1
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Rogers MS, Gordon AM, Rappe TM, Goodpaster JD, Lipscomb JD. Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase. Biochemistry 2023; 62:507-523. [PMID: 36583545 PMCID: PMC9854337 DOI: 10.1021/acs.biochem.2c00610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18O2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Rieske-type iron-sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD3-salicylate-d8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD3-salicylate-d8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp2 → sp3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the aryl-methyl hydroxylation.
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Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adrian M. Gordon
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Rappe
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Cook EN, Hooe SL, Dickie DA, Machan CW. Homogeneous Catalytic Reduction of O 2 to H 2O by a Terpyridine-Based FeN 3O Complex. Inorg Chem 2022; 61:8387-8392. [PMID: 35594192 DOI: 10.1021/acs.inorgchem.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a new terpyridine-based FeN3O catalyst, Fe(tpytbupho)Cl2, which reduces O2 to H2O. Variable concentration and variable temperature spectrochemical studies with decamethylferrocene as a chemical reductant in acetonitrile solution enabled the elucidation of key reaction parameters for the catalytic reduction of O2 to H2O by Fe(tpytbupho)Cl2. These mechanistic studies suggest that a 2 + 2 mechanism is operative, where hydrogen peroxide is produced as a discrete intermediate, prior to further reduction to H2O. Consistent with this proposal, the spectrochemically measured first-order rate constant k (s-1) value for H2O2 reduction is larger than that for O2 reduction. Further, significant H2O2 production is observed under hydrodynamic conditions in rotating ring-disk electrode measurements, where the product can be swept away from the cathode surface before further reduction occurs.
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Affiliation(s)
- Emma N Cook
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
| | - Shelby L Hooe
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
| | - Diane A Dickie
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
| | - Charles W Machan
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
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3
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Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
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Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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4
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Yeh CCG, Mokkawes T, Bradley J, Le Brun NE, de Visser S. Second coordination sphere effects on the mechanistic pathways for dioxygen activation by a ferritin: involvement of a Tyr radical and the identification of a cation binding site. Chembiochem 2022; 23:e202200257. [PMID: 35510795 PMCID: PMC9401865 DOI: 10.1002/cbic.202200257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/05/2022] [Indexed: 11/09/2022]
Abstract
Ferritins are ubiquitous diiron enzymes involved in iron(II) detoxification and oxidative stress responses and can act as metabolic iron stores. The overall reaction mechanisms of ferritin enzymes are still unclear, particularly concerning the role of the conserved, near catalytic center Tyr residue. Thus, we carried out a computational study of a ferritin using a large cluster model of well over 300 atoms including its first- and second-coordination sphere. The calculations reveal important insight into the structure and reactivity of ferritins. Specifically, the active site Tyr residue delivers a proton and electron in the catalytic cycle prior to iron(II) oxidation. In addition, the calculations highlight a likely cation binding site at Asp65, which through long-range electrostatic interactions, influences the electronic configuration and charge distributions of the metal center. The results are consistent with experimental observations but reveal novel detail of early mechanistic steps that lead to an unusual mixed-valent iron(III)-iron(II) center.
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Affiliation(s)
- Chieh-Chih George Yeh
- The University of Manchester, Department of Chemical Engineering, Oxford Road, Manchester, UNITED KINGDOM
| | - Thirakorn Mokkawes
- The University of Manchester, Department of Chemical Engineering, Manchester, UNITED KINGDOM
| | - Justin Bradley
- University of East Anglia, School of Chemistry, UNITED KINGDOM
| | - Nick E Le Brun
- University of East Anglia, School of Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
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5
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Csizi K, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
Rieske dioxygenases belong to the non-heme iron family of oxygenases and catalyze important cis-dihydroxylation as well as O-/N-dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non-heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O 2 activation. Here, we studied the role of the substrate in the key elementary reaction leading to O 2 activation from a theoretical perspective by systematically considering (i) the 6-coordinate to 5-coordinate conversion of the non-heme FeII upon abstraction of a water ligand, (ii) binding of O 2 , and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin-state-dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non-heme FeII center through thermoneutral H2 O reorientation and exothermic O 2 binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe-oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6-coordinate non-heme FeII sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non-heme FeII in agreement with a strategy that avoids unproductive O 2 activation.
