mediator of inflammation and believed to be up-regulated in many forms of cancer. Described here are first-of-a-kind studies of COX-2-catalyzed oxidation of the substrate analogue linoleic acid. Very large (≥20) temperature-independent deuterium kinetic isotope effects (KIEs) on the rate constant for enzyme turnover were observed, due to hydrogen atom abstraction from the bisallylic C-H(D) of the fatty acid. The magnitude of the KIE depends on the O(2) concentration, consistent with reversible H/D tunneling mediated by the catalytic Y·. At physiological levels of O(2), retention of the hydrogen initially abstracted by the catalytic tyrosine results in strongly temperature-dependent KIEs on O-H(D) homolysis, also characteristic of nuclear tunneling.
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Affiliation(s)
- Husain H Danish
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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15
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Lundström SL, Levänen B, Nording M, Klepczynska-Nyström A, Sköld M, Haeggström JZ, Grunewald J, Svartengren M, Hammock BD, Larsson BM, Eklund A, Wheelock ÅM, Wheelock CE. Asthmatics exhibit altered oxylipin profiles compared to healthy individuals after subway air exposure. PLoS One 2011; 6:e23864. [PMID: 21897859 PMCID: PMC3163588 DOI: 10.1371/journal.pone.0023864] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 07/26/2011] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Asthma is a chronic inflammatory lung disease that causes significant morbidity and mortality worldwide. Air pollutants such as particulate matter (PM) and oxidants are important factors in causing exacerbations in asthmatics, and the source and composition of pollutants greatly affects pathological implications. OBJECTIVES This randomized crossover study investigated responses of the respiratory system to Stockholm subway air in asthmatics and healthy individuals. Eicosanoids and other oxylipins were quantified in the distal lung to provide a measure of shifts in lipid mediators in association with exposure to subway air relative to ambient air. METHODS Sixty-four oxylipins representing the cyclooxygenase (COX), lipoxygenase (LOX) and cytochrome P450 (CYP) metabolic pathways were screened using liquid chromatography-tandem mass spectrometry (LC-MS/MS) of bronchoalveolar lavage (BAL)-fluid. Validations through immunocytochemistry staining of BAL-cells were performed for 15-LOX-1, COX-1, COX-2 and peroxisome proliferator-activated receptor gamma (PPARγ). Multivariate statistics were employed to interrogate acquired oxylipin and immunocytochemistry data in combination with patient clinical information. RESULTS Asthmatics and healthy individuals exhibited divergent oxylipin profiles following exposure to ambient and subway air. Significant changes were observed in 8 metabolites of linoleic- and α-linolenic acid synthesized via the 15-LOX pathway, and of the COX product prostaglandin E(2) (PGE(2)). Oxylipin levels were increased in healthy individuals following exposure to subway air, whereas asthmatics evidenced decreases or no change. CONCLUSIONS Several of the altered oxylipins have known or suspected bronchoprotective or anti-inflammatory effects, suggesting a possible reduced anti-inflammatory response in asthmatics following exposure to subway air. These observations may have ramifications for sensitive subpopulations in urban areas.
