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Thomas J, Mokkawes T, Senft L, Dey A, Gordon JB, Ivanovic-Burmazovic I, de Visser SP, Goldberg DP. Axial Ligation Impedes Proton-Coupled Electron-Transfer Reactivity of a Synthetic Compound-I Analogue. J Am Chem Soc 2024; 146:12338-12354. [PMID: 38669456 DOI: 10.1021/jacs.3c08950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The nature of the axial ligand in high-valent iron-oxo heme enzyme intermediates and related synthetic catalysts is a critical structural element for controlling proton-coupled electron-transfer (PCET) reactivity of these species. Herein, we describe the generation and characterization of three new 6-coordinate, iron(IV)-oxo porphyrinoid-π-cation-radical complexes and report their PCET reactivity together with a previously published 5-coordinate analogue, FeIV(O)(TBP8Cz+•) (TBP8Cz = octakis(p-tert-butylphenyl)corrolazinato3-) (2) (Cho, K. A high-valent iron-oxo corrolazine activates C-H bonds via hydrogen-atom transfer. J. Am. Chem. Soc. 2012, 134, 7392-7399). The new complexes FeIV(O)(TBP8Cz+•)(L) (L = 1-methyl imidazole (1-MeIm) (4a), 4-dimethylaminopyridine (DMAP) (4b), cyanide (CN-)(4c)) can be generated from either oxidation of the ferric precursors or by addition of L to the Compound-I (Cpd-I) analogue at low temperatures. These complexes were characterized by UV-vis, electron paramagnetic resonance (EPR), and Mössbauer spectroscopies, and cryospray ionization mass spectrometry (CSI-MS). Kinetic studies using 4-OMe-TEMPOH as a test substrate indicate that coordination of a sixth axial ligand dramatically lowers the PCET reactivity of the Cpd-I analogue (rates up to 7000 times slower). Extensive density functional theory (DFT) calculations together with the experimental data show that the trend in reactivity with the axial ligands does not correlate with the thermodynamic driving force for these reactions or the calculated strengths of the O-H bonds being formed in the FeIV(O-H) products, pointing to non-Bell-Evans-Polanyi behavior. However, the PCET reactivity does follow a trend with the bracketed reduction potential of Cpd-I analogues and calculated electron affinities. The combined data suggest a concerted mechanism (a concerted proton electron transfer (CPET)) and an asynchronous movement of the electron/proton pair in the transition state.
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Affiliation(s)
- Jithin Thomas
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thirakorn Mokkawes
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Laura Senft
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr., 5-13, Haus D, 81377 München, Germany
| | - Aniruddha Dey
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Jesse B Gordon
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Ivana Ivanovic-Burmazovic
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr., 5-13, Haus D, 81377 München, Germany
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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2
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Gérard E, Mokkawes T, Johannissen LO, Warwicker J, Spiess RR, Blanford CF, Hay S, Heyes DJ, de Visser SP. How Is Substrate Halogenation Triggered by the Vanadium Haloperoxidase from Curvularia inaequalis? ACS Catal 2023; 13:8247-8261. [PMID: 37342830 PMCID: PMC10278073 DOI: 10.1021/acscatal.3c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/05/2023] [Indexed: 06/23/2023]
Abstract
Vanadium haloperoxidases (VHPOs) are unique enzymes in biology that catalyze a challenging halogen transfer reaction and convert a strong aromatic C-H bond into C-X (X = Cl, Br, I) with the use of a vanadium cofactor and H2O2. The VHPO catalytic cycle starts with the conversion of hydrogen peroxide and halide (X = Cl, Br, I) into hypohalide on the vanadate cofactor, and the hypohalide subsequently reacts with a substrate. However, it is unclear whether the hypohalide is released from the enzyme or otherwise trapped within the enzyme structure for the halogenation of organic substrates. A substrate-binding pocket has never been identified for the VHPO enzyme, which questions the role of the protein in the overall reaction mechanism. Probing its role in the halogenation of small molecules will enable further engineering of the enzyme and expand its substrate scope and selectivity further for use in biotechnological applications as an environmentally benign alternative to current organic chemistry synthesis. Using a combined experimental and computational approach, we elucidate the role of the vanadium haloperoxidase protein in substrate halogenation. Activity studies show that binding of the substrate to the enzyme is essential for the reaction of the hypohalide with substrate. Stopped-flow measurements demonstrate that the rate-determining step is not dependent on substrate binding but partially on hypohalide formation. Using a combination of molecular mechanics (MM) and molecular dynamics (MD) simulations, the substrate binding area in the protein is identified and even though the selected substrates (methylphenylindole and 2-phenylindole) have limited hydrogen-bonding abilities, they are found to bind relatively strongly and remain stable in a binding tunnel. A subsequent analysis of the MD snapshots characterizes two small tunnels leading from the vanadate active site to the surface that could fit small molecules such as hypohalide, halide, and hydrogen peroxide. Density functional theory studies using electric field effects show that a polarized environment in a specific direction can substantially lower barriers for halogen transfer. A further analysis of the protein structure indeed shows a large dipole orientation in the substrate-binding pocket that could enable halogen transfer through an applied local electric field. These findings highlight the importance of the enzyme in catalyzing substrate halogenation by providing an optimal environment to lower the energy barrier for this challenging aromatic halide insertion reaction.
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Affiliation(s)
- Emilie
F. Gérard
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, United Kingdom
| | - Thirakorn Mokkawes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, United Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jim Warwicker
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- School
of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester 13 9PL, United
Kingdom
| | - Reynard R. Spiess
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Christopher F. Blanford
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Materials, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, United Kingdom
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3
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Kobayashi K, Ito YT, Kasu Y, Horitani M, Kozawa T. Intramolecular electron transfer from biopterin to Fe II-O 2 complex in nitric oxide synthases occurs at very different rates between bacterial and mammalian enzymes: Direct observation of a catalytically active intermediate. J Inorg Biochem 2023; 238:112035. [PMID: 36327499 DOI: 10.1016/j.jinorgbio.2022.112035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/05/2022] [Accepted: 10/17/2022] [Indexed: 11/21/2022]
Abstract
Nitric oxide synthase (NOS) is a cytochrome P450-type mono‑oxygenase that catalyzes the oxidation of L-arginine to nitric oxide. We previously observed that intramolecular electron transfer from biopterin to Fe2+-O2 in Deinococcus radiodurans NOS (DrNOS) using pulse radiolysis. However, the rate of electron transfer in DrNOS (2.2 × 103 s-1) contrasts with a reported corresponding rate (11 s-1) in a mammalian NOS determined using rapid freeze-quench (RFQ) EPR. We applied pulse radiolysis to Bacillus subtilis NOS (bsNOS) and to rat neural NOS oxygenase domain NOS (mNOS). Concurrently, RFQ EPR was used to trap a pterin radical during single-turnover enzyme reactions of the enzymes. By using the pulse radiolysis method, hydrated electrons (eaq-) reduced the heme iron of NOS enzymes. Subsequently, ferrous heme reacted with O2 to form a Fe2+-O2 intermediate. In the presence of pterin, the intermediate of bsNOS was found to convert to other intermediate in the time range of milliseconds. A similar process was determined to have occurred after pulse radiolysis of the pterin-bound mNOS, though the rate was much slower. The intermediates of all of the NOS enzymes further converted to the original ferric form in the time range of seconds. When using the RFQ method, pterin radicals were formed very rapidly in both DrNOS and bsNOS in the time range of milliseconds. In contrast, the pterin radical in mNOS was observed to form slowly, at a rate of ∼20 s-1.
