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Gong Z, Wang L, Xu Y, Xie D, Qi X, Nam W, Guo M. Enhanced Reactivities of Iron(IV)-Oxo Porphyrin Species in Oxidation Reactions Promoted by Intramolecular Hydrogen-Bonding. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310333. [PMID: 38477431 PMCID: PMC11109629 DOI: 10.1002/advs.202310333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/19/2024] [Indexed: 03/14/2024]
Abstract
High-valent iron-oxo species are one of the common intermediates in both biological and biomimetic catalytic oxidation reactions. Recently, hydrogen-bonding (H-bonding) has been proved to be critical in determining the selectivity and reactivity. However, few examples have been established for mechanistic insights into the H-bonding effect. Moreover, intramolecular H-bonding effect on both C-H activation and oxygen atom transfer (OAT) reactions in synthetic porphyrin model system has not been investigated yet. In this study, a series of heme-containing iron(IV)-oxo porphyrin species with or without intramolecular H-bonding are synthesized and characterized. Kinetic studies revealed that intramolecular H-bonding can significantly enhance the reactivity of iron(IV)-oxo species in OAT, C-H activation, and electron-transfer reactions. This unprecedented unified H-bonding effect is elucidated by theoretical calculations, which showed that intramolecular H-bonding interactions lower the energy of the anti-bonding orbital of iron(IV)-oxo porphyrin species, resulting in the enhanced reactivities in oxidation reactions irrespective of the reaction type. To the best of the knowledge, this is the first extensive investigation on the intramolecular H-bonding effect in heme system. The results show that H-bonding interactions have a unified effect with iron(IV)-oxo porphyrin species in all three investigated reactions.
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Affiliation(s)
- Zhe Gong
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Liwei Wang
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Yiran Xu
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Duanfeng Xie
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Xiaotian Qi
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Wonwoo Nam
- Department of Chemistry and Nano ScienceEwha Womans UniversitySeoul03760South Korea
| | - Mian Guo
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
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2
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Cao Y, Hay S, de Visser SP. An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by Nonheme Iron Lysine-4-hydroxylase Enzymes through Proton-Coupled Electron Transfer. J Am Chem Soc 2024; 146:11726-11739. [PMID: 38636166 PMCID: PMC11066847 DOI: 10.1021/jacs.3c14574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs in nature; however, little is known about the factors that govern the regio- and stereoselectivity of these enzymes. To understand how KDOs can selectively hydroxylate their substrate, we did a comprehensive computational study into the mechanisms and features of 4-lysine dioxygenase. In particular, we selected a snapshot from the MD simulation on KDO5 and created large QM cluster models (A, B, and C) containing 297, 312, and 407 atoms, respectively. The largest model predicts regioselectivity that matches experimental observation with rate-determining hydrogen atom abstraction from the C4-H position, followed by fast OH rebound to form 4-hydroxylysine products. The calculations show that in model C, the dipole moment is positioned along the C4-H bond of the substrate and, therefore, the electrostatic and electric field perturbations of the protein assist the enzyme in creating C4-H hydroxylation selectivity. Furthermore, an active site Tyr233 residue is identified that reacts through proton-coupled electron transfer akin to the axial Trp residue in cytochrome c peroxidase. Thus, upon formation of the iron(IV)-oxo species in the catalytic cycle, the Tyr233 phenol loses a proton to the nearby Asp179 residue, while at the same time, an electron is transferred to the iron to create an iron(III)-oxo active species. This charged tyrosyl residue directs the dipole moment along the C4-H bond of the substrate and guides the selectivity to the C4-hydroxylation of the substrate.
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Affiliation(s)
- Yuanxin Cao
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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3
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Hardy FG, Wong HPH, de Visser SP. Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin. Chemistry 2024; 30:e202400019. [PMID: 38323740 DOI: 10.1002/chem.202400019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.
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Affiliation(s)
- Fintan G Hardy
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Henrik P H Wong
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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4
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Satpathy JK, Yadav R, Bagha UK, Kumar D, Sastri CV, de Visser SP. Enhanced Reactivity through Equatorial Sulfur Coordination in Nonheme Iron(IV)-Oxo Complexes: Insights from Experiment and Theory. Inorg Chem 2024; 63:6752-6766. [PMID: 38551622 DOI: 10.1021/acs.inorgchem.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Sulfur ligation in metalloenzymes often gives the active site unique properties, whether it is the axial cysteinate ligand in the cytochrome P450s or the equatorial sulfur/thiol ligation in nonheme iron enzymes. To understand sulfur ligation to iron complexes and how it affects the structural, spectroscopic, and intrinsic properties of the active species and the catalysis of substrates, we pursued a systematic study and compared sulfur with amine-ligated iron(IV)-oxo complexes. We synthesized and characterized a biomimetic N4S-ligated iron(IV)-oxo complex and compared the obtained results with an analogous N5-ligated iron(IV)-oxo complex. Our work shows that the amine for sulfur replacement in the equatorial ligand framework leads to a rate enhancement for oxygen atom and hydrogen atom transfer reactions. Moreover, the sulfur-ligated iron(IV)-oxo complex reacts through a different reaction mechanism as compared to the N5-ligated iron(IV)-oxo complex, where the former reacts through hydride transfer with the latter reacting via radical pathways. We show that the reactivity differences are caused by a dramatic change in redox potential between the two complexes. Our studies highlight the importance of implementing a sulfur ligand into the equatorial ligand framework of nonheme iron(IV)-oxo complexes and how it affects the physicochemical properties of the oxidant and its reactivity.
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Affiliation(s)
- Jagnyesh K Satpathy
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Rolly Yadav
- 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
| | - Devesh Kumar
- Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow 226025, UP, India
| | - 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
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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5
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Ali HS, de Visser SP. Catalytic divergencies in the mechanism of L-arginine hydroxylating nonheme iron enzymes. Front Chem 2024; 12:1365494. [PMID: 38406558 PMCID: PMC10884159 DOI: 10.3389/fchem.2024.1365494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024] Open
Abstract
Many enzymes in nature utilize a free arginine (L-Arg) amino acid to initiate the biosynthesis of natural products. Examples include nitric oxide synthases, which generate NO from L-Arg for blood pressure control, and various arginine hydroxylases involved in antibiotic biosynthesis. Among the groups of arginine hydroxylases, several enzymes utilize a nonheme iron(II) active site and let L-Arg react with dioxygen and α-ketoglutarate to perform either C3-hydroxylation, C4-hydroxylation, C5-hydroxylation, or C4-C5-desaturation. How these seemingly similar enzymes can react with high specificity and selectivity to form different products remains unknown. Over the past few years, our groups have investigated the mechanisms of L-Arg-activating nonheme iron dioxygenases, including the viomycin biosynthesis enzyme VioC, the naphthyridinomycin biosynthesis enzyme NapI, and the streptothricin biosynthesis enzyme OrfP, using computational approaches and applied molecular dynamics, quantum mechanics on cluster models, and quantum mechanics/molecular mechanics (QM/MM) approaches. These studies not only highlight the differences in substrate and oxidant binding and positioning but also emphasize on electronic and electrostatic differences in the substrate-binding pockets of the enzymes. In particular, due to charge differences in the active site structures, there are changes in the local electric field and electric dipole moment orientations that either strengthen or weaken specific substrate C-H bonds. The local field effects, therefore, influence and guide reaction selectivity and specificity and give the enzymes their unique reactivity patterns. Computational work using either QM/MM or density functional theory (DFT) on cluster models can provide valuable insights into catalytic reaction mechanisms and produce accurate and reliable data that can be used to engineer proteins and synthetic catalysts to perform novel reaction pathways.