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Affiliation(s)
- Susanna L. Lundström
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden
| | - Bettina Levänen
- Division of Respiratory Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Malin Nording
- Department of Entomology and Cancer Research Center, University of California Davis, Davis, California, United States of America
- Department of Public Health and Clinical Medicine, Respiratory Medicine and Allergy, Umeå University, Umeå, Sweden
| | - Anna Klepczynska-Nyström
- Division of Occupational and Environmental Medicine, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Sköld
- Division of Respiratory Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Z. Haeggström
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden
| | - Johan Grunewald
- Division of Respiratory Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Svartengren
- Division of Occupational and Environmental Medicine, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Bruce D. Hammock
- Department of Entomology and Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Britt-Marie Larsson
- Division of Occupational and Environmental Medicine, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Anders Eklund
- Division of Respiratory Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Åsa M. Wheelock
- Division of Respiratory Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (CEW); (AMW)
| | - Craig E. Wheelock
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (CEW); (AMW)
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16
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Huff GS, Doncheva IS, Brinkley DW, Angeles-Boza AM, Mukherjee A, Cramer CJ, Roth JP. Experimental and Computational Investigations of Oxygen Reactivity in a Heme and Tyrosyl Radical-Containing Fatty Acid α-(Di)oxygenase. Biochemistry 2011; 50:7375-89. [DOI: 10.1021/bi201016h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Gregory S. Huff
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Irina S. Doncheva
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis,
Minnesota 55455, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
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17
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Lü JM, Rogge CE, Wu G, Kulmacz RJ, van der Donk WA, Tsai AL. Cyclooxygenase reaction mechanism of PGHS--evidence for a reversible transition between a pentadienyl radical and a new tyrosyl radical by nitric oxide trapping. J Inorg Biochem 2011; 105:356-65. [PMID: 21403766 DOI: 10.1016/j.jinorgbio.2010.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Incubation of prostaglandin H synthase-1 (PGHS-1) under anaerobic conditions with peroxide and arachidonic acid leads to two major radical species: a pentadienyl radical and a radical with a narrow EPR spectrum. The proportions of the two radicals are sensitive to temperature, favoring the narrow radical species at 22 °C. The EPR characteristics of this latter radical are somewhat similar to the previously reported narrow-singlet tyrosine radical NS1a and are insensitive to deuterium labeling of AA. To probe the origin and structure of this radical, we combined EPR analysis with nitric oxide (NO) trapping of tyrosine and substrate derived radicals for both PGHS-1 and -2. Formation of 3-nitrotyrosine in the proteins was analyzed by immunoblotting, whereas NO adducts to AA and AA metabolites were analyzed by mass spectrometry and by chromatography of (14)C-labeled products. The results indicate that both nitrated tyrosine residues and NO-AA adducts formed upon NO trapping. The NO-AA adduct was predominantly an oxime at C11 of AA with three conjugated double bonds, as indicated by absorption at 275 nm and by mass spectral analysis. This adduct amounted to 10% and 20% of the heme concentration of PGHS-1 and -2, respectively. For PGHS-1, the yield of NO-AA adduct matched the yield of the narrow radical signal obtained in parallel EPR experiments. High frequency EPR characterization of this narrow radical, reported in an accompanying paper, supports assignment to a new tyrosyl radical, NS1c, rather than an AA-based radical. To reconcile the results from EPR and NO-trapping studies, we propose that the NS1c is in equilibrium with an AA pentadienyl radical, and that the latter reacts preferentially with NO.
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Affiliation(s)
- Jian-Ming Lü
- Department of Internal Medicine, University of Texas Medical School at Houston, Houston, Texas 77030, USA
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18
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Cyclooxygenase reaction mechanism of prostaglandin H synthase from deuterium kinetic isotope effects. J Inorg Biochem 2011; 105:382-90. [PMID: 21394223 DOI: 10.1016/j.jinorgbio.2010.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cyclooxygenase catalysis by prostaglandin H synthase (PGHS) is thought to involve a multistep mechanism with several radical intermediates. The proposed mechanism begins with transfer of the C13 pro-(S) hydrogen atom from the substrate arachidonic acid (AA) to the Tyr385 radical in PGHS, followed by oxygen insertion and several bond rearrangements. The importance of the hydrogen-transfer step to controlling the overall kinetics of cyclooxygenase catalysis has not been directly examined. We quantified the non-competitive primary kinetic isotope effect (KIE) for both PGHS-1 and -2 using unlabeled AA and several deuterated AAs, including 13-pro-(S) d-AA, 13,13-d(2)-AA and 10, 10, 13,13-d(4)-AA. The primary KIE for steady-state cyclooxygenase catalysis, (D)k(cat), ranged between 1.8 and 2.3 in oxygen electrode measurements. The intrinsic KIE of AA radical formation by C13 pro-(S) hydrogen abstraction in PGHS-1 was estimated to be 1.9-2.3 using rapid freeze-quench EPR kinetic analysis of anaerobic reactions and computer modeling to a mechanism that includes slow formation of a pentadienyl AA radical and rapid equilibration of the AA radical with a tyrosyl radical, NS1c. The observation of similar values for steady-state and pre-steady state KIEs suggests that hydrogen abstraction is a rate-limiting step in cyclooxygenase catalysis. The large difference of the observed KIE from that of lipoxygenase indicates very different mechanism of hydrogen transfer.