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
| | - Yuko Tsutsui Ito
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Yuri Kasu
- Department of Applied Biochemistry and Food Science, Saga University, Honjo-machi Saga, 840-8502, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry and Food Science, Saga University, Honjo-machi Saga, 840-8502, Japan; The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Takahiro Kozawa
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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4
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Field MJ, Oyala PH, Green MT. 17O Electron Nuclear Double Resonance Analysis of Compound I: Inverse Correlation between Oxygen Spin Population and Electron Donation. J Am Chem Soc 2022; 144:19272-19283. [PMID: 36240444 DOI: 10.1021/jacs.2c05459] [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
Although the activation of inert C-H bonds by metal-oxo complexes has been widely studied, important questions remain, particularly regarding the role of oxygen spin population (i.e., unpaired electrons on the oxo ligand) in facilitating C-H bond cleavage. In order to shed light on this issue, we have utilized 17O electron nuclear double resonance spectroscopy to measure the oxygen spin populations of three compound I intermediates in heme enzymes with different reactivities toward C-H bonds: chloroperoxidase, cytochrome P450, and a selenolate (selenocysteinyl)-ligated cytochrome P450. The experimental data suggest an inverse correlation between oxygen spin population and electron donation from the axial ligand. We have explored the implications of this result using a Hückel-type molecular orbital model and constrained density functional theory calculations. These investigations have allowed us to examine the relationship between oxygen spin population, oxygen charge, electron donation from the axial ligand, and reactivity.
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Affiliation(s)
- Mackenzie J Field
- Department of Chemistry and Department of Molecular Biology and Biochemistry, University of California, Irvine, California92697, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Michael T Green
- Department of Chemistry and Department of Molecular Biology and Biochemistry, University of California, Irvine, California92697, United States
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5
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Gérard EF, Yadav V, Goldberg DP, de Visser SP. What Drives Radical Halogenation versus Hydroxylation in Mononuclear Nonheme Iron Complexes? A Combined Experimental and Computational Study. J Am Chem Soc 2022; 144:10752-10767. [PMID: 35537044 PMCID: PMC9228086 DOI: 10.1021/jacs.2c01375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Nonheme iron halogenases
are unique enzymes in nature that selectively
activate an aliphatic C–H bond of a substrate to convert it
into C–X (X = Cl/Br, but not F/I). It is proposed that they
generate an FeIII(OH)(X) intermediate in their catalytic
cycle. The analogous FeIII(OH) intermediate in nonheme
iron hydroxylases transfers OH• to give alcohol
product, whereas the halogenases transfer X• to
the carbon radical substrate. There remains significant debate regarding
what factors control their remarkable selectivity of the halogenases.
The reactivity of the complexes FeIII(BNPAPh2O)(OH)(X) (X = Cl, Br) with a secondary carbon radical (R•) is described. It is found that X• transfer occurs
with a secondary carbon radical, as opposed to OH• transfer with tertiary radicals. Comprehensive computational studies
involving density functional theory were carried out to examine the
possible origins of this selectivity. The calculations reproduce the
experimental findings, which indicate that halogen transfer is not
observed for the tertiary radicals because of a nonproductive equilibrium
that results from the endergonic nature of these reactions, despite
a potentially lower reaction barrier for the halogenation pathway.
In contrast, halogen transfer is favored for secondary carbon radicals,
for which the halogenated product complex is thermodynamically more
stable than the reactant complex. These results are rationalized by
considering the relative strengths of the C–X bonds that are
formed for tertiary versus secondary carbon centers. The computational
analysis also shows that the reaction barrier for halogen transfer
is significantly dependent on secondary coordination sphere effects,
including steric and H-bonding interactions.
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Affiliation(s)
- Emilie F Gérard
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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6
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Experimental guidelines for trapping paramagnetic reaction intermediates in radical S-adenosylmethionine enzymes. Methods Enzymol 2022; 666:451-468. [DOI: 10.1016/bs.mie.2022.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Mubarak MQE, Gérard EF, Blanford CF, Hay S, de Visser SP. How Do Vanadium Chloroperoxidases Generate Hypochlorite from Hydrogen Peroxide and Chloride? A Computational Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03490] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Emilie F. Gérard
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Christopher F. Blanford
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Materials, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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8
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Pagnier A, Yang H, Jodts RJ, James CD, Shepard EM, Impano S, Broderick WE, Hoffman BM, Broderick JB. Radical SAM Enzyme Spore Photoproduct Lyase: Properties of the Ω Organometallic Intermediate and Identification of Stable Protein Radicals Formed during Substrate-Free Turnover. J Am Chem Soc 2020; 142:18652-18660. [PMID: 32966073 DOI: 10.1021/jacs.0c08585] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spore photoproduct lyase is a radical S-adenosyl-l-methionine (SAM) enzyme with the unusual property that addition of SAM to the [4Fe-4S]1+ enzyme absent substrate results in rapid electron transfer to SAM with accompanying homolytic S-C5' bond cleavage. Herein, we demonstrate that this unusual reaction forms the organometallic intermediate Ω in which the unique Fe atom of the [4Fe-4S] cluster is bound to C5' of the 5'-deoxyadenosyl radical (5'-dAdo•). During catalysis, homolytic cleavage of the Fe-C5' bond liberates 5'-dAdo• for reaction with substrate, but here, we use Ω formation without substrate to determine the thermal stability of Ω. The reaction of Geobacillus thermodenitrificans SPL (GtSPL) with SAM forms Ω within ∼15 ms after mixing. By monitoring the decay of Ω through rapid freeze-quench trapping at progressively longer times we find an ambient temperature decay time of the Ω Fe-C5' bond of τ ≈ 5-6 s, likely shortened by enzymatic activation as is the case with the Co-C5' bond of B12. We have further used hand quenching at times up to 10 min, and thus with multiple SAM turnovers, to probe the fate of the 5'-dAdo• radical liberated by Ω. In the absence of substrate, Ω undergoes low-probability conversion to a stable protein radical. The WT enzyme with valine at residue 172 accumulates a Val•; mutation of Val172 to isoleucine or cysteine results in accumulation of an Ile• or Cys• radical, respectively. The structures of the radical in WT, V172I, and V172C variants have been established by detailed EPR/DFT analyses.
