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Lee CWZ, Mubarak MQE, Green AP, de Visser SP. How Does Replacement of the Axial Histidine Ligand in Cytochrome c Peroxidase by N δ-Methyl Histidine Affect Its Properties and Functions? A Computational Study. Int J Mol Sci 2020; 21:ijms21197133. [PMID: 32992593 PMCID: PMC7583937 DOI: 10.3390/ijms21197133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/27/2022] Open
Abstract
Heme peroxidases have important functions in nature related to the detoxification of H2O2. They generally undergo a catalytic cycle where, in the first stage, the iron(III)-heme-H2O2 complex is converted into an iron(IV)-oxo-heme cation radical species called Compound I. Cytochrome c peroxidase Compound I has a unique electronic configuration among heme enzymes where a metal-based biradical is coupled to a protein radical on a nearby Trp residue. Recent work using the engineered Nδ-methyl histidine-ligated cytochrome c peroxidase highlighted changes in spectroscopic and catalytic properties upon axial ligand substitution. To understand the axial ligand effect on structure and reactivity of peroxidases and their axially Nδ-methyl histidine engineered forms, we did a computational study. We created active site cluster models of various sizes as mimics of horseradish peroxidase and cytochrome c peroxidase Compound I. Subsequently, we performed density functional theory studies on the structure and reactivity of these complexes with a model substrate (styrene). Thus, the work shows that the Nδ-methyl histidine group has little effect on the electronic configuration and structure of Compound I and little changes in bond lengths and the same orbital occupation is obtained. However, the Nδ-methyl histidine modification impacts electron transfer processes due to a change in the reduction potential and thereby influences reactivity patterns for oxygen atom transfer. As such, the substitution of the axial histidine by Nδ-methyl histidine in peroxidases slows down oxygen atom transfer to substrates and makes Compound I a weaker oxidant. These studies are in line with experimental work on Nδ-methyl histidine-ligated cytochrome c peroxidases and highlight how the hydrogen bonding network in the second coordination sphere has a major impact on the function and properties of the enzyme.
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Affiliation(s)
- Calvin W. Z. Lee
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Anthony P. Green
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Correspondence: ; Tel.: +44-161-306-4882
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Kamiya K, Kuwabara A, Harada T, Nakanishi S. Electrochemical Formation of Fe(IV)=O Derived from H 2 O 2 on a Hematite Electrode as an Active Catalytic Site for Selective Hydrocarbon Oxidation Reactions. Chemphyschem 2019; 20:648-650. [PMID: 30659730 DOI: 10.1002/cphc.201801207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/17/2019] [Indexed: 11/05/2022]
Abstract
The high-valence iron species (Fe(IV)=O) in the cytochrome P450 enzyme superfamily is generated via the activation of O2 , and serves as the active center of selective hydrocarbon oxidation reactions. Furthermore, P450 can employ an alternate route to produce Fe(IV)=O, even from H2 O2 without O2 activation. Meanwhile, Fe(IV)=O has recently been revealed to be the reactive intermediate during H2 O oxidation to O2 on hematite electrodes. Herein, we demonstrated the generation of Fe(IV)=O on hematite electrodes during the electrochemical oxidative decomposition of H2 O2 using in situ UV-visible absorption spectra. The generation of Fe(IV)=O on hematite electrodes from H2 O2 exhibited 100 mV lower overpotential than that from H2 O. This is because H2 O2 serves not only as the oxygen source of Fe(IV)=O, but also as the additional oxidant. Finally, we confirmed that the Fe(IV)=O generated on hematite electrodes can serve as the catalytic site for styrene epoxidation reactions.
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Affiliation(s)
- Kazuhide Kamiya
- Department of Chemical Science and Engineering Graduate School of Engineering Science, Osaka University 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.,Research Center for Solar Energy Chemistry, Osaka University 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Akito Kuwabara
- Department of Chemical Science and Engineering Graduate School of Engineering Science, Osaka University 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Takashi Harada
- Research Center for Solar Energy Chemistry, Osaka University 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Shuji Nakanishi
- Department of Chemical Science and Engineering Graduate School of Engineering Science, Osaka University 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.,Research Center for Solar Energy Chemistry, Osaka University 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
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Wei WJ, Siegbahn PEM, Liao RZ. Theoretical Study of the Mechanism of the Nonheme Iron Enzyme EgtB. Inorg Chem 2017; 56:3589-3599. [PMID: 28277674 DOI: 10.1021/acs.inorgchem.6b03177] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
EgtB is a nonheme iron enzyme catalyzing the C-S bond formation between γ-glutamyl cysteine (γGC) and N-α-trimethyl histidine (TMH) in the ergothioneine biosynthesis. Density functional calculations were performed to elucidate and delineate the reaction mechanism of this enzyme. Two different mechanisms were considered, depending on whether the sulfoxidation or the S-C bond formation takes place first. The calculations suggest that the S-O bond formation occurs first between the thiolate and the ferric superoxide, followed by homolytic O-O bond cleavage, very similar to the case of cysteine dioxygenase. Subsequently, proton transfer from a second-shell residue Tyr377 to the newly generated iron-oxo moiety takes place, which is followed by proton transfer from the TMH imidazole to Tyr377, facilitated by two crystallographically observed water molecules. Next, the S-C bond is formed between γGC and TMH, followed by proton transfer from the imidazole CH moiety to Tyr377, which was calculated to be the rate-limiting step for the whole reaction, with a barrier of 17.9 kcal/mol in the quintet state. The calculated barrier for the rate-limiting step agrees quite well with experimental kinetic data. Finally, this proton is transferred back to the imidazole nitrogen to form the product. The alternative thiyl radical attack mechanism has a very high barrier, being 25.8 kcal/mol, ruling out this possibility.