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19
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Tsai AL, Wu G, Rogge CE, Lü JM, Peng S, van der Donk WA, Palmer G, Gerfen GJ, Kulmacz RJ. Structural comparisons of arachidonic acid-induced radicals formed by prostaglandin H synthase-1 and -2. J Inorg Biochem 2011; 105:366-74. [PMID: 21421123 DOI: 10.1016/j.jinorgbio.2010.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 11/15/2010] [Accepted: 11/19/2010] [Indexed: 11/15/2022]
Abstract
Cyclooxygenase catalysis by prostaglandin H synthase (PGHS)-1 and -2 involves reaction of a peroxide-induced Tyr385 radical with arachidonic acid (AA) to form an AA radical that reacts with O(2). The potential for isomeric AA radicals and formation of an alternate tyrosyl radical at Tyr504 complicate analysis of radical intermediates. We compared the EPR spectra of PGHS-1 and -2 reacted with peroxide and AA or specifically deuterated AA in anaerobic, single-turnover experiments. With peroxide-treated PGHS-2, the carbon-centered radical observed after AA addition was consistently a pentadienyl radical; a variable wide-singlet (WS) contribution from mixture of Tyr385 and Tyr504 radicals was also present. Analogous reactions with PGHS-1 produced EPR signals consistent with varying proportions of pentadienyl and tyrosyl radicals, and two additional EPR signals. One, insensitive to oxygen exposure, is the narrow singlet tyrosyl radical with clear hyperfine features found previously in inhibitor-pretreated PGHS-1. The second type of EPR signal is a narrow singlet lacking detailed hyperfine features that disappeared upon oxygen exposure. This signal was previously ascribed to an allyl radical, but high field EPR analysis indicated that ~90% of the signal originates from a novel tyrosyl radical, with a small contribution from a carbon-centered species. The radical kinetics could be resolved by global analysis of EPR spectra of samples trapped at various times during anaerobic reaction of PGHS-1 with a mixture of peroxide and AA. The improved understanding of the dynamics of AA and tyrosyl radicals in PGHS-1 and -2 will be useful for elucidating details of the cyclooxygenase mechanism, particularly the H-transfer between tyrosyl radical and AA.
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Affiliation(s)
- Ah-lim Tsai
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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20
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Nadler A, Koch C, Brodhun F, Wehland JD, Tittmann K, Feussner I, Diederichsen U. Influence of Substrate Dideuteration on the Reaction of the Bifunctional Heme Enzyme Psi Factor Producing Oxygenase A (PpoA). Chembiochem 2011; 12:728-37. [DOI: 10.1002/cbic.201000669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Indexed: 11/06/2022]
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21
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Mukherjee A, Angeles-Boza AM, Huff GS, Roth JP. Catalytic mechanism of a heme and tyrosyl radical-containing fatty acid α-(di)oxygenase. J Am Chem Soc 2010; 133:227-38. [PMID: 21166399 DOI: 10.1021/ja104180v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The steady-state catalytic mechanism of a fatty acid α-(di)oxygenase is examined, revealing that a persistent tyrosyl radical (Tyr379(•)) effects O(2) insertion into C(α)-H bonds of fatty acids. The initiating C(α)-H homolysis step is characterized by apparent rate constants and deuterium kinetic isotope effects (KIEs) that increase hyperbolically upon raising the concentration of O(2). These results are consistent with H(•) tunneling, transitioning from a reversible to an irreversible regime. The limiting deuterium KIEs increase from ∼30 to 120 as the fatty acid chain is shortened from that of the native substrate. In addition, activation barriers increase in a manner that reflects decreased fatty acid binding affinities. Anaerobic isotope exchange experiments provide compelling evidence that Tyr379(•) initiates catalysis by H(•) abstraction. C(α)-H homolysis is kinetically driven by O(2) trapping of the α-carbon radical and reduction of a putative peroxyl radical intermediate to a 2(R)-hydroperoxide product. These findings add to a body of work which establishes large-scale hydrogen tunneling in proteins. This particular example is novel because it involves a protein-derived amino acid radical.
