1
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Dinda S, Roy T, Samanta S, Banerjee K, Cox N, Dey A. Proton-Coupled Electron Transfer between a Pendant Thiol and a Ferrous Dioxygen Adduct. Inorg Chem 2024; 63:21313-21322. [PMID: 39432325 DOI: 10.1021/acs.inorgchem.4c03802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2024]
Abstract
The mechanism of thiol oxidation by O2, as catalyzed by ferrous porphyrins, is investigated by trapping intermediates of the transformation at low temperatures and subsequently characterizing them using continuous wave and pulsed electron paramagnetic resonance and resonance Raman spectroscopy. A Fe(III)-O2•- species is initially formed in an iron porphyrin with a pendant thiol functional group, which undergoes proton-coupled electron transfer (PCET) (not HAT) to form an Fe(III)-OOH species. Following O-O bond homolysis, this forms a Fe(IV)═O species with concomitant oxidation of the thiol to an RSO3H group.
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Affiliation(s)
- Souvik Dinda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & B Raja S C Mullick Road, Kolkata, WB 700032, India
| | - Triparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & B Raja S C Mullick Road, Kolkata, WB 700032, India
| | - Soumya Samanta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & B Raja S C Mullick Road, Kolkata, WB 700032, India
| | - Kumarjit Banerjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & B Raja S C Mullick Road, Kolkata, WB 700032, India
| | - Nicholas Cox
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & B Raja S C Mullick Road, Kolkata, WB 700032, India
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2
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Kass D, Katz S, Özgen H, Mebs S, Haumann M, García-Serres R, Dau H, Hildebrandt P, Lohmiller T, Ray K. A Bioinspired Nonheme Fe III-(O 22-)-Cu II Complex with an St = 1 Ground State. J Am Chem Soc 2024; 146:24808-24817. [PMID: 38967560 PMCID: PMC11403606 DOI: 10.1021/jacs.4c04492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Cytochrome c oxidase (CcO) is a heme copper oxidase (HCO) that catalyzes the natural reduction of oxygen to water. A profound understanding of some of the elementary steps leading to the intricate 4e-/4H+ reduction of O2 is presently lacking. A total spin St = 1 FeIII-(O22-)-CuII (IP) intermediate is proposed to reduce the overpotentials associated with the reductive O-O bond rupture by allowing electron transfer from a tyrosine moiety without the necessity of any spin-surface crossing. Direct evidence of the involvement of IP in the CcO catalytic cycle is, however, missing. A number of heme copper peroxido complexes have been prepared as synthetic models of IP, but all of them possess the catalytically nonrelevant St = 0 ground state resulting from antiferromagnetic coupling between the S = 1/2 FeIII and CuII centers. In a complete nonheme approach, we now report the spectroscopic characterization and reactivity of the FeIII-(O22-)-CuII intermediates 1 and 2, which differ only by a single -CH3 versus -H substituent on the central amine of the tridentate ligands binding to copper. Complex 1 with an end-on peroxido core and ferromagnetically (St = 1) coupled FeIII and CuII centers performs H-bonding-mediated O-O bond cleavage in the presence of phenol to generate oxoiron(IV) and exchange-coupled copper(II) and PhO• moieties. In contrast, the μ-η2:η1 peroxido complex 2, with a St = 0 ground state, is unreactive toward phenol. Thus, the implications for spin topology contributions to O-O bond cleavage, as proposed for the heme FeIII-(O22-)-CuII intermediate in CcO, can be extended to nonheme chemistry.
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Affiliation(s)
- Dustin Kass
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Sagie Katz
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Hivda Özgen
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Stefan Mebs
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ricardo García-Serres
- Université Grenoble Alpes, CEA, CNRS, Laboratoire de Chimie et Biologie des Métaux, 38000 Grenoble, France
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Thomas Lohmiller
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
- EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 16, 12489 Berlin, Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
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3
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Albert T, Kumar A, Caranto J, Moënne-Loccoz P. Vibrational analyses of the reaction of oxymyoglobin with NO using a photolabile caged NO donor at cryogenic temperatures. J Inorg Biochem 2024; 258:112633. [PMID: 38852292 PMCID: PMC11216511 DOI: 10.1016/j.jinorgbio.2024.112633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/17/2024] [Accepted: 06/01/2024] [Indexed: 06/11/2024]
Abstract
The NO dioxygenation reaction catalyzed by heme-containing globin proteins is a crucial aerobic detoxification pathway. Accordingly, the second order reaction of NO with oxymyoglobin and oxyhemoglobin has been the focus of a large number of kinetic and spectroscopic studies. Stopped-flow and rapid-freeze-quench (RFQ) measurements have provided evidence for the formation of a Fe(III)-nitrato complex with millisecond lifetime prior to release of the nitrate product, but the temporal resolution of these techniques is insufficient for the characterization of precursor species. Most mechanistic models assume the formation of an initial Fe(III)-peroxynitrite species prior to homolytic cleavage of the OO bond and recombination of the resulting NO2 and Fe(IV)=O species. Here we report vibrational spectroscopy measurements for the reaction of oxymyoglobin with a photolabile caged NO donor at cryogenic temperatures. We show that this approach offers efficient formation and trapping of the Fe(III)-nitrato, enzyme-product, complex at 180 K. Resonance Raman spectra of the Fe(III)-nitrato complex trapped via RFQ in the liquid phase and photolabile NO release at cryogenic temperatures are indistinguishable, demonstrating the complementarity of these approaches. Caged NO is released by irradiation <180 K but diffusion into the heme pocket is fully inhibited. Our data provide no evidence for Fe(III)-peroxynitrite of Fe(IV)=O species, supporting low activation energies for the NO to nitrate conversion at the oxymyoglobin reaction site. Photorelease of NO at cryogenic temperatures allows monitoring of the reaction by transmittance FTIR which provides valuable quantitative information and promising prospects for the detection of protein sidechain reorganization events in NO-reacting metalloenzymes.
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Affiliation(s)
- Therese Albert
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA
| | - Arun Kumar
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL 32816, USA
| | - Jonathan Caranto
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL 32816, USA
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.
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4
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Gera R, De P, Singh KK, Jannuzzi SAV, Mohanty A, Velasco L, Kulbir, Kumar P, Marco JF, Nagarajan K, Pecharromán C, Rodríguez-Pascual PM, DeBeer S, Moonshiram D, Gupta SS, Dasgupta J. Trapping an Elusive Fe(IV)-Superoxo Intermediate Inside a Self-Assembled Nanocage in Water at Room Temperature. J Am Chem Soc 2024; 146:21729-21741. [PMID: 39078020 DOI: 10.1021/jacs.4c05849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Molecular cavities that mimic natural metalloenzymes have shown the potential to trap elusive reaction intermediates. Here, we demonstrate the formation of a rare yet stable Fe(IV)-superoxo intermediate at room temperature subsequent to dioxygen binding at the Fe(III) site of a (Et4N)2[FeIII(Cl)(bTAML)] complex confined inside the hydrophobic interior of a water-soluble Pd6L412+ nanocage. Using a combination of electron paramagnetic resonance, Mössbauer, Raman/IR vibrational, X-ray absorption, and emission spectroscopies, we demonstrate that the cage-encapsulated complex has a Fe(IV) oxidation state characterized by a stable S = 1/2 spin state and a short Fe-O bond distance of ∼1.70 Å. We find that the O2 reaction in confinement is reversible, while the formed Fe(IV)-superoxo complex readily reacts when presented with substrates having weak C-H bonds, highlighting the lability of the O-O bond. We envision that such optimally trapped high-valent superoxos can show new classes of reactivities catalyzing both oxygen atom transfer and C-H bond activation reactions.
