1
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Satpathy JK, Yadav R, Bagha UK, Kumar D, Sastri CV, de Visser SP. Enhanced Reactivity through Equatorial Sulfur Coordination in Nonheme Iron(IV)-Oxo Complexes: Insights from Experiment and Theory. Inorg Chem 2024; 63:6752-6766. [PMID: 38551622 DOI: 10.1021/acs.inorgchem.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Sulfur ligation in metalloenzymes often gives the active site unique properties, whether it is the axial cysteinate ligand in the cytochrome P450s or the equatorial sulfur/thiol ligation in nonheme iron enzymes. To understand sulfur ligation to iron complexes and how it affects the structural, spectroscopic, and intrinsic properties of the active species and the catalysis of substrates, we pursued a systematic study and compared sulfur with amine-ligated iron(IV)-oxo complexes. We synthesized and characterized a biomimetic N4S-ligated iron(IV)-oxo complex and compared the obtained results with an analogous N5-ligated iron(IV)-oxo complex. Our work shows that the amine for sulfur replacement in the equatorial ligand framework leads to a rate enhancement for oxygen atom and hydrogen atom transfer reactions. Moreover, the sulfur-ligated iron(IV)-oxo complex reacts through a different reaction mechanism as compared to the N5-ligated iron(IV)-oxo complex, where the former reacts through hydride transfer with the latter reacting via radical pathways. We show that the reactivity differences are caused by a dramatic change in redox potential between the two complexes. Our studies highlight the importance of implementing a sulfur ligand into the equatorial ligand framework of nonheme iron(IV)-oxo complexes and how it affects the physicochemical properties of the oxidant and its reactivity.
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Affiliation(s)
- Jagnyesh K Satpathy
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Rolly Yadav
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Umesh K Bagha
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Devesh Kumar
- Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow 226025, UP, India
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Sam P de Visser
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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2
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Ansari M, Bhattacharjee S, Pantazis DA. Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II. J Am Chem Soc 2024; 146:9640-9656. [PMID: 38530124 PMCID: PMC11009960 DOI: 10.1021/jacs.3c13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024]
Abstract
Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.
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Affiliation(s)
- Mursaleem Ansari
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Sinjini Bhattacharjee
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
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3
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Awasthi A, Mallojjala SC, Kumar R, Eerlapally R, Hirschi JS, Draksharapu A. Altering the Localization of an Unpaired Spin in a Formal Ni(V) Species. Chemistry 2024; 30:e202302824. [PMID: 37903027 PMCID: PMC10841873 DOI: 10.1002/chem.202302824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
The participation of both ligand and the metal center in the redox events has been recognized as one of the ways to attain the formal high valent complexes for the late 3d metals, such as Ni and Cu. Such an approach has been employed successfully to stabilize a Ni(III) bisphenoxyl diradical species in which there exist an equilibrium between the ligand and the Ni localized resultant spin. The present work, however, broadens the scope of the previously reported three oxidized equivalent species by conveying the approaches that tend to affect the reported equilibrium in CH3 CN at 233 K. Various spectroscopic characterization revealed that employing exogenous N-donor ligands like 1-methyl imidazole and pyridine favors the formation of the Ni centered localized spin though axial binding. In contrast, due to its steric hinderance, quinoline favors an exclusive ligand localized radical species. DFT studies shed light on the novel intermediates' complex electronic structure. Further, the three oxidized equivalent species with the Ni centered spin was examined for its hydrogen atom abstraction ability stressing their key role in alike reactions.
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Affiliation(s)
- Ayushi Awasthi
- Southern Laboratories-208 A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | | | - Rakesh Kumar
- Southern Laboratories-208 A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Raju Eerlapally
- Southern Laboratories-208 A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Jennifer S Hirschi
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Apparao Draksharapu
- Southern Laboratories-208 A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
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4
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Jeong D, Selverstone Valentine J, Cho J. Bio-inspired mononuclear nonheme metal peroxo complexes: Synthesis, structures and mechanistic studies toward understanding enzymatic reactions. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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5
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Wang M, Chen Y, Yu Z, Hou Y, Jiang R, Li S, Chen J, Tang W, Pang H, Xie W. Unraveling the π-interaction of NiFe-based metal-organic frameworks with enhanced oxygen evolution: Optimizing electronic structure and facilitating electron transfer modulation. J Colloid Interface Sci 2023; 640:1-14. [PMID: 36827844 DOI: 10.1016/j.jcis.2023.02.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Metal-organic frameworks (MOFs) with conjugation carboxylate ligands as electrocatalysts can significantly improve oxygen evolution reaction (OER), but the role of π-interaction on the reactive sites of OER is often neglected. We intend to unravel the mechanism of how π-interaction enhances OER performance. The results of Rietveld refinement, density functional theory (DFT) calculations, and in-situ Raman spectra show that π-interaction can efficiently modulate the local spin configuration of metal centers, facilitate γ-Ni1-xFexOOH active species with high-valence Ni sites modified by high-spin Fe, accelerate electron transfer, optimize the d-band center together with the beneficial rate-determining step of OER. NiFe-BPDC MOFs/NF with 0.8559 eV π-interaction energy generated γ-Ni1-xFexOOH in only 60 s at 1.4 V, demonstrating that π-interaction promotes the rapid generation of highly active reactive sites. Furthermore, the results of in-situ Raman and electron paramagnetic resonance (EPR) spectra reveal that the deprotonation and deoxygenation steps of OER are accompanied by changes in the oxidation state of metal ions and the generation of oxygen vacancies on the surface of catalysts. In addition, NiFe-BPDC MOFs/NF rapidly completes the deprotonation and deoxygenation steps, and it requires only 288 mV overpotential to reach 100 mA/cm2 with 100 h of stability, suggesting promising industrial application.
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Affiliation(s)
- Mi Wang
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Yushan Chen
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Zebin Yu
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China.
| | - Yanping Hou
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Ronghua Jiang
- School of Chemical and Environmental Engineering, Shaoguan University, Shaoguan 512005, China
| | - Shuang Li
- School of Environmental Science and Technology, Dalian University of Technology, Dalian 116023, China
| | - Jianhua Chen
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Wenjun Tang
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Han Pang
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Wenhui Xie
- State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures, School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
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6
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Ramos DR, Furtmüller PG, Obinger C, Peña-Gallego Á, Pérez-Juste I, Santaballa JA. Common Reactivity and Properties of Heme Peroxidases: A DFT Study of Their Origin. Antioxidants (Basel) 2023; 12:antiox12020303. [PMID: 36829861 PMCID: PMC9952403 DOI: 10.3390/antiox12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Electronic structure calculations using the density-functional theory (DFT) have been performed to analyse the effect of water molecules and protonation on the heme group of peroxidases in different redox (ferric, ferrous, compounds I and II) and spin states. Shared geometries, spectroscopic properties at the Soret region, and the thermodynamics of peroxidases are discussed. B3LYP and M06-2X density functionals with different basis sets were employed on a common molecular model of the active site (Fe-centred porphine and proximal imidazole). Computed Gibbs free energies indicate that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) centre in native ferric peroxidases, with a water molecule located at a non-bonding distance. Protonation of the ferryl oxygen of compound II is discussed in terms of thermodynamics, Fe-O bond distances, and redox properties. It is demonstrated that this protonation is necessary to account for the experimental data, and computed Gibbs free energies reveal pKa values of compound II about 8.5-9.0. Computation indicates that the general oxidative properties of peroxidase intermediates, as well as their reactivity towards water and protons and Soret bands, are mainly controlled by the iron porphyrin and its proximal histidine ligand.
