1
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Csizi KS, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
Rieske dioxygenases belong to the non‐heme iron family of oxygenases and catalyze important cis‐dihydroxylation as well as O‐/N‐dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non‐heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O2
activation. Here, we studied the role of the substrate in the key elementary reaction leading to O2
activation from a theoretical perspective by systematically considering (i) the 6‐coordinate to 5‐coordinate conversion of the non‐heme FeII upon abstraction of a water ligand, (ii) binding of O2
, and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin‐state‐dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non‐heme FeII
center through thermoneutral H2O reorientation and exothermic O2
binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe‐oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6‐coordinate non‐heme FeII
sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non‐heme FeII
in agreement with a strategy that avoids unproductive O2
activation.
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Affiliation(s)
- Katja-Sophia Csizi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Lina Eckert
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Christoph Brunken
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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2
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Cao X, Song H, Li XX, Zhao Y, Qiao Q, Wang Y. Which is the real oxidant in the competitive ligand self-hydroxylation and substrate oxidation, a biomimetic iron(II)-hydroperoxo species or an oxo-iron(IV)-hydroxy one? Dalton Trans 2022; 51:7571-7580. [DOI: 10.1039/d2dt00797e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nonheme iron(II)-hydroperoxo species (FeII-(η2-OOH)) 1 and the concomitant oxo-iron(IV)-hydroxyl one 2 are proposed as the key intermediates of a large class of 2-oxoglutarate dependent dioxygenases (e.g., isopenicillin N synthase). Extensive...
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3
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Blanquart C, Linot C, Cartron PF, Tomaselli D, Mai A, Bertrand P. Epigenetic Metalloenzymes. Curr Med Chem 2019; 26:2748-2785. [PMID: 29984644 DOI: 10.2174/0929867325666180706105903] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Abstract
Epigenetics controls the expression of genes and is responsible for cellular phenotypes. The fundamental basis of these mechanisms involves in part the post-translational modifications (PTMs) of DNA and proteins, in particular, the nuclear histones. DNA can be methylated or demethylated on cytosine. Histones are marked by several modifications including acetylation and/or methylation, and of particular importance are the covalent modifications of lysine. There exists a balance between addition and removal of these PTMs, leading to three groups of enzymes involved in these processes: the writers adding marks, the erasers removing them, and the readers able to detect these marks and participating in the recruitment of transcription factors. The stimulation or the repression in the expression of genes is thus the result of a subtle equilibrium between all the possibilities coming from the combinations of these PTMs. Indeed, these mechanisms can be deregulated and then participate in the appearance, development and maintenance of various human diseases, including cancers, neurological and metabolic disorders. Some of the key players in epigenetics are metalloenzymes, belonging mostly to the group of erasers: the zinc-dependent histone deacetylases (HDACs), the iron-dependent lysine demethylases of the Jumonji family (JMJ or KDM) and for DNA the iron-dependent ten-eleven-translocation enzymes (TET) responsible for the oxidation of methylcytosine prior to the demethylation of DNA. This review presents these metalloenzymes, their importance in human disease and their inhibitors.
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Affiliation(s)
- Christophe Blanquart
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Camille Linot
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.,Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Philippe Bertrand
- Réseau Epigénétique du Cancéropôle Grand Ouest, France.,Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B27, 86073, Poitiers cedex 09, France
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4
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Zhao Y, Hu JC, Cui JT, Xu LL, Ma JB. Fe 2 O + Cation Mediated Propane Oxidation by Dioxygen in the Gas Phase. Chemistry 2018; 24:5920-5926. [PMID: 29424048 DOI: 10.1002/chem.201705997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 11/11/2022]
Abstract
The mass-selected Fe2 O+ cation mediated propane oxidation by O2 was investigated by mass spectrometry and density functional theory calculations. In the reaction of Fe2 O+ with C3 H8 , H2 was liberated by C-H bond activation to give Fe2 OC3 H6+ . Interestingly, when a mixture of C3 H8 /O2 was introduced into the reactor, an intense signal that corresponded to the Fe2 O2+ cation was present; the experiments indicated that O2 was activated in its reaction with Fe2 O(C3 H6 )+ to give Fe2 O2+ and C3 H6 O (acetone or propanal). A Langmuir-Hinshelwood-like mechanism was adopted in the propane oxidation reaction by O2 on gas-phase Fe2 O+ cations. In comparison with the absence of Fe2 O2+ in the reaction of Fe2 O+ with O2 , the ligand effect of C3 H6 on Fe2 OC3 H6+ is important in the oxygen activation reaction. The theoretical results are consistent with the experimental observations. The propane oxidation by O2 in the presence of Fe2 O+ might be applied as a model for alkane and O2 activations over iron oxide catalysts, and the mechanisms and kinetic data are useful for understanding corresponding heterogeneous reactions.