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Affiliation(s)
- Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry and the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, Manchester, United Kingdom
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6
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Zhu C, D'Agostino C, de Visser SP. Mechanism of CO 2 Reduction to Methanol with H 2 on an Iron(II)-scorpionate Catalyst. Chemistry 2023; 29:e202302832. [PMID: 37694535 DOI: 10.1002/chem.202302832] [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: 09/07/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/12/2023]
Abstract
CO2 utilization is an important process in the chemical industry with great environmental power. In this work we show how CO2 and H2 can be reacted to form methanol on an iron(II) center and highlight the bottlenecks for the reaction and what structural features of the catalyst are essential for efficient turnover. The calculations predict the reactions to proceed through three successive reaction cycles that start with heterolytic cleavage of H2 followed by sequential hydride and proton transfer processes. The H2 splitting process is an endergonic process and hence high pressures will be needed to overcome this step and trigger the hydrogenation reaction. Moreover, H2 cleavage into a hydride and proton requires a metal to bind hydride and a nearby source to bind the proton, such as an amide or pyrazolyl group, which the scorpionate ligand used here facilitates. As such the computations highlight the non-innocence of the ligand scaffold through proton shuttle from H2 to substrate as an important step in the reaction mechanism.
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Affiliation(s)
- Chengxu Zhu
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Carmine D'Agostino
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Dipartimento di Ingegneria Civile, Chimica, Ambientale e dei Materiali (DICAM), Alma Mater Studiorum, Università di Bologna, Via Terracini, 28, 40131, Bologna, Italy
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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7
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Ali HS, de Visser S, de Visser SP. Electrostatic perturbations in the substrate-binding pocket of taurine/α-ketoglutarate dioxygenase determine its selectivity. Chemistry 2021; 28:e202104167. [PMID: 34967481 PMCID: PMC9304159 DOI: 10.1002/chem.202104167] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Indexed: 11/17/2022]
Abstract
Taurine/α‐ketoglutarate dioxygenase is an important enzyme that takes part in the cysteine catabolism process in the human body and selectively hydroxylates taurine at the C1‐position. Recent computational studies showed that in the gas‐phase the C2−H bond of taurine is substantially weaker than the C1−H bond, yet no evidence exists of 2‐hydroxytaurine products. To this end, a detailed computational study on the selectivity patterns in TauD was performed. The calculations show that the second‐coordination sphere and the protonation states of residues play a major role in guiding the enzyme to the right selectivity. Specifically, a single proton on an active site histidine residue can change the regioselectivity of the reaction through its electrostatic perturbations in the active site and effectively changes the C1−H and C2−H bond strengths of taurine. This is further emphasized by many polar and hydrogen bonding interactions of the protein cage in TauD with the substrate and the oxidant that weaken the pro‐R C1−H bond and triggers a chemoselective reaction process. The large cluster models reproduce the experimental free energy of activation excellently.
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Affiliation(s)
- Hafiz Saqib Ali
- The University of Manchester, School of Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
| | - Sam P de Visser
- The University of Manchester, Department of Chemical Engineering, UNITED KINGDOM
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8
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Lin YT, Ali HS, de Visser S. Biodegradation of herbicides by a plant nonheme iron dioxygenase: mechanism and selectivity of substrate analogues. Chemistry 2021; 28:e202103982. [PMID: 34911156 DOI: 10.1002/chem.202103982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 11/11/2022]
Abstract
Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogs by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C 2 -hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R - and S -methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R -isomer give high rebound barriers.
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Affiliation(s)
- Yen-Ting Lin
- UoM: The University of Manchester, Chemical Engineering and Analytical Science, UNITED KINGDOM
| | - Hafiz S Ali
- UoM: The University of Manchester, Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
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9
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Yeh CCG, Pierides C, Jameson GNL, de Visser SP. Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study. Chemistry 2021; 27:13793-13806. [PMID: 34310770 DOI: 10.1002/chem.202101878] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 11/09/2022]
Abstract
Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.
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Affiliation(s)
- C-C George Yeh
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Christos Pierides
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Guy N L Jameson
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Vic, 3010, Australia
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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10
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Latifi R, Palluccio TD, Ye W, Minnick JL, Glinton KS, Rybak-Akimova EV, de Visser SP, Tahsini L. pH Changes That Induce an Axial Ligand Effect on Nonheme Iron(IV) Oxo Complexes with an Appended Aminopropyl Functionality. Inorg Chem 2021; 60:13821-13832. [PMID: 34291939 DOI: 10.1021/acs.inorgchem.1c01312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonheme iron enzymes often utilize a high-valent iron(IV) oxo species for the biosynthesis of natural products, but their high reactivity often precludes structural and functional studies of these complexes. In this work, a combined experimental and computational study is presented on a biomimetic nonheme iron(IV) oxo complex bearing an aminopyridine macrocyclic ligand and its reactivity toward olefin epoxidation upon changes in the identity and coordination ability of the axial ligand. Herein, we show a dramatic effect of the pH on the oxygen-atom-transfer (OAT) reaction with substrates. In particular, these changes have occurred because of protonation of the axial-bound pendant amine group, where its coordination to iron is replaced by a solvent molecule or anionic ligand. This axial ligand effect influences the catalysis, and we observe enhanced cyclooctene epoxidation yields and turnover numbers in the presence of the unbound protonated pendant amine group. Density functional theory studies were performed to support the experiments and highlight that replacement of the pendant amine with a neutral or anionic ligand dramatically lowers the rate-determining barriers of cyclooctene epoxidation. The computational work further establishes that the change in OAT is due to electrostatic interactions of the pendant amine cation that favorably affect the barrier heights.