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Affiliation(s)
- Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-10691 Stockholm, Sweden
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
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Jalalvand AR, Gholivand MB, Goicoechea HC, Skov T, Mansouri K. Mimicking enzymatic effects of cytochrome P450 by an efficient biosensor for in vitro detection of DNA damage. Int J Biol Macromol 2015; 79:1004-10. [DOI: 10.1016/j.ijbiomac.2015.05.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 05/24/2015] [Accepted: 05/25/2015] [Indexed: 10/24/2022]
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Sil D, Khan FST, Rath SP. Axial Thiophenolate Coordination on Diiron(III)bisporphyrin: Influence of Heme–Heme Interactions on Structure, Function and Electrochemical Properties of the Individual Heme Center. Inorg Chem 2014; 53:11925-36. [DOI: 10.1021/ic5011677] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debangsu Sil
- Department of Chemistry, Indian Institute of Technology Kanpur
, Kanpur-208016, India
| | | | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur
, Kanpur-208016, India
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Ni Y, Wang P, Song H, Lin X, Kokot S. Electrochemical detection of benzo(a)pyrene and related DNA damage using DNA/hemin/nafion–graphene biosensor. Anal Chim Acta 2014; 821:34-40. [DOI: 10.1016/j.aca.2014.03.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/05/2014] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
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Lopes GR, Pinto DCGA, Silva AMS. Horseradish peroxidase (HRP) as a tool in green chemistry. RSC Adv 2014. [DOI: 10.1039/c4ra06094f] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The horseradish peroxidase (HRP) potential in organic synthesis.
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Affiliation(s)
- Guido R. Lopes
- Department of Chemistry & QOPNA
- University of Aveiro
- 3810-193 Aveiro, Portugal
| | | | - Artur M. S. Silva
- Department of Chemistry & QOPNA
- University of Aveiro
- 3810-193 Aveiro, Portugal
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Kumar D, Sastry GN, de Visser SP. Effect of the axial ligand on substrate sulfoxidation mediated by iron(IV)-oxo porphyrin cation radical oxidants. Chemistry 2011; 17:6196-205. [PMID: 21469227 DOI: 10.1002/chem.201003187] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Indexed: 11/09/2022]
Abstract
Cytochromes P450 catalyze a range of different oxygen-transfer processes including aliphatic and aromatic hydroxylation, epoxidation, and sulfoxidation reactions. Herein, we have investigated substrate sulfoxidation mediated by models of P450 enzymes as well as by biomimetic oxidants using density functional-theory methods and we have rationalized the sulfoxidation reaction barriers and rate constants. We carried out two sets of calculations: first, we calculated the sulfoxidation by an iron(IV)-oxo porphyrin cation radical oxidant [Fe(IV)=O(Por(+.))SH] that mimics the active site of cytochrome P450 enzymes with a range of different substrates, and second, we studied one substrate (dimethyl sulfide) with a selection of different iron(IV)-oxo porphyrin cation radical oxidants [Fe(IV)=O(Por(+.))L] with varying axial ligands L. The study presented herein shows that the barrier height for substrate sulfoxidation correlates linearly with the ionization potential of the substrate, thus reflecting the electron-transfer processes in the rate-determining step of the reaction. Furthermore, the axial ligand of the oxidant influences the pK(a) value of the iron(IV)-oxo group, and, as a consequence, the bond dissociation energy (BDE(OH) value correlates with the barrier height for the reverse sulfoxidation reaction. These studies have generalized substrate-sulfoxidation reactions and have shown how they fundamentally compare with substrate hydroxylation and epoxidation reactions.
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Affiliation(s)
- Devesh Kumar
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India.
