1
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Marques HM. Electron transfer in biological systems. J Biol Inorg Chem 2024:10.1007/s00775-024-02076-8. [PMID: 39424709 DOI: 10.1007/s00775-024-02076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 09/27/2024] [Indexed: 10/21/2024]
Abstract
Examples of how metalloproteins feature in electron transfer processes in biological systems are reviewed. Attention is focused on the electron transport chains of cellular respiration and photosynthesis, and on metalloproteins that directly couple electron transfer to a chemical reaction. Brief mention is also made of extracellular electron transport. While covering highlights of the recent and the current literature, this review is aimed primarily at introducing the senior undergraduate and the novice postgraduate student to this important aspect of bioinorganic chemistry.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa.
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2
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Devi T, Dutta K, Deutscher J, Mebs S, Kuhlmann U, Haumann M, Cula B, Dau H, Hildebrandt P, Ray K. A high-spin alkylperoxo-iron(iii) complex with cis-anionic ligands: implications for the superoxide reductase mechanism. Chem Sci 2024; 15:528-533. [PMID: 38179538 PMCID: PMC10762717 DOI: 10.1039/d3sc05603a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
The N3O macrocycle of the 12-TMCO ligand stabilizes a high spin (S = 5/2) [FeIII(12-TMCO)(OOtBu)Cl]+ (3-Cl) species in the reaction of [FeII(12-TMCO)(OTf)2] (1-(OTf)2) with tert-butylhydroperoxide (tBuOOH) in the presence of tetraethylammonium chloride (NEt4Cl) in acetonitrile at -20 °C. In the absence of NEt4Cl the oxo-iron(iv) complex 2 [FeIV(12-TMCO)(O)(CH3CN)]2+ is formed, which can be further converted to 3-Cl by adding NEt4Cl and tBuOOH. The role of the cis-chloride ligand in the stabilization of the FeIII-OOtBu moiety can be extended to other anions including the thiolate ligand relevant to the enzyme superoxide reductase (SOR). The present study underlines the importance of subtle electronic changes and secondary interactions in the stability of the biologically relevant metal-dioxygen intermediates. It also provides some rationale for the dramatically different outcomes of the chemistry of iron(iii)peroxy intermediates formed in the catalytic cycles of SOR (Fe-O cleavage) and cytochrome P450 (O-O bond lysis) in similar N4S coordination environments.
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Affiliation(s)
- Tarali Devi
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
- Department of Inorganic and Physical Chemistry, Indian Institute of Science Bangalore Karnataka-560012 India
| | - Kuheli Dutta
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Jennifer Deutscher
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Stefan Mebs
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Uwe Kuhlmann
- Institut für Chemie, Technische Universität Berlin Fakultät II, Straße des 17. Juni 135 10623 Berlin Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Beatrice Cula
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Fakultät II, Straße des 17. Juni 135 10623 Berlin Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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3
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Hu S, Guo R, Gao Y, Chen F. Oxoiron(IV)-dominated Heterogeneous Fenton-like Mechanism of Fe-Doped MoS 2. Chem Asian J 2023; 18:e202201134. [PMID: 36459407 DOI: 10.1002/asia.202201134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/04/2022]
Abstract
Oxoiron(IV) species are a critical intermediate in the Fe-based Fenton-like process at circumneutral pH, and its oxidative reactivity is closely related to the ligands. An optional inorganic host material, MoS2 , is selected to construct a highly reactive sulfur ligand coordinated Fe species in this work. The Fe species doped in MoS2 is presented as the FeII centre and triggers the transformation of the 2H phase to the octahedral 1T phase MoS2 . The role of the interaction between doped Fe and the MoS2 host lattice on the formation of oxoiron(IV) is studied. A significant Fenton-like reactivity and a remarkable accumulation of oxoiron(IV) species were observed for Fe-MoS2 . The quenching experiment was implemented to disclose the predominant role of oxoiron(IV) species in the Fe-MoS2 /H2 O2 Fenton-like system. Furthermore, oxoiron(IV) species could transform into the ⋅O2 - and 1 O2 , which further expedites the Fenton-like reaction.
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Affiliation(s)
- Shiyu Hu
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, P. R. China
| | - Rujia Guo
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, P. R. China
| | - Yiqian Gao
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, P. R. China
| | - Feng Chen
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, P. R. China
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4
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Rajakumara E, Saniya D, Bajaj P, Rajeshwari R, Giri J, Davari MD. Hijacking Chemical Reactions of P450 Enzymes for Altered Chemical Reactions and Asymmetric Synthesis. Int J Mol Sci 2022; 24:ijms24010214. [PMID: 36613657 PMCID: PMC9820634 DOI: 10.3390/ijms24010214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/25/2022] Open
Abstract
Cytochrome P450s are heme-containing enzymes capable of the oxidative transformation of a wide range of organic substrates. A protein scaffold that coordinates the heme iron, and the catalytic pocket residues, together, determine the reaction selectivity and regio- and stereo-selectivity of the P450 enzymes. Different substrates also affect the properties of P450s by binding to its catalytic pocket. Modulating the redox potential of the heme by substituting iron-coordinating residues changes the chemical reaction, the type of cofactor requirement, and the stereoselectivity of P450s. Around hundreds of P450s are experimentally characterized, therefore, a mechanistic understanding of the factors affecting their catalysis is increasingly vital in the age of synthetic biology and biotechnology. Engineering P450s can enable them to catalyze a variety of chemical reactions viz. oxygenation, peroxygenation, cyclopropanation, epoxidation, nitration, etc., to synthesize high-value chiral organic molecules with exceptionally high stereo- and regioselectivity and catalytic efficiency. This review will focus on recent studies of the mechanistic understandings of the modulation of heme redox potential in the engineered P450 variants, and the effect of small decoy molecules, dual function small molecules, and substrate mimetics on the type of chemical reaction and the catalytic cycle of the P450 enzymes.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502284, India
- Correspondence: (E.R.); (M.D.D.)
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502284, India
| | - Priyanka Bajaj
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Rajanna Rajeshwari
- Department of Plant Pathology, College of Horticulture, University of Horticultural Sciences, Bagalkot Campus, GKVK, Bengaluru 560064, India
| | - Jyotsnendu Giri
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502284, India
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
- Correspondence: (E.R.); (M.D.D.)