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Affiliation(s)
- Katja‐Sophia Csizi
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Lina Eckert
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Christoph Brunken
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas B. Hofstetter
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
| | - Markus Reiher
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
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6
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Tomboc GM, Park Y, Lee K, Jin K. Directing transition metal-based oxygen-functionalization catalysis. Chem Sci 2021; 12:8967-8995. [PMID: 34276926 PMCID: PMC8261717 DOI: 10.1039/d1sc01272j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/07/2021] [Indexed: 11/21/2022] Open
Abstract
This review presents the recent progress of oxygen functionalization reactions based on non-electrochemical (conventional organic synthesis) and electrochemical methods. Although both methods have their advantages and limitations, the former approach has been used to synthesize a broader range of organic substances as the latter is limited by several factors, such as poor selectivity and high energy cost. However, because electrochemical methods can replace harmful terminal oxidizers with external voltage, organic electrosynthesis has emerged as greener and more eco-friendly compared to conventional organic synthesis. The progress of electrochemical methods toward oxygen functionalization is presented by an in-depth discussion of different types of electrically driven-chemical organic synthesis, with particular attention to recently developed electrochemical systems and catalyst designs. We hope to direct the attention of readers to the latest breakthroughs of traditional oxygen functionalization reactions and to the potential of electrochemistry for the transformation of organic substrates to useful end products.
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Affiliation(s)
- Gracita M Tomboc
- Department of Chemistry and Research Institute for Natural Sciences, Korea University Seoul 02841 Republic of Korea
| | - Yeji Park
- Department of Chemistry and Research Institute for Natural Sciences, Korea University Seoul 02841 Republic of Korea
| | - Kwangyeol Lee
- Department of Chemistry and Research Institute for Natural Sciences, Korea University Seoul 02841 Republic of Korea
| | - Kyoungsuk Jin
- Department of Chemistry and Research Institute for Natural Sciences, Korea University Seoul 02841 Republic of Korea
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7
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Pattanayak S, Cantú Reinhard FG, Rana A, Gupta SS, de Visser SP. The Equatorial Ligand Effect on the Properties and Reactivity of Iron(V) Oxo Intermediates. Chemistry 2019; 25:8092-8104. [DOI: 10.1002/chem.201900708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Santanu Pattanayak
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Atanu Rana
- Indian Association for the Cultivation of Sciences 2A Raja S. C. Mullick Road Kolkata 700032 India
| | - Sayam Sen Gupta
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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8
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Szaleniec M, Wojtkiewicz AM, Bernhardt R, Borowski T, Donova M. Bacterial steroid hydroxylases: enzyme classes, their functions and comparison of their catalytic mechanisms. Appl Microbiol Biotechnol 2018; 102:8153-8171. [PMID: 30032434 PMCID: PMC6153880 DOI: 10.1007/s00253-018-9239-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022]
Abstract
The steroid superfamily includes a wide range of compounds that are essential for living organisms of the animal and plant kingdoms. Structural modifications of steroids highly affect their biological activity. In this review, we focus on hydroxylation of steroids by bacterial hydroxylases, which take part in steroid catabolic pathways and play an important role in steroid degradation. We compare three distinct classes of metalloenzymes responsible for aerobic or anaerobic hydroxylation of steroids, namely: cytochrome P450, Rieske-type monooxygenase 3-ketosteroid 9α-hydroxylase, and molybdenum-containing steroid C25 dehydrogenases. We analyze the available literature data on reactivity, regioselectivity, and potential application of these enzymes in organic synthesis of hydroxysteroids. Moreover, we describe mechanistic hypotheses proposed for all three classes of enzymes along with experimental and theoretical evidences, which have provided grounds for their formulation. In case of the 3-ketosteroid 9α-hydroxylase, such a mechanistic hypothesis is formulated for the first time in the literature based on studies conducted for other Rieske monooxygenases. Finally, we provide comparative analysis of similarities and differences in the reaction mechanisms utilized by bacterial steroid hydroxylases.