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Affiliation(s)
- Daniel R. Ramos
- Chemical Reactivity & Photoreactivity Group (React!), Department of Chemistry, CICA & Faculty of Sciences, Universidade da Coruña, Campus da Zapateira, E-15071 A Coruña, Spain
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
- Correspondence: (D.R.R.); (J.A.S.)
| | - Paul G. Furtmüller
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Ángeles Peña-Gallego
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
| | - Ignacio Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
| | - J. Arturo Santaballa
- Chemical Reactivity & Photoreactivity Group (React!), Department of Chemistry, CICA & Faculty of Sciences, Universidade da Coruña, Campus da Zapateira, E-15071 A Coruña, Spain
- Correspondence: (D.R.R.); (J.A.S.)
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7
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Lučić M, Wilson MT, Tosha T, Sugimoto H, Shilova A, Axford D, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB. ACS Catal 2022; 12:13349-13359. [PMID: 36366763 PMCID: PMC9638988 DOI: 10.1021/acscatal.2c03754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/05/2022] [Indexed: 11/30/2022]
Abstract
![]()
Controlling the reactivity
of high-valent Fe(IV)–O
catalytic
intermediates, Compounds I and II, generated in heme enzymes upon
reaction with dioxygen or hydrogen peroxide, is important for function.
It has been hypothesized that the presence (wet) or absence (dry)
of distal heme pocket water molecules can influence whether Compound
I undergoes sequential one-electron additions or a concerted two-electron
reduction. To test this hypothesis, we investigate the role of water
in the heme distal pocket of a dye-decolorizing peroxidase utilizing
a combination of serial femtosecond crystallography and rapid kinetic
studies. In a dry distal heme site, Compound I reduction proceeds
through a mechanism in which Compound II concentration is low. This
reaction shows a strong deuterium isotope effect, indicating that
reduction is coupled to proton uptake. The resulting protonated Compound
II (Fe(IV)–OH) rapidly reduces to the ferric state, giving
the appearance of a two-electron transfer process. In a wet site,
reduction of Compound I is faster, has no deuterium effect, and yields
highly populated Compound II, which is subsequently reduced to the
ferric form. This work provides a definitive experimental test of
the hypothesis advanced in the literature that relates sequential
or concerted electron transfer to Compound I in wet or dry distal
heme sites.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park,
Essex, ColchesterCO4 3SQ, U.K
| | - Michael T. Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park,
Essex, ColchesterCO4 3SQ, U.K
| | - Takehiko Tosha
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo, Hyogo679-5148Japan
| | | | - Anastasya Shilova
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, DidcotOX11 0DE, U.K
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, DidcotOX11 0DE, U.K
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, DidcotOX11 0DE, U.K
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park,
Essex, ColchesterCO4 3SQ, U.K
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, DidcotOX11 0DE, U.K
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park,
Essex, ColchesterCO4 3SQ, U.K
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8
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Revealing *OOH key intermediates and regulating H 2O 2 photoactivation by surface relaxation of Fenton-like catalysts. Proc Natl Acad Sci U S A 2022; 119:e2205562119. [PMID: 36037332 PMCID: PMC9457417 DOI: 10.1073/pnas.2205562119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogen peroxide (H2O2) molecules play important roles in many green chemical reactions. However, the high activation energy limits their application efficiency, and there is still huge controversy about the activation path of H2O2 molecules over the presence of *OOH intermediates. Here, we confirmed the formation of the key species *OOH in the heterogeneous system, via in situ shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS), isotope labeling, and theoretical calculation. In addition, we found that compared with *H2O2, *OOH was more conducive to the charge transfer behavior with the catalyst and the activation of an O-O bond. Furthermore, we proposed to improve the local coordination structure and electronic density of the YFeO3 catalyst by regulating the surface relaxation with Ti modification so as to reduce the activation barrier of H2O2 and to improve the production efficiency of •OH. As a result, the kinetics rates of the Fenton-like (photo-Fenton) reaction had been significantly increased several times. The •OH free radical activity mechanism and molecular transformation pathways of 4-chloro phenol (4-CP) were also revealed. This may provide a clearer vision for the further study of H2O2 activation and suggest a means of designing catalysts for efficient H2O2 activation.
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9
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Dedushko MA, Greiner MB, Downing AN, Coggins M, Kovacs JA. Electronic Structure and Reactivity of Dioxygen-Derived Aliphatic Thiolate-Ligated Fe-Peroxo and Fe(IV) Oxo Compounds. J Am Chem Soc 2022; 144:8515-8528. [PMID: 35522532 DOI: 10.1021/jacs.1c07656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Herein, we examine the electronic and geometric structural properties of O2-derived aliphatic thiolate-ligated Fe-peroxo, Fe-hydroxo, and Fe(IV) oxo compounds. The latter cleaves strong C-H bonds (96 kcal mol-1) on par with the valine C-H bond cleaved by isopencillin N synthase (IPNS). Stopped-flow kinetics studies indicate that the barrier to O2 binding to [FeII(SMe2N4(tren))]+ (3) is extremely low (Ea = 36(2) kJ mol-1), as theoretically predicted for IPNS. Dioxygen binding to 3 is shown to be reversible, and a superoxo intermediate, [FeIII(SMe2N4(tren))(O2)]+ (6), forms in the first 25 ms of the reaction at -40 °C prior to the rate-determining (Ea = 46(2) kJ mol-1) formation of peroxo-bridged [(SMe2N4(tren))Fe(III)]2(μ-O2)2+ (7). A log(kobs) vs log([Fe]) plot for the formation of 7 is consistent with the second-order dependence on iron, and H2O2 assays are consistent with a 2:1 ratio of Fe/H2O2. Peroxo 7 is shown to convert to ferric-hydroxo [FeIII(SMe2N(tren))(OH)]+ (9, g⊥ = 2.24, g∥ = 1.96), the identity of which was determined via its independent synthesis. Rates of the conversion 7 → 9 are shown to be dependent on the X-H bond strength of the H-atom donor, with a kH/kD = 4 when CD3OD is used in place of CH3OH as a solvent. A crystallographically characterized cis thiolate-ligated high-valent iron oxo, [FeIV(O)(SMe2N4(tren))]+ (11), is shown to form en route to hydroxo 9. Electronic structure calculations were shown to be consistent with 11 being an S = 1 Fe(IV)═O with an unusually high νFe-O stretching frequency at 918 cm-1 in line with the extremely short Fe-O bond (1.603(7) Å).