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5
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Wu C, Wu Y, He X, Hong R, Lee H, Feng K, Ping‐Yu Chen P. Modeling Heme Peroxidase: Heme Saddling Facilitates Reactions with Hyperperoxides To Form High‐Valent Fe
IV
‐Oxo Species. Chemistry 2022; 28:e202201139. [DOI: 10.1002/chem.202201139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Chang‐Quan Wu
- Department of Chemistry National Chung Hsing University 145 Xingda Rd., South Dist. Taichung City 402 Taiwan (R.O.C
| | - Yi‐Wen Wu
- Department of Chemistry National Chung Hsing University 145 Xingda Rd., South Dist. Taichung City 402 Taiwan (R.O.C
| | - Xuan‐Han He
- Department of Chemistry National Chung Hsing University 145 Xingda Rd., South Dist. Taichung City 402 Taiwan (R.O.C
| | - Ruo‐Ting Hong
- Department of Chemistry National Chung Hsing University 145 Xingda Rd., South Dist. Taichung City 402 Taiwan (R.O.C
| | - Hao‐Chien Lee
- Department of Chemistry National Chung Hsing University 145 Xingda Rd., South Dist. Taichung City 402 Taiwan (R.O.C
| | - Kang‐Yen Feng
- Department of Chemistry National Chung Hsing University 145 Xingda Rd., South Dist. Taichung City 402 Taiwan (R.O.C
| | - Peter Ping‐Yu Chen
- Department of Chemistry National Chung Hsing University 145 Xingda Rd., South Dist. Taichung City 402 Taiwan (R.O.C
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6
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Huang J, Xu Q, Liu Z, Jain N, Tyagi M, Wei DQ, Hong L. Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density. Molecules 2021; 26:5693. [PMID: 34577164 PMCID: PMC8470667 DOI: 10.3390/molecules26185693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Many enzymes, particularly in one single family, with highly conserved structures and folds exhibit rather distinct substrate specificities. The underlying mechanism remains elusive, the resolution of which is of great importance for biochemistry, biophysics, and bioengineering. Here, we performed a neutron scattering experiment and molecular dynamics (MD) simulations on two structurally similar CYP450 proteins; CYP101 primarily catalyzes one type of ligands, then CYP2C9 can catalyze a large range of substrates. We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus restricting its selection on substrates. Moreover, we performed MD simulations on 146 different kinds of CYP450 proteins, spanning distinct biological categories including Fungi, Archaea, Bacteria, Protista, Animalia, and Plantae, and found the above mechanism generally valid. We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus differentiate their substrate specificities to meet the specific biological needs. As this mechanism is well-controllable and easy to be implemented, we expect it to be generally applicable in future enzymatic engineering to develop proteins of desired substrate specificities.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Nitin Jain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA;
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA;
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Peng Cheng Laboratory, Shenzhen 518055, China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
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7
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Mukherjee G, Satpathy JK, Bagha UK, Mubarak MQE, Sastri CV, de Visser SP. Inspiration from Nature: Influence of Engineered Ligand Scaffolds and Auxiliary Factors on the Reactivity of Biomimetic Oxidants. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01993] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Jagnyesh K. Satpathy
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Umesh K. Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Fakulti Sains dan Teknologi, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan Malaysia
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Sam P. de Visser
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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8
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Mukherjee M, Dey A. A heterogeneous bio-inspired peroxide shunt for catalytic oxidation of organic molecules. Chem Commun (Camb) 2020; 56:11593-11596. [PMID: 32852503 DOI: 10.1039/d0cc03468a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heme enzymes are capable of catalytically oxidising organic substrates using peroxide via the formation of a high-valent intermediate. Iron porphyrins with three different axial ligands are created on self-assembled monolayer-modified gold electrodes, which can oxidize C-H bonds and epoxidize alkenes efficiently. The kinetic isotope effects suggest that the hydrogen atom transfer reaction by a highly reactive oxidant is likely to be the rate-determining step. Effect of different axial ligands and different secondary structures of the iron porphyrin confirms that the thiolate axial ligand with a hydrophobic distal pocket is the most efficient for this oxidation chemistry.
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Affiliation(s)
- Manjistha Mukherjee
- School of Chemical Science, Indian Association for the Cultivation of Science, Kolkata, India.
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9
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Ortmayer M, Fisher K, Basran J, Wolde-Michael EM, Heyes DJ, Levy C, Lovelock SL, Anderson JLR, Raven EL, Hay S, Rigby SEJ, Green AP. Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code. ACS Catal 2020; 10:2735-2746. [PMID: 32550044 PMCID: PMC7273622 DOI: 10.1021/acscatal.9b05129] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/22/2020] [Indexed: 01/14/2023]
Abstract
![]()
Nature
employs a limited number of genetically encoded axial ligands
to control diverse heme enzyme activities. Deciphering the functional
significance of these ligands requires a quantitative understanding of how their electron-donating
capabilities modulate the structures and reactivities of the iconic
ferryl intermediates compounds I and II. However, probing these relationships
experimentally has proven to be challenging as ligand substitutions
accessible via conventional mutagenesis do not allow fine tuning of
electron donation and typically abolish catalytic function. Here,
we exploit engineered translation components to replace the histidine
ligand of cytochrome c peroxidase (CcP) by a less electron-donating Nδ-methyl histidine (Me-His) with little effect on the enzyme structure.
The rate of formation (k1) and the reactivity
(k2) of compound I are unaffected by ligand
substitution. In contrast, proton-coupled electron transfer to compound
II (k3) is 10-fold slower in CcP Me-His, providing a direct link between electron donation
and compound II reactivity, which can be explained by weaker electron
donation from the Me-His ligand (“the push”) affording
an electron-deficient ferryl oxygen with reduced proton affinity (“the
pull”). The deleterious effects of the Me-His ligand can be
fully compensated by introducing a W51F mutation designed to increase
“the pull” by removing a hydrogen bond to the ferryl
oxygen. Analogous substitutions in ascorbate peroxidase lead to similar
activity trends to those observed in CcP, suggesting
that a common mechanistic strategy is employed by enzymes using distinct
electron transfer pathways. Our study highlights how noncanonical
active site substitutions can be used to directly probe and deconstruct
highly evolved bioinorganic mechanisms.
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Affiliation(s)
- Mary Ortmayer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Karl Fisher
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Emmanuel M. Wolde-Michael
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Colin Levy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Sarah L. Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - J. L. Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Emma L. Raven
- School of Chemistry, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Stephen E. J. Rigby
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Anthony P. Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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10
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Ahadi E, Hosseini-Monfared H, Spieß A, Janiak C. Photocatalytic asymmetric epoxidation of trans-stilbene with manganese–porphyrin/graphene-oxide nanocomposite and molecular oxygen: axial ligand effect. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00441c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An efficient, visible light-driven manganese–porphyrin photocatalyst was developed for the asymmetric epoxidation of trans-stilbene by molecular oxygen under mild conditions.