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Affiliation(s)
- Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher D James
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
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9
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Mubarak MQE, Visser SP. Computational Study on the Catalytic Reaction Mechanism of Heme Haloperoxidase Enzymes. Isr J Chem 2019. [DOI: 10.1002/ijch.201900099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
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10
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Sajadimehr Y, Moosavi‐Movahedi Z, Haghighi MG, Miyardan AB, Nourisefat M, Moosavi‐Movahedi AA. Iron‐Porphyrin/Cysteine/PEG as Pseudo‐Chloroperoxidase Nanozyme. ChemistrySelect 2019. [DOI: 10.1002/slct.201901649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Yazdan Sajadimehr
- Chemistry and Chemical Engineering Research Center of Iran Tehran Iran
| | | | | | | | - Maryam Nourisefat
- Institute of Biochemistry and BiophysicsUniversity of Tehran Tehran Iran
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11
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Timmins A, Fowler NJ, Warwicker J, Straganz GD, de Visser SP. Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? Front Chem 2018; 6:513. [PMID: 30425979 PMCID: PMC6218459 DOI: 10.3389/fchem.2018.00513] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases.
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Affiliation(s)
- Amy Timmins
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Nicholas J. Fowler
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Grit D. Straganz
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- Institute of Molecular Biosciences, Graz University, Graz, Austria
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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12
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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13
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Morozov AN, Chatfield DC. How the Proximal Pocket May Influence the Enantiospecificities of Chloroperoxidase-Catalyzed Epoxidations of Olefins. Int J Mol Sci 2016; 17:E1297. [PMID: 27517911 PMCID: PMC5000694 DOI: 10.3390/ijms17081297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/28/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
Chloroperoxidase-catalyzed enantiospecific epoxidations of olefins are of significant biotechnological interest. Typical enantiomeric excesses are in the range of 66%-97% and translate into free energy differences on the order of 1 kcal/mol. These differences are generally attributed to the effect of the distal pocket. In this paper, we show that the influence of the proximal pocket on the electron transfer mechanism in the rate-limiting event may be just as significant for a quantitatively accurate account of the experimentally-measured enantiospecificities.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
| | - David C Chatfield
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
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14
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Horitani M, Shisler K, Broderick WE, Hutcheson RU, Duschene KS, Marts AR, Hoffman BM, Broderick JB. Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond. Science 2016; 352:822-5. [PMID: 27174986 DOI: 10.1126/science.aaf5327] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/29/2016] [Indexed: 11/02/2022]
Abstract
Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes.
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Affiliation(s)
- Masaki Horitani
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Krista Shisler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Rachel U Hutcheson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Kaitlin S Duschene
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Amy R Marts
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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15
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Nami F, Gast P, Groenen EJJ. Rapid Freeze-Quench EPR Spectroscopy: Improved Collection of Frozen Particles. APPLIED MAGNETIC RESONANCE 2016; 47:643-653. [PMID: 27340337 PMCID: PMC4875044 DOI: 10.1007/s00723-016-0783-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/18/2016] [Indexed: 05/22/2023]
Abstract
Rapid freeze-quench (RFQ) in combination with electron paramagnetic resonance (EPR) spectroscopy at X-band is a proven technique to trap and characterize paramagnetic intermediates of biochemical reactions. Preparation of suitable samples is still cumbersome, despite many attempts to remedy this problem, and limits the wide applicability of RFQ EPR. We present a method, which improves the collection of freeze-quench particles from isopentane and their packing in an EPR tube. The method is based on sucking the particle suspension into an EPR tube with a filter at the bottom. This procedure results in a significant reduction of the required volume of reactants, which allows the economical use of valuable reactants such as proteins. The approach also enables the successful collection of smaller frozen particles, which are generated at higher flow rates. The method provides for a reproducible, efficient and fast collection of the freeze-quench particles and can be easily adapted to RFQ EPR at higher microwave frequencies than X-band.
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Affiliation(s)
- Faezeh Nami
- Huygens-Kamerlingh Onnes Laboratory, Department of Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
| | - Peter Gast
- Huygens-Kamerlingh Onnes Laboratory, Department of Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
| | - Edgar J. J. Groenen
- Huygens-Kamerlingh Onnes Laboratory, Department of Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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16
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Oszajca M, Franke A, Brindell M, Stochel G, van Eldik R. Redox cycling in the activation of peroxides by iron porphyrin and manganese complexes. ‘Catching’ catalytic active intermediates. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.01.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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17
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Morozov AN, Pardillo AD, Chatfield DC. Chloroperoxidase-Catalyzed Epoxidation of Cis-β-Methylstyrene: NH-S Hydrogen Bonds and Proximal Helix Dipole Change the Catalytic Mechanism and Significantly Lower the Reaction Barrier. J Phys Chem B 2015; 119:14350-63. [PMID: 26452587 DOI: 10.1021/acs.jpcb.5b06731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH-S) is a conserved feature of heme-thiolate enzymes such as chloroperoxidase (CPO) and cytochrome P450 (P450). In CPO, the effect of NH-S bonds is amplified by the dipole moment of the proximal helix. Our gas-phase DFT studies show that the proximal pocket effect significantly enhances CPO's reactivity toward the epoxidation of olefinic substrates. Comparison of models with and without proximal pocket residues shows that with them, the barrier for Cβ-O bond formation is lowered by about ∼4.6 kcal/mol, while Cα-O-Cβ ring closure becomes barrierless. The dipole moment of the proximal helix was estimated to contribute 1/3 of the decrease, while the rest is attributed to the effect of NH-S bonds. The decrease of the reaction barrier correlates with increased electron density transfer to residues of the proximal pocket. The effect is most pronounced on the doublet spin surface and involves a change in the electron-transfer mechanism. A full enzyme QMMM study on the doublet spin surface gives about the same barrier as the gas-phase DFT study. The free-energy barrier was estimated to be in agreement with the experimental results for the CPO-catalyzed epoxidation of styrene.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - Armando D Pardillo
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - David C Chatfield
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
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18
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Saitow M, Kurashige Y, Yanai T. Fully Internally Contracted Multireference Configuration Interaction Theory Using Density Matrix Renormalization Group: A Reduced-Scaling Implementation Derived by Computer-Aided Tensor Factorization. J Chem Theory Comput 2015; 11:5120-31. [DOI: 10.1021/acs.jctc.5b00270] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masaaki Saitow
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yuki Kurashige
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department
of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takeshi Yanai
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department
of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
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19
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Pardillo AD, Morozov AN, Chatfield DC. Proximal Pocket Hydrogen Bonds Significantly Influence the Mechanism of Chloroperoxidase Compound I Formation. J Phys Chem B 2015; 119:12590-602. [DOI: 10.1021/acs.jpcb.5b06324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Armando D. Pardillo
- Department of Chemistry and
Biochemistry, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, United States
| | - Alexander N. Morozov
- Department of Chemistry and
Biochemistry, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, United States
| | - David C. Chatfield
- Department of Chemistry and
Biochemistry, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, United States
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20
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Campomanes P, Rothlisberger U, Alfonso-Prieto M, Rovira C. The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase. J Am Chem Soc 2015; 137:11170-8. [DOI: 10.1021/jacs.5b06796] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Mercedes Alfonso-Prieto
- Departament de Química Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08208 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08208 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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21
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Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:113-51. [PMID: 26415843 DOI: 10.1016/bs.apcsb.2015.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis of haloalkanes. Currently, however, industry utilizes few applications of biological haloperoxidases and halogenases, but efforts are being worked on to understand their catalytic mechanism, so that their catalytic function can be upscaled. In this review, we summarize experimental and computational studies on the catalytic mechanism of a range of haloperoxidases and halogenases with structurally very different catalytic features and cofactors. This chapter gives an overview of heme-dependent haloperoxidases, nonheme vanadium-dependent haloperoxidases, and flavin adenine dinucleotide-dependent haloperoxidases. In addition, we discuss the S-adenosyl-l-methionine fluoridase and nonheme iron/α-ketoglutarate-dependent halogenases. In particular, computational efforts have been applied extensively for several of these haloperoxidases and halogenases and have given insight into the essential structural features that enable these enzymes to perform the unusual halogen atom transfer to substrates.