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Affiliation(s)
- Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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22
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Ashley DC, Brinkley DW, Roth JP. Oxygen Isotope Effects as Structural and Mechanistic Probes in Inorganic Oxidation Chemistry. Inorg Chem 2010; 49:3661-75. [DOI: 10.1021/ic901778g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Daniel C. Ashley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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23
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Prostaglandin H synthase: resolved and unresolved mechanistic issues. Arch Biochem Biophys 2009; 493:103-24. [PMID: 19728984 DOI: 10.1016/j.abb.2009.08.019] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 08/25/2009] [Accepted: 08/26/2009] [Indexed: 11/20/2022]
Abstract
The cyclooxygenase and peroxidase activities of prostaglandin H synthase (PGHS)-1 and -2 have complex kinetics, with the cyclooxygenase exhibiting feedback activation by product peroxide and irreversible self-inactivation, and the peroxidase undergoing an independent self-inactivation process. The mechanistic bases for these complex, non-linear steady-state kinetics have been gradually elucidated by a combination of structure/function, spectroscopic and transient kinetic analyses. It is now apparent that most aspects of PGHS-1 and -2 catalysis can be accounted for by a branched chain radical mechanism involving a classic heme-based peroxidase cycle and a radical-based cyclooxygenase cycle. The two cycles are linked by the Tyr385 radical, which originates from an oxidized peroxidase intermediate and begins the cyclooxygenase cycle by abstracting a hydrogen atom from the fatty acid substrate. Peroxidase cycle intermediates have been well characterized, and peroxidase self-inactivation has been kinetically linked to a damaging side reaction involving the oxyferryl heme oxidant in an intermediate that also contains the Tyr385 radical. The cyclooxygenase cycle intermediates are poorly characterized, with the exception of the Tyr385 radical and the initial arachidonate radical, which has a pentadiene structure involving C11-C15 of the fatty acid. Oxygen isotope effect studies suggest that formation of the arachidonate radical is reversible, a conclusion consistent with electron paramagnetic resonance spectroscopic observations, radical trapping by NO, and thermodynamic calculations, although moderate isotope selectivity was found for the H-abstraction step as well. Reaction with peroxide also produces an alternate radical at Tyr504 that is linked to cyclooxygenase activation efficiency and may serve as a reservoir of oxidizing equivalent. The interconversions among radicals on Tyr385, on Tyr504, and on arachidonate, and their relationships to regulation and inactivation of the cyclooxygenase, are still under active investigation for both PGHS isozymes.
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24
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Raber ML, Freeman MF, Townsend CA. Dissection of the stepwise mechanism to beta-lactam formation and elucidation of a rate-determining conformational change in beta-lactam synthetase. J Biol Chem 2008; 284:207-217. [PMID: 18955494 DOI: 10.1074/jbc.m805390200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clavulanic acid is a widely used beta-lactamase inhibitor whose key beta-lactam core is formed by beta-lactam synthetase. beta-Lactam synthetase exhibits a Bi-Ter mechanism consisting of two chemical steps, acyl-adenylation followed by beta-lactam formation. 32PPi-ATP exchange assays showed the first irreversible step of catalysis is acyl-adenylation. From a small, normal solvent isotope effect (1.38 +/- 0.04), it was concluded that beta-lactam synthesis contributes at least partially to kcat. Site-specific mutation of Lys-443 identified this residue as the ionizable group at pKa approximately 8.1 apparent in the pH-kcat profile that stabilizes the beta-lactam-forming step. Viscosity studies demonstrated that a protein conformational change was also partially rate-limiting on kcat attenuating the observed solvent isotope effect on beta-lactam formation. Adherence to Kramers' theory gave a slope of 1.66 +/- 0.08 from a plot of log(o kcat/kcat) versus log(eta/eta(o)) consistent with opening of a structured loop visible in x-ray data preceding product release. Internal "friction" within the enzyme contributes to a slope of > 1 in this analysis. Correspondingly, earlier in the catalytic cycle ordering of a mobile active site loop upon substrate binding was manifested by an inverse solvent isotope effect (0.67 +/- 0.15) on kcat/Km. The increased second-order rate constant in heavy water was expected from ordering of this loop over the active site imposing torsional strain. Finally, an Eyring plot displayed a large enthalpic change accompanying loop movement (DeltaH approximately 20 kcal/mol) comparable to the chemical barrier of beta-lactam formation.