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Affiliation(s)
- Yue Zhao
- The Institute for Chemical Physics, Key Laboratory of Cluster Science, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 102488, Beijing, P. R. China
| | - Ji-Chuang Hu
- The Institute for Chemical Physics, Key Laboratory of Cluster Science, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 102488, Beijing, P. R. China
| | - Jia-Tong Cui
- The Institute for Chemical Physics, Key Laboratory of Cluster Science, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 102488, Beijing, P. R. China
| | - Lin-Lin Xu
- The Institute for Chemical Physics, Key Laboratory of Cluster Science, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 102488, Beijing, P. R. China
| | - Jia-Bi Ma
- The Institute for Chemical Physics, Key Laboratory of Cluster Science, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 102488, Beijing, P. R. China
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5
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Pandey B, Jaccob M, Rajaraman G. Mechanistic insights into intramolecular ortho-amination/hydroxylation by nonheme Fe IV[double bond, length as m-dash]NTs/Fe IV[double bond, length as m-dash]O species: the σ vs. the π channels. Chem Commun (Camb) 2018; 53:3193-3196. [PMID: 28220156 DOI: 10.1039/c6cc08761b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Comparative oxidative abilities of nonheme FeIV[double bond, length as m-dash]NTs and FeIV[double bond, length as m-dash]O species using DFT has been explored. Our calculations reveal that the FeIV[double bond, length as m-dash]NTs is found to be a stronger oxidant in two electron transfer reactions and react exclusively via π channels while the FeIV[double bond, length as m-dash]O species is found to be a stronger oxidant when the σ-pathway is activated such as in HAT reactions.
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Affiliation(s)
- Bhawana Pandey
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India.
| | - Madhavan Jaccob
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India. and Department of Chemistry, Loyola College, Chennai 600 034, Tamil Nadu, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India.
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6
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Ji JN, Chen SL. Asymmetric abstraction of two chemically-equivalent methylene hydrogens: significant enantioselectivity of endoperoxide presented by fumitremorgin B endoperoxidase. Phys Chem Chem Phys 2018; 20:26500-26505. [DOI: 10.1039/c8cp05637d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unique enantioselectivity for an R-chiral endoperoxy ring in verruculogen biosynthesis originates from asymmetric abstraction of two chemically-equivalent methylene hydrogens.
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Affiliation(s)
- Jian-Nan Ji
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
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7
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Synthesis, structural, catecholase, tyrosinase and DFT studies of pyrazoloquinoxaline derivatives. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Gasselhuber B, Graf MMH, Jakopitsch C, Zamocky M, Nicolussi A, Furtmüller PG, Oostenbrink C, Carpena X, Obinger C. Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase. Biochemistry 2016; 55:3528-41. [PMID: 27293030 PMCID: PMC4928148 DOI: 10.1021/acs.biochem.6b00436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Catalase-peroxidases
(KatGs) are unique bifunctional heme peroxidases
with an additional posttranslationally formed redox-active Met-Tyr-Trp
cofactor that is essential for catalase activity. On the basis of
studies of bacterial KatGs, controversial mechanisms of hydrogen peroxide
oxidation were proposed. The recent discovery of eukaryotic KatGs
with differing pH optima of catalase activity now allows us to scrutinize
those postulated reaction mechanisms. In our study, secreted KatG
from the fungus Magnaporthe grisea (MagKatG2) was used to analyze the role of a remote KatG-typical mobile
arginine that was shown to interact with the Met-Tyr-Trp adduct in
a pH-dependent manner in bacterial KatGs. Here we present crystal
structures of MagKatG2 at pH 3.0, 5.5, and 7.0 and
investigate the mobility of Arg461 by molecular dynamics simulation.