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22
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Bagai I, Sarangi R, Fleischhacker A, Sharma A, Hoffman BM, Zuiderweg ERP, Ragsdale SW. Spectroscopic studies reveal that the heme regulatory motifs of heme oxygenase-2 are dynamically disordered and exhibit redox-dependent interaction with heme. Biochemistry 2015; 54:2693-708. [PMID: 25849895 PMCID: PMC4423204 DOI: 10.1021/bi501489r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/09/2015] [Indexed: 11/28/2022]
Abstract
Heme oxygenase (HO) catalyzes a key step in heme homeostasis: the O2- and NADPH-cytochrome P450 reductase-dependent conversion of heme to biliverdin, Fe, and CO through a process in which the heme participates both as a prosthetic group and as a substrate. Mammals contain two isoforms of this enzyme, HO2 and HO1, which share the same α-helical fold forming the catalytic core and heme binding site, as well as a membrane spanning helix at their C-termini. However, unlike HO1, HO2 has an additional 30-residue N-terminus as well as two cysteine-proline sequences near the C-terminus that reside in heme regulatory motifs (HRMs). While the role of the additional N-terminal residues of HO2 is not yet understood, the HRMs have been proposed to reversibly form a thiol/disulfide redox switch that modulates the affinity of HO2 for ferric heme as a function of cellular redox poise. To further define the roles of the N- and C-terminal regions unique to HO2, we used multiple spectroscopic techniques to characterize these regions of the human HO2. Nuclear magnetic resonance spectroscopic experiments with HO2 demonstrate that, when the HRMs are in the oxidized state (HO2(O)), both the extra N-terminal and the C-terminal HRM-containing regions are disordered. However, protein NMR experiments illustrate that, under reducing conditions, the C-terminal region gains some structure as the Cys residues in the HRMs undergo reduction (HO2(R)) and, in experiments employing a diamagnetic protoporphyrin, suggest a redox-dependent interaction between the core and the HRM domains. Further, electron nuclear double resonance and X-ray absorption spectroscopic studies demonstrate that, upon reduction of the HRMs to the sulfhydryl form, a cysteine residue from the HRM region ligates to a ferric heme. Taken together with EPR measurements, which show the appearance of a new low-spin heme signal in reduced HO2, it appears that a cysteine residue(s) in the HRMs directly interacts with a second bound heme.
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Affiliation(s)
- Ireena Bagai
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Ritimukta Sarangi
- Stanford
Synchrotron
Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Angela
S. Fleischhacker
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Ajay Sharma
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Erik R. P. Zuiderweg
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Stephen W. Ragsdale
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48019, United States
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23
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Elenewski JE, Hackett JC. Ab initio dynamics of the cytochrome P450 hydroxylation reaction. J Chem Phys 2015; 142:064307. [PMID: 25681906 PMCID: PMC4367892 DOI: 10.1063/1.4907733] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/27/2015] [Indexed: 01/01/2023] Open
Abstract
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
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Affiliation(s)
- Justin E Elenewski
- Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540, USA
| | - John C Hackett
- Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540, USA
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24
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Structure and bonding analysis of intermediate model heme-imidazole and heme-thiolate enzymes complexed with formate, acetate and nitrate: A theoretical study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Abstract
Electron-nuclear double resonance (ENDOR) is a method that probes the local structure of paramagnetic centers via their hyperfine interactions with nearby magnetic nuclei. Here we describe the use of this technique to structurally characterize the ATPase active site of the RNA helicase DbpA, where Mg(2+)-ATP binds. This is achieved by substituting the EPR (electron paramagnetic resonance) silent Mg(2+) ion with paramagnetic, EPR active, Mn(2+) ion. (31)P ENDOR provides the interaction of the Mn(2+) with the nucleotide (ADP, ATP and its analogs) through the phosphates. The ENDOR spectra clearly distinguish between ATP- and ADP-binding modes. In addition, by preparing (13)C-enriched DbpA, (13)C ENDOR is used to probe the interaction of the Mn(2+) with protein residues. This combination allows tracking structural changes in the Mn(2+) coordination shell, in the ATPase site, in different states of the protein, namely with and without RNA and with different ATP analogs. Here, a detailed description of sample preparation and the ENDOR measurement methodology is provided, focusing on measurements at W-band (95 GHz) where sensitivity is high and spectral interpretations are relatively simple.
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26
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Sun S, Sono M, Du J, Dawson JH. Evidence of the Direct Involvement of the Substrate TCP Radical in Functional Switching from Oxyferrous O2 Carrier to Ferric Peroxidase in the Dual-Function Hemoglobin/Dehaloperoxidase from Amphitrite ornata. Biochemistry 2014; 53:4956-69. [DOI: 10.1021/bi5002757] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shengfang Sun
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Masanori Sono
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jing Du
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - John H. Dawson
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- School
of Medicine, University of South Carolina, Columbia, South Carolina 29208, United States
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27
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Davydov R, Laryukhin M, Ledbetter-Rogers A, Sono M, Dawson JH, Hoffman BM. Electron paramagnetic resonance and electron-nuclear double resonance studies of the reactions of cryogenerated hydroperoxoferric-hemoprotein intermediates. Biochemistry 2014; 53:4894-903. [PMID: 25046203 PMCID: PMC4144713 DOI: 10.1021/bi500296d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The fleeting ferric peroxo and hydroperoxo
intermediates of dioxygen
activation by hemoproteins can be readily trapped and characterized
during cryoradiolytic reduction of ferrous hemoprotein–O2 complexes at 77 K. Previous cryoannealing studies suggested
that the relaxation of cryogenerated hydroperoxoferric intermediates
of myoglobin (Mb), hemoglobin, and horseradish peroxidase (HRP), either
trapped directly at 77 K or generated by cryoannealing of a trapped
peroxo-ferric state, proceeds through dissociation of bound H2O2 and formation of the ferric heme without formation
of the ferryl porphyrin π-cation radical intermediate, compound
I (Cpd I). Herein we have reinvestigated the mechanism of decays of
the cryogenerated hydroperoxyferric intermediates of α- and
β-chains of human hemoglobin, HRP, and chloroperoxidase (CPO).