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Affiliation(s)
- Rahul Gera
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
- Department of Education in Science and Mathematics, Regional Institute of Education - Mysuru, NCERT, Mysuru 570006, India
| | - Puja De
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Kundan K Singh
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, Maharashtra 411008, India
- Chemistry Department, Indian Institute of Technology, Dharwad 580007, India
| | - Sergio A V Jannuzzi
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Aisworika Mohanty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Lucia Velasco
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Kulbir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - Pankaj Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - J F Marco
- Instituto de Quimica Fisica Blas Cabrera, Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid 28006, Spain
| | - Kalaivanan Nagarajan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Carlos Pecharromán
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - P M Rodríguez-Pascual
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Serena DeBeer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Dooshaye Moonshiram
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Sayam Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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5
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Snyder SN, Chiura T, Mak PJ. Resonance Raman Characterization of O 2-Binding Heme Proteins. Methods Mol Biol 2023; 2648:27-41. [PMID: 37039983 DOI: 10.1007/978-1-0716-3080-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
A vast array of critical in vivo processes and pathways are dependent on a multitude of O2-binding heme proteins which contain a diverse range of functions. Resonance Raman (rR) spectroscopy is an ideal technique for structural investigation of these proteins, providing information about the geometry of the Fe-O-O fragment and its electrostatic interactions with the distal active site. Characterization of these oxy adducts is an endeavor that is complicated by their instability for many heme proteins in solution, an obstacle which can be overcome by applying the rR technique to cryogenically frozen samples. We describe here how to measure rR spectra of heme proteins with stable oxy forms, as well as the technical adaptations required to measure unstable samples at 77 K.
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Affiliation(s)
- Samuel N Snyder
- Department of Chemistry, Saint Louis University, Saint Louis, MO, USA
| | - Tapiwa Chiura
- Department of Chemistry, Saint Louis University, Saint Louis, MO, USA
| | - Piotr J Mak
- Department of Chemistry, Saint Louis University, Saint Louis, MO, USA.
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6
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Nath AK, Roy M, Dey C, Dey A, Dey SG. Spin state dependent peroxidase activity of heme bound amyloid β peptides relevant to Alzheimer's disease. Chem Sci 2022; 13:14305-14319. [PMID: 36545147 PMCID: PMC9749105 DOI: 10.1039/d2sc05008k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
The colocalization of heme rich deposits in the senile plaque of Aβ in the cerebral cortex of the Alzheimer's disease (AD) brain along with altered heme homeostasis and heme deficiency symptoms in AD patients has invoked the association of heme in AD pathology. Heme bound Aβ complexes, depending on the concentration of the complex or peptide to heme ratio, exhibit an equilibrium between a high-spin mono-His bound peroxidase-type active site and a low-spin bis-His bound cytochrome b type active site. The high-spin heme-Aβ complex shows higher peroxidase activity than free heme, where compound I is the reactive oxidant. It is also capable of oxidizing neurotransmitters like serotonin in the presence of peroxide, owing to the formation of compound I. The low-spin bis-His heme-Aβ complex on the other hand shows enhanced peroxidase activity relative to high-spin heme-Aβ. It reacts with H2O2 to produce two stable intermediates, compound 0 and compound I, which are characterized by absorption, EPR and resonance Raman spectroscopy. The stability of compound I of low-spin heme-Aβ is accountable for its enhanced peroxidase activity and oxidation of the neurotransmitter serotonin. The effect of the second sphere Tyr10 residue of Aβ on the formation and stability of the intermediates of low-spin heme-Aβ has also been investigated. The higher stability of compound I for low-spin heme-Aβ is likely due to H-bonding interactions involving Tyr10 in the distal pocket.
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Affiliation(s)
- Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
| | - Chinmay Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
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7
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Geeraerts Z, Stiller OR, Lukat-Rodgers GS, Rodgers KR. Roles of High-Valent Hemes and pH Dependence in Halite Decomposition Catalyzed by Chlorite Dismutase from Dechloromonas aromatica. ACS Catal 2022; 12:8641-8657. [DOI: 10.1021/acscatal.2c01428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zachary Geeraerts
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Olivia R. Stiller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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8
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Parsons BJ. Kinetic simulations of the effect of antioxidants on the metmyoglobin reactions with hydrogen peroxide and their relevance and application to the Trolox equivalent equivalent antioxidant assay. INT J CHEM KINET 2021. [DOI: 10.1002/kin.21500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Barry J. Parsons
- School of Clinical and Applied Sciences Leeds Beckett University Leeds UK
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9
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Kim H, Rogler PJ, Sharma SK, Schaefer AW, Solomon EI, Karlin KD. Ferric Heme Superoxide Reductive Transformations to Ferric Heme (Hydro)Peroxide Species: Spectroscopic Characterization and Thermodynamic Implications for H‐Atom Transfer (HAT). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hyun Kim
- Chemistry Department Johns Hopkins University Baltimore MD 21218 USA
| | - Patrick J. Rogler
- Chemistry Department Johns Hopkins University Baltimore MD 21218 USA
| | - Savita K. Sharma
- Chemistry Department Johns Hopkins University Baltimore MD 21218 USA
| | | | | | - Kenneth D. Karlin
- Chemistry Department Johns Hopkins University Baltimore MD 21218 USA
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10
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Kim H, Rogler PJ, Sharma SK, Schaefer AW, Solomon EI, Karlin KD. Ferric Heme Superoxide Reductive Transformations to Ferric Heme (Hydro)Peroxide Species: Spectroscopic Characterization and Thermodynamic Implications for H-Atom Transfer (HAT). Angew Chem Int Ed Engl 2021; 60:5907-5912. [PMID: 33348450 PMCID: PMC7920932 DOI: 10.1002/anie.202013791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Indexed: 01/07/2023]
Abstract
A new end-on low-spin ferric heme peroxide, [(PIm )FeIII -(O22- )]- (PIm -P), and subsequently formed hydroperoxide species, [(PIm )FeIII -(OOH)] (PIm -HP) are generated utilizing the iron-porphyrinate PIm with its tethered axial base imidazolyl group. Measured thermodynamic parameters, the ferric heme superoxide [(PIm )FeIII -(O2⋅- )] (PIm -S) reduction potential (E°') and the PIm -HP pKa value, lead to the finding of the OO-H bond-dissociation free energy (BDFE) of PIm -HP as 69.5 kcal mol-1 using a thermodynamic square scheme and Bordwell relationship. The results are validated by the observed oxidizing ability of PIm -S via hydrogen-atom transfer (HAT) compared to that of the F8 superoxide complex, [(F8 )FeIII -(O2.- )] (S) (F8 =tetrakis(2,6-difluorophenyl)porphyrinate, without an internally appended axial base imidazolyl), as determined from reactivity comparison of superoxide complexes PIm -S and S with the hydroxylamine (O-H) substrates TEMPO-H and ABNO-H.