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Affiliation(s)
- Maksym A Dedushko
- Department of Chemistry, University of Washington, Campus Box 351700, Seattle, Washington 98195-1700, United States
| | - Maria B Greiner
- Department of Chemistry, University of Washington, Campus Box 351700, Seattle, Washington 98195-1700, United States
| | - Alexandra N Downing
- Department of Chemistry, University of Washington, Campus Box 351700, Seattle, Washington 98195-1700, United States
| | - Michael Coggins
- Department of Chemistry, University of Washington, Campus Box 351700, Seattle, Washington 98195-1700, United States
| | - Julie A Kovacs
- Department of Chemistry, University of Washington, Campus Box 351700, Seattle, Washington 98195-1700, United States
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10
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Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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11
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Lučić M, Wilson MT, Svistunenko DA, Owen RL, Hough MA, Worrall JAR. Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of Fe IV = O formation in bacterial dye-decolorizing peroxidases. J Biol Inorg Chem 2021; 26:743-761. [PMID: 34477969 PMCID: PMC8463360 DOI: 10.1007/s00775-021-01896-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, Oxfordshire, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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12
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Mukherjee G, Satpathy JK, Bagha UK, Mubarak MQE, Sastri CV, de Visser SP. Inspiration from Nature: Influence of Engineered Ligand Scaffolds and Auxiliary Factors on the Reactivity of Biomimetic Oxidants. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01993] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Jagnyesh K. Satpathy
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Umesh K. Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Fakulti Sains dan Teknologi, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan Malaysia
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Sam P. de Visser
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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13
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Kwon H, Basran J, Pathak C, Hussain M, Freeman SL, Fielding AJ, Bailey AJ, Stefanou N, Sparkes HA, Tosha T, Yamashita K, Hirata K, Murakami H, Ueno G, Ago H, Tono K, Yamamoto M, Sawai H, Shiro Y, Sugimoto H, Raven EL, Moody PCE. XFEL Crystal Structures of Peroxidase Compound II. Angew Chem Int Ed Engl 2021; 60:14578-14585. [PMID: 33826799 PMCID: PMC8251747 DOI: 10.1002/anie.202103010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 01/07/2023]
Abstract
Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an FeIV =O or FeIV -OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated FeIV =O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme.
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Affiliation(s)
- Hanna Kwon
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Chinar Pathak
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Mahdi Hussain
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Samuel L. Freeman
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Alistair J. Fielding
- Centre for Natural Products Discovery, Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityJames Parsons Building, Byrom StreetLiverpoolL3 3AFUK
| | - Anna J. Bailey
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Natalia Stefanou
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Hazel A. Sparkes
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | - Keitaro Yamashita
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Present address: MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB1 0QHUK
| | - Kunio Hirata
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hironori Murakami
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | - Go Ueno
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hideo Ago
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Hitomi Sawai
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | - Yoshitsugu Shiro
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | | | - Emma L. Raven
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Peter C. E. Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
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14
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Kwon H, Basran J, Pathak C, Hussain M, Freeman SL, Fielding AJ, Bailey AJ, Stefanou N, Sparkes HA, Tosha T, Yamashita K, Hirata K, Murakami H, Ueno G, Ago H, Tono K, Yamamoto M, Sawai H, Shiro Y, Sugimoto H, Raven EL, Moody PCE. XFEL Crystal Structures of Peroxidase Compound II. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:14699-14706. [PMID: 38505375 PMCID: PMC10947387 DOI: 10.1002/ange.202103010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 03/21/2024]
Abstract
Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an FeIV=O or FeIV-OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated FeIV=O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme.
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Affiliation(s)
- Hanna Kwon
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Chinar Pathak
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Mahdi Hussain
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Samuel L. Freeman
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Alistair J. Fielding
- Centre for Natural Products Discovery, Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityJames Parsons Building, Byrom StreetLiverpoolL3 3AFUK
| | - Anna J. Bailey
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Natalia Stefanou
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Hazel A. Sparkes
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | - Keitaro Yamashita
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Present address: MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB1 0QHUK
| | - Kunio Hirata
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hironori Murakami
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | - Go Ueno
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hideo Ago
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Hitomi Sawai
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | - Yoshitsugu Shiro
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | | | - Emma L. Raven
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Peter C. E. Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
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15
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Deutscher J, Gerschel P, Warm K, Kuhlmann U, Mebs S, Haumann M, Dau H, Hildebrandt P, Apfel UP, Ray K. A bioinspired oxoiron(IV) motif supported on a N 2S 2 macrocyclic ligand. Chem Commun (Camb) 2021; 57:2947-2950. [PMID: 33621306 DOI: 10.1039/d1cc00250c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A mononuclear oxoiron(iv) complex 1-trans bearing two equatorial sulfur ligations is synthesized and characterized as an active-site model of the elusive sulfur-ligated FeIV[double bond, length as m-dash]O intermediates in non-heme iron oxygenases. The introduction of sulfur ligands weakens the Fe[double bond, length as m-dash]O bond and enhances the oxidative reactivity of the FeIV[double bond, length as m-dash]O unit with a diminished deuterium kinetic isotope effect, thereby providing a compelling rationale for nature's use of the cis-thiolate ligated oxoiron(iv) motif in key metabolic transformations.
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Affiliation(s)
- Jennifer Deutscher
- Institut für Chemie Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
| | - Philipp Gerschel
- Anorganische Chemie 1 Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Katrin Warm
- Institut für Chemie Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
| | - Uwe Kuhlmann
- Institut für Chemie Technische, Universität Berlin, Fakultät II Straße des 17, Juni 135, 10623, Berlin, Germany
| | - Stefan Mebs
- Institut für Physik Freie, Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Michael Haumann
- Institut für Physik Freie, Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Holger Dau
- Institut für Physik Freie, Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Peter Hildebrandt
- Institut für Chemie Technische, Universität Berlin, Fakultät II Straße des 17, Juni 135, 10623, Berlin, Germany
| | - Ulf-Peter Apfel
- Anorganische Chemie 1 Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany and Department of Electrosynthesis, Fraunhofer UMSICHT, Osterfelder Str. 3, 46047 Oberhausen, Germany
| | - Kallol Ray
- Institut für Chemie Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
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16
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Ledray AP, Krest CM, Yosca TH, Mittra K, Green MT. Ascorbate Peroxidase Compound II Is an Iron(IV) Oxo Species. J Am Chem Soc 2020; 142:10.1021/jacs.0c09108. [PMID: 33170000 PMCID: PMC8107191 DOI: 10.1021/jacs.0c09108] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The protonation state of the iron(IV) oxo (or ferryl) form of ascorbate peroxidase compound II (APX-II) is a subject of debate. It has been reported that this intermediate is best described as an iron(IV) hydroxide species. Neutron diffraction data obtained from putative APX-II crystals indicate a protonated oxygenic ligand at 1.88 Å from the heme iron. This finding, if correct, would be unprecedented. A basic iron(IV) oxo species has yet to be spectroscopically observed in a histidine-ligated heme enzyme. The importance of ferryl basicity lies in its connection to our fundamental understanding of C-H bond activation. Basic ferryl species have been proposed to facilitate the oxidation of inert C-H bonds, reactions that are unknown for histidine-ligated hemes enzymes. To provide further insight into the protonation status of APX-II, we examined the intermediate using a combination of Mössbauer and X-ray absorption spectroscopies. Our data indicate that APX-II is an iron(IV) oxo species with an Fe-O bond distance of 1.68 Å, a K-edge pre-edge absorption of 18 units, and Mössbauer parameters of ΔEq = 1.65 mm/s and δ = 0.03 mm/s.