Data suggest that at pH ≥4.5 Arg461 mostly interacts with the
deprotonated adduct Tyr. Elimination of Arg461 by mutation to Ala
slightly increases the thermal stability but does not alter the active
site architecture or the kinetics of cyanide binding. However, the
variant Arg461Ala lost the wild-type-typical optimum of catalase activity
at pH 5.25 (kcat = 6450 s–1) but exhibits a broad plateau between pH 4.5 and 7.5 (kcat = 270 s–1 at pH 5.5). Moreover,
significant differences in the kinetics of interconversion of redox
intermediates of wild-type and mutant protein mixed with either peroxyacetic
acid or hydrogen peroxide are observed. These findings together with
published data from bacterial KatGs allow us to propose a role of
Arg461 in the H2O2 oxidation reaction of KatG.
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Affiliation(s)
- Bernhard Gasselhuber
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Michael M H Graf
- Department of Material Sciences and Process Engineering, Institute for Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Christa Jakopitsch
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Marcel Zamocky
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria.,Institute of Molecular Biology, Slovak Academy of Sciences , Dubravska cesta 21, SK-84551 Bratislava, Slovakia
| | - Andrea Nicolussi
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute for Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Xavi Carpena
- Institut de Biologia Molecular (IBMB-CSIC) , Parc Cientific de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
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9
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Wang L, Hu L, Zhang H, Chen H, Deng L. Three-Coordinate Iron(IV) Bisimido Complexes with Aminocarbene Ligation: Synthesis, Structure, and Reactivity. J Am Chem Soc 2015; 137:14196-207. [DOI: 10.1021/jacs.5b09579] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lei Wang
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of
Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Lianrui Hu
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hezhong Zhang
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of
Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Liang Deng
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of
Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
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10
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Kruft BI, Magliozzo RS, Jarzęcki AA. Density Functional Theory Insights into the Role of the Methionine–Tyrosine–Tryptophan Adduct Radical in the KatG Catalase Reaction: O2 Release from the Oxyheme Intermediate. J Phys Chem A 2015; 119:6850-66. [DOI: 10.1021/jp511358p] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bonnie I. Kruft
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Andrzej A. Jarzęcki
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
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11
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Sun X, Sun X, Geng C, Zhao H, Li J. Benchmark study on methanol C-H and O-H bond activation by bare [Fe(IV)O](2+). J Phys Chem A 2014; 118:7146-58. [PMID: 25091205 DOI: 10.1021/jp505662x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a high-level computational study on methanol C-H and O-H bond cleavages by bare [Fe(IV)O](2+), as well as benchmarks of various density functional theory (DFT) methods. We considered direct and concerted hydrogen transfer (DHT and CHT) pathways, respectively. The potential energy surfaces were constructed at the CCSD(T)/def2-TZVPP//B3LYP/def2-TZVP level of theory. Mechanistically, (1) the C-H bond cleavage is dominant and the O-H activation only plays minor role on the PESs; (2) the DHT from methyl should be the most practical channel; and (3) electronic structure analysis demonstrates the proton and electron transfer coupling behavior along the reaction coordinates. The solvent effect is evident and plays distinct roles in regulating the two bond activations in different mechanisms during the catalysis. The effect of optimizing the geometries using different density functionals was also studied, showing that it is not meaningful to discuss which DFT method could give the accurate prediction of the geometries, especially for transition structures. Furthermore, the gold-standard CCSD(T) method was used to benchmark 19 different density functionals with different Hartree-Fock exchange fractions. The results revealed that (i) the structural factor plays a minor role in the single point energy (SPE) calculations; (ii) reaction energy prediction is quite challenging for DFT methods; (iii) the mean absolute deviations (MADs) reflect the problematic description of the DFs when dealing with metal oxidation state change, giving a strong correlation on the HF exchange in the DFs. Knowledge from this study should be of great value for computational chemistry, especially for the de novo design of transition metal catalysts.