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Affiliation(s)
- Hyun Kim
- Chemistry Department, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Patrick J Rogler
- Chemistry Department, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Savita K Sharma
- Chemistry Department, Johns Hopkins University, Baltimore, MD, 21218, USA
| | | | - Edward I Solomon
- Chemistry Department, Stanford University, Stanford, CA, 94305, USA
| | - Kenneth D Karlin
- Chemistry Department, Johns Hopkins University, Baltimore, MD, 21218, USA
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11
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Usai R, Kaluka D, Mak PJ, Liu Y, Kincaid JR. Resonance Raman spectroscopic studies of peroxo and hydroperoxo intermediates in lauric acid (LA)-bound cytochrome P450 119. J Inorg Biochem 2020; 208:111084. [PMID: 32470906 DOI: 10.1016/j.jinorgbio.2020.111084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 03/07/2020] [Accepted: 03/29/2020] [Indexed: 11/30/2022]
Abstract
Cytochromes P450 bind and cleave dioxygen to generate a potent intermediate compound I, capable of hydroxylating inert hydrocarbon substrates. Cytochrome P450 119, a bacterial cytochrome P450 that serves as a good model system for the study of the intermediate states in the P450 catalytic cycle. CYP119 is found in high temperature and sulfur rich environments. Though the natural substrate and redox partner are still unknown, a potential application of such thermophilic P450s is utilizing them as biocatalysts in biotechnological industry; e.g., the synthesis of organic compounds otherwise requiring hostile environments like extremes of pH or temperature. In the present work the oxygenated complex of this enzyme bound to lauric acid, a surrogate substrate known to have a good binding affinity, was studied by a combination of cryoradiolysis and resonance Raman spectroscopy, to trap and characterize active site structures of the key fleeting enzymatic intermediates, including the peroxo and hydroperoxo species.
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Affiliation(s)
- Remigio Usai
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Daniel Kaluka
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Piotr J Mak
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - Yilin Liu
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, United States.
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12
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Kim H, Rogler PJ, Sharma SK, Schaefer AW, Solomon EI, Karlin KD. Heme-Fe III Superoxide, Peroxide and Hydroperoxide Thermodynamic Relationships: Fe III-O 2•- Complex H-Atom Abstraction Reactivity. J Am Chem Soc 2020; 142:3104-3116. [PMID: 31913628 PMCID: PMC7034651 DOI: 10.1021/jacs.9b12571] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Establishing redox and thermodynamic relationships between metal-ion-bound O2 and its reduced (and protonated) derivatives is critically important for a full understanding of (bio)chemical processes involving dioxygen processing. Here, a ferric heme peroxide complex, [(F8)FeIII-(O22-)]- (P) (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a superoxide complex, [(F8)FeIII-(O2•-)] (S), are shown to be redox interconvertible. Using Cr(η-C6H6)2, an equilibrium state where S and P are present is established in tetrahydrofuran (THF) at -80 °C, allowing determination of the reduction potential of S as -1.17 V vs Fc+/0. P could be protonated with 2,6-lutidinium triflate, yielding the low-spin ferric hydroperoxide species, [(F8)FeIII-(OOH)] (HP). Partial conversion of HP back to P using a derivatized phosphazene base gave a P/HP equilibrium mixture, leading to the determination of pKa = 28.8 for HP (THF, -80 °C). With the measured reduction potential and pKa, the O-H bond dissociation free energy (BDFE) of hydroperoxide species HP was calculated to be 73.5 kcal/mol, employing the thermodynamic square scheme and Bordwell relationship. This calculated O-H BDFE of HP, in fact, lines up with an experimental demonstration of the oxidizing ability of S via hydrogen atom transfer (HAT) from TEMPO-H (2,2,6,6-tetramethylpiperdine-N-hydroxide, BDFE = 66.5 kcal/mol in THF), forming the hydroperoxide species HP and TEMPO radical. Kinetic studies carried out with TEMPO-H(D) reveal second-order behavior, kH = 0.5, kD = 0.08 M-1 s-1 (THF, -80 °C); thus, the hydrogen/deuterium kinetic isotope effect (KIE) = 6, consistent with H-atom abstraction by S being the rate-determining step. This appears to be the first case where experimentally derived thermodynamics lead to a ferric heme hydroperoxide OO-H BDFE determination, that FeIII-OOH species being formed via HAT reactivity of the partner ferric heme superoxide complex.
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Affiliation(s)
- Hyun Kim
- 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
| | - Savita K Sharma
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Andrew W Schaefer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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13
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Rodriguez-Mackenzie AD, Arbelo-Lopez HD, Wymore T, Lopez-Garriga J. A reaction pathway to compound 0 intermediates in oxy-myoglobin through interactions with hydrogen sulfide and His64. J Mol Graph Model 2019; 94:107465. [PMID: 31670138 DOI: 10.1016/j.jmgm.2019.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022]
Abstract
Myoglobin (Mb) binds oxygen with high affinity as a low spin singlet complex and thus functions as an oxygen storage protein. Yet, hybrid Density Functional Theory/Molecular Mechanical (DFT/MM) calculations of oxy-Mb models predict that the O2 bond is much less resistant to breaking in the presence of hydrogen sulfide (H2S) compared with water. Specifically, a hydrogen atom from H2S can be transferred to the distal oxygen atom through homolytic cleavage of the S-H bond to form the intermediate Compound (Cpd) 0 structure and a thiyl radical. In the presence of a neutral His64 (Nε protonation, His64-ε) and H2S, only a metastable Cpd 0 would be formed as the active site is devoid of any additional proton donor to fully break the O2 bond. In contrast, the calculations predict that the triplet state is significantly favored over the open shell singlet diradical state throughout the entire reaction coordinate in the presence of H2S and a positively charged His64. Furthermore, a positively charged His64 can readily donate a proton to Cpd 0 to fully break the O2 bond resulting in a configuration analogous to reported reaction models of a hemoglobin mutant bound to H2O2 with H2S present. Typically, exotic techniques are required to generate Cpd 0 but under the conditions just described the intermediate is readily detected in UV-Vis spectra at room temperature. The effect is observed as a 2 nm red shift of the Soret band from 414 nm to 416 nm (pH 5.0, His64-εδ) and from 416 nm to 418 nm (pH 6.6, His64-ε).
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Affiliation(s)
| | - Hector D Arbelo-Lopez
- Department of Chemistry, University of Puerto Rico Mayaguez Campus, Mayaguez, 00680, Puerto Rico
| | - Troy Wymore
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, United States.
| | - Juan Lopez-Garriga
- Department of Chemistry, University of Puerto Rico Mayaguez Campus, Mayaguez, 00680, Puerto Rico.