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Affiliation(s)
- Reza Latifi
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Taryn D Palluccio
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Wanhua Ye
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jennifer L Minnick
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Kwame S Glinton
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Elena V Rybak-Akimova
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Laleh Tahsini
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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11
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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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12
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Ali HS, Henchman RH, Visser SP. Mechanism of Oxidative Ring‐Closure as Part of the Hygromycin Biosynthesis Step by a Nonheme Iron Dioxygenase. ChemCatChem 2021. [DOI: 10.1002/cctc.202100393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemistry The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Richard H. Henchman
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemistry The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Sam P. Visser
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemical Engineering and Analytical Science The University of Manchester Oxford Road Manchester M13 9PL UK
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13
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Ali HS, Henchman RH, de Visser SP. What Determines the Selectivity of Arginine Dihydroxylation by the Nonheme Iron Enzyme OrfP? Chemistry 2020; 27:1795-1809. [PMID: 32965733 DOI: 10.1002/chem.202004019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/22/2020] [Indexed: 12/13/2022]
Abstract
The nonheme iron enzyme OrfP reacts with l-Arg selectively to form the 3R,4R-dihydroxyarginine product, which in mammals can inhibit the nitric oxide synthase enzymes involved in blood pressure control. To understand the mechanisms of dioxygen activation of l-Arg by OrfP and how it enables two sequential oxidation cycles on the same substrate, we performed a density functional theory study on a large active site cluster model. We show that substrate binding and positioning in the active site guides a highly selective reaction through C3 -H hydrogen atom abstraction. This happens despite the fact that the C3 -H and C4 -H bond strengths of l-Arg are very similar. Electronic differences in the two hydrogen atom abstraction pathways drive the reaction with an initial C3 -H activation to a low-energy 5 σ-pathway, while substrate positioning destabilizes the C4 -H abstraction and sends it over the higher-lying 5 π-pathway. We show that substrate and monohydroxylated products are strongly bound in the substrate binding pocket and hence product release is difficult and consequently its lifetime will be long enough to trigger a second oxygenation cycle.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,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.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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14
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Ali HS, Henchman RH, de Visser SP. Lignin Biodegradation by a Cytochrome P450 Enzyme: A Computational Study into Syringol Activation by GcoA. Chemistry 2020; 26:13093-13102. [PMID: 32613677 PMCID: PMC7590115 DOI: 10.1002/chem.202002203] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 12/12/2022]
Abstract
A recently characterized cytochrome P450 isozyme GcoA activates lignin components through a selective O-demethylation or alternatively an acetal formation reaction. These are important reactions in biotechnology and, because lignin is readily available; it being the main component in plant cell walls. In this work we present a density functional theory study on a large active site model of GcoA to investigate syringol activation by an iron(IV)-oxo heme cation radical oxidant (Compound I) leading to hemiacetal and acetal products. Several substrate-binding positions were tested and full energy landscapes calculated. The study shows that substrate positioning determines the product distributions. Thus, with the phenol group pointing away from the heme, an O-demethylation is predicted, whereas an initial hydrogen-atom abstraction of the weak phenolic O-H group would trigger a pathway leading to ring-closure to form acetal products. Predictions on how to engineer P450 GcoA to get more selective product distributions are given.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
| | - Richard H. Henchman
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
| | - Sam P. de Visser
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of Chemical Engineering and Analytical ScienceThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
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15
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Yeh CG, Hörner G, Visser SP. Computational Study on O–O Bond Formation on a Mononuclear Non‐Heme Iron Center. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Chieh‐Chih George Yeh
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street M1 7DN Manchester UK
| | - Gerald Hörner
- Institut für Anorganische Chemie IV / NW I Universität Bayreuth Universitätsstraße 30 95440 Bayreuth Germany
| | - Sam P. Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street M1 7DN Manchester UK
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16
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Li H, Liu Y. Mechanistic Investigation of Isonitrile Formation Catalyzed by the Nonheme Iron/α-KG-Dependent Decarboxylase (ScoE). ACS Catal 2020. [DOI: 10.1021/acscatal.9b05411] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hong Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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17
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Mukherjee G, Reinhard FGC, Bagha UK, Sastri CV, de Visser SP. Sluggish reactivity by a nonheme iron(iv)-tosylimido complex as compared to its oxo analogue. Dalton Trans 2020; 49:5921-5931. [DOI: 10.1039/d0dt00018c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparative spectroscopic and computational study of reactivity between ferryl-tosylimido and ferryl-oxo complexes of two biomimetic model systems. The Fe(iv)-tosylimido complex was found to be sluggish in comparison to its fellow oxo counterpart.
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Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Fabián G. Cantú Reinhard
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | | | | | - Sam P. de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
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18
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Ghafoor S, Mansha A, de Visser SP. Selective Hydrogen Atom Abstraction from Dihydroflavonol by a Nonheme Iron Center Is the Key Step in the Enzymatic Flavonol Synthesis and Avoids Byproducts. J Am Chem Soc 2019; 141:20278-20292. [PMID: 31749356 DOI: 10.1021/jacs.9b10526] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The plant non-heme iron dioxygenase flavonol synthase performs a regioselective desaturation reaction as part of the biosynthesis of the signaling molecule flavonol that triggers the growing of leaves and flowers. These compounds also have health benefits for humans. Desaturation of aliphatic compounds generally proceeds through two consecutive hydrogen atom abstraction steps from two adjacent carbon atoms and in nature often is performed by a high-valent iron(IV)-oxo species. We show that the order of the hydrogen atom abstraction steps, however, is opposite of those expected from the C-H bond strengths in the substrate and determines the product distributions. As such, flavonol synthase follows a negative catalysis mechanism. Using density functional theory methods on large active-site model complexes, we investigated pathways for desaturation and hydroxylation by an iron(IV)-oxo active-site model. Contrary to thermochemical predictions, we find that the oxidant abstracts the hydrogen atom from the strong C2-H bond rather than the weaker C3-H bond of the substrate first. We analyze the origin of this unexpected selective hydrogen atom abstraction pathway and find that the alternative C3-H hydrogen atom abstraction would be followed by a low-energy and competitive substrate hydroxylation mechanism hence, should give considerable amount of byproducts. Our computational modeling studies show that substrate positioning in flavonol synthase is essential, as it guides the reactivity to a chemo- and regioselective substrate desaturation from the C2-H group, leading to desaturation products efficiently.