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Affiliation(s)
- Aaron P Ledray
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Courtney M Krest
- Roach & Associates, Limited Liability Company, Seymour, Wisconsin 54942, United States
| | - Timothy H Yosca
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Kaustuv Mittra
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Michael T Green
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
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17
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Weitz AC, Biswas S, Rizzolo K, Elliott S, Bominaar EL, Hendrich MP. Electronic State of the His/Tyr-Ligated Heme of BthA by Mössbauer and DFT Analysis. Inorg Chem 2020; 59:10223-10233. [PMID: 32602712 DOI: 10.1021/acs.inorgchem.0c01349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The BthA protein from the microorganism Burkholderia thailandensis contains two hemes with axial His/OH2 and His/Tyr coordinations separated by the closest interheme distance of 14 Å. BthA has a similar structure and belongs to the same family of multiheme cytochrome c peroxidases as MauG, which performs long-range oxidation of the partner protein methylamine dehydrogenase. Magnetic Mössbauer spectroscopy of the diferric state of BthA corroborates previous structural work identifying a high-spin (His/OH2) peroxidatic heme and a low-spin (His/Tyr) electron transfer heme. Unlike MauG, addition of H2O2 fully converts the diferric form of BthA to a stable 2e- oxidized state, allowing a new assessment of this state. The peroxidatic heme is found to be oxidized to a canonical compound II, S = 1 oxoiron(IV) heme. In contrast, the electronic properties of the oxidized His/Tyr heme are puzzling. The isomer shift of the His/Tyr heme (0.17 mm/s) is close to that of the precursor S = 1/2 Fe3+ heme (0.21 mm/s) which suggests oxidation of the Tyr. However, the spin-dipolar hyperfine coupling constants are found here to be the same as those for the ferryl peroxidatic heme, indicating that the His/Tyr heme is also a compound II, S = 1 Fe4+ heme and ruling out oxidation of the Tyr. DFT calculations indicate that the unusually high isomer shift is not attributable to the rare axial His/Tyr heme coordination. The calculations are only compatible with spectroscopy for an unusually long Fe4+-OTyr distance, which is presumably under the influence of the protein environment of the His/Tyr heme moiety in the H2O2 oxidized state of the protein. The results offer new insights into how high valence intermediates can be tuned by the protein environment for performing long-range oxidation.
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Affiliation(s)
- Andrew C Weitz
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Saborni Biswas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kim Rizzolo
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sean Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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18
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Bhunia S, Rana A, Dey SG, Ivancich A, Dey A. A designed second-sphere hydrogen-bond interaction that critically influences the O-O bond activation for heterolytic cleavage in ferric iron-porphyrin complexes. Chem Sci 2020; 11:2681-2695. [PMID: 34084327 PMCID: PMC8157560 DOI: 10.1039/c9sc04388h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/26/2020] [Indexed: 12/18/2022] Open
Abstract
Heme hydroperoxidases catalyze the oxidation of substrates by H2O2. The catalytic cycle involves the formation of a highly oxidizing species known as Compound I, resulting from the two-electron oxidation of the ferric heme in the active site of the resting enzyme. This high-valent intermediate is formed upon facile heterolysis of the O-O bond in the initial FeIII-OOH complex. Heterolysis is assisted by the histidine and arginine residues present in the heme distal cavity. This chemistry has not been successfully modeled in synthetic systems up to now. In this work, we have used a series of iron(iii) porphyrin complexes (FeIIIL2(Br), FeIIIL3(Br) and FeIIIMPh(Br)) with covalently attached pendent basic groups (pyridine and primary amine) mimicking the histidine and arginine residues in the distal-pocket of natural heme enzymes. The presence of pendent basic groups, capable of 2nd sphere hydrogen bonding interactions, leads to almost 1000-fold enhancement in the rate of Compound I formation from peracids relative to analogous complexes without these residues. The short-lived Compound I intermediate formed at cryogenic temperatures could be detected using UV-vis electronic absorption spectroscopy and also trapped to be unequivocally identified by 9 GHz EPR spectroscopy at 4 K. The broad (2000 G) and axial EPR spectrum of an exchange-coupled oxoferryl-porphyrin radical species, [FeIV[double bond, length as m-dash]O Por˙+] with g eff ⊥ = 3.80 and g eff ‖ = 1.99, was observed upon a reaction of the FeIIIL3(Br) porphyrin complex with m-CPBA. The characterization of the reactivity of the FeIII porphyrin complexes with a substrate in the presence of an oxidant like m-CPBA by UV-vis electronic absorption spectroscopy showed that they are capable of oxidizing two equivalents of inorganic and organic substrate(s) like ferrocene, 2,4,6-tritertiary butyl phenol and o-phenylenediamine. These oxidations are catalytic with a turnover number (TON) as high as 350. Density Functional Theory (DFT) calculations show that the mechanism of O-O bond activation by 2nd sphere hydrogen bonding interaction from these pendent basic groups, which are protonated by a peracid, involves polarization of the O-O σ-bond, leading to lowering of the O-O σ*-orbital allowing enhanced back bonding from the iron center. These results demonstrate how inclusion of 2nd sphere hydrogen bonding interaction can play a critical role in O-O bond heterolysis.
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Affiliation(s)
- Sarmistha Bhunia
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Atanu Rana
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Somdatta Ghosh Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Anabella Ivancich
- CNRS, Aix-Marseille Univ, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479 Marseille France
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
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19
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Mubarak MQE, Visser SP. Computational Study on the Catalytic Reaction Mechanism of Heme Haloperoxidase Enzymes. Isr J Chem 2019. [DOI: 10.1002/ijch.201900099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
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20
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Ehudin MA, Gee LB, Sabuncu S, Braun A, Moenne-Loccoz P, Hedman B, Hodgson KO, Solomon EI, Karlin KD. Tuning the Geometric and Electronic Structure of Synthetic High-Valent Heme Iron(IV)-Oxo Models in the Presence of a Lewis Acid and Various Axial Ligands. J Am Chem Soc 2019; 141:5942-5960. [PMID: 30860832 PMCID: PMC6611672 DOI: 10.1021/jacs.9b00795] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
High-valent ferryl species (e.g., (Por)FeIV═O, Cmpd-II) are observed or proposed key oxidizing intermediates in the catalytic cycles of heme-containing enzymes (P-450s, peroxidases, catalases, and cytochrome c oxidase) involved in biological respiration and oxidative metabolism. Herein, various axially ligated iron(IV)-oxo complexes were prepared to examine the influence of the identity of the base. These were generated by addition of various axial ligands (1,5-dicyclohexylimidazole (DCHIm), a tethered-imidazole system, and sodium derivatives of 3,5-dimethoxyphenolate and imidazolate). Characterization was carried out via UV-vis, electron paramagnetic resonance (EPR), 57Fe Mössbauer, Fe X-ray absorption (XAS), and 54/57Fe resonance Raman (rR) spectroscopies to confirm their formation and compare the axial ligand perturbation on the electronic and geometric structures of these heme iron(IV)-oxo species. Mössbauer studies confirmed that the axially ligated derivatives were iron(IV) and six-coordinate complexes. XAS and 54/57Fe rR data correlated with slight elongation of the iron-oxo bond with increasing donation from the axial ligands. The first reported synthetic H-bonded iron(IV)-oxo heme systems were made in the presence of the protic Lewis acid, 2,6-lutidinium triflate (LutH+), with (or without) DCHIm. Mössbauer, rR, and XAS spectroscopic data indicated the formation of molecular Lewis acid ferryl adducts (rather than full protonation). The reduction potentials of these novel Lewis acid adducts were bracketed through addition of outer-sphere reductants. The oxidizing capabilities of the ferryl species with or without Lewis acid vary drastically; addition of LutH+ to F8Cmpd-II (F8 = tetrakis(2,6-difluorophenyl)porphyrinate) increased its reduction potential by more than 890 mV, experimentally confirming that H-bonding interactions can increase the reactivity of ferryl species.