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14
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Kim B, Jeong D, Ohta T, Cho J. Nucleophilic reactivity of a copper(II)-hydroperoxo complex. Commun Chem 2019. [DOI: 10.1038/s42004-019-0187-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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15
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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16
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Singha A, Dey A. Hydrogen atom abstraction by synthetic heme ferric superoxide and hydroperoxide species. Chem Commun (Camb) 2019; 55:5591-5594. [PMID: 31021337 DOI: 10.1039/c9cc01423c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To date, artificial dioxygen adducts of heme have not been demonstrated to be able to oxidize organic substrates in sharp contrast to their non-heme analogues and naturally occurring enzymes like heme dioxygenases. To address this apparent anomaly, an iron porphyrin complex is synthesized which includes a pendant quinol group. The corresponding dioxygen bound iron porphyrin species is demonstrated to perform hydrogen atom transfer (HAT) from the quinol group appended to the porphyrin ligand. The resultant ferric peroxide, formed by the first HAT, performs a 2nd HAT generating a ferryl species (FeIV[double bond, length as m-dash]O) and resulting in the 2e-/2H+ oxidation of the pendant hydroquinone to quinone.
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Affiliation(s)
- Asmita Singha
- School of Chemical Science, Indian Association for the Cultivation of Science, Kolkata, India.
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17
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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: 156] [Impact Index Per Article: 22.3] [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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18
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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19
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Reed JH, Shi Y, Zhu Q, Chakraborty S, Mirts EN, Petrik ID, Bhagi-Damodaran A, Ross M, Moënne-Loccoz P, Zhang Y, Lu Y. Manganese and Cobalt in the Nonheme-Metal-Binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-Inactive Mechanism. J Am Chem Soc 2017; 139:12209-12218. [PMID: 28768416 PMCID: PMC5673108 DOI: 10.1021/jacs.7b05800] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The presence of a nonheme metal, such as copper and iron, in the heme-copper oxidase (HCO) superfamily is critical to the enzymatic activity of reducing O2 to H2O, but the exact mechanism the nonheme metal ion uses to confer and fine-tune the activity remains to be understood. We herein report that manganese and cobalt can bind to the same nonheme site and confer HCO activity in a heme-nonheme biosynthetic model in myoglobin. While the initial rates of O2 reduction by the Mn, Fe, and Co derivatives are similar, the percentages of reactive oxygen species (ROS) formation are 7%, 4%, and 1% and the total turnovers are 5.1 ± 1.1, 13.4 ± 0.7, and 82.5 ± 2.5, respectively. These results correlate with the trends of nonheme-metal-binding dissociation constants (35, 22, and 9 μM) closely, suggesting that tighter metal binding can prevent ROS release from the active site, lessen damage to the protein, and produce higher total turnover numbers. Detailed spectroscopic, electrochemical, and computational studies found no evidence of redox cycling of manganese or cobalt in the enzymatic reactions and suggest that structural and electronic effects related to the presence of different nonheme metals lead to the observed differences in reactivity. This study of the roles of nonheme metal ions beyond the Cu and Fe found in native enzymes has provided deeper insights into nature's choice of metal ion and reaction mechanism and allows for finer control of the enzymatic activity, which is a basis for the design of efficient catalysts for the oxygen reduction reaction in fuel cells.
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Affiliation(s)
- Julian H. Reed
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yelu Shi
- Department of Biomedical Engineering, Chemistry, and Biological
Sciences, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Qianhong Zhu
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, Portland, OR,
97239, USA
| | - Saumen Chakraborty
- Department of Chemistry & Biochemistry, University of
Mississippi, Oxford, Mississippi, 38677, USA
| | - Evan N. Mirts
- Center for Biophysics and Quantitative Biology, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign,
Urbana, IL, 61801, USA
| | - Ambika Bhagi-Damodaran
- Department of Pharmaceutical Chemistry, University of California,
San Francisco, San Francisco, CA, 94143, USA
| | - Matthew Ross
- Department of Chemistry, Northwestern University, Evanston, IL,
60208, USA
| | - Pierre Moënne-Loccoz
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, Portland, OR,
97239, USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry, and Biological
Sciences, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign,
Urbana, IL, 61801, USA
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20
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Bhagi-Damodaran A, Michael MA, Zhu Q, Reed J, Sandoval BA, Mirts EN, Chakraborty S, Moënne-Loccoz P, Zhang Y, Lu Y. Why copper is preferred over iron for oxygen activation and reduction in haem-copper oxidases. Nat Chem 2017; 9:257-263. [PMID: 28221360 PMCID: PMC5321616 DOI: 10.1038/nchem.2643] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/09/2016] [Indexed: 01/13/2023]
Abstract
Haem-copper oxidase (HCO) catalyses the natural reduction of oxygen to water using a haem-copper centre. Despite decades of research on HCOs, the role of non-haem metal and the reason for nature's choice of copper over other metals such as iron remains unclear. Here, we use a biosynthetic model of HCO in myoglobin that selectively binds different non-haem metals to demonstrate 30-fold and 11-fold enhancements in the oxidase activity of Cu- and Fe-bound HCO mimics, respectively, as compared with Zn-bound mimics. Detailed electrochemical, kinetic and vibrational spectroscopic studies, in tandem with theoretical density functional theory calculations, demonstrate that the non-haem metal not only donates electrons to oxygen but also activates it for efficient O-O bond cleavage. Furthermore, the higher redox potential of copper and the enhanced weakening of the O-O bond from the higher electron density in the d orbital of copper are central to its higher oxidase activity over iron. This work resolves a long-standing question in bioenergetics, and renders a chemical-biological basis for the design of future oxygen-reduction catalysts.
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Affiliation(s)
| | - Matthew A. Michael
- Department of Biomedical Engineering, Chemistry, and
Biological Sciences, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Qianhong Zhu
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, 3181 SW Sam Jackson Park
Road, Portland, OR, USA
| | - Julian Reed
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, USA
| | - Braddock A. Sandoval
- Department of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, USA
| | - Evan N. Mirts
- Center for Biophysics and Quantitative Biology, University
of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Saumen Chakraborty
- Department of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, USA
| | - Pierre Moënne-Loccoz
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, 3181 SW Sam Jackson Park
Road, Portland, OR, USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry, and
Biological Sciences, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University
of Illinois at Urbana-Champaign, Urbana, IL, USA
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21
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Nagaraju P, Ohta T, Liu JG, Ogura T, Naruta Y. The secondary coordination sphere controlled reactivity of a ferric-superoxo heme: unexpected conversion to a ferric hydroperoxo intermediate by reaction with a high-spin ferrous heme. Chem Commun (Camb) 2016; 52:7213-6. [PMID: 27105471 DOI: 10.1039/c6cc02162j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A bio-inspired heme complex involving both a proton donor and an axial imidazole ligand reduces the activation energy for the formation of a ferric hydroperoxo intermediate. A high-spin ferrous heme is shown to be capable of reducing its superoxy species to generate a ferric hydroperoxo intermediate for the first time.