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Affiliation(s)
- Sidra Ghafoor
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , United Kingdom.,Department of Chemistry , Government College University Faisalabad , New Campus, Jhang Road , Faisalabad 38000 , Pakistan
| | - Asim Mansha
- Department of Chemistry , Government College University Faisalabad , New Campus, Jhang Road , Faisalabad 38000 , Pakistan
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , United Kingdom
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19
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Mubarak MQE, de Visser SP. Reactivity patterns of vanadium(iv/v)-oxo complexes with olefins in the presence of peroxides: a computational study. Dalton Trans 2019; 48:16899-16910. [PMID: 31670737 DOI: 10.1039/c9dt03048d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vanadium porphyrin complexes are naturally occurring substances found in crude oil and have been shown to have medicinal properties as well. Little is known on their activities with substrates; therefore, we decided to perform a detailed density functional theory study on the properties and reactivities of vanadium(iv)- and vanadium(v)-oxo complexes with a TPPCl8 or 2,3,7,8,12,13,17,18-octachloro-meso-tetraphenylporphyrinato ligand system. In particular, we investigated the reactivity of [VV(O)(TPPCl8)]+ and [VIV(O)(TPPCl8)] with cyclohexene in the presence of H2O2 or HCO4-. The work shows that vanadium(iv)-oxo and vanadium(v)-oxo are sluggish oxidants by themselves and react with olefins slowly. However, in the presence of hydrogen peroxide, these metal-oxo species can be transformed into a side-on vanadium-peroxo complex, which reacts with substrates more efficiently. Particularly with anionic axial ligands, the side-on vanadium-peroxo and vanadium-oxo complexes produced epoxides from cyclohexene via small barrier heights. In addition to olefin epoxidation, we investigated aliphatic hydroxylation mechanisms by the same oxidants and some oxidants show efficient and viable cyclohexene hydroxylation mechanisms. The work implies that vanadium-oxo and vanadium-peroxo complexes can react with double bonds through epoxidation, and under certain conditions also undergo hydroxylation, but the overall reactivity is highly dependent on the equatorial ligand, the local environment and the presence or absence of anionic axial ligands.
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Affiliation(s)
- M Qadri E Mubarak
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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20
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Singh W, Quinn D, Moody TS, Huang M. Reaction Mechanism of Histone Demethylation in αKG-dependent Non-Heme Iron Enzymes. J Phys Chem B 2019; 123:7801-7811. [PMID: 31469562 DOI: 10.1021/acs.jpcb.9b06064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Histone demethylases (KDMs) catalyze histone lysine demethylation, an important epigenetic process that controls gene expression in eukaryotes, and represent important cancer drug targets for cancer treatment. Demethylation of histone is comprised of sequential reaction steps including oxygen activation, decarboxylation, and demethylation. The initial oxygen binding and activation steps have been studied. However, the information on the complete catalytic reaction cycle is limited, which has impeded the structure-based design of inhibitors targeting KDMs. Here we report the mechanism of the complete reaction steps catalyzed by a representative nonheme iron αKG-dependent KDM, PHF8 using QM/MM approaches. The atomic-level understanding on the complete reaction mechanism of PHF8 would shed light on the structure-based design of selective inhibitors targeting KDMs to intervene in cancer epigenetics.
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Affiliation(s)
- Warispreet Singh
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom.,Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Derek Quinn
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Thomas S Moody
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom.,Arran Chemical Company Limited , Unit 1 Monksland Industrial Estate , Athlone , Co. Roscommon , Ireland
| | - Meilan Huang
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom
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21
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Davethu PA, de Visser SP. CO2 Reduction on an Iron-Porphyrin Center: A Computational Study. J Phys Chem A 2019; 123:6527-6535. [DOI: 10.1021/acs.jpca.9b05102] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Paul A. Davethu
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, the University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam P. de Visser
- The 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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22
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Pattanayak S, Cantú Reinhard FG, Rana A, Gupta SS, de Visser SP. The Equatorial Ligand Effect on the Properties and Reactivity of Iron(V) Oxo Intermediates. Chemistry 2019; 25:8092-8104. [DOI: 10.1002/chem.201900708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Santanu Pattanayak
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Atanu Rana
- Indian Association for the Cultivation of Sciences 2A Raja S. C. Mullick Road Kolkata 700032 India
| | - Sayam Sen Gupta
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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23
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Mukherjee G, Alili A, Barman P, Kumar D, Sastri CV, de Visser SP. Interplay Between Steric and Electronic Effects: A Joint Spectroscopy and Computational Study of Nonheme Iron(IV)-Oxo Complexes. Chemistry 2019; 25:5086-5098. [PMID: 30720909 DOI: 10.1002/chem.201806430] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Indexed: 01/05/2023]
Abstract
Iron is an essential element in nonheme enzymes that plays a crucial role in many vital oxidative transformations and metabolic reactions in the human body. Many of those reactions are regio- and stereospecific and it is believed that the selectivity is guided by second-coordination sphere effects in the protein. Here, results are shown of a few engineered biomimetic ligand frameworks based on the N4Py (N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) scaffold and the second-coordination sphere effects are studied. For the first time, selective substitutions in the ligand framework have been shown to tune the catalytic properties of the iron(IV)-oxo complexes by regulating the steric and electronic factors. In particular, a better positioning of the oxidant and substrate in the rate-determining transition state lowers the reaction barriers. Therefore, an optimum balance between steric and electronic factors mediates the ideal positioning of oxidant and substrate in the rate-determining transition state that affects the reactivity of high-valent reaction intermediates.
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Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Aligulu Alili
- The Manchester Institute of Biotechnology and School of Chemical, Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Prasenjit Barman
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Devesh Kumar
- Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, 226025, UP, India
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sam P de Visser
- The 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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24
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Timmins A, Fowler NJ, Warwicker J, Straganz GD, de Visser SP. Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? Front Chem 2018; 6:513. [PMID: 30425979 PMCID: PMC6218459 DOI: 10.3389/fchem.2018.00513] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases.
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Affiliation(s)
- Amy Timmins
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Nicholas J. Fowler
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Grit D. Straganz
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- Institute of Molecular Biosciences, Graz University, Graz, Austria
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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25
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Timmins A, Quesne MG, Borowski T, de Visser SP. Group Transfer to an Aliphatic Bond: A Biomimetic Study Inspired by Nonheme Iron Halogenases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01673] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Amy Timmins
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Matthew G. Quesne
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Sam P. de Visser
- The 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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Postils V, Saint-André M, Timmins A, Li XX, Wang Y, Luis JM, Solà M, de Visser SP. Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes. Int J Mol Sci 2018; 19:E1974. [PMID: 29986417 PMCID: PMC6073316 DOI: 10.3390/ijms19071974] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 02/03/2023] Open
Abstract
The cytochromes P450 are drug metabolizing enzymes in the body that typically react with substrates through a monoxygenation reaction. During the catalytic cycle two reduction and protonation steps generate a high-valent iron (IV)-oxo heme cation radical species called Compound I. However, with sufficient reduction equivalents present, the catalytic cycle should be able to continue to the reduced species of Compound I, called Compound II, rather than a reaction of Compound I with substrate. In particular, since electron transfer is usually on faster timescales than atom transfer, we considered this process feasible and decided to investigate the reaction computationally. In this work we present a computational study using density functional theory methods on active site model complexes alongside quantum mechanics/molecular mechanics calculations on full enzyme structures of cytochrome P450 enzymes. Specifically, we focus on the relative reactivity of Compound I and II with a model substrate for O⁻H bond activation. We show that generally the barrier heights for hydrogen atom abstraction are higher in energy for Compound II than Compound I for O⁻H bond activation. Nevertheless, for the activation of such bonds, Compound II should still be an active oxidant under enzymatic conditions. As such, our computational modelling predicts that under high-reduction environments the cytochromes P450 can react with substrates via Compound II but the rates will be much slower.