The latter two proteins are well-known to form spectroscopically detectable
quasistable Cpds I. Peroxoferric intermediates are trapped during
77 K cryoreduction of oxy Mb, α-chains, and β-chains of
human hemoglobin and CPO. They convert into hydroperoxoferric intermediates
during annealing at temperatures above 160 K. The hydroperoxoferric
intermediate of HRP is trapped directly at 77 K. All studied hydroperoxoferric
intermediates decay with measurable rates at temperatures above 170
K with appreciable solvent kinetic isotope effects. The hydroperoxoferric
intermediate of β-chains converts to the S =
3/2 Cpd I, which in turn decays to an electron paramagnetic resonance
(EPR)-silent product at temperature above 220 K. For all the other
hemoproteins studied, cryoannealing of the hydroperoxo intermediate
directly yields an EPR-silent majority product. In each case, a second
follow-up 77 K γ-irradiation of the annealed samples yields
low-spin EPR signals characteristic of cryoreduced ferrylheme (compound
II, Cpd II). This indicates that in general the hydroperoxoferric
intermediates relax to Cpd I during cryoanealing at low temperatures,
but when this state is not captured by reaction with a bound substrate,
it is reduced to Cpd II by redox-active products of radiolysis.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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28
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Sazama GT, Betley TA. Multiple, disparate redox pathways exhibited by a tris(pyrrolido)ethane iron complex. Inorg Chem 2013; 53:269-81. [PMID: 24320208 DOI: 10.1021/ic402210j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Iron(III) complexes of the tris(pyrrolide)ethane trianion have been synthesized by reaction of one- and two-electron oxidants with [(tpe)Fe(THF)][Li(THF)4] (tpe = tris(5-mesitylpyrrolyl)ethane). X-ray crystallography, (57)Fe Mössbauer, (1)H NMR and EPR spectroscopy, SQUID magnetometry, and density functional theory calculations were employed to rigorously establish the iron 3+ oxidation state. All oxidants employed are proposed to operate via an inner-sphere electron transfer mechanism. Dialkyl peroxides and dibenzyldisulfide served to oxidize iron by one electron, and group transfer of an aryl nitrene unit to the Fe(2+) starting material resulted in formation of Fe(3+) amido species following H-atom abstraction by a presumed nitrenoid intermediate. Single electron transfer to and from diphenyldiazoalkane was also observed to yield a diphenyldiazomethanyl radical anion antiferromagnetically coupled to the S = 5/2 Fe(3+). Isolation of Fe(3+) complexes of tpe, in comparison with previous results wherein the tpe ligand was the redox active moiety, presents an unusual juxtaposition of two noncommunicating redox reservoirs, each accessible via different reaction pathways (namely, inner- and outer-sphere electron transfer).
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Affiliation(s)
- Graham T Sazama
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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29
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Elenewski JE, Hackett JC. Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin. J Comput Chem 2013; 34:1647-60. [PMID: 23670855 PMCID: PMC3711018 DOI: 10.1002/jcc.23311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 03/18/2013] [Accepted: 04/07/2013] [Indexed: 11/11/2022]
Abstract
The cytochromes P450 constitute a ubiquitous family of metalloenzymes, catalyzing manifold reactions of biological and synthetic importance via a thiolate-ligated iron-oxo (IV) porphyrin radical species denoted compound I (Cpd I). Experimental investigations have implicated this intermediate in a broad spectrum of biophysically interesting phenomena, further augmenting the importance of a Cpd I model system. Ab initio molecular dynamics, including Car-Parrinello and path integral methods, conjoin electronic structure theory with finite temperature simulation, affording tools most valuable to approach such enzymes. These methods are typically driven by density functional theory (DFT) in a plane-wave pseudopotential framework; however, existing studies of Cpd I have been restricted to localized Gaussian basis sets. The appropriate choice of density functional and pseudopotential for such simulations is accordingly not obvious. To remedy this situation, a systematic benchmarking of thiolate-ligated Cpd I is performed using several generalized-gradient approximation (GGA) functionals in the Martins-Troullier and Vanderbilt ultrasoft pseudopotential schemes. The resultant electronic and structural parameters are compared to localized-basis DFT calculations using GGA and hybrid density functionals. The merits and demerits of each scheme are presented in the context of reproducing existing experimental and theoretical results for Cpd I.
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Affiliation(s)
- Justin E. Elenewski
- Goodwin Research Laboratory, Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540
| | - John C Hackett
- Goodwin Research Laboratory, Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540
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30
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Zhang R, He Q, Chatfield D, Wang X. Paramagnetic nuclear magnetic resonance relaxation and molecular mechanics studies of the chloroperoxidase-indole complex: insights into the mechanism of chloroperoxidase-catalyzed regioselective oxidation of indole. Biochemistry 2013; 52:3688-701. [PMID: 23634952 DOI: 10.1021/bi4002437] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To unravel the mechanism of chloroperoxidase (CPO)-catalyzed regioselective oxidation of indole, we studied the structure of the CPO-indole complex using nuclear magnetic resonance (NMR) relaxation measurements and computational techniques. The dissociation constant (KD) of the CPO-indole complex was calculated to be approximately 21 mM. The distances (r) between protons of indole and the heme iron calculated via NMR relaxation measurements and molecular docking revealed that the pyrrole ring of indole is oriented toward the heme with its 2-H pointing directly at the heme iron. Both KD and r values are independent of pH in the range of 3.0-6.5. The stability and structure of the CPO-indole complex are also independent of the concentration of chloride or iodide ion. Molecular docking suggests the formation of a hydrogen bond between the NH group of indole and the carboxyl O of Glu 183 in the binding of indole to CPO. Simulated annealing of the CPO-indole complex using r values from NMR experiments as distance restraints reveals that the van der Waals interactions were much stronger than the Coulomb interactions in the binding of indole to CPO, indicating that the association of indole with CPO is primarily governed by hydrophobic rather than electrostatic interactions. This work provides the first experimental and theoretical evidence of the long-sought mechanism that leads to the "unexpected" regioselectivity of the CPO-catalyzed oxidation of indole. The structure of the CPO-indole complex will serve as a lighthouse in guiding the design of CPO mutants with tailor-made activities for biotechnological applications.
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Affiliation(s)
- Rui Zhang
- Department of Chemistry and Biochemistry, Florida International University , Miami, Florida 33199, United States
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Kaufmann R, Yadid I, Goldfarb D. A novel microfluidic rapid freeze-quench device for trapping reactions intermediates for high field EPR analysis. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 230:220-226. [PMID: 23481860 DOI: 10.1016/j.jmr.2013.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 06/01/2023]
Abstract
Rapid freeze quench electron paramagnetic resonance (RFQ)-EPR is a method for trapping short lived intermediates in chemical reactions and subjecting them to EPR spectroscopy investigation for their characterization. Two (or more) reacting components are mixed at room temperature and after some delay the mixture is sprayed into a cold trap and transferred into the EPR tube. A major caveat in using commercial RFQ-EPR for high field EPR applications is the relatively large amount of sample needed for each time point, a major part of which is wasted as the dead volume of the instrument. The small sample volume (∼2μl) needed for high field EPR spectrometers, such as W-band (∼3.5T, 95GHz), that use cavities calls for the development of a microfluidic based RFQ-EPR apparatus. This is particularly important for biological applications because of the difficulties often encountered in producing large amounts of intrinsically paramagnetic proteins and spin labeled nucleic acid and proteins. Here we describe a dedicated microfluidic based RFQ-EPR apparatus suitable for small volume samples in the range of a few μl. The device is based on a previously published microfluidic mixer and features a new ejection mechanism and a novel cold trap that allows collection of a series of different time points in one continuous experiment. The reduction of a nitroxide radical with dithionite, employing the signal of Mn(2+) as an internal standard was used to demonstrate the performance of the microfluidic RFQ apparatus.
