1
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Li J, Tan W, Li X, Zhang P, Jin P, Fan J, Li K. Silver Ion-Facilitated Singular Poulos-Kraut Mechanism of O-O Heterolysis to Enhance the Light Activation of H 2O 2 over Peroxidase-Mimicking Photonanozymes. Anal Chem 2023; 95:12435-12442. [PMID: 37566745 DOI: 10.1021/acs.analchem.3c02095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
The Poulos-Kraut heterolytic O-O cleavage mechanism is essential for natural peroxidases to activate H2O2. Current existing peroxidase-mimicking nanozymes, including photonanozymes (PNZs), however, are generally believed to prefer the Fenton-type mechanism of O-O homolysis, which produces •OH radicals. Here, Ag+ ions are introduced into TiO2 PNZs to boost the hot hole-driven O-O heterolysis for the expedited H2O2 activation in the peroxidase-like photonanozymatic reaction while inhibiting the Fenton-type O-O homolysis. The Ag+-facilitated Poulos-Kraut heterolytic O-O cleavage mechanism for H2O2 activation is explicated in terms of the speedy capture and exhaustion of photogenerated electrons by Ag+ and the dissociation of the peroxo-oxygen bridge in Ti-O-OH promoted by accumulated hot holes. Moreover, the enhanced photonanozymatic activity of TiO2 PNZs enables the construction of a rapid colorimetric sensing platform for Ag+ determination. This work provides valuable insights into the mechanism of H2O2 activation and exemplifies a novel photoregulation strategy for controlling reaction pathways in nanozymes.
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Affiliation(s)
- Jinzhao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Wenlong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Xu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Pei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Peng Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Jinsong Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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2
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Hong YH, Lee YM, Nam W, Fukuzumi S. Reaction Intermediates in Artificial Photosynthesis with Molecular Catalysts. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Young Hyun Hong
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul03760, Korea
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul03760, Korea
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3
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Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
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Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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4
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Tian G, Hao G, Chen X, Liu Y. Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET: Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC. Inorg Chem 2021; 60:13539-13549. [PMID: 34382397 DOI: 10.1021/acs.inorgchem.1c01864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peroxide-dependent coproheme decarboxylase ChdC from Geobacillus stearothermophilus catalyzes two key steps in the synthesis of heme b, i.e., two sequential oxidative decarboxylations of coproporphyrinogen III (coproheme III) at propionate groups P2 and P4. In the binding site of coproheme III, P2 and P4 are anchored by different residues (Tyr144, Arg217, and Ser222 for P2 and Tyr113, Lys148, and Trp156 for P4); however, strong experimental evidence supports that the generated Tyr144 radical acts as an unique intermediary for hydrogen atom transfer (HAT) from both reactive propionates. So far, the reaction details are still unclear. Herein, we carried out quantum mechanics/molecular mechanics calculations to explore the decarboxylation mechanism of coproheme III. In our calculations, the coproheme Cpd I, Fe(IV) = O coupled to a porphyrin radical cation (por•+) with four propionate groups, was used as a reactant model. Our calculations reveal that Tyr144 is directly involved in the decarboxylation of propionate group P2. First, the proton-coupled electron transfer (PCET) occurs from Tyr144 to P2, generating a Tyr144 radical, which then abstracts a hydrogen atom from the Cβ of P2. The β-H extraction was calculated to be the rate-limiting step of decarboxylation. It is the porphyrin radical cation (por•+) that makes the PCET from Tyr144 to P2 to be quite easy to initiate the decarboxylation. Finally, the electron transfers from the Cβ• through the porphyrin to the iron center, leading to the decarboxylation of P2. Importantly, the decarboxylation of P4 mediated by Lys148 was calculated to be very difficult, which suggests that after the P2 decarboxylation, the generated harderoheme III intermediate should rebind or rotate in the active site so that the propionate P4 occupies the binding site of P2, and Tyr144 again mediates the decarboxylation of P4. Thus, our calculations support the fact that Tyr144 is responsible for the decarboxylation of both P2 and P4.