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Affiliation(s)
- Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland.
| | - Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland
| | - Rita Bernhardt
- Lehrstuhl für Biochemie, Universität des Saarlandes, Campus B2 2, 66123, Saarbrücken, Germany
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland
| | - Marina Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Oblast, 142290, Russia
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9
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Sutherlin KD, Rivard BS, Böttger LH, Liu LV, Rogers MS, Srnec M, Park K, Yoda Y, Kitao S, Kobayashi Y, Saito M, Seto M, Hu M, Zhao J, Lipscomb JD, Solomon EI. NRVS Studies of the Peroxide Shunt Intermediate in a Rieske Dioxygenase and Its Relation to the Native Fe II O 2 Reaction. J Am Chem Soc 2018; 140:5544-5559. [PMID: 29618204 PMCID: PMC5973823 DOI: 10.1021/jacs.8b01822] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The Rieske dioxygenases are a major subclass of mononuclear nonheme iron enzymes that play an important role in bioremediation. Recently, a high-spin FeIII-(hydro)peroxy intermediate (BZDOp) has been trapped in the peroxide shunt reaction of benzoate 1,2-dioxygenase. Defining the structure of this intermediate is essential to understanding the reactivity of these enzymes. Nuclear resonance vibrational spectroscopy (NRVS) is a recently developed synchrotron technique that is ideal for obtaining vibrational, and thus structural, information on Fe sites, as it gives complete information on all vibrational normal modes containing Fe displacement. In this study, we present NRVS data on BZDOp and assign its structure using these data coupled to experimentally calibrated density functional theory calculations. From this NRVS structure, we define the mechanism for the peroxide shunt reaction. The relevance of the peroxide shunt to the native FeII/O2 reaction is evaluated. For the native FeII/O2 reaction, an FeIII-superoxo intermediate is found to react directly with substrate. This process, while uphill thermodynamically, is found to be driven by the highly favorable thermodynamics of proton-coupled electron transfer with an electron provided by the Rieske [2Fe-2S] center at a later step in the reaction. These results offer important insight into the relative reactivities of FeIII-superoxo and FeIII-hydroperoxo species in nonheme Fe biochemistry.
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Affiliation(s)
- Kyle D. Sutherlin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Brent S. Rivard
- Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lei V. Liu
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Martin Srnec
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- J. HeyrovskýInstitute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Kiyoung Park
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Shinji Kitao
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
| | | | - Makina Saito
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
| | - Michael Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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10
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Barragan AM, Schulten K, Solov'yov IA. Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc 1 Complex. J Phys Chem B 2016; 120:11369-11380. [PMID: 27661199 DOI: 10.1021/acs.jpcb.6b07394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bc1 complex is a critical enzyme for the ATP production in photosynthesis and cellular respiration. Its biochemical function relies on the so-called Q-cycle, which is well established and operates via quinol substrates that bind inside the protein complex. Despite decades of research, the quinol-protein interaction, which initiates the Q-cycle, has not yet been completely described. Furthermore, the initial charge transfer reactions of the Q-cycle lack a physical description. The present investigation utilizes classical molecular dynamics simulations in tandem with quantum density functional theory calculations, to provide a complete and consistent quantitative description of the primary events that occur within the bc1 complex upon quinol binding. In particular, the electron and proton transfer reactions that trigger the Q-cycle in the bc1 complex from Rhodobacter capsulatus are studied. The coupled nature of these charge transfer reactions was revealed by obtaining the transition energy path connecting configurations of the Qo-site prior and after the transfers. The analysis of orbitals and partial charge distribution of the different states of the Qo-site has further supported the conclusion. Finally, key structural elements of the bc1 complex that trigger the charge transfer reactions were established, manifesting the importance of the environment in the process, which is furthermore evidenced by free energy calculations.
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Affiliation(s)
- Angela M Barragan
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense M, Denmark
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11
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Husen P, Solov'yov IA. Spontaneous Binding of Molecular Oxygen at the Qo-Site of the bc1 Complex Could Stimulate Superoxide Formation. J Am Chem Soc 2016; 138:12150-8. [PMID: 27447781 DOI: 10.1021/jacs.6b04849] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A key part of the respiratory and photosynthetic pathways is the bc1 protein complex embedded in the inner membrane of mitochondria and the plasma membrane of photosynthetic bacteria. The protein complex pumps protons across the membrane to maintain an electrostatic potential, which is in turn used to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecular dynamics simulations, we investigate here the migration of molecular oxygen in the bc1 complex in order to identify possible reaction sites that could lead to superoxide formation. It is found, in particular, that oxygen penetrates spontaneously the Qo binding site of the bc1 complex in the presence of an intermediate semiquinone radical, thus making the Qo-site a strong candidate for being a center of superoxide production.