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Affiliation(s)
- Verònica Postils
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Maud Saint-André
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Amy Timmins
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Xiao-Xi Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Yong Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Josep M Luis
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
| | - Sam P de Visser
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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27
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Ibdah A, Alduwikat S. Thermochemistry and Bond Nature of Oxo and Thio Ligands in Rhenium(V) Catalysts and Rhenium(VII) Intermediates: Density Functional Calculations. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Abdellatif Ibdah
- Department of Chemistry Jordan University of Science and Technology Irbid Jordan
| | - Salwa Alduwikat
- Department of Chemistry Jordan University of Science and Technology Irbid Jordan
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28
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de Visser SP. Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases. CHEM REC 2018; 18:1501-1516. [PMID: 29878456 DOI: 10.1002/tcr.201800033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/05/2023]
Abstract
Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO2 . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase.
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Affiliation(s)
- 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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29
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Cantú Reinhard FG, Fornarini S, Crestoni ME, de Visser SP. Hydrogen Atom vs. Hydride Transfer in Cytochrome P450 Oxidations: A Combined Mass Spectrometry and Computational Study. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology; School of Chemical Engineering and Analytical Science; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco; Università di Roma “La Sapienza”; Piazzale Aldo Moro 5 00185 Roma Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco; Università di Roma “La Sapienza”; Piazzale Aldo Moro 5 00185 Roma Italy
| | - Sam P. de Visser
- Manchester Institute of Biotechnology; School of Chemical Engineering and Analytical Science; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
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30
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Gani TZH, Kulik HJ. Understanding and Breaking Scaling Relations in Single-Site Catalysis: Methane to Methanol Conversion by FeIV═O. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03597] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Terry Z. H. Gani
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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31
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Mukherjee G, Lee CWZ, Nag SS, Alili A, Cantú Reinhard FG, Kumar D, Sastri CV, de Visser SP. Dramatic rate-enhancement of oxygen atom transfer by an iron(iv)-oxo species by equatorial ligand field perturbations. Dalton Trans 2018; 47:14945-14957. [DOI: 10.1039/c8dt02142b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The reactivity and characterization of a novel iron(iv)-oxo species is reported that gives enhanced reactivity as a result of second-coordination sphere perturbations of the ligand system.
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Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Calvin W. Z. Lee
- The Manchester Institute of Biotechnology and the School of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | | | - Aligulu Alili
- The Manchester Institute of Biotechnology and the School of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | - Fabián G. Cantú Reinhard
- The Manchester Institute of Biotechnology and the School of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | - Devesh Kumar
- Department of Applied Physics
- School for Physical Sciences
- Babasaheb Bhimrao Ambedkar University
- Lucknow 226025
- India
| | | | - Sam P. de Visser
- The Manchester Institute of Biotechnology and the School of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
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Timmins A, de Visser SP. How Are Substrate Binding and Catalysis Affected by Mutating Glu 127 and Arg 161 in Prolyl-4-hydroxylase? A QM/MM and MD Study. Front Chem 2017; 5:94. [PMID: 29170737 PMCID: PMC5684110 DOI: 10.3389/fchem.2017.00094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/24/2017] [Indexed: 11/13/2022] Open
Abstract
Prolyl-4-hydroxylase is a vital enzyme for human physiology involved in the biosynthesis of 4-hydroxyproline, an essential component for collagen formation. The enzyme performs a unique stereo- and regioselective hydroxylation at the C4 position of proline despite the fact that the C5 hydrogen atoms should be thermodynamically easier to abstract. To gain insight into the mechanism and find the origin of this regioselectivity, we have done a quantum mechanics/molecular mechanics (QM/MM) study on wildtype and mutant structures. In a previous study (Timmins et al., 2017) we identified several active site residues critical for substrate binding and positioning. In particular, the Glu127 and Arg161 were shown to form multiple hydrogen bonding and ion-dipole interactions with substrate and could thereby affect the regio- and stereoselectivity of the reaction. In this work, we decided to test that hypothesis and report a QM/MM and molecular dynamics (MD) study on prolyl-4-hydroxylase and several active site mutants where Glu127 or Arg161 are mutated for Asp, Gln, or Lys. Thus, the R161D and R161Q mutants give very high barriers for hydrogen atom abstraction from any proline C-H bond and therefore will be inactive. The R161K mutant, by contrast, sees the regio- and stereoselectivity of the reaction change but still is expected to hydroxylate proline at room temperature. By contrast, the Glu127 mutants E127D and E127Q show possible changes in regioselectivity with the former being more probable to react compared to the latter.
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Affiliation(s)
| | - Sam P. de Visser
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
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Timmins A, Saint-André M, de Visser SP. Understanding How Prolyl-4-hydroxylase Structure Steers a Ferryl Oxidant toward Scission of a Strong C-H Bond. J Am Chem Soc 2017; 139:9855-9866. [PMID: 28657747 DOI: 10.1021/jacs.7b02839] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prolyl-4-hydroxylase (P4H) is a non-heme iron hydroxylase that regio- and stereospecifically hydroxylates proline residues in a peptide chain into R-4-hydroxyproline, which is essential for collagen cross-linking purposes in the human body. Surprisingly, in P4H, a strong aliphatic C-H bond is activated, while thermodynamically much weaker aliphatic C-H groups, that is, at the C3 and C5 positions, are untouched. Little is known on the origins of the high regio- and stereoselectivity of P4H and many non-heme and heme enzymes in general, and insight into this matter may be relevant to Biotechnology as well as Drug Development. The active site of the protein contains two aromatic residues (Tyr140 and Trp243) that we expected to be crucial for guiding the regioselectivity of the reaction. We performed a detailed quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) study on wild-type and mutant structures. The work shows that Trp243 is involved in key protein loop-loop interactions that affect the shape and size of the substrate binding pocket and its mutation has major long-range effects. By contrast, the Tyr140 residue is shown to guide the regio- and stereoselectivity by holding the substrate and ferryl oxidant in a specific orientation through hydrogen bonding and π-stacking interactions. Compelling evidence is found that the Tyr140 residue is involved in expelling the product from the binding pocket after the reaction is complete. It is shown that mutations where the hydrogen bonding network that involves the Tyr140 and Trp243 residues is disrupted lead to major changes in folding of the protein and the size and shape of the substrate binding pocket. Specifically, the Trp243 residue positions the amino acid side chains of Arg161 and Glu127 in specific orientations with substrate. As such, the P4H enzyme is a carefully designed protein with a subtle and rigid secondary structure that enables the binding of substrate, guides the regioselectivity, and expels product efficiently.