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Affiliation(s)
- Perumandla Nagaraju
- Institute of Science and Technology Research, Chubu University, Kasugai, Aichi 487-8501, Japan.
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22
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Samuni U, Czapski G, Goldstein S. Nitroxide radicals as research tools: Elucidating the kinetics and mechanisms of catalase-like and "suicide inactivation" of metmyoglobin. Biochim Biophys Acta Gen Subj 2016; 1860:1409-16. [PMID: 27062906 DOI: 10.1016/j.bbagen.2016.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/28/2016] [Accepted: 04/04/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Metmyoglobin (MbFe(III)) reaction with H(2)O(2) has been a subject of study over many years. H(2)O(2) alone promotes heme destruction frequently denoted "suicide inactivation," yet the mechanism underlying H(2)O(2) dismutation associated with MbFe(III) inactivation remains obscure. METHODS MbFe(III) reaction with excess H(2)O(2) in the absence and presence of the nitroxide was studied at pH 5.3-8.1 and 25°C by direct determination of reaction rate constants using rapid-mixing stopped-flow technique, by following H(2)O(2) depletion, O(2) evolution, spectral changes of the heme protein, and the fate of the nitroxide by EPR spectroscopy. RESULTS The rates of both H(2)O(2) dismutation and heme inactivation processes depend on [MbFe(III)], [H(2)O(2)] and pH. Yet the inactivation stoichiometry is independent of these variables and each MbFe(III) molecule catalyzes the dismutation of 50±10 H(2)O(2) molecules until it is inactivated. The nitroxide catalytically enhances the catalase-like activity of MbFe(III) while protecting the heme against inactivation. The rate-determining step in the absence and presence of the nitroxide is the reduction of MbFe(IV)O by H(2)O(2) and by nitroxide, respectively. CONCLUSIONS The nitroxide effects on H(2)O(2) dismutation catalyzed by MbFe(III) demonstrate that MbFe(IV)O reduction by H(2)O(2) is the rate-determining step of this process. The proposed mechanism, which adequately fits the pro-catalytic and protective effects of the nitroxide, implies the intermediacy of a compound I-H(2)O(2) adduct, which decomposes to a MbFe(IV)O and an inactivated heme at a ratio of 25:1. GENERAL SIGNIFICANCE The effects of nitroxides are instrumental in elucidating the mechanism underlying the catalysis and inactivation routes of heme proteins.
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Affiliation(s)
- Uri Samuni
- Department of Chemistry and Biochemistry, Queens College, City University of New York, Flushing, NY 11367, USA
| | - Gideon Czapski
- The Accelerator Laboratory, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Sara Goldstein
- The Accelerator Laboratory, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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23
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Sengupta K, Chatterjee S, Dey A. Catalytic H2O2 Disproportionation and Electrocatalytic O2 Reduction by a Functional Mimic of Heme Catalase: Direct Observation of Compound 0 and Compound I in Situ. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02668] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kushal Sengupta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Sudipta Chatterjee
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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24
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Mak PJ, Thammawichai W, Wiedenhoeft D, Kincaid JR. Resonance Raman Spectroscopy Reveals pH-Dependent Active Site Structural Changes of Lactoperoxidase Compound 0 and Its Ferryl Heme O–O Bond Cleavage Products. J Am Chem Soc 2014; 137:349-61. [DOI: 10.1021/ja5107833] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Piotr J. Mak
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Warut Thammawichai
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Dennis Wiedenhoeft
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - James R. Kincaid
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
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25
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Ohta T, Liu JG, Naruta Y. Resonance Raman characterization of mononuclear heme-peroxo intermediate models. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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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: 4.8] [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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27
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Ibrahim M, Kincaid JR. Spectroscopic studies of peroxo/hydroperoxo derivatives of heme proteins and model compounds. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424604000209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The spectroscopic characterization of peroxo- and hydroperoxo- intermediates of heme proteins and enzymes has long interested scientists studying the structure and function of these important biochemical systems. Until very recently, little progress had been made in studying these fleeting intermediates by vibrational spectroscopic methods. In this brief review, recent studies reporting the Resonance Raman and Infrared spectra of such intermediates and pertinent model compounds are reviewed and compared to corresponding studies utilizing electronic absorption and electron paramagnetic resonance spectrometric methods.
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Affiliation(s)
- Mohammed Ibrahim
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - James R. Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
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28
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Cryoradiolysis and cryospectroscopy for studies of heme-oxygen intermediates in cytochromes p450. Methods Mol Biol 2012; 875:375-91. [PMID: 22573452 DOI: 10.1007/978-1-61779-806-1_20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryogenic radiolytic reduction is one of the most straightforward and convenient methods of generation and stabilization of reactive iron-oxygen intermediates for mechanistic studies in chemistry and biochemistry. The method is based on one-electron reduction of the precursor complex in frozen solution via exposure to the ionizing radiation at cryogenic temperatures. Such approach allows for accumulation of the fleeting reactive complexes which otherwise could not be generated at sufficient amount for structural and mechanistic studies. Application of this method allowed for characterizing of peroxo-ferric and hydroperoxo-ferric intermediates, which are common for the oxygen activation mechanism in cytochromes P450, heme oxygenases, and nitric oxide synthases, as well as for the peroxide metabolism by peroxidases and catalases.
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29
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Mak PJ, Denisov IG, Grinkova YV, Sligar SG, Kincaid JR. Defining CYP3A4 structural responses to substrate binding. Raman spectroscopic studies of a nanodisc-incorporated mammalian cytochrome P450. J Am Chem Soc 2011; 133:1357-66. [PMID: 21207936 DOI: 10.1021/ja105869p] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Resonance Raman (RR) spectroscopy is used to help define active site structural responses of nanodisc-incorporated CYP3A4 to the binding of three substrates: bromocriptine (BC), erythromycin (ERY), and testosterone (TST). We demonstrate that nanodisc-incorporated assemblies reveal much more well-defined active site RR spectroscopic responses as compared to those normally obtained with the conventional, detergent-stabilized, sampling strategies. While ERY and BC are known to bind to CYP3A4 with a 1:1 stoichiometry, only the BC induces a substantial conversion from low- to high-spin state, as clearly manifested in the RR spectra acquired herein. The third substrate, TST, displays significant homotropic interactions within CYP3A4, the active site binding up to 3 molecules of this substrate, with the functional properties varying in response to binding of individual substrate molecules. While such behavior seemingly suggests the possibility that each substrate binding event induces functionally important heme structural changes, up to this time spectroscopic evidence for such structural changes has not been available. The current RR spectroscopic studies show clearly that accommodation of different size substrates, and different loading of TST, do not significantly affect the structure of the substrate-bound ferric heme. However, it is here demonstrated that the nature and number of bound substrates do have an extraordinary influence on the conformation of bound exogenous ligands, such as CO or dioxygen and its reduced forms, implying an effective mechanism whereby substrate structure can impact reactivity of intermediates so as to influence function, as reflected in the diverse reactivity of this drug metabolizing cytochrome.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53233, United States
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30
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Kitagishi H, Tamaki M, Ueda T, Hirota S, Ohta T, Naruta Y, Kano K. Oxoferryl Porphyrin/Hydrogen Peroxide System Whose Behavior is Equivalent to Hydroperoxoferric Porphyrin. J Am Chem Soc 2010; 132:16730-2. [DOI: 10.1021/ja106798a] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Mariko Tamaki
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Takunori Ueda
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Shun Hirota
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Takehiro Ohta
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yoshinori Naruta
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Koji Kano
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
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Cytochromes P450 in nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:223-9. [PMID: 20685623 DOI: 10.1016/j.bbapap.2010.05.017] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 05/17/2010] [Accepted: 05/24/2010] [Indexed: 01/20/2023]
Abstract
Nanodiscs have proven to be a versatile tool for the study all types of membrane proteins, including receptors, transporters, enzymes and viral antigens. The self-assembled Nanodisc system provides a robust and common means for rendering these targets soluble in aqueous media while providing a native like bilayer environment that maintains functional activity. This system has thus provided a means for studying the extensive collection of membrane bound cytochromes P450 with the same biochemical and biophysical tools that have been previously limited to use with the soluble P450s. These include a plethora of spectroscopic, kinetic and surface based methods. Significant improvements in homogeneity and stability of these preparations open new possibilities for detailed analysis of equilibrium and steady-state kinetic characteristics of catalytic mechanisms of human cytochromes P450 involved in xenobiotic metabolism and in steroid biosynthesis. The experimental methods developed for physico-chemical and functional studies of membrane cytochromes P450 incorporated in Nanodiscs allow for more detailed understanding of the scientific questions along the lines pioneered by Professor Klaus Ruckpaul and his array of colleagues and collaborators.