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Affiliation(s)
- Elahe Ahadi
- Department of Chemistry
- University of Zanjan
- Zanjan
- Iran
| | | | - Alex Spieß
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine-Universität Düsseldorf
- 40204 Düsseldorf
- Germany
| | - Christoph Janiak
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine-Universität Düsseldorf
- 40204 Düsseldorf
- Germany
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11
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Dalton R, Lee SB, Claw KG, Prasad B, Phillips BR, Shen DD, Wong LH, Fade M, McDonald MG, Dunham MJ, Fowler DM, Rettie AE, Schuetz E, Thornton TA, Nickerson DA, Gaedigk A, Thummel KE, Woodahl EL. Interrogation of CYP2D6 Structural Variant Alleles Improves the Correlation Between CYP2D6 Genotype and CYP2D6-Mediated Metabolic Activity. Clin Transl Sci 2019; 13:147-156. [PMID: 31536170 PMCID: PMC6951848 DOI: 10.1111/cts.12695] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 01/03/2023] Open
Abstract
The cytochrome P450 2D6 (CYP2D6) gene locus is challenging to accurately genotype due to numerous single nucleotide variants and complex structural variation. Our goal was to determine whether the CYP2D6 genotype‐phenotype correlation is improved when diplotype assignments incorporate structural variation, identified by the bioinformatics tool Stargazer, with next‐generation sequencing data. Using CYP2D6 activity measured with substrates dextromethorphan and metoprolol, activity score explained 40% and 34% of variability in metabolite formation rates, respectively, when diplotype calls incorporated structural variation, increasing from 36% and 31%, respectively, when diplotypes did not incorporate structural variation. We also investigated whether the revised Clinical Pharmacogenetics Implementation Consortium (CPIC) recommendations for translating genotype to phenotype improve CYP2D6 activity predictions over the current system. Although the revised recommendations do not improve the correlation between activity score and CYP2D6 activity, perhaps because of low frequency of the CYP2D6*10 allele, the correlation with metabolizer phenotype group was significantly improved for both substrates. We also measured the function of seven rare coding variants: one (A449D) exhibited decreased (44%) and another (R474Q) increased (127%) activity compared with reference CYP2D6.1 protein. Allele‐specific analysis found that A449D is part of a novel CYP2D6*4 suballele, CYP2D6*4.028. The novel haplotype containing R474Q was designated CYP2D6*138 by PharmVar; another novel haplotype containing R365H was designated CYP2D6*139. Accuracy of CYP2D6 phenotype prediction is improved when the CYP2D6 gene locus is interrogated using next‐generation sequencing coupled with structural variation analysis. Additionally, revised CPIC genotype to phenotype translation recommendations provides an improvement in assigning CYP2D6 activity.
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Affiliation(s)
- Rachel Dalton
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | - Seung-Been Lee
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Katrina G Claw
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Brian R Phillips
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Danny D Shen
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Lai Hong Wong
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Mitch Fade
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Matthew G McDonald
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Maitreya J Dunham
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Douglas M Fowler
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Erin Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, & Therapeutic Innovation, Children's Mercy Kansas City and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
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12
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Quesne MG, Silveri F, de Leeuw NH, Catlow CRA. Advances in Sustainable Catalysis: A Computational Perspective. Front Chem 2019; 7:182. [PMID: 31032245 PMCID: PMC6473102 DOI: 10.3389/fchem.2019.00182] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/07/2019] [Indexed: 11/13/2022] Open
Abstract
The enormous challenge of moving our societies to a more sustainable future offers several exciting opportunities for computational chemists. The first principles approach to "catalysis by design" will enable new and much greener chemical routes to produce vital fuels and fine chemicals. This prospective outlines a wide variety of case studies to underscore how the use of theoretical techniques, from QM/MM to unrestricted DFT and periodic boundary conditions, can be applied to biocatalysis and to both homogeneous and heterogenous catalysts of all sizes and morphologies to provide invaluable insights into the reaction mechanisms they catalyze.
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13
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Hsieh CC, Liu YC, Tseng MC, Chiang MH, Horng YC. Dioxygen activation by a dinuclear thiolate-ligated Fe(ii) complex. Dalton Trans 2019; 48:379-386. [PMID: 30516213 DOI: 10.1039/c8dt04491k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dioxygen activation by FeII thiolate complexes is relatively rare in biological and chemical systems because the sulfur site is at least as vulnerable as the iron site to oxidative modification. O2 activation by FeII-SR complexes with thiolate bound trans to the O2 binding site generally affords the FeIV[double bond, length as m-dash]O intermediate and oxidized thiolate. On the other hand, O2 activation by Fe(ii)-SR complexes with thiolate bound cis to the O2 binding site generates FeIII-O-FeIII or S-oxygenated complexes. The postulated FeIV[double bond, length as m-dash]O intermediate has only been identified in isopenicillin N synthase recently. We demonstrated here that O2 activation by a dinuclear FeII thiolate-rich complex produces a mononuclear FeIII complex and water with a supply of electron donors. The thiolate is bound cis to the postulated dioxygen binding site, and no FeIII-O-FeIII or S-oxygenated complex was observed. Although we have not detected the transient intermediate by spectroscopic measurements, the FeIV[double bond, length as m-dash]O intermediate is suggested to exist by theoretical calculation, and P-oxidation and hydride-transfer experiments. In addition, an unprecedented FeIII-O2-FeIII complex supported by thiolates was observed during the reaction by using a coldspray ionization time-of-flight mass (CSI-TOF MS) instrument. This is also supported by low-temperature UV-vis measurements. The intramolecular NHO[double bond, length as m-dash]FeIV hydrogen bonding, calculated by DFT, probably fine tunes the O2-activation process for intramolecular hydrogen abstraction, avoiding the S-oxygenation at cis-thiolate.
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Affiliation(s)
- Chang-Chih Hsieh
- Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan.
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14
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Balaraman P, Plettner E. Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1). Biochim Biophys Acta Gen Subj 2018; 1863:304-312. [PMID: 30391161 DOI: 10.1016/j.bbagen.2018.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 11/29/2022]
Abstract
The camphor-degrading microorganism, Pseudomonas putida strain ATCC 17453, is an aerobic, gram-negative soil bacterium that uses camphor as its sole carbon and energy source. The genes responsible for the catabolic degradation of camphor are encoded on the extra-chromosomal CAM plasmid. A monooxygenase, cytochrome P450cam, mediates hydroxylation of camphor to 5-exo-hydroxycamphor as the first and committed step in the camphor degradation pathway, requiring a dioxygen molecule (O2) from air. Under low O2 levels, P450cam catalyzes the production of borneol via an unusual reduction reaction. We have previously shown that borneol downregulates the expression of P450cam. To understand the function of P450cam and the consequences of down-regulation by borneol under low O2 conditions, we have studied chemotaxis of camphor induced and non-induced P. putida strain ATCC 17453. We have tested camphor, borneol, oxidized camphor metabolites and known bacterial attractants (d)-glucose, (d) - and (l)-glutamic acid for their elicitation chemotactic behavior. In addition, we have used 1-phenylimidazole, a P450cam inhibitor, to investigate if P450cam plays a role in the chemotactic ability of P. putida in the presence of camphor. We found that camphor, a chemoattractant, became toxic and chemorepellent when P450cam was inhibited. We have also evaluated the effect of borneol on chemotaxis and found that the bacteria chemotaxed away from camphor in the presence of borneol. This is the first report of the chemotactic behaviour of P. putida ATCC 17453 and the essential role of P450cam in this process.