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Affiliation(s)
- Ge Tian
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China.,School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Gangping Hao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China
| | - Xiaohua Chen
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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5
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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6
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Nesterova OV, Nesterov DS, Vranovičová B, Boča R, Pombeiro AJL. Heterometallic Cu IIFe III and Cu IIMn III alkoxo-bridged complexes revealing a rare hexanuclear M 6(μ-X) 7(μ 3-X) 2 molecular core. Dalton Trans 2018; 47:10941-10952. [PMID: 30019733 DOI: 10.1039/c8dt02290a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The novel hexanuclear complexes [Cu4Fe2(OH)(Piv)4(tBuDea)4Cl]·0.5CH3CN (1) and [Cu4Mn2(OH)(Piv)4(tBuDea)4Cl] (2) were prepared through one-pot self-assembly reactions of copper powder and iron(ii) or manganese(ii) chloride with N-tert-butyldiethanolamine (H2tBuDea) and pivalic acid (HPiv) in acetonitrile. Crystallographic studies revealed the uncommon molecular core type M6(μ-X)7(μ3-X)2 in 1 and 2, which can be viewed as a combination of two trimetallic M3(μ-X)2(μ3-X) fragments joined by three bridging atoms. The analysis and classification of the hexanuclear complexes having a M3(μ-X)2(μ3-X) moiety as a core forming fragment using data from the Cambridge Structural Database (CSD) were performed. Variable-temperature (1.8-300 K) magnetic susceptibility measurements of 1 showed a decrease of the effective magnetic moment value at low temperature, indicative of antiferromagnetic coupling between the magnetic centres (JFe-Cu/hc = -6.9 cm-1, JCu-Cu/hc = -4.1 cm-1, JFe-Fe/hc = -24.2 cm-1). Complex 1 acts as a catalyst in the reaction of mild oxidation of cyclohexane with H2O2, showing the yields of products, cyclohexanol and cyclohexanone, up to 17% using pyrazinecarboxylic acid as a promoter. In the oxidation of cis-1,2-dimethylcyclohexane with m-chloroperoxybenzoic acid (m-CPBA), 70% of retention of stereoconfiguration was observed for tertiary alcohols. Compound 1 also catalyses the amidation of cyclohexane with benzamide. In all three catalytic reactions the by-products were investigated in detail and discussed.
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Affiliation(s)
- Oksana V Nesterova
- Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisboa, Portugal.
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7
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Pang J, Zhao Y, Liu HL, Wang K. A single nanoparticle-based real-time monitoring of biocatalytic progress and detection of hydrogen peroxide. Talanta 2018; 185:581-585. [PMID: 29759244 DOI: 10.1016/j.talanta.2018.04.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/02/2018] [Accepted: 04/07/2018] [Indexed: 11/19/2022]
Abstract
This paper reported a new method to observe the catalytic progress of the natural horseradish peroxidase (HRP) in-situ on single gold nanoparticles (GNPs) by the combination of dark field imaging and plasmonic resonance scattering spectra. The produced single HRP-GNP exhibited localized catalytic property toward H2O2-Diaminobenzidine (DAB), which could be used to detect the concentration of H2O2 in micro/nanospace. The linear range for H2O2 sensing was from 0.01 μM to 5 μM with a detection limit of 10 nM. The new design strategy could be applied for a broader bioanalysis situation by substituting the HRP with other specified biocatalyst.
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Affiliation(s)
- Jie Pang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, PR China.
| | - Yun Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, PR China
| | - Hai-Ling Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, PR China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, PR China.
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8
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Abderrahim M, Arribas SM, Condezo-Hoyos L. A novel pyrogallol red-based assay to assess catalase activity: Optimization by response surface methodology. Talanta 2017; 166:349-356. [DOI: 10.1016/j.talanta.2017.01.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/19/2017] [Accepted: 01/24/2017] [Indexed: 01/15/2023]
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9
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10
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Khan S, Yang KR, Ertem MZ, Batista VS, Brudvig GW. Mechanism of Manganese-Catalyzed Oxygen Evolution from Experimental and Theoretical Analyses of 18O Kinetic Isotope Effects. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01976] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sahr Khan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ke R. Yang
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Mehmed Z. Ertem
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
- Chemistry
Department, Brookhaven National Laboratory, Building 555A, Upton, New
York 11973, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gary W. Brudvig
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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11
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Chatterjee S, Sengupta K, Samanta S, Das PK, Dey A. Concerted Proton–Electron Transfer in Electrocatalytic O2 Reduction by Iron Porphyrin Complexes: Axial Ligands Tuning H/D Isotope Effect. Inorg Chem 2015; 54:2383-92. [DOI: 10.1021/ic5029959] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sudipta Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Kushal Sengupta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Subhra Samanta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Pradip Kumar Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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12
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Simpson N, Adamczyk K, Hithell G, Shaw DJ, Greetham GM, Towrie M, Parker AW, Hunt NT. The effect on structural and solvent water molecules of substrate binding to ferric horseradish peroxidase. Faraday Discuss 2015; 177:163-79. [DOI: 10.1039/c4fd00161c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast, multi-dimensional infrared spectroscopy, in the form of 2D-IR and pump–probe measurements, has been employed to investigate the effect of substrate binding on the structural dynamics of the horseradish peroxidase (HRP) enzyme. Using nitric oxide bound to the ferric haem of HRP as a sensitive probe of local dynamics, we report measurements of the frequency fluctuations (spectral diffusion) and vibrational lifetime of the NO stretching mode with benzohydroxamic acid (BHA) located in the substrate-binding position at the periphery of the haem pocket, in both D2O and H2O solvents. The results reveal that, with BHA bound to the enzyme, the local structural dynamics are insensitive to H/D exchange. These results are in stark contrast to those found in studies of the substrate-free enzyme, which demonstrated that the local chemical and dynamic environment of the haem ligand is influenced by water molecules. In light of the large changes in solvent accessibility caused by substrate binding, we discuss the potential for varying roles for the solvent in the haem pocket of HRP at different stages along the reaction coordinate of the enzymatic mechanism.