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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: 155] [Impact Index Per Article: 11.1] [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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Wang Y, Li D, Han K, Shaik S. An Acyl Group Makes a Difference in the Reactivity Patterns of Cytochrome P450 Catalyzed N-Demethylation of Substituted N,N-Dimethylbenzamides—High Spin Selective Reactions. J Phys Chem B 2010; 114:2964-70. [DOI: 10.1021/jp9097974] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Wang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China, and The Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Dongmei Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China, and The Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China, and The Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Sason Shaik
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China, and The Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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de Visser SP, Nam W. The effect and influence of cis-ligands on the electronic and oxidizing properties of nonheme oxoiron biomimetics. A density functional study. J Phys Chem A 2009; 112:12887-95. [PMID: 18616332 DOI: 10.1021/jp8018556] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory studies on the nature of the cis effect and cis influence of ligands on oxoiron nonheme complexes have been performed. A detailed analysis of the electronic and oxidizing properties of [Fe(IV)O(TPA)L](+) with L = F(-), Cl(-), and Br(-) and TPA = tris-(2-pyridylmethyl)amine are presented and compared with [Fe(IV)O(TPA)NCCH(3)](2+). The calculations show that the electronic cis effect is determined by favorable orbital overlap between first-row elements with the metal, which are missing between the metal and second- and third-row elements. As a consequence, the metal 3d block is split into a one-below-two set of orbitals with L = Cl(-) and Br(-), and the HOMO/LUMO energy gap is widened with respect to the system with L = F(-). However, this larger HOMO/LUMO gap does not lead to large differences in electron affinities of the complexes. Moreover, a quantum mechanical analysis of the binding of the ligand shows that it is built up from a large electric field effect of the ligand on the oxoiron species and a much smaller quantum mechanical effect due to orbital overlap. These contributions are of similar strength for the three tested halogen cis ligands and result in similar reactivity patterns with substrates. The calculations show that [Fe(IV)O(TPA)L](+) with L = F(-), Cl(-), and Br(-) have closely lying triplet and quintet spin states, but only the quintet spin state is reactive with substrates. Therefore, the efficiency of the oxidant will be determined by the triplet-quintet spin state crossing of the reaction. The reaction of styrene with a doubly charged reactant, that is, [Fe(V)O(TPA)L](2+) with L = F(-), Cl(-), and Br(-) or [Fe(V)O(TPA)NCCH(3)](3+), leads to an initial electron transfer from the substrate to the metal followed by a highly exothermic epoxidation mechanism. These reactivity differences are mainly determined by the overall charge of the system rather than the nature of the cis ligand.
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Affiliation(s)
- Sam P de Visser
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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de Visser S, Tahsini L, Nam W. How Does the Axial Ligand of Cytochrome P450 Biomimetics Influence the Regioselectivity of Aliphatic versus Aromatic Hydroxylation? Chemistry 2009; 15:5577-87. [DOI: 10.1002/chem.200802234] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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de Visser SP, Tan LS. Is the bound substrate in nitric oxide synthase protonated or neutral and what is the active oxidant that performs substrate hydroxylation? J Am Chem Soc 2008; 130:12961-74. [PMID: 18774806 DOI: 10.1021/ja8010995] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present here results of a series of density functional theory (DFT) studies on enzyme active site models of nitric oxide synthase (NOS) and address the key steps in the catalytic cycle whereby the substrate (L-arginine) is hydroxylated to N(omega)-hydroxo-arginine. It has been proposed that the mechanism follows a cytochrome P450-type catalytic cycle; however, our calculations find an alternative low energy pathway whereby the bound L-arginine substrate has two important functions in the catalytic cycle, namely first as a proton donor and later as the substrate in the reaction mechanism. Thus, the DFT studies show that the oxo-iron active species (compound I) cannot abstract a proton and neither a hydrogen atom from protonated L-arginine due to the strength of the N-H bonds of the substrate. However, the hydroxylation of neutral arginine by compound I and its one electron reduced form (compound II) requires much lower barriers and is highly exothermic. Detailed analysis of proton transfer mechanisms shows that the basicity of the dioxo dianion and the hydroperoxo-iron (compound 0) intermediates in the catalytic cycle are larger than that of arginine, which makes it likely that protonated arginine donates one of the two protons needed during the first catalytic cycle of NOS. Therefore, DFT predicts that in NOS enzymes arginine binds to the active site in its protonated form, but is deprotonated during the oxygen activation process in the catalytic cycle by either the dioxo dianion species or compound 0. As a result of the low ionization potential of neutral arginine, the actual hydroxylation reaction starts with an initial electron transfer from the substrate to compound I to create compound II followed by a concerted hydrogen abstraction/radical rebound from the substrate. These studies indicate that compound II is the actual oxidant in NOS enzymes that performs the hydroxylation reaction of arginine, which is in sharp contrast with the cytochromes P450 where compound II was shown to be a sluggish oxidant. This is the first example of an enzyme where compound II is able to participate in the reaction mechanism. Moreover, arginine hydroxylation by NOS enzymes is catalyzed in a significantly different way from the cytochromes P450 although the active sites of the two enzyme classes are very similar in structure. Detailed studies of environmental effects on the reaction mechanism show that environmental perturbations as appear in the protein have little effect and do not change the energies of the reaction. Finally, a valence bond curve crossing model has been set up to explain the obtained reaction mechanisms for the hydrogen abstraction processes in P450 and NOS enzymes.
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Affiliation(s)
- Sam P de Visser
- Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom.
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