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Affiliation(s)
- Priyadarshini Balaraman
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Erika Plettner
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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15
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Zhang W, Du L, Li F, Zhang X, Qu Z, Han L, Li Z, Sun J, Qi F, Yao Q, Sun Y, Geng C, Li S. Mechanistic Insights into Interactions between Bacterial Class I P450 Enzymes and Redox Partners. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02913] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Lei Du
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Fengwei Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Zepeng Qu
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Lei Han
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Jingran Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Fengxia Qi
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Qiuping Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Yue Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
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16
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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17
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Enzymatic Activation of the Emerging Drug Resveratrol. Appl Biochem Biotechnol 2017; 185:248-256. [PMID: 29124656 DOI: 10.1007/s12010-017-2645-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
The plant originated stilbene "resveratrol" (3,4',5-trans-trihydroxystilbene) is well known for its diverse health benefits including anti-tumor, anti-inflammatory, anti-microbial, and anti-oxidant properties. Besides a significant amount of reports on different aspects of its application as prodrug in the last 50 years, still, a strategy leading to the production of the active drug is missing. The aim of this work was to evaluate the enzymatic activation of prodrug resveratrol to the effective drug piceatannol, without engaging expensive cofactors. Five different heme proteins were analyzed for the transformation of resveratrol. Kinetic parameters of resveratrol transformation and analysis of the transformed products were conducted through HPLC and GC-MS. Effect of pH and organic solvent on the transformation process had also been evaluated. Among all tested heme proteins, only a variant of cytochrome P450BM3 from Bacillus megaterium (CYPBM3F87A) was found suitable for piceatannol production. The most suitable pH for the reaction conditions was 8.5, while organic solvents did not show any effect on transformation. For resveratrol transformation, the turnover rate (k cat) was 21.7 (± 0.6) min-1, the affinity constant (K M) showed a value of 55.7 (± 16.7) μM for a catalytic efficiency (k cat/K M) of 389 min-1 mM-1. GC-MS analysis showed that the only product from resveratrol transformation by cytochrome P450BM3 is the biologically active piceatannol. The enzymatic transformation of resveratrol, an emerging compound with medical interest, to active product piceatannol by a variant of cytochrome P450BM3 in the absence of expensive NADPH cofactor is demonstrated. This enzymatic process is economically attractive and can be scaled up to cover the increasing medical demand for piceatannol.
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18
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19
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Onderko EL, Silakov A, Yosca TH, Green MT. Characterization of a selenocysteine-ligated P450 compound I reveals direct link between electron donation and reactivity. Nat Chem 2017. [DOI: 10.1038/nchem.2781] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Li N, Zheng Y, Jiang X, Zhang R, Chen W. Generation of reactive cobalt oxo oxamate radical species for biomimetic oxidation of contaminants. RSC Adv 2017. [DOI: 10.1039/c7ra08317c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bio-inspired formation of [CoIVO˙]− species: cobalt oxo radical intermediate was directly observed in ESI-MS.
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Affiliation(s)
- Nan Li
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Yun Zheng
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Xuemei Jiang
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Ran Zhang
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Wenxing Chen
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
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21
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Affiliation(s)
- Timothy H. Yosca
- Departments of Chemistry & Molecular Biology and Biochemistry; University of California-Irvine, Irvine; California 92697 USA
| | - Michael T. Green
- Departments of Chemistry & Molecular Biology and Biochemistry; University of California-Irvine, Irvine; California 92697 USA
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22
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McIntosh JA, Heel T, Buller AR, Chio L, Arnold FH. Structural Adaptability Facilitates Histidine Heme Ligation in a Cytochrome P450. J Am Chem Soc 2015; 137:13861-5. [PMID: 26299431 PMCID: PMC4635421 DOI: 10.1021/jacs.5b07107] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/29/2022]
Abstract
Almost all known members of the cytochrome P450 (CYP) superfamily conserve a key cysteine residue that coordinates the heme iron. Although mutation of this residue abolishes monooxygenase activity, recent work has shown that mutation to either serine or histidine unlocks non-natural carbene- and nitrene-transfer activities. Here we present the first crystal structure of a histidine-ligated P450. The T213A/C317H variant of the thermostable CYP119 from Sulfolobus acidocaldarius maintains heme iron coordination through the introduced ligand, an interaction that is accompanied by large changes in the overall protein structure. We also find that the axial cysteine C317 may be substituted with any other amino acid without abrogating folding and heme cofactor incorporation. Several of the axial mutants display unusual spectral features, suggesting that they have active sites with unique steric and electronic properties. These novel, highly stable enzyme active sites will be fruitful starting points for investigations of non-natural P450 catalysis and mechanisms.
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Affiliation(s)
- John A. McIntosh
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Thomas Heel
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Andrew R. Buller
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Linda Chio
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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23
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Vandemeulebroucke A, Aldag C, Stiebritz MT, Reiher M, Hilvert D. Kinetic Consequences of Introducing a Proximal Selenocysteine Ligand into Cytochrome P450cam. Biochemistry 2015; 54:6692-703. [DOI: 10.1021/acs.biochem.5b00939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- An Vandemeulebroucke
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Caroline Aldag
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin T. Stiebritz
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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24
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Ji L, Faponle AS, Quesne MG, Sainna MA, Zhang J, Franke A, Kumar D, van Eldik R, Liu W, de Visser SP. Drug metabolism by cytochrome p450 enzymes: what distinguishes the pathways leading to substrate hydroxylation over desaturation? Chemistry 2015; 21:9083-92. [PMID: 25924594 DOI: 10.1002/chem.201500329] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Indexed: 01/05/2023]
Abstract
Cytochrome P450 enzymes are highly versatile biological catalysts in our body that react with a broad range of substrates. Key functions in the liver include the metabolism of drugs and xenobiotics. One particular metabolic pathway that is poorly understood relates to the P450 activation of aliphatic groups leading to either hydroxylation or desaturation pathways. A DFT and QM/MM study has been carried out on the factors that determine the regioselectivity of aliphatic hydroxylation over desaturation of compounds by P450 isozymes. The calculations establish multistate reactivity patterns, whereby the product distributions differ on each of the spin-state surfaces; hence spin-selective product formation was found. The electronic and thermochemical factors that determine the bifurcation pathways were analysed and a model that predicts the regioselectivity of aliphatic hydroxylation over desaturation pathways was established from valence bond and molecular orbital theories. Thus, the difference in energy of the OH versus the OC bond formed and the π-conjugation energy determines the degree of desaturation products. In addition, environmental effects of the substrate binding pocket that affect the regioselectivities were identified. These studies imply that bioengineering P450 isozymes for desaturation reactions will have to include modifications in the substrate binding pocket to restrict the hydroxylation rebound reaction.