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Affiliation(s)
- Peter Husen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Odense 5230, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Odense 5230, Denmark
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12
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Rivard BS, Rogers MS, Marell DJ, Neibergall MB, Chakrabarty S, Cramer CJ, Lipscomb JD. Rate-Determining Attack on Substrate Precedes Rieske Cluster Oxidation during Cis-Dihydroxylation by Benzoate Dioxygenase. Biochemistry 2015; 54:4652-64. [PMID: 26154836 DOI: 10.1021/acs.biochem.5b00573] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rieske dearomatizing dioxygenases utilize a Rieske iron-sulfur cluster and a mononuclear Fe(II) located 15 Å across a subunit boundary to catalyze O2-dependent formation of cis-dihydrodiol products from aromatic substrates. During catalysis, O2 binds to the Fe(II) while the substrate binds nearby. Single-turnover reactions have shown that one electron from each metal center is required for catalysis. This finding suggested that the reactive intermediate is Fe(III)-(H)peroxo or HO-Fe(V)═O formed by O-O bond scission. Surprisingly, several kinetic phases were observed during the single-turnover Rieske cluster oxidation. Here, the Rieske cluster oxidation and product formation steps of a single turnover of benzoate 1,2-dioxygenase are investigated using benzoate and three fluorinated analogues. It is shown that the rate constant for product formation correlates with the reciprocal relaxation time of only the fastest kinetic phase (RRT-1) for each substrate, suggesting that the slower phases are not mechanistically relevant. RRT-1 is strongly dependent on substrate type, suggesting a role for substrate in electron transfer from the Rieske cluster to the mononuclear iron site. This insight, together with the substrate and O2 concentration dependencies of RRT-1, indicates that a reactive species is formed after substrate and O2 binding but before electron transfer from the Rieske cluster. Computational studies show that RRT-1 is correlated with the electron density at the substrate carbon closest to the Fe(II), consistent with initial electrophilic attack by an Fe(III)-superoxo intermediate. The resulting Fe(III)-peroxo-aryl radical species would then readily accept an electron from the Rieske cluster to complete the cis-dihydroxylation reaction.
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Affiliation(s)
- Brent S Rivard
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Melanie S Rogers
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel J Marell
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew B Neibergall
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sarmistha Chakrabarty
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher J Cramer
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D Lipscomb
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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13
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Ali ME, Staemmler V, Marx D. Magnetostructural dynamics of Rieske versus ferredoxin iron-sulfur cofactors. Phys Chem Chem Phys 2015; 17:6289-96. [PMID: 25648433 DOI: 10.1039/c4cp05465b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The local chemical environment of the [2Fe-2S] cofactor hosted by ferredoxin and Rieske-type proteins is fundamentally different due to the presence of distinct ligands at the two iron centers in the case of Rieske proteins, whereas they are identical in ferredoxins. This renders Rieske [2Fe-2S] cores chemically asymmetric and results in more complex vibrational spectra as compared to ferredoxin. Likewise, one would expect other properties, for instance the dynamics of the magnetic exchange coupling constant J, to be also more complex. Applying ab initio molecular dynamics using our recently introduced spin-constrained two-determinant extended broken symmetry (CEBS) approach to Rieske and ferredoxin model complexes at 300 K, we extract the molecular fluctuations and the resulting magnetostructural cross-correlations involving the antiferromagnetic exchange interaction J(t). This analysis demonstrates that the details of the magnetostructural dynamics are indeed distinctly different for Rieske and ferredoxin cofactors, while the time averages of 〈J〉 are shown to be essentially identical. In particular, the frequency window between about 200 and 350 cm(-1), is a "fingerprint region" that allows one to distinguish chemically asymmetric from symmetric cofactors and thus Rieske proteins from ferredoxins.
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Affiliation(s)
- Md Ehesan Ali
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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14
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Barragan AM, Crofts AR, Schulten K, Solov'yov IA. Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex. J Phys Chem B 2014; 119:433-47. [PMID: 25372183 PMCID: PMC4297238 DOI: 10.1021/jp510022w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Enzymes of the bc1 complex family power
the biosphere through their central role in respiration and photosynthesis.