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Affiliation(s)
- Amy Timmins
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Maud Saint-André
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - 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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Li XX, Postils V, Sun W, Faponle AS, Solà M, Wang Y, Nam W, de Visser SP. Reactivity Patterns of (Protonated) Compound II and Compound I of Cytochrome P450: Which is the Better Oxidant? Chemistry 2017; 23:6406-6418. [PMID: 28295741 DOI: 10.1002/chem.201700363] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Indexed: 01/27/2023]
Abstract
The cytochromes P450 are versatile enzymes in human physiology that perform substrate hydroxylation reactions extremely efficiently. In this work, we present results of a computational study on the reactivity patterns of Compound I, Compound II, and protonated Compound II with model substrates, and we address the question of which of these compounds is the most effective oxidant? All calculations, regardless of the substrate, implicated that Compound I is the superior oxidant of the three. However, Compound II and protonated Compound II were found to react with free energies of activation that are only a few kcal mol-1 higher in energy than those obtained with Compound I. Therefore, Compound II and protonated Compound II should be able to react with aliphatic groups with moderate C-H bond strengths. We have analysed all results in detail and have given electronic, thermochemical, valence bond, and molecular orbital rationalizations on the reactivity differences and explained experimental product distributions. Overall, the findings implied that alternative oxidants could operate alongside Compound I in complex reaction mechanisms of enzymatic and synthetic iron porphyrinoid complexes.
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Affiliation(s)
- Xiao-Xi Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou, 730000, P. R. China
| | - Verònica Postils
- Institut de Química Computacional i Catàlisi (IQCC) and Department de Química, Universitat de Girona, Campus de Montilivi, C/ Maria Aurèlia Capmany 6, 17003, Girona, Catalonia, Spain.,The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Wei Sun
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou, 730000, P. R. China
| | - Abayomi S Faponle
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Department de Química, Universitat de Girona, Campus de Montilivi, C/ Maria Aurèlia Capmany 6, 17003, Girona, Catalonia, Spain
| | - Yong Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou, 730000, P. R. China
| | - Wonwoo Nam
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou, 730000, P. R. China.,Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Korea
| | - Sam P de Visser
- The 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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Cantú Reinhard FG, de Visser SP. Oxygen Atom Transfer Using an Iron(IV)-Oxo Embedded in a Tetracyclic N-Heterocyclic Carbene System: How Does the Reactivity Compare to Cytochrome P450 Compound I? Chemistry 2017; 23:2935-2944. [PMID: 28052598 DOI: 10.1002/chem.201605505] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Indexed: 12/21/2022]
Abstract
N-Heterocyclic carbenes (NHC) are commonly featured as ligands in transition metal catalysis. Recently, a cyclic system containing four NHC groups with a central iron atom was synthesized and its iron(IV)-oxo species, [FeIV (O)(cNHC4 )]2+ , was characterized. This tetracyclic NHC ligand system may give the iron(IV)-oxo species unique catalytic properties as compared to traditional non-heme and heme iron ligand systems. Therefore, we performed a computational study on the structure and reactivity of the [FeIV (O)(cNHC4 )]2+ complex in substrate hydroxylation and epoxidation reactions. The reactivity patterns are compared with cytochrome P450 Compound I and non-heme iron(IV)-oxo models and it is shown that the [FeIV (O)(cNHC4 )]2+ system is an effective oxidant with oxidative power analogous to P450 Compound I. Unfortunately, in polar solvents, a solvent molecule will bind to the sixth ligand position and decrease the catalytic activity of the oxidant. A molecular orbital and valence bond analysis provides insight into the origin of the reactivity differences and makes predictions of how to further exploit these systems in chemical catalysis.
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Affiliation(s)
- Fabián G Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - 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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36
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Khan FST, Pandey AK, Rath SP. Remarkable Anion-Dependent Spin-State Switching in Diiron(III) μ-Hydroxo Bisporphyrins: What Role do Counterions Play? Chemistry 2016; 22:16124-16137. [PMID: 27682429 DOI: 10.1002/chem.201603163] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 12/20/2022]
Abstract
Addition of 2,4,6-trinitrophenol (HTNP) to an ethene-bridged diiron(III) μ-oxo bisporphyrin (1) in CH2 Cl2 initially leads to the formation of diiron(III) μ-hydroxo bisporphyrin (2⋅TNP) with a phenolate counterion that, after further addition of HTNP or dissolution in a nonpolar solvent, converts to a diiron(III) complex with axial phenoxide coordination (3⋅(TNP)2 ). The progress of the reaction from μ-oxo to μ-hydroxo to axially ligated complex has been monitored in solution by using 1 H NMR spectroscopy because their signals appear in three different and distinct spectral regions. The X-ray structure of 2⋅TNP revealed that the nearly planar TNP counterion fits perfectly within the bisporphyrin cavity to form a strong hydrogen bond with the μ-hydroxo group, which thus stabilizes the two equivalent iron centers. In contrast, such counterions as I5 , I3 , BF4 , SbF6 , and PF6 are found to be tightly associated with one of the porphyrin rings and, therefore, stabilize two different spin states of iron in one molecule. A spectroscopic investigation of 2⋅TNP has revealed the presence of two equivalent iron centers with a high-spin state (S=5/2) in the solid state that converts to intermediate spin (S=3/2) in solution. An extensive computational study by using a range of DFT methods was performed on 2⋅TNP and 2+ , and clearly supports the experimentally observed spin flip triggered by hydrogen-bonding interactions. The counterion is shown to perturb the spin-state ordering through, for example, hydrogen-bonding interactions, switched positions between counterion and axial ligand, ion-pair interactions, and charge polarization. The present investigation thus provides a clear rationalization of the unusual counterion-specific spin states observed in the μ-hydroxo bisporphyrins that have so far remained the most outstanding issue.
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Affiliation(s)
| | - Anjani Kumar Pandey
- 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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37
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Morozov AN, Chatfield DC. How the Proximal Pocket May Influence the Enantiospecificities of Chloroperoxidase-Catalyzed Epoxidations of Olefins. Int J Mol Sci 2016; 17:E1297. [PMID: 27517911 PMCID: PMC5000694 DOI: 10.3390/ijms17081297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/28/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
Chloroperoxidase-catalyzed enantiospecific epoxidations of olefins are of significant biotechnological interest. Typical enantiomeric excesses are in the range of 66%-97% and translate into free energy differences on the order of 1 kcal/mol. These differences are generally attributed to the effect of the distal pocket. In this paper, we show that the influence of the proximal pocket on the electron transfer mechanism in the rate-limiting event may be just as significant for a quantitatively accurate account of the experimentally-measured enantiospecificities.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
| | - David C Chatfield
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
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38
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Mechanistic study on rhenium(V) dimer catalysis for the oxygen atom transfer from pyridine oxide to Ph3E (E = P, As): experiment and computational study. REACTION KINETICS MECHANISMS AND CATALYSIS 2016. [DOI: 10.1007/s11144-016-1012-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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39
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Nagaraju P, Ohta T, Liu JG, Ogura T, Naruta Y. The secondary coordination sphere controlled reactivity of a ferric-superoxo heme: unexpected conversion to a ferric hydroperoxo intermediate by reaction with a high-spin ferrous heme. Chem Commun (Camb) 2016; 52:7213-6. [PMID: 27105471 DOI: 10.1039/c6cc02162j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A bio-inspired heme complex involving both a proton donor and an axial imidazole ligand reduces the activation energy for the formation of a ferric hydroperoxo intermediate. A high-spin ferrous heme is shown to be capable of reducing its superoxy species to generate a ferric hydroperoxo intermediate for the first time.