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Affiliation(s)
- Melanie A. Ehudin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Leland B. Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Sinan Sabuncu
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Pierre Moenne-Loccoz
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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21
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Liu Y, Huo Z, Song Z, Zhang C, Ren D, Zhong H, Jin F. Preparing a magnetic activated carbon with expired beverage as carbon source and KOH as activator. J Taiwan Inst Chem Eng 2019. [DOI: 10.1016/j.jtice.2018.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 582] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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23
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Affiliation(s)
- Paolo Pirovano
- School of Chemistry and CRANN/AMBER Nanoscience Institute; Trinity College Dublin; The University of Dublin; College Green 2 Dublin Ireland
| | - Aidan R. McDonald
- School of Chemistry and CRANN/AMBER Nanoscience Institute; Trinity College Dublin; The University of Dublin; College Green 2 Dublin Ireland
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24
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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: 7.3] [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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Zaragoza JPT, Yosca TH, Siegler MA, Moënne-Loccoz P, Green MT, Goldberg DP. Direct Observation of Oxygen Rebound with an Iron-Hydroxide Complex. J Am Chem Soc 2017; 139:13640-13643. [PMID: 28930448 DOI: 10.1021/jacs.7b07979] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The rebound mechanism for alkane hydroxylation was invoked over 40 years ago to help explain reactivity patterns in cytochrome P450, and subsequently has been used to provide insight into a range of biological and synthetic systems. Efforts to model the rebound reaction in a synthetic system have been unsuccessful, in part because of the challenge in preparing a suitable metal-hydroxide complex at the correct oxidation level. Herein we report the synthesis of such a complex. The reaction of this species with a series of substituted radicals allows for the direct interrogation of the rebound process, providing insight into this uniformly invoked, but previously unobserved process.
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Affiliation(s)
- Jan Paulo T Zaragoza
- Department of Chemistry, The Johns Hopkins University , 3400 N Charles Street, Baltimore, Maryland 21218, United States
| | - Timothy H Yosca
- Department of Chemistry and Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University , 3400 N Charles Street, Baltimore, Maryland 21218, United States
| | - Pierre Moënne-Loccoz
- Division of Environmental and Biomolecular Systems, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Michael T Green
- Department of Chemistry and Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University , 3400 N Charles Street, Baltimore, Maryland 21218, United States
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Dornevil K, Davis I, Fielding AJ, Terrell JR, Ma L, Liu A. Cross-linking of dicyclotyrosine by the cytochrome P450 enzyme CYP121 from Mycobacterium tuberculosis proceeds through a catalytic shunt pathway. J Biol Chem 2017; 292:13645-13657. [PMID: 28667013 DOI: 10.1074/jbc.m117.794099] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
CYP121, the cytochrome P450 enzyme in Mycobacterium tuberculosis that catalyzes a single intramolecular C-C cross-linking reaction in the biosynthesis of mycocyclosin, is crucial for the viability of this pathogen. This C-C coupling reaction represents an expansion of the activities carried out by P450 enzymes distinct from oxygen insertion. Although the traditional mechanism for P450 enzymes has been well studied, it is unclear whether CYP121 follows the general P450 mechanism or uses a different catalytic strategy for generating an iron-bound oxidant. To gain mechanistic insight into the CYP121-catalyzed reaction, we tested the peroxide shunt pathway by using rapid kinetic techniques to monitor the enzyme activity with its substrate dicyclotyrosine (cYY) and observed the formation of the cross-linked product mycocyclosin by LC-MS. In stopped-flow experiments, we observed that cYY binding to CYP121 proceeds in a two-step process, and EPR spectroscopy indicates that the binding induces active site reorganization and uniformity. Using rapid freeze-quenching EPR, we observed the formation of a high-spin intermediate upon the addition of peracetic acid to the enzyme-substrate complex. This intermediate exhibits a high-spin (S = 5/2) signal with g values of 2.00, 5.77, and 6.87. Likewise, iodosylbenzene could also produce mycocyclosin, implicating compound I as the initial oxidizing species. Moreover, we also demonstrated that CYP121 performs a standard peroxidase type of reaction by observing substrate-based radicals. On the basis of these results, we propose plausible free radical-based mechanisms for the C-C bond coupling reaction.
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Affiliation(s)
- Kednerlin Dornevil
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Ian Davis
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Andrew J Fielding
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
| | - James R Terrell
- the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Li Ma
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
| | - Aimin Liu
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
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27
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Lang J, Maréchal A, Couture M, Santolini J. Reaction Intermediates and Molecular Mechanism of Peroxynitrite Activation by NO Synthases. Biophys J 2017; 111:2099-2109. [PMID: 27851935 DOI: 10.1016/j.bpj.2016.05.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022] Open
Abstract
The activation of the peroxynitrite anion (PN) by hemoproteins, which leads to its detoxification or, on the contrary to the enhancement of its cytotoxic activity, is a reaction of physiological importance that is still poorly understood. It has been known for some years that the reaction of hemoproteins, notably cytochrome P450, with PN leads to the buildup of an intermediate species with a Soret band at ∼435 nm (I435). The nature of this intermediate is, however, debated. On the one hand, I435 has been presented as a compound II species that can be photoactivated to compound I. A competing alternative involves the assignment of I435 to a ferric-nitrosyl species. Similar to cytochromes P450, the buildup of I435 occurs in nitric oxide synthases (NOSs) upon their reaction with excess PN. Interestingly, the NOS isoforms vary in their capacity to detoxify/activate PN, although they all show the buildup of I435. To better understand PN activation/detoxification by heme proteins, a definitive assignment of I435 is needed. Here we used a combination of fine kinetic analysis under specific conditions (pH, PN concentrations, and PN/NOSs ratios) to probe the formation of I435. These studies revealed that I435 is not formed upon homolytic cleavage of the O-O bond of PN, but instead arises from side reactions associated with excess PN. Characterization of I435 by resonance Raman spectroscopy allowed its identification as a ferric iron-nitrosyl complex. Our study indicates that the model used so far to depict PN interactions with hemo-thiolate proteins, i.e., leading to the formation and accumulation of compound II, needs to be reconsidered.