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Liu JG, Ohta T, Yamaguchi S, Ogura T, Sakamoto S, Maeda Y, Naruta Y. Spectroscopic characterization of a hydroperoxo-heme intermediate: conversion of a side-on peroxo to an end-on hydroperoxo complex. Angew Chem Int Ed Engl 2010; 48:9262-7. [PMID: 19882613 DOI: 10.1002/anie.200904572] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jin-Gang Liu
- Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka, 812-8581, Japan
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Liu JG, Ohta T, Yamaguchi S, Ogura T, Sakamoto S, Maeda Y, Naruta Y. Spectroscopic Characterization of a HydroperoxoâHeme Intermediate: Conversion of a Side-On Peroxo to an End-On Hydroperoxo Complex. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904572] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Abstract
In contrast to the wide spectrum of cytochrome P450 monooxygenases, there are only 2 heme-based dioxygenases in humans: tryptophan dioxygenase (hTDO) and indoleamine 2,3-dioxygenase (hIDO). hTDO and hIDO catalyze the same oxidative ring cleavage reaction of L-tryptophan to N-formyl kynurenine, the initial and rate-limiting step of the kynurenine pathway. Despite immense interest, the mechanism by which the 2 enzymes execute the dioxygenase reaction remains elusive. Here, we report experimental evidence for a key ferryl intermediate of hIDO that supports a mechanism in which the 2 atoms of dioxygen are inserted into the substrate via a consecutive 2-step reaction. This finding introduces a paradigm shift in our understanding of the heme-based dioxygenase chemistry, which was previously believed to proceed via simultaneous incorporation of both atoms of dioxygen into the substrate. The ferryl intermediate is not observable during the hTDO reaction, highlighting the structural differences between the 2 dioxygenases, as well as the importance of stereoelectronic factors in modulating the reactions.
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Denisov IG, Mak PJ, Makris TM, Sligar SG, Kincaid JR. Resonance Raman characterization of the peroxo and hydroperoxo intermediates in cytochrome P450. J Phys Chem A 2009; 112:13172-9. [PMID: 18630867 DOI: 10.1021/jp8017875] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Resonance Raman (RR) studies of intermediates generated by cryoreduction of the oxyferrous complex of the D251N mutant of cytochrome P450(cam) (CYP101) are reported. Owing to the fact that proton delivery to the active site is hindered in this mutant, the unprotonated peroxo-ferric intermediate is observed as the primary species after radiolytic reduction of the oxy-complex in frozen solutions at 77 K. In as much as previous EPR and ENDOR studies have shown that annealing of this species to approximately 180 K results in protonation of the distal oxygen atom to form the hydroperoxo intermediate, this system has been exploited to permit direct RR interrogation of the changes in the Fe-O and O-O bonds caused by the reduction and subsequent protonation. Our results show that the nu(O-O) mode decreases from a superoxo-like frequency near approximately 1130 cm(-1) to 792 cm(-1) upon reduction. The latter frequency, as well as its lack of sensitivity to H/D exchange, is consistent with heme-bound peroxide formulation. This species also exhibits a nu(Fe-O) mode, the 553 cm(-1) frequency of which is higher than that observed for the nonreduced oxy P450 precursor (537 cm(-1)), implying a strengthened Fe-O linkage upon reduction. Upon subsequent protonation, the resulting Fe-O-OH fragment exhibits a lowered nu(O-O) mode at 774 cm(-1), whereas the nu(Fe-O) increases to 564 cm(-1). Both modes exhibit a downshift upon H/D exchange, as expected for a hydroperoxo-ferric formulation. These experimental RR data are compared with those previously acquired for the wild-type protein, and the shifts observed upon reduction and subsequent protonation are discussed with reference to theoretical predictions.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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37
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Hersleth HP, Hsiao YW, Ryde U, Görbitz CH, Andersson KK. The influence of X-rays on the structural studies of peroxide-derived myoglobin intermediates. Chem Biodivers 2008; 5:2067-2089. [PMID: 18972498 DOI: 10.1002/cbdv.200890189] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In recent years, the awareness of potential radiation damage of metal centers in protein crystals during crystallographic data collection has received increasing attention. The radiation damage can lead to radiation-induced changes and reduction of the metal sites. One of the research fields where these concerns have been comprehensively addressed is the study of the reaction intermediates of the heme peroxidase and oxygenase reaction cycles. For both the resting states and the high-valent intermediates, the X-rays used in the structure determination have given undesired side effects through radiation-induced changes to the trapped intermediates. However, X-rays have been used to generate and trap the peroxy/hydroperoxy state in crystals. In this review, the structural work and the influence of X-rays on these intermediates in myoglobin are summarized and viewed in light of analogous studies on similar intermediates in peroxidases and oxygenases.