These enzymes couple the oxidation of quinol molecules by cytochrome c to the transfer of protons across the membrane, to generate
a proton-motive force that drives ATP synthesis. Key for the function
of the bc1 complex is the initial redox
process that involves a bifurcated electron transfer in which the
two electrons from a quinol substrate are passed to different electron
acceptors in the bc1 complex. The electron
transfer is coupled to proton transfer. The overall mechanism of quinol
oxidation by the bc1 complex is well enough
characterized to allow exploration at the atomistic level, but details
are still highly controversial. The controversy stems from the uncertain
binding motifs of quinol at the so-called Qo active site of the bc1 complex.
Here we employ a combination of classical all atom molecular dynamics
and quantum chemical calculations to reveal the binding modes of quinol
at the Qo-site of the bc1 complex from Rhodobacter capsulatus. The calculations suggest a novel configuration of amino acid residues
responsible for quinol binding and support a mechanism for proton-coupled
electron transfer from quinol to iron–sulfur cluster through
a bridging hydrogen bond from histidine that stabilizes the reaction
complex.
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Affiliation(s)
- Angela M Barragan
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 W. Green Street, Urbana, Illinois 61801, United States
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15
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The iron-sulfur core in Rieske proteins is not symmetric. J Biol Inorg Chem 2014; 19:1287-93. [PMID: 25151276 DOI: 10.1007/s00775-014-1185-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
At variance with ferredoxins, Rieske-type proteins contain a chemically asymmetric iron-sulfur cluster. Nevertheless, X-ray crystallography apparently finds their [2Fe-2S] cores to be structurally symmetric or very close to symmetric (i.e. the four iron-sulfur bonds in the [2Fe-2S] core are equidistant). Using a combination of advanced density-based approaches, including finite-temperature molecular dynamics to access thermal fluctuations and free-energy profiles, in conjunction with correlated wavefunction-based methods we clearly predict an asymmetric core structure. This reveals a fundamental and intrinsic difference within the iron-sulfur clusters hosted by Rieske proteins and ferredoxins and thus opens up a new dimension for the ongoing efforts in understanding the role of Rieske-type [2Fe-2S] cluster in electron transfer processes that occur in almost all biological systems.
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16
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Kamachi T, Kouno T, Doitomi K, Yoshizawa K. Generation of adenosyl radical from S-adenosylmethionine (SAM) in biotin synthase. J Inorg Biochem 2011; 105:850-7. [DOI: 10.1016/j.jinorgbio.2011.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 03/16/2011] [Accepted: 03/16/2011] [Indexed: 10/18/2022]
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17
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Kuznetsov AM, Zueva EM, Masliy AN, Krishtalik LI. Redox potential of the Rieske iron-sulfur protein quantum-chemical and electrostatic study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:347-59. [PMID: 20026009 DOI: 10.1016/j.bbabio.2009.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 12/04/2009] [Accepted: 12/08/2009] [Indexed: 11/15/2022]
Abstract
Quantum-chemical study of structures, energies, and effective partial charge distribution for several models of the Rieske protein redox center is performed in terms of the B3LYP density functional method in combination with the broken symmetry approach using three different atomic basis sets. The structure of the redox complex optimized in vacuum differs markedly from that inside the protein. This means that the protein matrix imposes some stress on the active site resulting in distortion of its structure. The redox potentials calculated for the real active site structure are in a substantially better agreement with the experiment than those calculated for the idealized structure. This shows an important role of the active site distortion in tuning its redox potential. The reference absolute electrode potential of the standard hydrogen electrode is used that accounts for the correction caused by the water surface potential. Electrostatic calculations are performed in the framework of the polarizable solute model. Two dielectric permittivities of the protein are employed: the optical permittivity for calculation of the intraprotein electric field, and the static permittivity for calculation of the dielectric response energy. Only this approach results in a reasonable agreement of the calculated and experimental redox potentials.
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Affiliation(s)
- Andrey M Kuznetsov
- Kazan State Technological University, ul. K. Marksa 68, 420015, Kazan, Russia.