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Affiliation(s)
- Niall Simpson
- Department of Physics
- University of Strathclyde
- SUPA
- Glasgow
- UK
| | | | - Gordon Hithell
- Department of Physics
- University of Strathclyde
- SUPA
- Glasgow
- UK
| | - Daniel J. Shaw
- Department of Physics
- University of Strathclyde
- SUPA
- Glasgow
- UK
| | - Gregory M. Greetham
- Central Laser Facility, Research Complex at Harwell
- STFC Rutherford Appleton Laboratory
- Didcot
- UK
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell
- STFC Rutherford Appleton Laboratory
- Didcot
- UK
| | - Anthony W. Parker
- Central Laser Facility, Research Complex at Harwell
- STFC Rutherford Appleton Laboratory
- Didcot
- UK
| | - Neil T. Hunt
- Department of Physics
- University of Strathclyde
- SUPA
- Glasgow
- UK
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13
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Hemin-histamine-montmorillonite clay conjugate as a model biocatalyst to mimic natural peroxidase. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5196-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Adamczyk K, Simpson N, Greetham GM, Gumiero A, Walsh MA, Towrie M, Parker AW, Hunt NT. Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site. Chem Sci 2014; 6:505-516. [PMID: 28936306 PMCID: PMC5588449 DOI: 10.1039/c4sc02752c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/22/2014] [Indexed: 11/24/2022] Open
Abstract
Ultrafast infrared spectroscopy provides insights into the dynamic nature of water in the active sites of catalase and peroxidase enzymes.
Understanding the impact of fast dynamics upon the chemical processes occurring within the active sites of proteins and enzymes is a key challenge that continues to attract significant interest, though direct experimental insight in the solution phase remains sparse. Similar gaps in our knowledge exist in understanding the role played by water, either as a solvent or as a structural/dynamic component of the active site. In order to investigate further the potential biological roles of water, we have employed ultrafast multidimensional infrared spectroscopy experiments that directly probe the structural and vibrational dynamics of NO bound to the ferric haem of the catalase enzyme from Corynebacterium glutamicum in both H2O and D2O. Despite catalases having what is believed to be a solvent-inaccessible active site, an isotopic dependence of the spectral diffusion and vibrational lifetime parameters of the NO stretching vibration are observed, indicating that water molecules interact directly with the haem ligand. Furthermore, IR pump–probe data feature oscillations originating from the preparation of a coherent superposition of low-frequency vibrational modes in the active site of catalase that are coupled to the haem ligand stretching vibration. Comparisons with an exemplar of the closely-related peroxidase enzyme family shows that they too exhibit solvent-dependent active-site dynamics, supporting the presence of interactions between the haem ligand and water molecules in the active sites of both catalases and peroxidases that may be linked to proton transfer events leading to the formation of the ferryl intermediate Compound I. In addition, a strong, water-mediated, hydrogen bonding structure is suggested to occur in catalase that is not replicated in peroxidase; an observation that may shed light on the origins of the different functions of the two enzymes.