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Affiliation(s)
- Hans-Petter Hersleth
- University of Oslo, Department of Molecular Biosciences, P. O. Box 1041 Blindern, N-0316 Oslo
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38
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Mak PJ, Kincaid JR. Resonance Raman spectroscopic studies of hydroperoxo derivatives of cobalt-substituted myoglobin. J Inorg Biochem 2008; 102:1952-7. [PMID: 18723225 DOI: 10.1016/j.jinorgbio.2008.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 07/11/2008] [Accepted: 07/14/2008] [Indexed: 11/15/2022]
Abstract
Recent progress in generating and stabilizing reactive heme protein enzymatic intermediates by cryoradiolytic reduction has prompted application of a range of spectroscopic approaches to effectively interrogate these species. The impressive potential of resonance Raman spectroscopy for characterizing such samples has been recently demonstrated in a number of studies of peroxo- and hydroperoxo-intermediates. While it is anticipated that this approach can be productively applied to the wide range of heme proteins whose reaction cycles naturally involve these peroxo- and hydroperoxo-intermediates, one limitation that sometimes arises is the lack of enhancement of the key intraligand nu(O-O) stretching mode in the native systems. The present work was undertaken to explore the utility of cobalt substitution to enhance both the nu(Co-O) and nu(O-O) modes of the CoOOH fragments of hydroperoxo forms of heme proteins bearing a trans-axial histidine linkage. Thus, having recently completed RR studies of hydroperoxo myoglobin, attention is now turned to its cobalt-substituted analogue. Spectra are acquired for samples prepared with (16)O(2) and (18)O(2) to reveal the nu(M-O) and nu(O-O) modes, the latter indeed being observed only for the cobalt-substituted proteins. In addition, spectra of samples prepared in deuterated solvents were also acquired, providing definitive evidence for the presence of the hydroperoxo-species.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
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39
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The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection. Biochem J 2008; 412:257-64. [DOI: 10.1042/bj20070921] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 01/22/2008] [Accepted: 01/23/2008] [Indexed: 11/17/2022]
Abstract
Myoglobin has the ability to react with hydrogen peroxide, generating high-valent complexes similar to peroxidases (compounds I and II), and in the presence of excess hydrogen peroxide a third intermediate, compound III, with an oxymyoglobin-type structure is generated from compound II. The compound III is, however, easily one-electron reduced to peroxymyoglobin by synchrotron radiation during crystallographic data collection. We have generated and solved the 1.30 Å (1 Å=0.1 nm) resolution crystal structure of the peroxymyoglobin intermediate, which is isoelectric to compound 0 and has a Fe–O distance of 1.8 Å and O–O bond of 1.3 Å in accordance with a FeII–O–O− (or FeIII–O–O2−) structure. The generation of the peroxy intermediate through reduction of compound III by X-rays shows the importance of using single-crystal microspectrophotometry when doing crystallography on metalloproteins. After having collected crystallographic data on a peroxy-generated myoglobin crystal, we were able (by a short annealing) to break the O–O bond leading to formation of compound II. These results indicate that the cryoradiolytic-generated peroxymyoglobin is biologically relevant through its conversion into compound II upon heating. Additionally, we have observed that the Xe1 site is occupied by a water molecule, which might be the leaving group in the compound II to compound III reaction.
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40
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Hersleth HP, Varnier A, Harbitz E, Røhr ÅK, Schmidt PP, Sørlie M, Cederkvist FH, Marchal S, Gorren AC, Mayer B, Uchida T, Schünemann V, Kitagawa T, Trautwein AX, Shimizu T, Lange R, Görbitz CH, Andersson KK. Reactive complexes in myoglobin and nitric oxide synthase. Inorganica Chim Acta 2008. [DOI: 10.1016/j.ica.2007.09.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Denisov IG, Dawson JH, Hager LP, Sligar SG. The ferric-hydroperoxo complex of chloroperoxidase. Biochem Biophys Res Commun 2007; 363:954-8. [PMID: 17920039 DOI: 10.1016/j.bbrc.2007.09.085] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Accepted: 09/19/2007] [Indexed: 10/22/2022]
Abstract
The hydroperoxo-ferric complex, or Compound 0 (Cpd 0), is an unstable transient intermediate common for oxygen activating heme enzymes such as the cytochromes P450, nitric oxide synthases, and heme oxygenases, as well as the peroxidases and catalases which utilize hydrogen peroxide as a source of oxygen and reducing equivalents. Detailed understanding of the mechanism of oxygen activation and formation of the higher valent catalytically active intermediates in heme enzyme catalysis requires the structural and spectroscopic characterization of this immediate precursor, Cpd 0. Using the method of cryoradiolytic reduction of the oxy-ferrous heme complex, we have prepared and characterized hydroperoxo-ferric complex in chloroperoxidase (CPO) and compared this to the same intermediate generated in cytochrome P450 CYP101. Optical absorption spectrum of Cpd 0 in CPO has a Soret band at 449 nm and poorly resolved alpha, beta bands at 576 and 546 nm.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, 116 Morrill Hall, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801, USA
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42
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Hersleth HP, Uchida T, Røhr AK, Teschner T, Schünemann V, Kitagawa T, Trautwein AX, Görbitz CH, Andersson KK. Crystallographic and Spectroscopic Studies of Peroxide-derived Myoglobin Compound II and Occurrence of Protonated FeIV–O. J Biol Chem 2007; 282:23372-86. [PMID: 17565988 DOI: 10.1074/jbc.m701948200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (<1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe-O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an Fe(IV)-O species with a single bond. The presence of Fe(IV) is indicated by a small isomer shift of delta = 0.07 mm/s from Mössbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.
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Affiliation(s)
- Hans-Petter Hersleth
- Department of Chemistry, University of Oslo, PO Box 1033, Blindern, Oslo N-0315, Norway
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43
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Ichikawa Y, Nakajima H, Watanabe Y. Characterization of peroxide-bound heme species generated in the reaction of thermally tolerant cytochrome c552 with hydrogen peroxide. Chembiochem 2007; 7:1582-9. [PMID: 16921577 DOI: 10.1002/cbic.200600135] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Peroxide-bound heme species have been considered difficult to detect under physiological conditions because of their intrinsically transient properties. Cytochrome c552 (cyt c552), from Thermus thermophirus HB8, bearing a mutation to an alanine at Met69 (M69A) reacts with hydrogen peroxide (H(2)O(2)) to generate a detectable hydroperoxo-ferric heme ([Fe(3+)--OOH]) species at ambient temperature. EPR measurements during appropriate reaction periods reveal that the [Fe(3+)--OOH] species is in a preequilibrium state between the resting form of the cyt c552 variant and a subsequent intermediate, compound II with a protein radical. Addition of ascorbic acid to the reaction mixture of the cyt c552 variant and H(2)O(2) does not affect the formation of the [Fe(3+)--OOH] species,a result suggesting that the species is incompetent for the oxidation of even an oxidatively fragile substrate such as ascorbic acid. Another variant bearing an additional mutation to aspartic acid at Val49 (V49D/M69A) reveals that a highly hydrophobic heme cavity in cyt c552 accounts for the generation of the durable [Fe(3+)--OOH] species. The less polar environment inside the cavity is expected to prevent H(2)O from approaching the cavity. This would suppress protonation of the distal oxygen atom of the [Fe(3+)--OOH] species and retard subsequent dissociation of H(2)O from the OOH moiety.