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Affiliation(s)
- Royi Kaufmann
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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32
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Collins DP, Isaac IS, Coulter ED, Hager PW, Ballou DP, Dawson JH. Reaction of ferric Caldariomyces fumago chloroperoxidase with meta-chloroperoxybenzoic acid: sequential formation of compound I, compound II and regeneration of the ferric state using one reactant. J PORPHYR PHTHALOCYA 2013. [DOI: 10.1142/s1088424612501234] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The mechanism of the reaction between ferric Caldariomyces fumago chloroperoxidase (CCPO) and meta-chloroperoxybenzoic acid (mCPBA) has been examined. It has previously been established that an Fe(IV) -oxo porphyrin radical species known as Compound I (Cpd I) is formed by two-electron oxidation of the native ferric enzyme by a variety of oxidants including organic peracids and hydroperoxides. Cpd I can return to the ferric state either by direct oxygen insertion into an organic substrate (e.g. a P450 oxygenase-like reaction), or by two consecutive one-electron additions, the first resulting in an intermediate Fe(IV) -oxo species known as Compound II (Cpd II). There has been much debate over the role of Cpd II and the details of its structure. In the present study, both CCPO Fe(IV) -oxo intermediates are formed, but unlike most CCPO reactions, Cpd I and Cpd II are formed using the same reactant, mCPBA. Thus, the peracid is used as an oxo donor to produce Cpd I and then as a reductant to reduce Cpd I to Cpd II, and finally, Cpd II to the ferric state. The observation of saturation kinetics with respect to mCPBA concentration for each step is consistent with the formation of CCPO-mCPBA complexes in each phase of the reaction. The original reaction mechanism for ferric CCPO with mCPBA was hypothesized to involve a scrambling mechanism with a unique Fe -OOO-C(O)R intermediate formed with no observed Cpd II intermediate. The data reported herein clearly demonstrate the formation of Cpd II in returning the oxidized enzyme back to its native ferric state.
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Affiliation(s)
- Daniel P. Collins
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Issa S. Isaac
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Eric D. Coulter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Paul W. Hager
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - David P. Ballou
- Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
- School of Medicine, University of South Carolina, Columbia, SC 29208, USA
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33
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Elenewski JE, Hackett JC. A GGA+U approach to effective electronic correlations in thiolate-ligated iron-oxo (IV) porphyrin. J Chem Phys 2013; 137:124311. [PMID: 23020335 DOI: 10.1063/1.4755290] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High-valent oxo-metal complexes exhibit correlated electronic behavior on dense, low-lying electronic state manifolds, presenting challenging systems for electronic structure methods. Among these species, the iron-oxo (IV) porphyrin denoted Compound I occupies a privileged position, serving a broad spectrum of catalytic roles. The most reactive members of this family bear a thiolate axial ligand, exhibiting high activity toward molecular oxygen activation and substrate oxidation. The default approach to such systems has entailed the use of hybrid density functionals or multi-configurational/multireference methods to treat electronic correlation. An alternative approach is presented based on the GGA+U approximation to density functional theory, in which a generalized gradient approximation (GGA) functional is supplemented with a localization correction to treat on-site correlation as inspired by the Hubbard model. The electronic structure of thiolate-ligated iron-oxo (IV) porphyrin and corresponding Coulomb repulsion U are determined both empirically and self-consistently, yielding spin-distributions, state level splittings, and electronic densities of states consistent with prior hybrid functional calculations. Comparison of this detailed electronic structure with model Hamiltonian calculations suggests that the localized 3d iron moments induce correlation in the surrounding electron gas, strengthening local moment formation. This behavior is analogous to strongly correlated electronic systems such as Mott insulators, in which the GGA+U scheme serves as an effective single-particle representation for the full, correlated many-body problem.
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Affiliation(s)
- Justin E Elenewski
- Institute for Structural Biology and Drug Discovery and Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 East Leigh Street, Richmond, Virginia 23219, USA
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34
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Morozov AN, Chatfield DC. Chloroperoxidase-catalyzed epoxidation of cis-β-methylstyrene: distal pocket flexibility tunes catalytic reactivity. J Phys Chem B 2012; 116:12905-14. [PMID: 23020548 DOI: 10.1021/jp302763h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chloroperoxidase, the most versatile heme protein, has a hybrid active site pocket that shares structural features with peroxidases and cytochrome P450s. The simulation studies presented here show that the enzyme possesses a remarkable ability to efficiently utilize its hybrid structure, assuming structurally different peroxidase-like and P450-like distal pocket faces and thereby enhancing the inherent catalytic capability of the active center. We find that, during epoxidation of cis-β-methylstyrene (CBMS), the native peroxidase-like aspect of the distal pocket is diminished as the polar Glu183 side chain is displaced away from the active center and the distal pocket takes on a more hydrophobic, P450-like, aspect. The P450-like distal pocket provides a significant enthalpic stabilization of ∼4 kcal/mol of the 14 kcal/mol reaction barrier for gas-phase epoxidation of CMBS by an oxyferryl heme-thiolate species. This stabilization comes from breathing of the distal pocket. As until recently the active site of chloroperoxidase was postulated to be inflexible, these results suggest a new conceptual understanding of the enzyme's versatility: catalytic reactivity is tuned by flexibility of the distal pocket.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.
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35
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Vidossich P, Alfonso-Prieto M, Rovira C. Catalases versus peroxidases: DFT investigation of H₂O₂ oxidation in models systems and implications for heme protein engineering. J Inorg Biochem 2012; 117:292-7. [PMID: 22883961 DOI: 10.1016/j.jinorgbio.2012.07.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 07/01/2012] [Accepted: 07/02/2012] [Indexed: 11/27/2022]
Abstract
Catalases and peroxidases are ubiquitous heme enzymes that catalyze the removal of hydrogen peroxide (H(2)O(2)). Both enzymes use one molecule of hydrogen peroxide to form a high valent iron intermediate named Compound I (Cpd I). However, whereas catalase Cpd I oxidizes a second H(2)O(2) molecule to oxygen, peroxidases use this intermediate to oxidize other substrates rather than H(2)O(2). The origin of the different reactivity of peroxidases and catalases is not known, but it is likely to be related to structural differences between the two heme active sites. Recent modeling studies suggest that the oxidation of H(2)O(2) by catalase Cpd I may take place by two hydrogen atom transfer steps. In this work, we investigate how catalases and peroxidases compare along the same hydrogen transfer steps to give hints into the question why peroxidases cannot efficiently oxidize H(2)O(2). The use of simplified models allows us to probe the direct effect of the proximal ligand (tyrosinate in catalases and histidine in peroxidases) without masking from the protein environment. We show that the nature of the fifth ligand (His in peroxidase and Tyr in catalase) has little effect on the energy barriers of the hydrogen transfer steps. On the contrary, the Cpd I-hydrogen peroxide (O(Fe)-O(peroxide)) distance affects significantly the reaction barriers. We propose that the distal side architecture of peroxidases do not allow to attain short O(Cpd I)-O(peroxide) distances, thus resulting in a lower efficiency towards H(2)O(2) oxidation.