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18
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Shimizu M, Katsuda N, Katsurada T, Mitani M, Yoshioka Y. Mechanism on Two-Electron Oxidation of Ubiquinol at the Qp Site in Cytochrome bc1 Complex: B3LYP Study with Broken Symmetry. J Phys Chem B 2008; 112:15116-26. [DOI: 10.1021/jp804387g] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Moriyuki Shimizu
- Chemistry Department for Materials, Graduate School of Engineering, Mie University, Kurima-machiya 1577, Tsu, Mie 514-8507, Japan
| | - Naoki Katsuda
- Chemistry Department for Materials, Graduate School of Engineering, Mie University, Kurima-machiya 1577, Tsu, Mie 514-8507, Japan
| | - Takeharu Katsurada
- Chemistry Department for Materials, Graduate School of Engineering, Mie University, Kurima-machiya 1577, Tsu, Mie 514-8507, Japan
| | - Masaki Mitani
- Chemistry Department for Materials, Graduate School of Engineering, Mie University, Kurima-machiya 1577, Tsu, Mie 514-8507, Japan
| | - Yasunori Yoshioka
- Chemistry Department for Materials, Graduate School of Engineering, Mie University, Kurima-machiya 1577, Tsu, Mie 514-8507, Japan
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19
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Chakrabarty S, Austin RN, Deng D, Groves JT, Lipscomb JD. Radical intermediates in monooxygenase reactions of rieske dioxygenases. J Am Chem Soc 2007; 129:3514-5. [PMID: 17341076 PMCID: PMC2720596 DOI: 10.1021/ja068188v] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarmistha Chakrabarty
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | | | - Dayi Deng
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - John T. Groves
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- E-mail:
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20
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Bassan A, Borowski T, Schofield CJ, Siegbahn PEM. Ethylene Biosynthesis by 1-Aminocyclopropane-1-Carboxylic Acid Oxidase: A DFT Study. Chemistry 2006; 12:8835-46. [PMID: 16933342 DOI: 10.1002/chem.200501459] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO(2), cyanide and two water molecules. A model including the mononuclear iron complex with ACC in the first coordination sphere was used to study the details of O-O bond cleavage and cyclopropane ring opening. Calculations imply that this unusual and complex reaction is triggered by a hydrogen atom abstraction step generating a radical on the amino nitrogen of ACC. Subsequently, cyclopropane ring opening followed by O-O bond heterolysis leads to a very reactive iron(IV)-oxo intermediate, which decomposes to ethylene and cyanoformate with very low energy barriers. The reaction is assisted by bicarbonate located in the second coordination sphere of the metal.
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Affiliation(s)
- Arianna Bassan
- Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 10691 Stockholm, Sweden.
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21
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Greene SN, Richards NGJ. Electronic structure, bonding, spectroscopy and energetics of Fe-dependent nitrile hydratase active-site models. Inorg Chem 2006; 45:17-36. [PMID: 16390037 DOI: 10.1021/ic050965p] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fe-type nitrile hydratase (NHase) is a non-heme Fe(III)-dependent enzyme that catalyzes the hydration of nitriles to the corresponding amides. Despite experimental studies of the enzyme and model Fe(III)-containing complexes, many questions concerning the electronic structure and spectroscopic transitions of the metal center remain unanswered. In addition, the catalytic mechanism of nitrile hydration has not yet been determined. We now report density functional theory (B3LYP/6-31G) calculations on three models of the Fe(III) center in the active site of NHase corresponding to hypothetical intermediates in the enzyme-catalyzed hydration of acetonitrile. Together with natural bond orbital (NBO) analysis of the chemical bonding in these active-site models and INDO/S CIS calculations of their electronic spectra, this theoretical investigation gives new insight into the molecular origin of the unusual low-spin preference and spectroscopic properties of the Fe(III) center. In addition, the low-energy electronic transition observed for the active form of NHase is assigned to a dd transition that is coupled with charge-transfer transitions involving the metal and its sulfur ligands. Calculations of isodesmic ligand-exchange reaction energies provide support for coordination of the Fe(III) center in free NHase by a water molecule rather than a hydroxide ion and suggest that the activation of the nitrile substrate by binding to the metal in the sixth coordination site during catalytic turnover cannot yet be definitively ruled out.
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Affiliation(s)
- Shannon N Greene
- Department of Chemistry, University of Florida, Gainesville, 32611-7200, USA
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22
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Abu-Omar MM, Loaiza A, Hontzeas N. Reaction mechanisms of mononuclear non-heme iron oxygenases. Chem Rev 2005; 105:2227-52. [PMID: 15941213 DOI: 10.1021/cr040653o] [Citation(s) in RCA: 457] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mahdi M Abu-Omar
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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