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Affiliation(s)
- Li Ji
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China)
| | - Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
| | - Matthew G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
| | - Mala A Sainna
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
| | - Jing Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China)
| | - Alicja Franke
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen (Germany)
| | - Devesh Kumar
- Department of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rai Bareilly Road, Lucknow 226 025 (India)
| | - Rudi van Eldik
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen (Germany).,Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow (Poland)
| | - Weiping Liu
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China).
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK).
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25
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Sainna MA, Sil D, Sahoo D, Martin B, Rath SP, Comba P, de Visser SP. Spin-State Ordering in Hydroxo-Bridged Diiron(III)bisporphyrin Complexes. Inorg Chem 2015; 54:1919-30. [DOI: 10.1021/ic502803b] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mala A. Sainna
- Manchester Institute
of Biotechnology and School of Chemical Engineering and Analytical
Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Debangsu Sil
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Dipankar Sahoo
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Bodo Martin
- Anorganisch-Chemisches Institüt and Interdisciplinary
Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer
Feld 270, 69120 Heidelberg, Germany
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Peter Comba
- Anorganisch-Chemisches Institüt and Interdisciplinary
Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer
Feld 270, 69120 Heidelberg, Germany
| | - Sam P. de Visser
- Manchester Institute
of Biotechnology and School of Chemical Engineering and Analytical
Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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26
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Miyamoto M, Yamashita T, Yasuhara Y, Hayasaki A, Hosokawa Y, Tsujino H, Uno T. Membrane Anchor of Cytochrome P450 Reductase Suppresses the Uncoupling of Cytochrome P450. Chem Pharm Bull (Tokyo) 2015; 63:286-94. [DOI: 10.1248/cpb.c15-00034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Taku Yamashita
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women’s University
| | - Yuki Yasuhara
- Graduate School of Pharmaceutical Sciences, Osaka University
| | | | - Yukari Hosokawa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | | | - Tadayuki Uno
- Graduate School of Pharmaceutical Sciences, Osaka University
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27
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Monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:1-61. [PMID: 26002730 DOI: 10.1007/978-3-319-16009-2_1] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review examines the monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 (CYP) enzymes in bacterial, archaeal and mammalian systems. CYP enzymes catalyze monooxygenation reactions by inserting one oxygen atom from O2 into an enormous number and variety of substrates. The catalytic versatility of CYP stems from its ability to functionalize unactivated carbon-hydrogen (C-H) bonds of substrates through monooxygenation. The oxidative prowess of CYP in catalyzing monooxygenation reactions is attributed primarily to a porphyrin π radical ferryl intermediate known as Compound I (CpdI) (Por•+FeIV=O), or its ferryl radical resonance form (FeIV-O•). CYP-mediated hydroxylations occur via a consensus H atom abstraction/oxygen rebound mechanism involving an initial abstraction by CpdI of a H atom from the substrate, generating a highly-reactive protonated Compound II (CpdII) intermediate (FeIV-OH) and a carbon-centered alkyl radical that rebounds onto the ferryl hydroxyl moiety to yield the hydroxylated substrate. CYP enzymes utilize hydroperoxides, peracids, perborate, percarbonate, periodate, chlorite, iodosobenzene and N-oxides as surrogate oxygen atom donors to oxygenate substrates via the shunt pathway in the absence of NAD(P)H/O2 and reduction-oxidation (redox) auxiliary proteins. It has been difficult to isolate the historically elusive CpdI intermediate in the native NAD(P)H/O2-supported monooxygenase pathway and to determine its precise electronic structure and kinetic and physicochemical properties because of its high reactivity, unstable nature (t½~2 ms) and short life cycle, prompting suggestions for participation in monooxygenation reactions of alternative CYP iron-oxygen intermediates such as the ferric-peroxo anion species (FeIII-OO-), ferric-hydroperoxo species (FeIII-OOH) and FeIII-(H2O2) complex.
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28
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Wang ZJ, Renata H, Peck NE, Farwell CC, Coelho PS, Arnold FH. Improved cyclopropanation activity of histidine-ligated cytochrome P450 enables the enantioselective formal synthesis of levomilnacipran. Angew Chem Int Ed Engl 2014; 53:6810-3. [PMID: 24802161 PMCID: PMC4120663 DOI: 10.1002/anie.201402809] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Indexed: 02/03/2023]
Abstract
Engineering enzymes capable of modes of activation unprecedented in nature will increase the range of industrially important molecules that can be synthesized through biocatalysis. However, low activity for a new function is often a limitation in adopting enzymes for preparative-scale synthesis, reaction with demanding substrates, or when a natural substrate is also present. By mutating the proximal ligand and other key active-site residues of the cytochrome P450 enzyme from Bacillus megaterium (P450-BM3), a highly active His-ligated variant of P450-BM3 that can be employed for the enantioselective synthesis of the levomilnacipran core was engineered. This enzyme, BM3-Hstar, catalyzes the cyclopropanation of N,N-diethyl-2-phenylacrylamide with an estimated initial rate of over 1000 turnovers per minute and can be used under aerobic conditions. Cyclopropanation activity is highly dependent on the electronic properties of the P450 proximal ligand, which can be used to tune this non-natural enzyme activity.