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Affiliation(s)
- Jérôme Lang
- Laboratory of Oxidative Stress and Detoxification, iBiTec-S/I2BC, UMR 9198, CEA-Centre National de la Recherche Scientifique Université Paris Sud, CEA Saclay, Gif-sur-Yvette Cedex, France; Department of Biochemistry, Université Laval, Laval, Québec, Canada
| | - Amandine Maréchal
- Laboratory of Oxidative Stress and Detoxification, iBiTec-S/I2BC, UMR 9198, CEA-Centre National de la Recherche Scientifique Université Paris Sud, CEA Saclay, Gif-sur-Yvette Cedex, France
| | - Manon Couture
- Department of Biochemistry, Université Laval, Laval, Québec, Canada
| | - Jérôme Santolini
- Laboratory of Oxidative Stress and Detoxification, iBiTec-S/I2BC, UMR 9198, CEA-Centre National de la Recherche Scientifique Université Paris Sud, CEA Saclay, Gif-sur-Yvette Cedex, France.
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Yosca TH, Ledray AP, Ngo J, Green MT. A new look at the role of thiolate ligation in cytochrome P450. J Biol Inorg Chem 2017; 22:209-220. [PMID: 28091754 PMCID: PMC5640440 DOI: 10.1007/s00775-016-1430-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/14/2016] [Indexed: 10/20/2022]
Abstract
Protonated ferryl (or iron(IV)hydroxide) intermediates have been characterized in several thiolate-ligated heme proteins that are known to catalyze C-H bond activation. The basicity of the ferryl intermediates in these species has been proposed to play a critical role in facilitating this chemistry, allowing hydrogen abstraction at reduction potentials below those that would otherwise lead to oxidative degradation of the enzyme. In this contribution, we discuss the events that led to the assignment and characterization of the unusual iron(IV)hydroxide species, highlighting experiments that provided a quantitative measure of the ferryl basicity, the iron(IV)hydroxide pKa. We then turn to the importance of the iron(IV)hydroxide state, presenting a new way of looking at the role of thiolate ligation in these systems.
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Affiliation(s)
- Timothy H Yosca
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California-Irvine, 4134, Natural Sciences 1, Irvine, CA 92697, USA
| | - Aaron P Ledray
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California-Irvine, 4134, Natural Sciences 1, Irvine, CA 92697, USA
| | - Joanna Ngo
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California-Irvine, 4134, Natural Sciences 1, Irvine, CA 92697, USA
| | - Michael T Green
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California-Irvine, 4134, Natural Sciences 1, Irvine, CA 92697, USA.
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29
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Yosca TH, Langston MC, Krest CM, Onderko EL, Grove TL, Livada J, Green MT. Spectroscopic Investigations of Catalase Compound II: Characterization of an Iron(IV) Hydroxide Intermediate in a Non-thiolate-Ligated Heme Enzyme. J Am Chem Soc 2016; 138:16016-16023. [PMID: 27960340 PMCID: PMC5987761 DOI: 10.1021/jacs.6b09693] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report on the protonation state of Helicobacter pylori catalase compound II. UV/visible, Mössbauer, and X-ray absorption spectroscopies have been used to examine the intermediate from pH 5 to 14. We have determined that HPC-II exists in an iron(IV) hydroxide state up to pH 11. Above this pH, the iron(IV) hydroxide complex transitions to a new species (pKa = 13.1) with Mössbauer parameters that are indicative of an iron(IV)-oxo intermediate. Recently, we discussed a role for an elevated compound II pKa in diminishing the compound I reduction potential. This has the effect of shifting the thermodynamic landscape toward the two-electron chemistry that is critical for catalase function. In catalase, a diminished potential would increase the selectivity for peroxide disproportionation over off-pathway one-electron chemistry, reducing the buildup of the inactive compound II state and reducing the need for energetically expensive electron donor molecules.
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Affiliation(s)
- Timothy H. Yosca
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Matthew C. Langston
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Courtney M. Krest
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Elizabeth L. Onderko
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Tyler L. Grove
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jovan Livada
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michael T. Green
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
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30
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Hill EA, Weitz AC, Onderko E, Romero-Rivera A, Guo Y, Swart M, Bominaar EL, Green MT, Hendrich MP, Lacy DC, Borovik AS. Reactivity of an Fe IV-Oxo Complex with Protons and Oxidants. J Am Chem Soc 2016; 138:13143-13146. [PMID: 27647293 PMCID: PMC5110122 DOI: 10.1021/jacs.6b07633] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-valent Fe-OH species are often invoked as key intermediates but have only been observed in Compound II of cytochrome P450s. To further address the properties of non-heme FeIV-OH complexes, we demonstrate the reversible protonation of a synthetic FeIV-oxo species containing a tris-urea tripodal ligand. The same protonated FeIV-oxo species can be prepared via oxidation, suggesting that a putative FeV-oxo species was initially generated. Computational, Mössbauer, XAS, and NRVS studies indicate that protonation of the FeIV-oxo complex most likely occurs on the tripodal ligand, which undergoes a structural change that results in the formation of a new intramolecular H-bond with the oxido ligand that aids in stabilizing the protonated adduct. We suggest that similar protonated high-valent Fe-oxo species may occur in the active sites of proteins. This finding further argues for caution when assigning unverified high-valent Fe-OH species to mechanisms.