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Affiliation(s)
- Xianhui Sun
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, P.R. China
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12
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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13
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Lundberg M, Borowski T. Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.03.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Miłaczewska A, Broclawik E, Borowski T. On the Catalytic Mechanism of (S)-2-Hydroxypropylphosphonic Acid Epoxidase (HppE): A Hybrid DFT Study. Chemistry 2012; 19:771-81. [DOI: 10.1002/chem.201202825] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Indexed: 11/10/2022]
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15
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Wójcik A, Broclawik E, Siegbahn PEM, Borowski T. Mechanism of benzylic hydroxylation by 4-hydroxymandelate synthase. A computational study. Biochemistry 2012; 51:9570-80. [PMID: 23126679 DOI: 10.1021/bi3010957] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxymandelate synthase (HMS) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) are highly related enzymes using the same substrates but catalyzing hydroxylation reactions yielding different products. The first steps of the HMS and HPPD catalytic reactions are believed to proceed in the same way and lead to an Fe(IV)═O-hydroxyphenylacetate (HPA) intermediate. Further down the catalytic cycles, HMS uses Fe(IV)═O to perform hydroxylation of the benzylic carbon, whereas in HPPD, the reactive oxoferryl intermediate attacks the aromatic ring of HPA. This study focuses on this part of the HMS catalytic cycle that starts from the oxoferryl intermediate and aims to identify interactions within the active site that are responsible for enzyme specificity. To this end, a HMS-Fe(IV)═O-HPA complex was modeled with molecular dynamics simulations. On the basis of the molecular dynamics-equilibrated structure, an active site model suitable for quantum chemical investigations was constructed and used for density functional theory (B3LYP) calculations of the mechanism of the native reaction of HMS, i.e., benzylic hydroxylation, and the alternative electrophilic attack on the ring, which is a step of the HPPD catalytic cycle. The most important result of this study is the finding that the conformation of the Ser201 side chain in the second coordination shell has a key role in directing the reaction of Fe(IV)═O into either the HMS or the HPPD channel.
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Affiliation(s)
- Anna Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
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16
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Chen H, Cho KB, Lai W, Nam W, Shaik S. Dioxygen Activation by a Non-Heme Iron(II) Complex: Theoretical Study toward Understanding Ferric–Superoxo Complexes. J Chem Theory Comput 2012; 8:915-26. [DOI: 10.1021/ct300015y] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hui Chen
- Beijing National Laboratory for Molecular
Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Kyung-Bin Cho
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Wenzhen Lai
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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17
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Gopakumar G, Belanzoni P, Baerends EJ. Hydroxylation catalysis by mononuclear and dinuclear iron oxo catalysts: a methane monooxygenase model system versus the Fenton reagent Fe(IV)O(H2O)5(2+). Inorg Chem 2011; 51:63-75. [PMID: 22221279 DOI: 10.1021/ic200754w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylation of aliphatic C-H bonds is a chemically and biologically important reaction, which is catalyzed by the oxidoiron group FeO(2+) in both mononuclear (heme and nonheme) and dinuclear complexes. We investigate the similarities and dissimilarities of the action of the FeO(2+) group in these two configurations, using the Fenton-type reagent [FeO(2+) in a water solution, FeO(H(2)O)(5)(2+)] and a model system for the methane monooxygenase (MMO) enzyme as representatives. The high-valent iron oxo intermediate MMOH(Q) (compound Q) is regarded as the active species in methane oxidation. We show that the electronic structure of compound Q can be understood as a dimer of two Fe(IV)O(2+) units. This implies that the insights from the past years in the oxidative action of this ubiquitous moiety in oxidation catalysis can be applied immediately to MMOH(Q). Electronically the dinuclear system is not fundamentally different from the mononuclear system. However, there is an important difference of MMOH(Q) from FeO(H(2)O)(5)(2+): the largest contribution to the transition state (TS) barrier in the case of MMOH(Q) is not the activation strain (which is in this case the energy for the C-H bond lengthening to the TS value), but it is the steric hindrance of the incoming CH(4) with the ligands representing glutamate residues. The importance of the steric factor in the dinuclear system suggests that it may be exploited, through variation in the ligand framework, to build a synthetic oxidation catalyst with the desired selectivity for the methane substrate.
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Affiliation(s)
- G Gopakumar
- Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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18
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Chen H, Lai W, Yao J, Shaik S. Perferryl FeV–Oxo Nonheme Complexes: Do They Have High-Spin or Low-Spin Ground States? J Chem Theory Comput 2011; 7:3049-53. [DOI: 10.1021/ct200614g] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui Chen
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wenzhen Lai
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Jiannian Yao
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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19
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Ghosh A. Ab initio wavefunctions in bioinorganic chemistry: More than a succès d'estime? J Biol Inorg Chem 2011; 16:819-20. [PMID: 21755384 PMCID: PMC3139065 DOI: 10.1007/s00775-011-0816-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 06/30/2011] [Indexed: 12/02/2022]
Affiliation(s)
- Abhik Ghosh
- Department of Chemistry and Center for Theoretical and Computational Chemistry, University of Tromsø, Norway.