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Affiliation(s)
| | | | - Nicole E. Peck
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA, 91125 (USA)
| | - Christopher C. Farwell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA, 91125 (USA)
| | - Pedro S. Coelho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA, 91125 (USA)
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA, 91125 (USA)
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Wang ZJ, Renata H, Peck NE, Farwell CC, Coelho PS, Arnold FH. Improved Cyclopropanation Activity of Histidine-Ligated Cytochrome P450 Enables the Enantioselective Formal Synthesis of Levomilnacipran. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402809] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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30
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Metal vs. chalcogen competition in the catalytic mechanism of cysteine dioxygenase. J Inorg Biochem 2013; 122:1-7. [DOI: 10.1016/j.jinorgbio.2013.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 12/25/2012] [Accepted: 01/11/2013] [Indexed: 11/18/2022]
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31
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Water oxidation by a cytochrome p450: mechanism and function of the reaction. PLoS One 2013; 8:e61897. [PMID: 23634216 PMCID: PMC3636257 DOI: 10.1371/journal.pone.0061897] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 03/18/2013] [Indexed: 12/18/2022] Open
Abstract
P450(cam) (CYP101A1) is a bacterial monooxygenase that is known to catalyze the oxidation of camphor, the first committed step in camphor degradation, with simultaneous reduction of oxygen (O2). We report that P450(cam) catalysis is controlled by oxygen levels: at high O2 concentration, P450(cam) catalyzes the known oxidation reaction, whereas at low O2 concentration the enzyme catalyzes the reduction of camphor to borneol. We confirmed, using (17)O and (2)H NMR, that the hydrogen atom added to camphor comes from water, which is oxidized to hydrogen peroxide (H2O2). This is the first time a cytochrome P450 has been observed to catalyze oxidation of water to H2O2, a difficult reaction to catalyze due to its high barrier. The reduction of camphor and simultaneous oxidation of water are likely catalyzed by the iron-oxo intermediate of P450(cam) , and we present a plausible mechanism that accounts for the 1:1 borneol:H2O2 stoichiometry we observed. This reaction has an adaptive value to bacteria that express this camphor catabolism pathway, which requires O2, for two reasons: 1) the borneol and H2O2 mixture generated is toxic to other bacteria and 2) borneol down-regulates the expression of P450(cam) and its electron transfer partners. Since the reaction described here only occurs under low O2 conditions, the down-regulation only occurs when O2 is scarce.
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Munro AW, Girvan HM, Mason AE, Dunford AJ, McLean KJ. What makes a P450 tick? Trends Biochem Sci 2013; 38:140-50. [DOI: 10.1016/j.tibs.2012.11.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/15/2012] [Accepted: 11/21/2012] [Indexed: 12/31/2022]
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Rebouças JS, James BR. Molecular Recognition Using Ruthenium(II) Porphyrin Thiol Complexes as Probes. Inorg Chem 2013; 52:1084-98. [DOI: 10.1021/ic302401m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Júlio S. Rebouças
- Departamento de Química, CCEN, Universidade Federal da Paraíba, João Pessoa, PB 58.051-900,
Brazil
| | - Brian R. James
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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Trzcionka J, Irvoas J, Pratviel G. The protonation state of trans axial water molecule switches: the reactivity of high-valent manganese-oxo porphyrin. NEW J CHEM 2013. [DOI: 10.1039/c3nj01004j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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35
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Hrycay EG, Bandiera SM. The monooxygenase, peroxidase, and peroxygenase properties of cytochrome P450. Arch Biochem Biophys 2012; 522:71-89. [DOI: 10.1016/j.abb.2012.01.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 12/22/2011] [Accepted: 01/04/2012] [Indexed: 12/30/2022]
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36
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Che X, Gao J, Zhang D, Liu C. How Do the Thiolate Ligand and Its Relative Position Control the Oxygen Activation in the Cysteine Dioxygenase Model? J Phys Chem A 2012; 116:5510-7. [DOI: 10.1021/jp3001515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xin Che
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Jun Gao
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Dongju Zhang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Chengbu Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100, P. R. China
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37
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Jankowska KI, Pagba CV, Piotrowiak P. Zinc-substituted cytochrome P450cam: characterization of protein conformers F420 and F450 by photoinduced electron transfer. Biochemistry 2012; 51:1431-8. [PMID: 22250969 DOI: 10.1021/bi201344h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metal substitution of heme proteins is widely applied in the study of biologically relevant electron transfer (ET) reactions. It has been shown that many modified proteins remain in their native conformation and can provide useful insights into the molecular mechanism of electron transfer between the native protein and its substrates. We investigated ET reactions between zinc-substituted cytochrome P450(cam) and small organic compounds such as quinones and ferrocene, which are capable of accessing the protein's hydrophobic channel and binding close to the active site, like its native substrate, camphor. Following the substitution method developed by Gunsalus and co-workers [Wagner, G. C., et al. (1981) J. Biol. Chem. 256, 6262-6265], we have identified two dominant forms of the zinc-substituted protein, F450 and F420, that exhibit different photophysical and photochemical properties. The ET behavior of F420 suggests that hydrophobic redox-active ligands are able to penetrate the hydrophobic channel and place themselves in the direct vicinity of the Zn-porphyrin. In contrast, the slower ET quenching rates observed in the case of F450 indicate that the association is weak and occurs outside of the protein channel. Therefore, we conclude that F420 corresponds to the open structure of the native cytochrome P450(cam) while F450 has a closed or partially closed channel that is characteristic of the camphor-containing cytochrome P450(cam). The existence of two distinct conformers of Zn-bound P450(cam) is consistent with the findings of Goodin and co-workers [Lee, Y.-T., et al. (2010) Biochemistry 49, 3412-3419] and has significant consequences for future electron transfer studies on this popular metalloenzyme.
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Affiliation(s)
- Katarzyna I Jankowska
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
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38
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Bruyneel F, Letondor C, Bastürk B, Gualandi A, Pordea A, Stoeckli-Evans H, Neier R. Catalytic Epoxidation of Alkenes by the Manganese Complex of a Reduced Porphyrinogen Macrocycle. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201100433] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Lang J, Santolini J, Couture M. The conserved Trp-Cys hydrogen bond dampens the "push effect" of the heme cysteinate proximal ligand during the first catalytic cycle of nitric oxide synthase. Biochemistry 2011; 50:10069-81. [PMID: 22023145 DOI: 10.1021/bi200965e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Residues surrounding and interacting with the heme proximal ligand are important for efficient catalysis by heme proteins. The nitric oxide synthases (NOSs) are thiolate-coordinated enzymes that catalyze the hydroxylation of l-Arg in the first of the two catalytic cycles needed to synthesize nitric oxide. In NOSs, the indole NH group of a conserved tryptophan [W56 of the bacterial NOS-like protein from Staphylococcus aureus (saNOS)] forms a hydrogen bond with the heme proximal cysteinate ligand. The purpose of this study was to determine the impact of increasing (W56F and W56Y variants) or decreasing (W56H variant) the electron density of the proximal cysteinate ligand on molecular oxygen (O(2)) activation using saNOS as a model. We show that the removal of the indole NH···S(-) bond for W56F and W56Y caused an increase in the electron density of the cysteinate. This was probed by the decrease of the midpoint reduction potential (E(1/2)) along with weakened σ-bonding and strengthened π-backbonding with distal ligands (CO and O(2)). On the other hand, the W56H variant showed stronger Fe-OO and Fe-CO bonds (strengthened σ-bonding) along with an elevated E(1/2), which is consistent with the formation of a strong NH···S(-) hydrogen bond from H56. We also show here that changing the electron density of the proximal thiolate controls its "push effect"; whereas the rates of both O(2) activation and autoxidation of the Fe(II)O(2) complex increase with the stronger push effect created by removing the indole NH···S(-) hydrogen bond (W56F and W56Y variants), the W56H variant showed an increased stability of the complex against autoxidation and a slower rate of O(2) activation. These results are discussed with regard to the roles played by the conserved tryptophan-cysteinate interaction in the first catalytic cycle of NOS.