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Affiliation(s)
- Perumandla Nagaraju
- Institute of Science and Technology Research, Chubu University, Kasugai, Aichi 487-8501, Japan.
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40
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Faponle AS, Quesne MG, de Visser SP. Origin of the Regioselective Fatty-Acid Hydroxylation versus Decarboxylation by a Cytochrome P450 Peroxygenase: What Drives the Reaction to Biofuel Production? Chemistry 2016; 22:5478-83. [PMID: 26918676 DOI: 10.1002/chem.201600739] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 11/11/2022]
Abstract
The cytochromes P450 are heme-based mono-oxygenases or peroxygenases involved in vital reaction processes for human health. A recently described P450 per-oxygenase, OleTJE , converts long-chain fatty acids to terminal olefins and as such may have biotechnological relevance in biodiesel production. However, the reaction produces significant amounts of α- and β-hydroxylation by-products, and their origin are poorly understood. Herein, we elucidate through a QM/MM study on the bifurcation pathways how the three possible products are generated and show how the enzyme can be further engineered for optimum desaturase activity. The studies showed that the polarity and the solvent accessibility of the substrate in the binding pocket destabilize the OH-rebound pathways and kinetically enable a thermodynamically otherwise unfavorable decarboxylation reaction. The origins of the bifurcation pathways are analyzed with valence-bond models that highlight the differences in reaction mechanism.
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Affiliation(s)
- 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
| | - 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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41
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Mittra K, Sengupta K, Singha A, Bandyopadhyay S, Chatterjee S, Rana A, Samanta S, Dey A. Second sphere control of spin state: Differential tuning of axial ligand bonds in ferric porphyrin complexes by hydrogen bonding. J Inorg Biochem 2016; 155:82-91. [DOI: 10.1016/j.jinorgbio.2015.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/02/2015] [Accepted: 11/10/2015] [Indexed: 11/16/2022]
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Quesne MG, Borowski T, de Visser SP. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs. Chemistry 2015; 22:2562-81. [PMID: 26696271 DOI: 10.1002/chem.201503802] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/08/2022]
Abstract
Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
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Affiliation(s)
- Matthew G Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland. .,Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - 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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43
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Ibdah A. Computational study on chain pathways for oxygen atom transfer catalyzed by a methyl(dithiolate) thiorhenium(V) compound. REACTION KINETICS MECHANISMS AND CATALYSIS 2015. [DOI: 10.1007/s11144-015-0896-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:113-51. [PMID: 26415843 DOI: 10.1016/bs.apcsb.2015.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis of haloalkanes. Currently, however, industry utilizes few applications of biological haloperoxidases and halogenases, but efforts are being worked on to understand their catalytic mechanism, so that their catalytic function can be upscaled. In this review, we summarize experimental and computational studies on the catalytic mechanism of a range of haloperoxidases and halogenases with structurally very different catalytic features and cofactors. This chapter gives an overview of heme-dependent haloperoxidases, nonheme vanadium-dependent haloperoxidases, and flavin adenine dinucleotide-dependent haloperoxidases. In addition, we discuss the S-adenosyl-l-methionine fluoridase and nonheme iron/α-ketoglutarate-dependent halogenases. In particular, computational efforts have been applied extensively for several of these haloperoxidases and halogenases and have given insight into the essential structural features that enable these enzymes to perform the unusual halogen atom transfer to substrates.
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45
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İşci Ü, Faponle AS, Afanasiev P, Albrieux F, Briois V, Ahsen V, Dumoulin F, Sorokin AB, de Visser SP. Site-selective formation of an iron(iv)-oxo species at the more electron-rich iron atom of heteroleptic μ-nitrido diiron phthalocyanines. Chem Sci 2015; 6:5063-5075. [PMID: 30155008 PMCID: PMC6088558 DOI: 10.1039/c5sc01811k] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/16/2015] [Indexed: 11/21/2022] Open
Abstract
A combination of MS and computation on μ-nitrido bridged diiron complexes reveals H2O2 binding to the complex and generates an oxidant capable of oxidizing methane.
Iron(iv)–oxo species have been identified as the active intermediates in key enzymatic processes, and their catalytic properties are strongly affected by the equatorial and axial ligands bound to the metal, but details of these effects are still unresolved. In our aim to create better and more efficient oxidants of H-atom abstraction reactions, we have investigated a unique heteroleptic diiron phthalocyanine complex. We propose a novel intramolecular approach to determine the structural features that govern the catalytic activity of iron(iv)–oxo sites. Heteroleptic μ-nitrido diiron phthalocyanine complexes having an unsubstituted phthalocyanine (Pc1) and a phthalocyanine ligand substituted with electron-withdrawing alkylsulfonyl groups (PcSO2R) were prepared and characterized. A reaction with terminal oxidants gives two isomeric iron(iv)–oxo and iron(iii)–hydroperoxo species with abundances dependent on the equatorial ligand. Cryospray ionization mass spectrometry (CSI-MS) characterized both hydroperoxo and diiron oxo species in the presence of H2O2. When m-CPBA was used as the oxidant, the formation of diiron oxo species (PcSO2R)FeNFe(Pc1)
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O was also evidenced. Sufficient amounts of these transient species were trapped in the quadrupole region of the mass-spectrometer and underwent a CID-MS/MS fragmentation. Analyses of fragmentation patterns indicated a preferential formation of hydroperoxo and oxo moieties at more electron-rich iron sites of both heteroleptic μ-nitrido complexes. DFT calculations show that both isomers are close in energy. However, the analysis of the iron(iii)–hydroperoxo bond strength reveals major differences for the (Pc1)FeN(PcSO2R)FeIIIOOH system as compared to (PcSO2R)FeN(Pc1)FeIIIOOH system, and, hence binding of a terminal oxidant will be preferentially on more electron-rich sides. Subsequent kinetics studies showed that these oxidants are able to even oxidize methane to formic acid efficiently.