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20
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Chen H, Lai W, Shaik S. Multireference and multiconfiguration ab initio methods in heme-related systems: what have we learned so far? J Phys Chem B 2011; 115:1727-42. [PMID: 21344948 DOI: 10.1021/jp110016u] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This work reviews the recent applications of ab initio multireference/multiconfiguration (MR/MC) electronic structure methods to heme-related systems, involving tetra-, penta-, and hexa-coordinate species, as well as the high-valent iron-oxo species. The current accuracy of these methods in the various systems is discussed, with special attention to potential sources of systematic errors. Thus, the review summarizes and tries to rationalize the key elements of MR/MC calculations, namely, the choice of the employed active space, especially the so-called double-shell effect that has already been recognized to be important in transition-metal-containing systems, and the impact of these elements on the spin-state energetics of heme species, as well as on the bonding mechanism of small molecules to the heme. It is shown that expansion of the MC wave function into one based on localized orbitals provides a compact and insightful view on some otherwise complex electronic structures. The effects of protein environment on the MR/MC results are summarized for the few available quantum mechanical/molecular mechanical (QM/MM) studies. Comparisons with corresponding DFT results are also made wherever available. Potential future directions are proposed.
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Affiliation(s)
- Hui Chen
- Institute of Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel.
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21
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Bernasconi L, Belanzoni P, Baerends EJ. An abiotic analogue of the diiron(iv)oxo “diamond core” of soluble methane monooxygenase generated by direct activation of O2 in aqueous Fe(ii)/EDTA solutions: thermodynamics and electronic structure. Phys Chem Chem Phys 2011; 13:15272-82. [DOI: 10.1039/c1cp21244c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Gryff-Keller A, Szczeciński P, Kraska-Dziadecka A. NMR and DFT calculation study on structures of 2-[2-nitro-4-(trifluoromethyl)benzoyl]cyclohexane-1,3-dione (NTBC) and its two metabolites isolated from urine of patients suffering from tyrosinemia type I. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Retegan M, Milet A, Jamet H. Comparative Theoretical Studies of the Phosphomonoester Hydrolysis Mechanism by Purple Acid Phosphatases. J Phys Chem A 2010; 114:7110-6. [DOI: 10.1021/jp100478f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Retegan
- DCM, Equipe Chimie Théorique, UMR CNRS 5250, ICMG, FR CNRS, Université J. Fourier, BP. 53, 38041 Grenoble Cedex, France
| | - A. Milet
- DCM, Equipe Chimie Théorique, UMR CNRS 5250, ICMG, FR CNRS, Université J. Fourier, BP. 53, 38041 Grenoble Cedex, France
| | - H. Jamet
- DCM, Equipe Chimie Théorique, UMR CNRS 5250, ICMG, FR CNRS, Université J. Fourier, BP. 53, 38041 Grenoble Cedex, France
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24
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Olsson E, Martinez A, Teigen K, Jensen VR. Water Dissociation and Dioxygen Binding in Phenylalanine Hydroxylase. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.200900489] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Belanzoni P, Bernasconi L, Baerends EJ. O2 Activation in a Dinuclear Fe(II)/EDTA Complex: Spin Surface Crossing As a Route to Highly Reactive Fe(IV)oxo Species. J Phys Chem A 2009; 113:11926-37. [DOI: 10.1021/jp9033672] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paola Belanzoni
- Department of Chemistry, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Theoretical Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0QX United Kingdom, and Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, South-Korea
| | - Leonardo Bernasconi
- Department of Chemistry, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Theoretical Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0QX United Kingdom, and Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, South-Korea
| | - Evert Jan Baerends
- Department of Chemistry, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Theoretical Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0QX United Kingdom, and Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, South-Korea
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26
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Michel C, Baerends EJ. What Singles out the FeO2+ Moiety? A Density-Functional Theory Study of the Methane-to-Methanol Reaction Catalyzed by the First Row Transition-Metal Oxide Dications MO(H2O)p2+, M = V−Cu. Inorg Chem 2009; 48:3628-38. [DOI: 10.1021/ic802095m] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carine Michel
- Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Evert Jan Baerends
- Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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27
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Bernasconi L, Baerends EJ. Generation of Ferryl Species through Dioxygen Activation in Iron/EDTA Systems: A Computational Study. Inorg Chem 2008; 48:527-40. [DOI: 10.1021/ic800998n] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Leonardo Bernasconi
- Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Evert Jan Baerends
- Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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28
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Lundberg M, Kawatsu T, Vreven T, Frisch MJ, Morokuma K. Transition States in a Protein Environment − ONIOM QM:MM Modeling of Isopenicillin N Synthesis. J Chem Theory Comput 2008; 5:222-34. [DOI: 10.1021/ct800457g] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcus Lundberg
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Tsutomu Kawatsu
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Thom Vreven