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Affiliation(s)
- Jérôme Lang
- Département de biochimie, de microbiologie et de bioinformatique, PROTEO and IBIS, pavillon Charles-Eugène Marchand, room 3163, Université Laval, Québec, Canada G1V 0A6
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40
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Identification of camphor oxidation and reduction products in Pseudomonas putida: new activity of the cytochrome P450cam system. J Chem Ecol 2011; 37:657-67. [PMID: 21562741 DOI: 10.1007/s10886-011-9959-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 04/12/2011] [Accepted: 04/25/2011] [Indexed: 10/18/2022]
Abstract
P450 enzymes are known for catalyzing hydroxylation reactions of non-activated C-H bonds. For example, P450(cam) from Pseudomonas putida oxidizes (1R)-(+)-camphor to 5-exo-hydroxy camphor and further to 5-ketocamphor. This hydroxylation reaction proceeds via a catalytic cycle in which the reduction of dioxygen (O(2)) is coupled to the oxidation of the substrate. We have observed that under conditions of low oxygen, P. putida and isolated P450(cam) reduce camphor to borneol. We characterized the formation of borneol under conditions of low oxygen or when the catalytic cycle is shunted by artificial oxidants like m-chloro perbenzoic acid, cumene hydroperoxide, etc. We also tested the toxicity of camphor and borneol with P. putida and Escherichia coli. We have found that in P. putida borneol is less toxic than camphor, whereas in E. coli borneol is more toxic than camphor. We discuss a potental ecological advantage of the camphor reduction reaction for P. putida.
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41
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Hieringer W, Flechtner K, Kretschmann A, Seufert K, Auwärter W, Barth JV, Görling A, Steinrück HP, Gottfried JM. The Surface Trans Effect: Influence of Axial Ligands on the Surface Chemical Bonds of Adsorbed Metalloporphyrins. J Am Chem Soc 2011; 133:6206-22. [DOI: 10.1021/ja1093502] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wolfgang Hieringer
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
| | - Ken Flechtner
- Lehrstuhl für Physikalische Chemie II and Interdisciplinary Center for Molecular Materials (ICMM), Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
| | - Andreas Kretschmann
- Lehrstuhl für Physikalische Chemie II and Interdisciplinary Center for Molecular Materials (ICMM), Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
| | - Knud Seufert
- Physik-Department E20, Technische Universität München, James-Franck-Strasse, 85748 Garching, Germany
| | - Willi Auwärter
- Physik-Department E20, Technische Universität München, James-Franck-Strasse, 85748 Garching, Germany
| | - Johannes V. Barth
- Physik-Department E20, Technische Universität München, James-Franck-Strasse, 85748 Garching, Germany
| | - Andreas Görling
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
| | - Hans-Peter Steinrück
- Lehrstuhl für Physikalische Chemie II and Interdisciplinary Center for Molecular Materials (ICMM), Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
| | - J. Michael Gottfried
- Lehrstuhl für Physikalische Chemie II and Interdisciplinary Center for Molecular Materials (ICMM), Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058 Erlangen, Germany
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42
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Sivaramakrishnan S, Ouellet H, Du J, McLean KJ, Medzihradszky KF, Dawson JH, Munro AW, Ortiz de Montellano PR. A novel intermediate in the reaction of seleno CYP119 with m-chloroperbenzoic acid. Biochemistry 2011; 50:3014-24. [PMID: 21381758 DOI: 10.1021/bi101728y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450-mediated monooxygenation generally proceeds via a reactive ferryl intermediate coupled to a ligand radical [Fe(IV)═O]+• termed Compound I (Cpd I). The proximal cysteine thiolate ligand is a critical determinant of the spectral and catalytic properties of P450 enzymes. To explore the effect of an increased level of donation of electrons by the proximal ligand in the P450 catalytic cycle, we recently reported successful incorporation of SeCys into the active site of CYP119, a thermophilic cytochrome P450. Here we report relevant physical properties of SeCYP119 and a detailed analysis of the reaction of SeCYP119 with m-chloroperbenzoic acid. Our results indicate that the selenolate anion reduces rather than stabilizes Cpd I and also protects the heme from oxidative destruction, leading to the generation of a new stable species with an absorbance maximum at 406 nm. This stable intermediate can be returned to the normal ferric state by reducing agents and thiols, in agreement with oxidative modification of the selenolate ligand itself. Thus, in the seleno protein, the oxidative damage shifts from the heme to the proximal ligand, presumably because (a) an increased level of donation of electrons more efficiently quenches reactive species such as Cpd I and (b) the protection of the thiolate ligand provided by the protein active site structure is insufficient to shield the more oxidizable selenolate ligand.
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Affiliation(s)
- Santhosh Sivaramakrishnan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, United States
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43
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Molecular basis for the inability of an oxygen atom donor ligand to replace the natural sulfur donor heme axial ligand in cytochrome P450 catalysis. Spectroscopic characterization of the Cys436Ser CYP2B4 mutant. Arch Biochem Biophys 2010; 507:119-25. [PMID: 21147058 DOI: 10.1016/j.abb.2010.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/06/2010] [Accepted: 12/07/2010] [Indexed: 11/21/2022]
Abstract
All cytochrome P450s (CYPs) contain a cysteinate heme iron proximal ligand that plays a crucial role in their mechanism of action. Conversion of the proximal Cys436 to Ser in NH(2)-truncated microsomal CYP2B4 (ΔCYP2B4) transforms the enzyme into a two-electron NADPH oxidase producing H(2)O(2) without monooxygenase activity [K.P. Vatsis, H.M. Peng, M.J. Coon, J. Inorg. Biochem. 91 (2002) 542-553]. To examine the effects of this ligation change on the heme iron spin-state and coordination structure of ΔC436S CYP2B4, the magnetic circular dichroism and electronic absorption spectra of several oxidation/ligation states of the variant have been measured and compared with those of structurally defined heme complexes. The spectra of the substrate-free ferric mutant are indicative of a high-spin five-coordinate structure ligated by anionic serinate. The spectroscopic properties of the dithionite-reduced (deoxyferrous) protein are those of a five-coordinate (high-spin) state, and it is concluded that the proximal ligand has been protonated to yield neutral serine (ROH-donor). Low-spin six-coordinate ferrous complexes of the mutant with neutral sixth ligands (NO, CO, and O(2)) examined are also likely ligated by neutral serine, as would be expected for ferric complexes with anionic sixth ligands such as the hydroperoxo-ferric catalytic intermediate. Ligation of the heme iron by neutral serine vs. deprotonated cysteine is likely the result of the large difference in their acidity. Thus, without the necessary proximal ligand push of the cysteinate, although the ΔC436S mutant can accept two electrons and two protons, it is unable to heterolytically cleave the O-O bond of the hydroperoxo-ferric species to generate Compound I and hydroxylate the substrate.