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Affiliation(s)
- Katrin Adamczyk
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Niall Simpson
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Gregory M Greetham
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Andrea Gumiero
- Diamond Light Source , Diamond House, Harwell Science and Innovation Campus , Didcot, Oxfordshire , OX11 0DE , UK
| | - Martin A Walsh
- Diamond Light Source , Diamond House, Harwell Science and Innovation Campus , Didcot, Oxfordshire , OX11 0DE , UK
| | - Michael Towrie
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Anthony W Parker
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Neil T Hunt
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
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15
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Tyrosine oxidation in heme oxygenase: examination of long-range proton-coupled electron transfer. J Biol Inorg Chem 2014; 19:1137-48. [PMID: 25023856 DOI: 10.1007/s00775-014-1169-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 06/05/2014] [Indexed: 01/01/2023]
Abstract
Heme oxygenase is responsible for the degradation of a histidine-ligated ferric protoporphyrin IX (Por) to biliverdin, CO, and the free ferrous ion. Described here are studies of tyrosyl radical formation reactions that occur after oxidizing Fe(III)(Por) to Fe(IV)=O(Por(·+)) in human heme oxygenase isoform-1 (hHO-1) and the structurally homologous protein from Corynebacterium diphtheriae (cdHO). Site-directed mutagenesis on hHO-1 probes the reduction of Fe(IV)=O(Por(·+)) by tyrosine residues within 11 Å of the prosthetic group. In hHO-1, Y58· is implicated as the most likely site of oxidation, based on the pH and pD dependent kinetics. The absence of solvent deuterium isotope effects in basic solutions of hHO-1 and cdHO contrasts with the behavior of these proteins in the acidic solution, suggesting that long-range proton-coupled electron transfer predominates over electron transfer.
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16
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Wang B, Li C, Cho KB, Nam W, Shaik S. The FeIII(H2O2) Complex as a Highly Efficient Oxidant in Sulfoxidation Reactions: Revival of an Underrated Oxidant in Cytochrome P450. J Chem Theory Comput 2013; 9:2519-25. [DOI: 10.1021/ct400190f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Binju Wang
- Institute of Chemistry and the
Lise Meitner-Minerva Center for Computational Quantum Chemistry, The
Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Chunsen Li
- Institute of Chemistry and the
Lise Meitner-Minerva Center for Computational Quantum Chemistry, The
Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Kyung-Bin Cho
- Department of Bioinspired Science,
Ewha Womans University, Seoul 120-750, Korea
| | - Wonwoo Nam
- Department of Bioinspired 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, 91904 Jerusalem, Israel
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17
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Shan G, Zheng S, Chen S, Chen Y, Liu Y. Detection of label-free H2O2 based on sensitive Au nanorods as sensor. Colloids Surf B Biointerfaces 2013; 102:327-30. [DOI: 10.1016/j.colsurfb.2012.07.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 11/17/2022]
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18
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Liu Y, Mukherjee A, Nahumi N, Ozbil M, Brown D, Angeles-Boza AM, Dooley DM, Prabhakar R, Roth JP. Experimental and Computational Evidence of Metal-O2 Activation and Rate-Limiting Proton-Coupled Electron Transfer in a Copper Amine Oxidase. J Phys Chem B 2012; 117:218-29. [DOI: 10.1021/jp3121484] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yi Liu
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Nadav Nahumi
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Doreen Brown
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - David M. Dooley
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
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19
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Sarma R, Angeles-Boza AM, Brinkley DW, Roth JP. Studies of the Di-iron(VI) Intermediate in Ferrate-Dependent Oxygen Evolution from Water. J Am Chem Soc 2012; 134:15371-86. [DOI: 10.1021/ja304786s] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rupam Sarma
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland
21218, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland
21218, United States
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland
21218, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland
21218, United States
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20
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Angeles-Boza AM, Roth JP. Oxygen Kinetic Isotope Effects upon Catalytic Water Oxidation by a Monomeric Ruthenium Complex. Inorg Chem 2012; 51:4722-9. [DOI: 10.1021/ic202745n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Alfredo M. Angeles-Boza
- Department