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Michael J. Frisch
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
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29
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Ye S, Tuttle T, Bill E, Simkhovich L, Gross Z, Thiel W, Neese F. The Electronic Structure of Iron Corroles: A Combined Experimental and Quantum Chemical Study. Chemistry 2008; 14:10839-51. [DOI: 10.1002/chem.200801265] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Borowski T, Blomberg MRA, Siegbahn PEM. Reaction mechanism of apocarotenoid oxygenase (ACO): a DFT study. Chemistry 2008; 14:2264-76. [PMID: 18181127 DOI: 10.1002/chem.200701344] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The mechanism of the oxidative cleavage catalyzed by apocarotenoid oxygenase (ACO) was studied by using a quantum chemical (DFT: B3 LYP) method. Based on the available crystal structure, relatively large models of the unusual active-site region, in which a ferrous ion is coordinated by four histidines and no negatively charged ligand, were selected and used in the computational investigation of the reaction mechanism. The results suggest that binding of dioxygen to the ferrous ion in the active site promotes one-electron oxidation of carotenoid leading to a substrate radical cation and a Fe-bound superoxide radical. Recombination of the two radicals, which can be realized in at least two different ways, yields a reactive peroxo species that subsequently evolves into either a dioxetane or an epoxide intermediate. The former easily decays into the final aldehyde products, whereas the oxidation of the epoxide to the proper products of the reaction requires involvement of a water molecule. The calculated activation barriers favor the dioxetane mechanism, yet the mechanism involving the epoxide intermediate cannot be ruled out.
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Affiliation(s)
- Tomasz Borowski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences ul. Niezapominajek 8, 30-239 Cracow, Poland.
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31
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Bernasconi L, Baerends EJ. The EDTA Complex of Oxidoiron(IV) as Realisation of an Optimal Ligand Environment for High Activity of FeO2+. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200701135] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Louwerse MJ, Vassilev P, Baerends EJ. Oxidation of Methanol by FeO2+ in Water: DFT Calculations in the Gas Phase and Ab Initio MD Simulations in Water Solution. J Phys Chem A 2008; 112:1000-12. [DOI: 10.1021/jp075914n] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manuel J. Louwerse
- Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Peter Vassilev
- Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Evert Jan Baerends
- Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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33
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Lundberg M, Siegbahn PEM, Morokuma K. The Mechanism for Isopenicillin N Synthase from Density-Functional Modeling Highlights the Similarities with Other Enzymes in the 2-His-1-carboxylate Family. Biochemistry 2007; 47:1031-42. [DOI: 10.1021/bi701577q] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcus Lundberg
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan, and Department of Physics, Quantum Chemistry Group, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Per E. M. Siegbahn
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan, and Department of Physics, Quantum Chemistry Group, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan, and Department of Physics, Quantum Chemistry Group, Stockholm University, SE-106 91 Stockholm, Sweden
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34
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Vidossich P, Alfonso-Prieto M, Carpena X, Loewen PC, Fita I, Rovira C. Versatility of the Electronic Structure of Compound I in Catalase-Peroxidases. J Am Chem Soc 2007; 129:13436-46. [DOI: 10.1021/ja072245i] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Pietro Vidossich
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Xavi Carpena
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Peter C. Loewen
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Ignacio Fita
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Carme Rovira
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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35
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Lundberg M, Morokuma K. Protein Environment Facilitates O2 Binding in Non-Heme Iron Enzyme. An Insight from ONIOM Calculations on Isopenicillin N Synthase (IPNS). J Phys Chem B 2007; 111:9380-9. [PMID: 17637052 DOI: 10.1021/jp071878g] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Binding of dioxygen to a non-heme enzyme has been modeled using the ONIOM combined quantum mechanical/molecular mechanical (QM/MM) method. For the present system, isopenicillin N synthase (IPNS), binding of dioxygen is stabilized by 8-10 kcal/mol for a QM:MM (B3LYP:Amber) protein model compared to a quantum mechanical model of the active site only. In the protein system, the free energy change of O2 binding is close to zero. Two major factors consistently stabilize O2 binding. The first effect, evaluated at the QM level, originates from a change in coordination geometry of the iron center. The active-site model artificially favors the deoxy state (O2 not bound) because it allows too-large rearrangements of the five-coordinate iron site. This error is corrected when the protein is included. The corresponding effect on binding energies is 3-6 kcal/mol, depending on the coordination mode of O2 (side-on or end-on). The second major factor that stabilizes O2 binding is van der Waals interactions between dioxygen and the surrounding enzyme. These interactions, 3-4 kcal/mol at the MM level, are neglected in models that include only the active site. Polarization of the active site by surrounding amino acids does not have a significant effect on the binding energy in the present system.