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Affiliation(s)
- Yusuke Ichikawa
- Department of Chemistry, Graduate School of Science Nagoya University, 464-8602 Nagoya, Japan
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44
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Mak PJ, Denisov IG, Victoria D, Makris TM, Deng T, Sligar SG, Kincaid JR. Resonance Raman detection of the hydroperoxo intermediate in the cytochrome P450 enzymatic cycle. J Am Chem Soc 2007; 129:6382-3. [PMID: 17461587 PMCID: PMC2574425 DOI: 10.1021/ja071426h] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Resonance Raman spectra of the hydroperoxo complex of camphor-bound CYP101 have been obtained by cryoradiolytic reduction of the oxygenated ferrous form that had been rapidly frozen in water-glycerol frozen solution; EPR spectroscopy was employed to confirm the identity of the trapped intermediate. The ν(O-O) mode, appearing at 799cm−1, is observed for the first time in a peroxo-heme adduct. It is assigned unambiguously by employing isotopomeric mixtures of oxygen gas containing 50% 16O18O, confirming the presence of an intact O-O fragment. The ν(Fe-O) mode is observed at 559 cm−1 (H2O). Furthermore, both modes shift down by 3 cm−1, documenting the formulation as a hydroperoxo-complex, in agreement with EPR data.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
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45
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Denisov IG, Victoria DC, Sligar SG. Cryoradiolytic reduction of heme proteins: Maximizing dose dependent yield. Radiat Phys Chem Oxf Engl 1993 2007; 76:714-721. [PMID: 18379640 DOI: 10.1016/j.radphyschem.2006.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Radiolytic reduction in frozen solutions and crystals is a useful method for generation of trapped intermediates in protein based radical reactions. In this communication we define the conditions which provide the maximum yield of one electron reduced myoglobin at 77 K using (60)Co γ-irradiation in aqueous glycerol glass. The yield reached 50% after 20 kGy, was almost complete at ∼160 kGy total dose, and does not depend on the protein concentration in the range 0.01 - 5 mM.
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Affiliation(s)
- Ilia G Denisov
- University of Illinois Urbana-Champaign, Department of Biochemistry, Urbana IL, 61801
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46
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Liu JG, Naruta Y, Tani F. A functional model of the cytochrome c oxidase active site: unique conversion of a heme-mu-peroxo-Cu(II) intermediate into heme- superoxo/Cu(I). Angew Chem Int Ed Engl 2006; 44:1836-40. [PMID: 15723432 DOI: 10.1002/anie.200462582] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jin-Gang Liu
- Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka, 812-8581, Japan
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47
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Bakac A. Kinetic and mechanistic studies of the reactions of transition metal-activated oxygen with inorganic substrates. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.02.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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48
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Kühnel K, Blankenfeldt W, Terner J, Schlichting I. Crystal structures of chloroperoxidase with its bound substrates and complexed with formate, acetate, and nitrate. J Biol Chem 2006; 281:23990-8. [PMID: 16790441 DOI: 10.1074/jbc.m603166200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chloroperoxidase (CPO) is a heme-thiolate enzyme that catalyzes hydrogen peroxide-dependent halogenation reactions. Structural data on substrate binding have not been available so far. CPO was therefore crystallized in the presence of iodide or bromide. One halide binding site was identified at the surface near a narrow channel that connects the surface with the heme. Two other halide binding sites were identified within and at the other end of this channel. Together, these sites suggest a pathway for access of halide anions to the active site. The structure of CPO complexed with its natural substrate cyclopentanedione was determined at a resolution of 1.8 A. This is the first example of a CPO structure with a bound organic substrate. In addition, structures of CPO bound with nitrate, acetate, and formate and of a ternary complex with dimethylsulfoxide (Me2SO) and cyanide were determined. These structures have implications for the mechanism of compound I formation. Before binding to the heme, the incoming hydrogen peroxide first interacts with Glu-183. The deprotonated Glu-183 abstracts a proton from hydrogen peroxide. The hydroperoxo-anion then binds at the heme, yielding compound 0. Glu-183 protonates the distal oxygen of compound 0, water is released, and compound I is formed.
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Affiliation(s)
- Karin Kühnel
- Abteilung Biomolekulare Mechanismen, Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
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49
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Terner J, Palaniappan V, Gold A, Weiss R, Fitzgerald MM, Sullivan AM, Hosten CM. Resonance Raman spectroscopy of oxoiron(IV) porphyrin π-cation radical and oxoiron(IV) hemes in peroxidase intermediates. J Inorg Biochem 2006; 100:480-501. [PMID: 16513173 DOI: 10.1016/j.jinorgbio.2006.01.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 01/04/2006] [Indexed: 11/15/2022]
Abstract
The catalytic cycle intermediates of heme peroxidases, known as compounds I and II, have been of long standing interest as models for intermediates of heme proteins, such as the terminal oxidases and cytochrome P450 enzymes, and for non-heme iron enzymes as well. Reports of resonance Raman signals for compound I intermediates of the oxo-iron(IV) porphyrin pi-cation radical type have been sometimes contradictory due to complications arising from photolability, causing compound I signals to appear similar to those of compound II or other forms. However, studies of synthetic systems indicated that protein based compound I intermediates of the oxoiron(IV) porphyrin pi-cation radical type should exhibit vibrational signatures that are different from the non-radical forms. The compound I intermediates of horseradish peroxidase (HRP), and chloroperoxidase (CPO) from Caldariomyces fumago do in fact exhibit unique and characteristic vibrational spectra. The nature of the putative oxoiron(IV) bond in peroxidase intermediates has been under discussion in the recent literature, with suggestions that the Fe(IV)O unit might be better described as Fe(IV)-OH. The generally low Fe(IV)O stretching frequencies observed for proteins have been difficult to mimic in synthetic ferryl porphyrins via electron donation from trans axial ligands alone. Resonance Raman studies of iron-oxygen vibrations within protein species that are sensitive to pH, deuteration, and solvent oxygen exchange, indicate that hydrogen bonding to the oxoiron(IV) group within the protein environment contributes to substantial lowering of Fe(IV)O frequencies relative to those of synthetic model compounds.
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Affiliation(s)
- James Terner
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
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50
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Sligar SG, Makris TM, Denisov IG. Thirty years of microbial P450 monooxygenase research: Peroxo-heme intermediates—The central bus station in heme oxygenase catalysis. Biochem Biophys Res Commun 2005; 338:346-54. [PMID: 16139790 DOI: 10.1016/j.bbrc.2005.08.094] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Indexed: 10/25/2022]
Abstract
Oxygen has always been recognized as an essential element of many life forms, initially through its role as a terminal electron acceptor for the energy-generating pathways of oxidative phosphorylation. In 1955, Hayaishi et al. [Mechanism of the pyrocatechase reaction, J. Am. Chem. Soc. 77 (1955) 5450-5451] presented the most important discovery that changed this simplistic view of how Nature uses atmospheric dioxygen. His discovery, the naming and mechanistic understanding of the first "oxygenase" enzyme, has provided a wonderful opportunity and scientific impetus for four decades of researchers. This volume provides an opportunity to recognize the breakthroughs of the "Hayaishi School." Notable have been the prolific contributions of Professor Ishimura et al. [Oxygen and life. Oxygenases, Oxidases and Lipid Mediators, International Congress Series, Elsevier, Amsterdam, 2002], a first-generation Hayaishi product, to characterization of the cytochrome P450 monooxygenases.
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Affiliation(s)
- Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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