of Chemistry, Johns Hopkins University, 3400 North Charles Street,
Baltimore, Maryland 21218, United States
| | - Justine P. Roth
- Department
of Chemistry, Johns Hopkins University, 3400 North Charles Street,
Baltimore, Maryland 21218, United States
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21
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Kundu S, Matito E, Walleck S, Pfaff FF, Heims F, Rábay B, Luis JM, Company A, Braun B, Glaser T, Ray K. O-O bond formation mediated by a hexanuclear iron complex supported on a stannoxane core. Chemistry 2012; 18:2787-91. [PMID: 22262528 DOI: 10.1002/chem.201102326] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Subrata Kundu
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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22
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Huff GS, Doncheva IS, Brinkley DW, Angeles-Boza AM, Mukherjee A, Cramer CJ, Roth JP. Experimental and Computational Investigations of Oxygen Reactivity in a Heme and Tyrosyl Radical-Containing Fatty Acid α-(Di)oxygenase. Biochemistry 2011; 50:7375-89. [DOI: 10.1021/bi201016h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Gregory S. Huff
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Irina S. Doncheva
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis,
Minnesota 55455, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
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23
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Dong S, Zhang P, Liu H, Li N, Huang T. Direct electrochemistry and electrocatalysis of hemoglobin in composite film based on ionic liquid and NiO microspheres with different morphologies. Biosens Bioelectron 2011; 26:4082-7. [DOI: 10.1016/j.bios.2011.03.039] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 03/28/2011] [Accepted: 03/29/2011] [Indexed: 11/27/2022]
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24
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Jin N, Lahaye DE, Groves JT. A “Push−Pull” Mechanism for Heterolytic O−O Bond Cleavage in Hydroperoxo Manganese Porphyrins. Inorg Chem 2010; 49:11516-24. [DOI: 10.1021/ic1015274] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ning Jin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Dorothée E. Lahaye
- 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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25
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Mandado M, Cordeiro MNDS. On the stability of metal-aminoacid complexes in water based on water-ligand exchange reactions and electronic properties: Detailed study on iron-glycine hexacoordinated complexes. J Comput Chem 2010; 31:2735-45. [DOI: 10.1002/jcc.21567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Vidossich P, Fiorin G, Alfonso-Prieto M, Derat E, Shaik S, Rovira C. On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation. J Phys Chem B 2010; 114:5161-9. [PMID: 20345187 DOI: 10.1021/jp911170b] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have investigated the dynamics of water molecules in the distal pocket of horseradish peroxidase to elucidate the role that they may play in the formation of the principal active species of the enzymatic cycle (compound I, Por(o+)-Fe(IV)=O) upon reaction of the resting Fe(III) state with hydrogen peroxide. The equilibrium molecular dynamics simulations show that, in accord with experimental evidence, the active site access channel is hydrated with an average of two to three water molecules within 5 A from the bound hydrogen peroxide. Although the channel is always hydrated, the specific conformations in which a water molecule bridges H(2)O(2) and the distal histidine, which were found (Derat; et al. J. Am. Chem. Soc. 2007, 129, 6346.) to display a low-energy barrier for the initial acid-base step of the reaction, occur with low probability but are relevant within the time scale of catalysis. Metadynamics simulations, which were used to reconstruct the free-energy landscape of water motion in the access channel, revealed that preferred interaction sites within the channel are separated by small energy barriers (<1.5 kcal/mol). Most importantly, water-bridged conformations lie on a shoulder just 1 kcal/mol above one local minimum and thus are easily accessible. Such an energy landscape appears as a requisite for the effectiveness of compound I formation, whereby the H-bonding pattern involving reactants and catalytic residues (including the intervening water molecule) has to rearrange to deliver the proton to the distal OH moiety of the hydrogen peroxide and thereby lead to heterolytic O-O cleavage. Our study provides an example of a system for which the "reactive configurations" (i.e., structures characterized by a low barrier for the chemical transformation) correspond to a minor population of the system and show how equilibrium molecular dynamics and free-energy calculations may conveniently be used to ascertain that such reactive conformations are indeed accessible to the system. Once again, the MD and QM/MM combination shows that a single water molecule acts as a biocatalyst in the cycle of HRP.