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Affiliation(s)
- Marcus Lundberg
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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36
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Bernasconi L, Louwerse MJ, Baerends EJ. The Role of Equatorial and Axial Ligands in Promoting the Activity of Non-Heme Oxidoiron(IV) Catalysts in Alkane Hydroxylation. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200601238] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Alfonso-Prieto M, Borovik A, Carpena X, Murshudov G, Melik-Adamyan W, Fita I, Rovira C, Loewen PC. The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations. J Am Chem Soc 2007; 129:4193-205. [PMID: 17358056 DOI: 10.1021/ja063660y] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A for HPC, suggestive of a Fe-O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por*+-FeIV=O, Por*+-FeIV=O...HisH+, Por*+-FeIV-OH+ and Por-FeIV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por*+-FeIV=O, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like "fluctuating" radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por*+-FeIV=O species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-FeIV-OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Centre especial de Recerca en Química Teorica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
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38
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Louwerse MJ, Jan Baerends E. Oxidative properties of FeO2+: electronic structure and solvation effects. Phys Chem Chem Phys 2007; 9:156-66. [PMID: 17164898 DOI: 10.1039/b613182d] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An electronic structure analysis is provided of the action of solvated FeO(2+), [FeO(H(2)O)(5)](2+), as a hydroxylation catalyst. It is emphasized that the oxo end of FeO(2+) does not form hydrogen bonds (as electron donor and H-bond acceptor) with H-bond donors nor with aliphatic C-H bonds, but it activates C-H bonds as an electron acceptor. It is extremely electrophilic, to the extent that it can activate even such poor electron donors as aliphatic C-H bonds, the C-H bond orbital acting as electron donor in a charge transfer type of interaction. Lower lying O-H bonding orbitals are less easily activated. The primary electron accepting orbital in a water environment is the 3sigma*alpha orbital, an antibonding combination of Fe-3d(z(2)) and O-2p(z), which is very low-lying relative to the pi*alpha compared with, for example, the sigma* orbital in O(2) relative to its pi*. This is ascribed to relatively small Fe-3d(z(2)) with O-2p(z) overlap, due to the nodal structure of the 3d(z(2)).The H-abstraction barrier is very low in the gas phase, but it is considerably enhanced in water solvent. This is shown to be due to strong screening effects of the dielectric medium, leading to relative destabilization of the levels of the charged [FeO(H(2)O)(5)](2+) species compared to those of the neutral substrate molecules, making it a less effective electron acceptor. The solvent directly affects the orbital interactions responsible for the catalytic reaction.
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Affiliation(s)
- Manuel J Louwerse
- Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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39
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Ghosh A. Transition metal spin state energetics and noninnocent systems: challenges for DFT in the bioinorganic arena. J Biol Inorg Chem 2006; 11:712-24. [PMID: 16841211 DOI: 10.1007/s00775-006-0135-4] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 06/14/2006] [Indexed: 11/25/2022]
Abstract
Although density functional theory (DFT) provides a generally good description of transition metal systems, we have identified several cases, involving Fe(III) porphyrins and related systems, where common functionals fail to correctly describe the energetics of the different low-lying spin states. The question of metal- versus ligand-centered oxidation in high-valent transition metal complexes is also a challenging one for DFT calculations, as I have tried to illustrate with examples from among porphyrin, corrole, biliverdine, and NO complexes. In a number of cases, I have compared results obtained with different exchange-correlation functionals; in addition, I have added a discussion on the relative performance of pure versus hybrid functionals. Finally, I have offered some thoughts on the role that traditional wavefunction-based ab initio methods, now essentially absent from the bioinorganic arena, might play in the future.
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Affiliation(s)
- Abhik Ghosh
- Department of Chemistry, University of Tromsø, 9037 Tromsø, Norway.
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