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Affiliation(s)
- Pietro Vidossich
- Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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36
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Morozov AN, D'Cunha C, Alvarez CA, Chatfield DC. Enantiospecificity of chloroperoxidase-catalyzed epoxidation: biased molecular dynamics study of a cis-β-methylstyrene/chloroperoxidase-compound I complex. Biophys J 2011; 100:1066-75. [PMID: 21320452 DOI: 10.1016/j.bpj.2010.12.3729] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 11/22/2010] [Accepted: 12/20/2010] [Indexed: 11/17/2022] Open
Abstract
Molecular dynamics simulations of an explicitly solvated cis-β-methylstyrene/chloroperoxidase-Compound I complex are performed to determine the cause of the high enantiospecificity of epoxidation. From the simulations, a two-dimensional free energy potential is calculated to distinguish binding potential wells from which reaction to 1S2R and 1R2S epoxide products may occur. Convergence of the free energy potential is accelerated with an adaptive biasing potential. Analysis of binding is followed by analysis of 1S2R and 1R2S reaction precursor structures in which the substrate, having left the binding wells, places its reactive double bond in steric proximity to the oxyferryl heme center. Structural analysis of binding and reaction precursor conformations is presented. We find that 1), a distortion of Glu(183) is important for CPO-catalyzed epoxidation as was postulated previously based on experimental results; 2), the free energy of binding does not provide significant differentiation between structures leading to the respective epoxide enantiomers; and 3), CPO's enantiospecificity toward cis-β-methylstyrene is likely to be caused by a specific group of residues which form a hydrophobic core surrounding the oxyferryl heme center.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA.
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37
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Radoń M, Broclawik E, Pierloot K. DFT and Ab Initio Study of Iron-Oxo Porphyrins: May They Have a Low-Lying Iron(V)-Oxo Electromer? J Chem Theory Comput 2011; 7:898-908. [DOI: 10.1021/ct1006168] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, Poland
| | - Ewa Broclawik
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Kraków, Poland
| | - Kristine Pierloot
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Heverlee-Leuven, Belgium
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38
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Alfonso-Prieto M, Oberhofer H, Klein ML, Rovira C, Blumberger J. Proton Transfer Drives Protein Radical Formation in Helicobacter pylori Catalase but Not in Penicillium vitale Catalase. J Am Chem Soc 2011; 133:4285-98. [DOI: 10.1021/ja1110706] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Alfonso-Prieto
- Computer Simulation & Modeling Laboratory, Parc Científic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Computational Molecular Science, Temple University, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - H. Oberhofer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - M. L. Klein
- Institute for Computational Molecular Science, Temple University, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - C. Rovira
- Computer Simulation & Modeling Laboratory, Parc Científic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - J. Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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39
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Jung C, Vries SD, Schünemann V. Spectroscopic characterization of cytochrome P450 Compound I. Arch Biochem Biophys 2011; 507:44-55. [DOI: 10.1016/j.abb.2010.12.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 11/25/2022]
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40
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Schmidt B, Mahmud G, Soh S, Kim SH, Page T, O’Halloran TV, Grzybowski BA, Hoffman BM. Design, Implementation, Simulation, and Visualization of a Highly Efficient RIM Microfluidic Mixer for Rapid Freeze-Quench of Biological Samples. APPLIED MAGNETIC RESONANCE 2011; 40:415-425. [PMID: 22180701 PMCID: PMC3237052 DOI: 10.1007/s00723-011-0195-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rapid freeze-quench (RFQ) trapping of short-lived reaction intermediates for spectroscopic study plays an important role in the characterization of biological reactions. Recently there has been considerable effort to achieve submillisecond reaction deadtimes. We present here a new, robust, high-velocity microfluidic mixer that enables such rapid freeze-quenching. It is a based on the mixing method of two impinging jets commonly used in reaction injection molding (RIM) of plastics. This method achieves efficient mixing by inducing chaotic flow at relatively low Reynolds numbers (Re =140). We present the first mathematical simulation and microscopic visualization of mixing in such RFQ micromixers, the results of which show that the impinging solutions efficiently mix within the mixing chamber. These tests, along with a practical demonstration in a RFQ setup that involves copper wheels, show this new mixer can in practice provide reaction deadtimes as low as 100 microseconds.
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Affiliation(s)
- Bryan Schmidt
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Goher Mahmud
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208
| | - Siowling Soh
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208
| | - Sun Hee Kim
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Taylor Page
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | | | - Bartosz A. Grzybowski
- Department of Chemistry, Northwestern University, Evanston, IL 60208
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
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41
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Jung C. The mystery of cytochrome P450 Compound I. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:46-57. [DOI: 10.1016/j.bbapap.2010.06.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 05/31/2010] [Accepted: 06/04/2010] [Indexed: 10/19/2022]
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42
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Luthra A, Denisov IG, Sligar SG. Spectroscopic features of cytochrome P450 reaction intermediates. Arch Biochem Biophys 2010; 507:26-35. [PMID: 21167809 DOI: 10.1016/j.abb.2010.12.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 12/06/2010] [Accepted: 12/07/2010] [Indexed: 11/24/2022]
Abstract
Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological kingdoms [1]. These enzymes are responsible for catalyzing dozens chemical oxidative transformations such as hydroxylation, epoxidation, N-demethylation, etc., with very broad range of substrates [2,3]. Historically these enzymes received their name from 'pigment 450' due to the unusual position of the Soret band in UV-vis absorption spectra of the reduced CO-saturated state [4,5]. Despite detailed biochemical characterization of many isozymes, as well as later discoveries of other 'P450-like heme enzymes' such as nitric oxide synthase and chloroperoxidase, the phenomenological term 'cytochrome P450' is still commonly used as indicating an essential spectroscopic feature of the functionally active protein which is now known to be due to the presence of a thiolate ligand to the heme iron [6]. Heme proteins with an imidazole ligand such as myoglobin and hemoglobin as well as an inactive form of P450 are characterized by Soret maxima at 420nm [7]. This historical perspective highlights the importance of spectroscopic methods for biochemical studies in general, and especially for heme enzymes, where the presence of the heme iron and porphyrin macrocycle provides rich variety of specific spectroscopic markers available for monitoring chemical transformations and transitions between active intermediates of catalytic cycle.
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Affiliation(s)
- Abhinav Luthra
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, Urbana, IL 61801, USA
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43
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Rittle J, Green MT. Cytochrome P450 compound I: capture, characterization, and C-H bond activation kinetics. Science 2010; 330:933-7. [PMID: 21071661 DOI: 10.1126/science.1193478] [Citation(s) in RCA: 986] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cytochrome P450 enzymes are responsible for the phase I metabolism of approximately 75% of known pharmaceuticals. P450s perform this and other important biological functions through the controlled activation of C-H bonds. Here, we report the spectroscopic and kinetic characterization of the long-sought principal intermediate involved in this process, P450 compound I (P450-I), which we prepared in approximately 75% yield by reacting ferric CYP119 with m-chloroperbenzoic acid. The Mössbauer spectrum of CYP119-I is similar to that of chloroperoxidase compound I, although its electron paramagnetic resonance spectrum reflects an increase in |J|/D, the ratio of the exchange coupling to the zero-field splitting. CYP119-I hydroxylates the unactivated C-H bonds of lauric acid [D(C-H) ~ 100 kilocalories per mole], with an apparent second-order rate constant of k(app) = 1.1 × 10(7) per molar per second at 4°C. Direct measurements put a lower limit of k ≥ 210 per second on the rate constant for bound substrate oxidation, whereas analyses involving kinetic isotope effects predict a value in excess of 1400 per second.