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Affiliation(s)
- Pietro Vidossich
- Laboratori de Simulació Computacional i Modelització, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
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27
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Zazza C, Palma A, Sanna N, Tatoli S, Aschi M. Computational Study on Compound I Redox-Active Species in Horseradish Peroxydase Enzyme: Conformational Fluctuations and Solvation Effects. J Phys Chem B 2010; 114:6817-24. [PMID: 20438084 DOI: 10.1021/jp101033w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Costantino Zazza
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| | - Amedeo Palma
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| | - Nico Sanna
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| | - Simone Tatoli
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| | - Massimiliano Aschi
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
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28
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Ashley DC, Brinkley DW, Roth JP. Oxygen Isotope Effects as Structural and Mechanistic Probes in Inorganic Oxidation Chemistry. Inorg Chem 2010; 49:3661-75. [DOI: 10.1021/ic901778g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Daniel C. Ashley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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29
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Direct electrochemistry and electrocatalysis of heme-proteins immobilized in porous carbon nanofiber/room-temperature ionic liquid composite film. Electrochim Acta 2010. [DOI: 10.1016/j.electacta.2009.12.101] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Krishnan S, Abeykoon A, Schenkman JB, Rusling JF. Control of electrochemical and ferryloxy formation kinetics of cyt P450s in polyion films by heme iron spin state and secondary structure. J Am Chem Soc 2010; 131:16215-24. [PMID: 19886700 DOI: 10.1021/ja9065317] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Voltammetry of cytochrome P450 (cyt P450) enzymes in ultrathin films with polyions was related for the first time to electronic and secondary structure. Heterogeneous electron transfer (hET) rate constants for reduction of the cyt P450s depended on heme iron spin state, with low spin cyt P450cam giving a value 40-fold larger than high spin human cyt P450 1A2, with mixed spin human P450 cyt 2E1 at an intermediate value. Asymmetric reduction-oxidation peak separations with increasing scan rates were explained by simulations featuring faster oxidation than reduction. Results are consistent with a square scheme in which oxidized and reduced forms of cyt P450s each participate in rapid conformational equilibria. Rate constants for oxidation of ferric cyt P450s in films by t-butyl hydroperoxide to active ferryloxy cyt P450s from rotating disk voltammetry suggested a weaker dependence on spin state, but in the reverse order of the observed hET reduction rates. Oxidation and reduction rates of cyt P450s in the films are also likely to depend on protein secondary structure around the heme iron.
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Affiliation(s)
- Sadagopan Krishnan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA
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31
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Zazza C, Palma A, Amadei A, Sanna N, Tatoli S, Aschi M. On the catalytic role of structural fluctuations in enzyme reactions: computational evidence on the formation of compound 0 in horseradish peroxidase. Faraday Discuss 2010. [DOI: 10.1039/b906614d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Cramer CJ, Truhlar DG. Density functional theory for transition metals and transition metal chemistry. Phys Chem Chem Phys 2009; 11:10757-816. [PMID: 19924312 DOI: 10.1039/b907148b] [Citation(s) in RCA: 1063] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.
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Affiliation(s)
- Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA.
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33
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Roth JP. Oxygen isotope effects as probes of electron transfer mechanisms and structures of activated O2. Acc Chem Res 2009; 42:399-408. [PMID: 19195996 DOI: 10.1021/ar800169z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Competitively determined oxygen ((18)O) isotope effects can be powerful probes of chemical and biological transformations involving molecular oxygen as well as superoxide and hydrogen peroxide. They play a complementary role to crystallography and spectroscopy in the study of activated oxygen intermediates by forging a link between electronic/vibrational structure and the bonding that occurs within ground and transition states along the reaction coordinate. Such analyses can be used to assess the plausibility of intermediates and their catalytic relevance in oxidative processes. This Account describes efforts to advance oxygen kinetic isotope effects ((18)O KIEs) and equilibrium isotope effects ((18)O EIEs) as mechanistic probes of reactive, oxygen-derived species. We focus primarily on transition metal mediated oxidations, outlining both advances over the past five years and current limitations of this approach. Computational methods are now being developed to probe transition states and the accompanying kinetic isotope effects. In particular, we describe the importance of using a full-frequency model to accurately predict the magnitudes as well as the temperature dependence of the isotope effects. Earlier studies have used a "cut-off model," which employs only a few isotopic vibrational modes, and such models tend to overestimate (18)O EIEs. Researchers in mechanistic biological inorganic chemistry would like to differentiate "inner-sphere" from "outer-sphere" reactivity of O(2), a designation that describes the extent of the bonding interaction between metal and oxygen in the transition state. Though this problem remains unsolved, we expect that this isotopic approach will help differentiate these processes. For example, comparisons of (18)O KIEs to (18)O EIEs provide benchmarks that allow us to calibrate computationally derived reaction coordinates. Once the physical origins of heavy atom isotope effects are better understood, researchers will be able to apply the competitive isotope fractionation technique to a wide range of pressing problems in small molecule chemistry and biochemistry.
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Affiliation(s)
- Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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34
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Smirnov VV, Lanci MP, Roth JP. Computational Modeling of Oxygen Isotope Effects on Metal-Mediated O2 Activation at Varying Temperatures. J Phys Chem A 2009; 113:1934-45. [DOI: 10.1021/jp807796c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valeriy V. Smirnov
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Michael P. Lanci
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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