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Affiliation(s)
- Mary L Raber
- Department of Chemistry and Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Michael F Freeman
- Department of Chemistry and Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Craig A Townsend
- Department of Chemistry and Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218.
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25
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Gupta A, Mukherjee A, Matsui K, Roth JP. Evidence for protein radical-mediated nuclear tunneling in fatty acid alpha-oxygenase. J Am Chem Soc 2008; 130:11274-5. [PMID: 18680254 DOI: 10.1021/ja8042273] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rice alpha-oxygenase (RalphaO) catalyzes the insertion of O2 into the Calpha-H bond of various fatty acids. The mechanism is thought to involve a tyrosyl radical as the oxidant on the basis of comparisons to the structurally homologous cyclooxygenase enzymes. Kinetic and spectroscopic results presented here for the wild-type RalphaO and the Tyr379Phe mutant indicate an irreversible H* abstraction mechanism and support the involvement of the proposed catalytic Tyr*. In addition, very large, weakly temperature dependent deuterium kinetic isotope effects (approximately 50) are observed, consistent with extensive nuclear tunneling. RalphaO, thus, presents a novel example where such quantum effects are associated with an amino acid radical-utilizing enzyme.
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Affiliation(s)
- Ankur Gupta
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore Maryland 21218, USA
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26
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Chen L, Lyubimov AY, Brammer L, Vrielink A, Sampson NS. The binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase. Biochemistry 2008; 47:5368-77. [PMID: 18410129 DOI: 10.1021/bi800228w] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The usage by enzymes of specific binding pathways for gaseous substrates or products is debated. The crystal structure of the redox enzyme cholesterol oxidase, determined at sub-angstrom resolution, revealed a hydrophobic tunnel that may serve as a binding pathway for oxygen and hydrogen peroxide. This tunnel is formed by a cascade of conformational rearrangements and connects the active site with the exterior surface of the protein. To elucidate the relationship between this tunnel and gas binding and release, three mutant enzymes were constructed to block the tunnel or its putative gate. Mutation of the proposed gating residue Asn485 to Asp or tunnel residue Phe359 or Gly347 to Trp or Asn reduces the catalytic efficiency of oxidation. The K mO 2 increases from 300 +/- 35 microM for the wild-type enzyme to 617 +/- 15 microM for the F359W mutant. The k cat for the F359W mutant-catalyzed reaction decreases 13-fold relative to that of the wild-type-catalyzed reaction. The N485D and G347N mutants could not be saturated with oxygen. Transfer of hydride from the sterol to the flavin prosthetic group is no longer rate-limiting for these tunnel mutants. The steady-state kinetics of both wild-type and tunnel mutant enzymes are consistent with formation of a ternary complex of steroid and oxygen during catalysis. Furthermore, kinetic cooperativity with respect to molecular oxygen is observed with the tunnel mutants, but not with the wild-type enzyme. A rate-limiting conformational change for binding and release of oxygen and hydrogen peroxide, respectively, is consistent with the cooperative kinetics. In the atomic-resolution structure of F359W, the indole ring of the tryptophan completely fills the tunnel and is observed in only a single conformation. The size of the indole is proposed to limit conformational rearrangement of residue 359 that leads to tunnel opening in the wild-type enzyme. Overall, these results substantiate the functional importance of the tunnel for substrate binding and product release.
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Affiliation(s)
- Lin Chen
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
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