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Affiliation(s)
- Ethan A. Hill
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697
| | - Andrew C. Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Elizabeth Onderko
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi & Dept. Química, Universitat de Girona, 17003, Spain
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi & Dept. Química, Universitat de Girona, 17003, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Michael T. Green
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | | | - David C. Lacy
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697
| | - A. S. Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697
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31
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Davydov R, Im S, Shanmugam M, Gunderson WA, Pearl NM, Hoffman BM, Waskell L. Role of the Proximal Cysteine Hydrogen Bonding Interaction in Cytochrome P450 2B4 Studied by Cryoreduction, Electron Paramagnetic Resonance, and Electron-Nuclear Double Resonance Spectroscopy. Biochemistry 2016; 55:869-83. [PMID: 26750753 DOI: 10.1021/acs.biochem.5b00744] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystallographic studies have shown that the F429H mutation of cytochrome P450 2B4 introduces an H-bond between His429 and the proximal thiolate ligand, Cys436, without altering the protein fold but sharply decreases the enzymatic activity and stabilizes the oxyferrous P450 2B4 complex. To characterize the influence of this hydrogen bond on the states of the catalytic cycle, we have used radiolytic cryoreduction combined with electron paramagnetic resonance (EPR) and (electron-nuclear double resonance (ENDOR) spectroscopy to study and compare their characteristics for wild-type (WT) P450 2B4 and the F429H mutant. (i) The addition of an H-bond to the axial Cys436 thiolate significantly changes the EPR signals of both low-spin and high-spin heme-iron(III) and the hyperfine couplings of the heme-pyrrole (14)N but has relatively little effect on the (1)H ENDOR spectra of the water ligand in the six-coordinate low-spin ferriheme state. These changes indicate that the H-bond introduced between His and the proximal cysteine decreases the extent of S → Fe electron donation and weakens the Fe(III)-S bond. (ii) The added H-bond changes the primary product of cryoreduction of the Fe(II) enzyme, which is trapped in the conformation of the parent Fe(II) state. In the wild-type enzyme, the added electron localizes on the porphyrin, generating an S = (3)/2 state with the anion radical exchange-coupled to the Fe(II). In the mutant, it localizes on the iron, generating an S = (1)/2 Fe(I) state. (iii) The additional H-bond has little effect on g values and (1)H-(14)N hyperfine couplings of the cryogenerated, ferric hydroperoxo intermediate but noticeably slows its decay during cryoannealing. (iv) In both the WT and the mutant enzyme, this decay shows a significant solvent kinetic isotope effect, indicating that the decay reflects a proton-assisted conversion to Compound I (Cpd I). (v) We confirm that Cpd I formed during the annealing of the cryogenerated hydroperoxy intermediate and that it is the active hydroxylating species in both WT P450 2B4 and the F429H mutant. (vi) Our data also indicate that the added H-bond of the mutation diminishes the reactivity of Cpd I.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
| | - Muralidharan Shanmugam
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - William A Gunderson
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Naw May Pearl
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
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32
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Oszajca M, Franke A, Brindell M, Stochel G, van Eldik R. Redox cycling in the activation of peroxides by iron porphyrin and manganese complexes. ‘Catching’ catalytic active intermediates. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.01.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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33
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Altun A. Combined QM/MM studies on spectroscopic parameters of Compound I, Compound II, and related intermediates of cytochrome P450cam. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Zhang Y, Biggs JD, Mukamel S. Characterizing the Intermediates Compound I and II in the Cytochrome P450 Catalytic Cycle with Nonlinear X-ray Spectroscopy: A Simulation Study. Chemphyschem 2015; 16:2006-14. [PMID: 25873009 DOI: 10.1002/cphc.201500064] [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: 01/27/2015] [Revised: 02/24/2015] [Indexed: 11/06/2022]
Abstract
Cytochrome P450 enzymes are an important family of biocatalysts that oxidize chemically inert CH bonds. There are many unresolved questions regarding the catalytic reaction intermediates, in particular P450 Compound I (Cpd-I) and II (Cpd-II). By using simple molecular models, we simulate various X-ray spectroscopy signals, including X-ray absorption near-edge structure (XANES), resonant inelastic X-ray scattering (RIXS), and stimulated X-ray Raman spectroscopy (SXRS) of the low- and high-spin states of Cpd-I and II. Characteristic peak patterns are presented and connected to the corresponding electronic structures. These X-ray spectroscopy techniques are complementary to more conventional infrared and optical spectroscopy and they help to elucidate the evolving electronic structures of transient species along the reaction path.
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Affiliation(s)
- Yu Zhang
- Dept. of Chemistry, University of California, 450 Rowland Hall, Irvine, California 92697 (USA).
| | - Jason D Biggs
- Dept. of Chemistry, University of California, 450 Rowland Hall, Irvine, California 92697 (USA)
| | - Shaul Mukamel
- Dept. of Chemistry, University of California, 450 Rowland Hall, Irvine, California 92697 (USA).
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35
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Smith AT, Pazicni S, Marvin KA, Stevens DJ, Paulsen KM, Burstyn JN. Functional divergence of heme-thiolate proteins: a classification based on spectroscopic attributes. Chem Rev 2015; 115:2532-58. [PMID: 25763468 DOI: 10.1021/cr500056m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aaron T Smith
- †Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208, United States
| | - Samuel Pazicni
- ‡Department of Chemistry, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Katherine A Marvin
- §Department of Chemistry, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032, United States
| | - Daniel J Stevens
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Katherine M Paulsen
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Judith N Burstyn
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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36
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Banerjee R, Proshlyakov Y, Lipscomb JD, Proshlyakov DA. Structure of the key species in the enzymatic oxidation of methane to methanol. Nature 2015; 518:431-4. [PMID: 25607364 PMCID: PMC4429310 DOI: 10.1038/nature14160] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022]
Abstract
Methane monooxygenase (MMO) catalyses the O2-dependent conversion of methane to methanol in methanotrophic bacteria, thereby preventing the atmospheric egress of approximately one billion tons of this potent greenhouse gas annually. The key reaction cycle intermediate of the soluble form of MMO (sMMO) is termed compound Q (Q). Q contains a unique dinuclear Fe(IV) cluster that reacts with methane to break an exceptionally strong 105 kcal mol(-1) C-H bond and insert one oxygen atom. No other biological oxidant, except that found in the particulate form of MMO, is capable of such catalysis. The structure of Q remains controversial despite numerous spectroscopic, computational and synthetic model studies. A definitive structural assignment can be made from resonance Raman vibrational spectroscopy but, despite efforts over the past two decades, no vibrational spectrum of Q has yet been obtained. Here we report the core structures of Q and the following product complex, compound T, using time-resolved resonance Raman spectroscopy (TR(3)). TR(3) permits fingerprinting of intermediates by their unique vibrational signatures through extended signal averaging for short-lived species. We report unambiguous evidence that Q possesses a bis-μ-oxo diamond core structure and show that both bridging oxygens originate from O2. This observation strongly supports a homolytic mechanism for O-O bond cleavage. We also show that T retains a single oxygen atom from O2 as a bridging ligand, while the other oxygen atom is incorporated into the product. Capture of the extreme oxidizing potential of Q is of great contemporary interest for bioremediation and the development of synthetic approaches to methane-based alternative fuels and chemical industry feedstocks. Insight into the formation and reactivity of Q from the structure reported here is an important step towards harnessing this potential.