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Affiliation(s)
- Ümit İşci
- Gebze Technical University , Department of Chemistry , P.O. Box 141, Gebze , 41400 Kocaeli , Turkey .
| | - 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 .
| | - Pavel Afanasiev
- Institut de Recherches sur la Catalyse et l'Environnement de Lyon (IRCELYON) , UMR 5256 , CNRS-Université Lyon 1 , 2, av. A. Einstein , 69626 Villeurbanne Cedex , France .
| | - Florian Albrieux
- Centre Commun de Spectrométrie de Masse UMR 5246 , CNRS-Université Claude Bernard Lyon 1 , Université de Lyon , Bâtiment Curien , 43, bd du 11 Novembre , 69622 Villeurbanne Cedex , France
| | - Valérie Briois
- Synchrotron Soleil , L'orme des merisiers, St-Aubin , 91192 Gif-sur-Yvette , France
| | - Vefa Ahsen
- Gebze Technical University , Department of Chemistry , P.O. Box 141, Gebze , 41400 Kocaeli , Turkey .
| | - Fabienne Dumoulin
- Gebze Technical University , Department of Chemistry , P.O. Box 141, Gebze , 41400 Kocaeli , Turkey .
| | - Alexander B Sorokin
- Institut de Recherches sur la Catalyse et l'Environnement de Lyon (IRCELYON) , UMR 5256 , CNRS-Université Lyon 1 , 2, av. A. Einstein , 69626 Villeurbanne Cedex , France .
| | - 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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46
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Karamzadeh B, Singh D, Nam W, Kumar D, de Visser SP. Properties and reactivities of nonheme iron(IV)-oxo versus iron(V)-oxo: long-range electron transfer versus hydrogen atom abstraction. Phys Chem Chem Phys 2015; 16:22611-22. [PMID: 25231726 DOI: 10.1039/c4cp03053b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent work of Nam and co-workers [J. Yoon, S. A. Wilson, Y. K. Jang, M. S. Seo, K. Nehru, B. Hedman, K. O. Hodgson, E. Bill, E. I. Solomon and W. Nam, Angew. Chem., Int. Ed., 2009, 48, 1257] on a biomimetic iron complex implicated a mixture of iron(IV)-oxo and iron(V)-oxo intermediates but the latter could not be spectroscopically characterized, hence its involvement was postulated. To gain insight into the relative activity of these iron(IV)-oxo versus iron(V)-oxo intermediates, we have performed an extensive density functional theory (DFT) study on the chemical properties of the chemical system of Nam et al., namely [Fe(O)(BQEN)(NCCH3)](2+/3+) with BQEN = N,N'-dimethyl-N,N'-bis(8-quinolyl)ethane-1,2-diamine and their reactivity in hydrogen atom abstraction from ethylbenzene. We show that the perceived iron(V)-oxo species actually is an iron(IV)-oxo ligand cation radical, similar to cytochrome P450 compound I. Moreover, this intermediate has an extremely large electron affinity and therefore can abstract electrons from substrates readily. In our particular system, this means that prior to the hydrogen atom abstraction, an electron is abstracted to form an iron(IV)-oxo species, which subsequently abstracts a hydrogen atom from the substrate. Thus, our calculations show for the first time how some nonheme iron complexes react by long-range electron transfer and others directly via hydrogen atom abstraction. We have rationalized our results with detailed thermochemical cycles that explain the observed reactivity patterns.
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Affiliation(s)
- Baharan Karamzadeh
- 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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47
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Sainna MA, Singh D, Kumar D, de Visser SP. A Trimetal Carbene with Reactivity Reminiscent of Fischer–Tropsch Catalysis. Organometallics 2015. [DOI: 10.1021/acs.organomet.5b00305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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
| | - Devendra Singh
- Department
of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow (U. P.) 226 025, India
| | - Devesh Kumar
- Department
of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow (U. P.) 226 025, India
| | - 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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48
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Sahoo D, Quesne MG, de Visser SP, Rath SP. Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 127:4878-4882. [PMID: 26109743 PMCID: PMC4470476 DOI: 10.1002/ange.201411399] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 11/16/2022]
Abstract
A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure of a five-coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=5/2) and intermediate spin (S=3/2) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen-bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations.
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Affiliation(s)
- Dipankar Sahoo
- Department of Chemistry, Indian Institute of Technology KanpurKanpur-208016 (India)
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK)
| | - Matthew G Quesne
- Department of Chemistry, Indian Institute of Technology KanpurKanpur-208016 (India)
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK)
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49
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Sallmann M, Kumar S, Chernev P, Nehrkorn J, Schnegg A, Kumar D, Dau H, Limberg C, de Visser SP. Structure and Mechanism Leading to Formation of the Cysteine Sulfinate Product Complex of a Biomimetic Cysteine Dioxygenase Model. Chemistry 2015; 21:7470-9. [DOI: 10.1002/chem.201500644] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Indexed: 01/10/2023]
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50
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Boaz NC, Bell SR, Groves JT. Ferryl protonation in oxoiron(IV) porphyrins and its role in oxygen transfer. J Am Chem Soc 2015; 137:2875-85. [PMID: 25651467 PMCID: PMC4363944 DOI: 10.1021/ja508759t] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ferryl porphyrins, P-Fe(IV)═O, are central reactive intermediates in the catalytic cycles of numerous heme proteins and a variety of model systems. There has been considerable interest in elucidating factors, such as terminal oxo basicity, that may control ferryl reactivity. Here, the sulfonated, water-soluble ferryl porphyrin complexes tetramesitylporphyrin, oxoFe(IV)TMPS (FeTMPS-II), its 2,6-dichlorophenyl analogue, oxoFe(IV)TDClPS (FeTDClPS-II), and two other analogues are shown to be protonated under turnover conditions to produce the corresponding bis-aqua-iron(III) porphyrin cation radicals. The results reveal a novel internal electromeric equilibrium, P-Fe(IV)═O ⇆ P(+)-Fe(III)(OH2)2. Reversible pKa values in the range of 4-6.3 have been measured for this process by pH-jump, UV-vis spectroscopy. Ferryl protonation has important ramifications for C-H bond cleavage reactions mediated by oxoiron(IV) porphyrin cation radicals in protic media. Both solvent O-H and substrate C-H deuterium kinetic isotope effects are observed for these reactions, indicating that hydrocarbon oxidation by these oxoiron(IV) porphyrin cation radicals occurs via a solvent proton-coupled hydrogen atom transfer from the substrate that has not been previously described. The effective FeO-H bond dissociation energies for FeTMPS-II and FeTDClPS-II were estimated from similar kinetic reactivities of the corresponding oxoFe(IV)TMPS(+) and oxoFe(IV)TDClPS(+) species to be ∼92-94 kcal/mol. Similar values were calculated from the two-proton P(+)-Fe(III)(OH2)2 pKa(obs) and the porphyrin oxidation potentials, despite a 230 mV range for the iron porphyrins examined. Thus, the iron porphyrin with the lower ring oxidation potential has a compensating higher basicity of the ferryl oxygen. The solvent-derived proton adds significantly to the driving force for C-H bond scission.
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Affiliation(s)
- Nicholas C. Boaz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Seth R. Bell
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - John T. Groves
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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