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Affiliation(s)
- Jonathan Rittle
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
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44
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Kumar D, Karamzadeh B, Sastry GN, de Visser SP. What factors influence the rate constant of substrate epoxidation by compound I of cytochrome P450 and analogous iron(IV)-oxo oxidants? J Am Chem Soc 2010; 132:7656-67. [PMID: 20481499 DOI: 10.1021/ja9106176] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cytochromes P450 are a versatile range of mono-oxygenase enzymes that catalyze a variety of different chemical reactions, of which the key reactions include aliphatic hydroxylation and C=C double bond epoxidation. To establish the fundamental factors that govern substrate epoxidation by these enzymes we have done a systematic density functional theory study on substrate epoxidation by the active species of P450 enzymes, namely the iron(IV)-oxo porphyrin cation radical oxidant or Compound I. We show here, for the first time, that the rate constant of substrate epoxidation, and hence the activation energy, correlates with the ionization potential of the substrate as well as with intrinsic electronic properties of the active oxidant such as the polarizability volume. To explain these findings we present an electron-transfer model for the reaction mechanism that explains the factors that determine the barrier heights and developed a valence bond (VB) curve crossing mechanism to rationalize the observed trends. In addition, we have found a correlation for substrate epoxidation reactions catalyzed by a range of heme and nonheme iron(IV)-oxo oxidants with the strength of the O-H bond in the iron-hydroxo complex, i.e. BDE(OH), which is supported by the VB model. Finally, the fundamental factors that determine the regioselectivity change between substrate hydroxylation and epoxidation are discussed. It is shown that the regioselectivity of aliphatic hydroxylation versus double bond epoxidation is not influenced by the choice of the oxidant but is purely substrate dependent.
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Affiliation(s)
- Devesh Kumar
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India.
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45
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Chen H, Song J, Lai W, Wu W, Shaik S. Multiple Low-Lying States for Compound I of P450cam and Chloroperoxidase Revealed from Multireference Ab Initio QM/MM Calculations. J Chem Theory Comput 2010; 6:940-53. [DOI: 10.1021/ct9006234] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hui Chen
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
| | - Jinshuai Song
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
| | - Wenzhen Lai
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
| | - Wei Wu
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
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46
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Lai W, Chen H, Cho KB, Shaik S. Effects of substrate, protein environment, and proximal ligand mutation on compound I and compound 0 of chloroperoxidase. J Phys Chem A 2010; 113:11763-71. [PMID: 19572690 DOI: 10.1021/jp902898s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper investigates the enzyme chloroperoxidase (CPO) by means of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. The effects of anionic substrate, protein environment, and proximal ligand mutation on the high-valent iron-oxo species, compound I (Cpd I), and the ferric hydroperoxide complex, compound 0 (Cpd 0), are studied. The results indicate that the presence of an anionic substrate (acetate) and the protonation state of one critical residue (Glu104) have a considerable impact on the relative stabilities of Cpd I and Cpd 0. In the absence of the substrate or when the substrate is protonated, Cpd I is considerably more stable, and its formation barrier is smaller than in the case where the substrate is in its anionic state and when Glu104 is deprotonated. This trend, which is shown to be a simple manifestation of the Hammond principle, reproduces the experimental observation that the working pH of the enzyme is acidic. Furthermore, in the absence of substrate (or when it is protonated), the relative Cpd 0/Cpd I energies are found to be a good index of Cpd I stability in heme enzymes and to follow the experimental order: horseradish peroxidase (HRP) > CPO > P450. In silico mutation of the proximal ligand from cysteine to selenocysteine was found to have no effect at all on the properties of Cpd I (e.g., spin density on the chalcogen, Mössbauer parameters, etc.) and its relative stability to Cpd 0 or on the corresponding barrier for formation. This surprising finding shows that the polar CPO pocket applies a leveling effect that stabilizes the anionic forms of the proximal ligands (CysS(-) and CysSe(-)). This in turn means that the Se-Cpd I of the mutant CPO is observable.
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Affiliation(s)
- Wenzhen Lai
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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47
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Shaik S, Cohen S, Wang Y, Chen H, Kumar D, Thiel W. P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations. Chem Rev 2009; 110:949-1017. [DOI: 10.1021/cr900121s] [Citation(s) in RCA: 791] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sason Shaik
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Shimrit Cohen
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Yong Wang
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Hui Chen
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Devesh Kumar
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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48
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Hessenauer-Ilicheva N, Franke A, Wolak M, Higuchi T, van Eldik R. Spectroscopic and Mechanistic Studies on Oxidation Reactions Catalyzed by the Functional Model SR Complex for Cytochrome P450: Influence of Oxidant, Substrate, and Solvent. Chemistry 2009; 15:12447-59. [DOI: 10.1002/chem.200901712] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Lai W, Chen H, Shaik S. What Kinds of Ferryl Species Exist for Compound II of Chloroperoxidase? A Dialog of Theory with Experiment. J Phys Chem B 2009; 113:7912-7. [DOI: 10.1021/jp902288q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Wenzhen Lai
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Hui Chen
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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50
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Wang Y, Chen H, Makino M, Shiro Y, Nagano S, Asamizu S, Onaka H, Shaik S. Theoretical and Experimental Studies of the Conversion of Chromopyrrolic Acid to an Antitumor Derivative by Cytochrome P450 StaP: The Catalytic Role of Water Molecules. J Am Chem Soc 2009; 131:6748-62. [DOI: 10.1021/ja9003365] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yong Wang
- The Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan, and Department of Biotechnology, Faculty of Engineering, and Biotechnology Research Center, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Hui Chen
- The Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan, and Department of Biotechnology, Faculty of Engineering, and Biotechnology Research Center, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Masatomo Makino
- The Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan, and Department of Biotechnology, Faculty of Engineering, and Biotechnology Research Center, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Yoshitsugu Shiro
- The Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan, and Department of Biotechnology, Faculty of Engineering, and Biotechnology Research Center, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Shingo Nagano
- The Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan, and Department of Biotechnology, Faculty of Engineering, and Biotechnology Research Center, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Shumpei Asamizu
- The Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan, and Department of Biotechnology, Faculty of Engineering, and Biotechnology Research Center, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Hiroyasu Onaka
- The Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan, and Department of Biotechnology, Faculty of Engineering, and Biotechnology Research Center, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Sason Shaik
- The Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan, and Department of Biotechnology, Faculty of Engineering, and Biotechnology Research Center, Toyama Prefectural University, Toyama 939-0398, Japan
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