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44
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McDonald AR, Bukowski MR, Farquhar ER, Jackson TA, Koehntop KD, Seo MS, De Hont RF, Stubna A, Halfen JA, Münck E, Nam W, Que L. Sulfur versus iron oxidation in an iron-thiolate model complex. J Am Chem Soc 2010; 132:17118-29. [PMID: 21070030 DOI: 10.1021/ja1045428] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the absence of base, the reaction of [Fe(II)(TMCS)]PF6 (1, TMCS = 1-(2-mercaptoethyl)-4,8,11-trimethyl-1,4,8,11-tetraazacyclotetradecane) with peracid in methanol at -20 °C did not yield the oxoiron(IV) complex (2, [Fe(IV)(O)(TMCS)]PF6), as previously observed in the presence of strong base (KO(t)Bu). Instead, the addition of 1 equiv of peracid resulted in 50% consumption of 1. The addition of a second equivalent of peracid resulted in the complete consumption of 1 and the formation of a new species 3, as monitored by UV-vis, ESI-MS, and Mössbauer spectroscopies. ESI-MS showed 3 to be formulated as [Fe(II)(TMCS) + 2O](+), while EXAFS analysis suggested that 3 was an O-bound iron(II)-sulfinate complex (Fe-O = 1.95 Å, Fe-S = 3.26 Å). The addition of a third equivalent of peracid resulted in the formation of yet another compound, 4, which showed electronic absorption properties typical of an oxoiron(IV) species. Mössbauer spectroscopy confirmed 4 to be a novel iron(IV) compound, different from 2, and EXAFS (Fe═O = 1.64 Å) and resonance Raman (ν(Fe═O) = 831 cm(-1)) showed that indeed an oxoiron(IV) unit had been generated in 4. Furthermore, both infrared and Raman spectroscopy gave indications that 4 contains a metal-bound sulfinate moiety (ν(s)(SO2) ≈ 1000 cm (-1), ν(as)(SO2) ≈ 1150 cm (-1)). Investigations into the reactivity of 1 and 2 toward H(+) and oxygen atom transfer reagents have led to a mechanism for sulfur oxidation in which 2 could form even in the absence of base but is rapidly protonated to yield an oxoiron(IV) species with an uncoordinated thiol moiety that acts as both oxidant and substrate in the conversion of 2 to 3.
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Affiliation(s)
- Aidan R McDonald
- Department of Chemistry and Center for Metals in Biocatalysis, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455, USA
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45
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Behera RK, Goyal S, Mazumdar S. Modification of the heme active site to increase the peroxidase activity of thermophilic cytochrome P450: A rational approach. J Inorg Biochem 2010; 104:1185-94. [DOI: 10.1016/j.jinorgbio.2010.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 11/28/2022]
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46
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Sun L, Wang Z, Jiang H, Tan X, Huang Z. Novel Conformational Transitions of Human Cytochrome P450 2C8 during Thermal and Acid-induced Unfolding. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Yang Y, Li C, Li W, Yi Z. Synthesis, Crystal Structure, Luminescence and Thermal Stability of a New Coordination Polymer Constructed by Europium(III) and 2,4-Dichlorophenoxyacetate. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Perera R, Sono M, Kinloch R, Zhang H, Tarasev M, Im SC, Waskell L, Dawson JH. Stabilization and spectroscopic characterization of the dioxygen complex of wild-type cytochrome P4502B4 (CYP2B4) and its distal side E301Q, T302A and proximal side F429H mutants at subzero temperatures. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:69-75. [PMID: 20637316 DOI: 10.1016/j.bbapap.2010.07.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 07/01/2010] [Accepted: 07/07/2010] [Indexed: 10/19/2022]
Abstract
Mammalian cytochrome P450 2B4 (CYP2B4) is a phenobarbital-inducible rabbit hepatic monooxygenase that catalyzes the N-demethylation of benzphetamine and metabolism of numerous other compounds. To probe the interactions of the heme environment and bound benzphetamine with the dioxygen (O₂) complex of CYP2B4, homogeneous O₂ complexes of the wild-type enzyme and three mutants at sites of conserved amino acids, two on the heme distal side (T302A and E301Q) and one on the proximal side (F429H), have been prepared and stabilized at ~-50°C in mixed solvents (60-70% v/v glycerol). We report that the magnetic circular dichroism and electronic absorption spectra of wild-type oxyferrous CYP2B4, in the presence and absence of substrate, are quite similar to those of the dioxygen complex of bacterial cytochrome P450-CAM (CYP101). However, the oxyferrous complexes of the T302A and E301Q CYP2B4 mutants have significantly perturbed electronic structure (~4 nm and ~3 nm red-shifted Soret features, respectively) compared to that of the wild-type oxyferrous complex. On the other hand, the heme proximal side mutant, CYP2B4 F429H, undergoes relatively facile conversion to a partially (~50%) denatured (P420) form upon reduction. The structural changes in the heme pocket environments of the CYP2B4 mutants that lead to the spectroscopic distinctions reported herein can be related to the differences in oxidation activities of wild-type CYP2B4 and its E301Q, T302A and F429H mutants.
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Affiliation(s)
- Roshan Perera
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
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49
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Jiang Y, Sivaramakrishnan S, Hayashi T, Cohen S, Moënne-Loccoz P, Shaik S, Ortiz de Montellano PR. Calculated and experimental spin state of seleno cytochrome P450. Angew Chem Int Ed Engl 2010; 48:7193-5. [PMID: 19718734 DOI: 10.1002/anie.200901485] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yongying Jiang
- Department of Pharmaceutical Chemistry, University of California, 600 16th street, San Francisco, CA 94158, USA
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50
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Sun L, Wang ZH, Ni FY, Tan XS, Huang ZX. The Role of Ile476 in the Structural Stability and Substrate Binding of Human Cytochrome P450 2C8. Protein J 2009; 29:32-43. [DOI: 10.1007/s10930-009-9218-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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