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Affiliation(s)
- Rahul Banerjee
- 1] Department of Biochemistry, Molecular Biology &Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA [2] Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Yegor Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - John D Lipscomb
- 1] Department of Biochemistry, Molecular Biology &Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA [2] Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Denis A Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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37
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Brines LM, Coggins MK, Poon PCY, Toledo S, Kaminsky W, Kirk ML, Kovacs JA. Water-soluble Fe(II)-H2O complex with a weak O-H bond transfers a hydrogen atom via an observable monomeric Fe(III)-OH. J Am Chem Soc 2015; 137:2253-64. [PMID: 25611075 DOI: 10.1021/ja5068405] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the metal ion properties that favor O-H bond formation versus cleavage should facilitate the development of catalysts tailored to promote a specific reaction, e.g., C-H activation or H2O oxidation. The first step in H2O oxidation involves the endothermic cleavage of a strong O-H bond (BDFE = 122.7 kcal/mol), promoted by binding the H2O to a metal ion, and by coupling electron transfer to proton transfer (PCET). This study focuses on details regarding how a metal ion's electronic structure and ligand environment can tune the energetics of M(HO-H) bond cleavage. The synthesis and characterization of an Fe(II)-H2O complex, 1, that undergoes PCET in H2O to afford a rare example of a monomeric Fe(III)-OH, 7, is described. High-spin 7 is also reproducibly generated via the addition of H2O to {[Fe(III)(O(Me2)N4(tren))]2-(μ-O)}(2+) (8). The O-H bond BDFE of Fe(II)-H2O (1) (68.6 kcal/mol) is calculated using linear fits to its Pourbaix diagram and shown to be 54.1 kcal/mol less than that of H2O and 10.9 kcal/mol less than that of [Fe(II)(H2O)6](2+). The O-H bond of 1 is noticeably weaker than the majority of reported M(n+)(HxO-H) (M = Mn, Fe; n+ = 2+, 3+; x = 0, 1) complexes. Consistent with their relative BDFEs, Fe(II)-H2O (1) is found to donate a H atom to TEMPO(•), whereas the majority of previously reported M(n+)-O(H) complexes, including [Mn(III)(S(Me2)N4(tren))(OH)](+) (2), have been shown to abstract H atoms from TEMPOH. Factors responsible for the weaker O-H bond of 1, such as differences in the electron-donating properties of the ligand, metal ion Lewis acidity, and electronic structure, are discussed.
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Affiliation(s)
- Lisa M Brines
- Department of Chemistry, University of Washington , Campus Box 351700, Seattle, Washington 98195-1700, United States
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Yosca TH, Behan RK, Krest CM, Onderko EL, Langston MC, Green MT. Setting an upper limit on the myoglobin iron(IV)hydroxide pK(a): insight into axial ligand tuning in heme protein catalysis. J Am Chem Soc 2014; 136:9124-31. [PMID: 24875119 PMCID: PMC4091272 DOI: 10.1021/ja503588n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To provide insight into the iron(IV)hydroxide pK(a) of histidine ligated heme proteins, we have probed the active site of myoglobin compound II over the pH range of 3.9-9.5, using EXAFS, Mössbauer, and resonance Raman spectroscopies. We find no indication of ferryl protonation over this pH range, allowing us to set an upper limit of 2.7 on the iron(IV)hydroxide pK(a) in myoglobin. Together with the recent determination of an iron(IV)hydroxide pK(a) ∼ 12 in the thiolate-ligated heme enzyme cytochrome P450, this result provides insight into Nature's ability to tune catalytic function through its choice of axial ligand.
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Affiliation(s)
- Timothy H Yosca
- Department of Chemistry, Pennsylvania State University , University Park, State College, Pennsylvania 16802, United States
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Stoian SA, Xue G, Bominaar EL, Que L, Münck E. Spectroscopic and theoretical investigation of a complex with an [O═Fe(IV)-O-Fe(IV)═O] core related to methane monooxygenase intermediate Q. J Am Chem Soc 2014; 136:1545-58. [PMID: 24380398 DOI: 10.1021/ja411376u] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Previous efforts to model the diiron(IV) intermediate Q of soluble methane monooxygenase have led to the synthesis of a diiron(IV) TPA complex, 2, with an O=Fe(IV)-O-Fe(IV)-OH core that has two ferromagnetically coupled Sloc = 1 sites. Addition of base to 2 at -85 °C elicits its conjugate base 6 with a novel O═Fe(IV)-O-Fe(IV)═O core. In frozen solution, 6 exists in two forms, 6a and 6b, that we have characterized extensively using Mössbauer and parallel mode EPR spectroscopy. The conversion between 2 and 6 is quantitative, but the relative proportions of 6a and 6b are solvent dependent. 6a has two equivalent high-spin (Sloc = 2) sites, which are antiferromagnetically coupled; its quadrupole splitting (0.52 mm/s) and isomer shift (0.14 mm/s) match those of intermediate Q. DFT calculations suggest that 6a assumes an anti conformation with a dihedral O═Fe-Fe═O angle of 180°. Mössbauer and EPR analyses show that 6b is a diiron(IV) complex with ferromagnetically coupled Sloc = 1 and Sloc = 2 sites to give total spin St = 3. Analysis of the zero-field splittings and magnetic hyperfine tensors suggests that the dihedral O═Fe-Fe═O angle of 6b is ∼90°. DFT calculations indicate that this angle is enforced by hydrogen bonding to both terminal oxo groups from a shared water molecule. The water molecule preorganizes 6b, facilitating protonation of one oxo group to regenerate 2, a protonation step difficult to achieve for mononuclear Fe(IV)═O complexes. Complex 6 represents an intriguing addition to the handful of diiron(IV) complexes that have been characterized.
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Affiliation(s)
- Sebastian A Stoian
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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Krewald V, Lassalle-Kaiser B, Boron TT, Pollock CJ, Kern J, Beckwith MA, Yachandra VK, Pecoraro VL, Yano J, Neese F, DeBeer S. The protonation states of oxo-bridged Mn(IV) dimers resolved by experimental and computational Mn K pre-edge X-ray absorption spectroscopy. Inorg Chem 2013; 52:12904-14. [PMID: 24161030 PMCID: PMC3911776 DOI: 10.1021/ic4008203] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In nature, the protonation of oxo bridges is a commonly encountered mechanism for fine-tuning chemical properties and reaction pathways. Often, however, the protonation states are difficult to establish experimentally. This is of particular importance in the oxygen evolving complex of photosystem II, where identification of the bridging oxo protonation states is one of the essential requirements toward unraveling the mechanism. In order to establish a combined experimental and theoretical protocol for the determination of protonation states, we have systematically investigated a series of Mn model complexes by Mn K pre-edge X-ray absorption spectroscopy. An ideal test case for selective bis-μ-oxo-bridge protonation in a Mn dimer is represented by the system [Mn(IV)2(salpn)2(μ-OHn)2](n+). Although the three species [Mn(IV)2(salpn)2(μ-O)2], [Mn(IV)2(salpn)2(μ-O)(μ-OH)](+) and [Mn(IV)2(salpn)2(μ-OH)2](2+) differ only in the protonation of the oxo bridges, they exhibit distinct differences in the pre-edge region while maintaining the same edge energy. The experimental spectra are correlated in detail to theoretically calculated spectra. A time-dependent density functional theory approach for calculating the pre-edge spectra of molecules with multiple metal centers is presented, using both high spin (HS) and broken symmetry (BS) electronic structure solutions. The most intense pre-edge transitions correspond to an excitation of the Mn 1s core electrons into the unoccupied orbitals of local e(g) character (d(z)(2) and d(xy) based in the chosen coordinate system). The lowest energy experimental feature is dominated by excitations of 1s-α electrons, and the second observed feature is primarily attributed to 1s-β electron excitations. The observed energetic separation is due to spin polarization effects in spin-unrestricted density functional theory and models final state multiplet effects. The effects of spin polarization on the calculated Mn K pre-edge spectra, in both the HS and BS solutions, are discussed in terms of the strength of the antiferromagnetic coupling and associated changes in the covalency of Mn-O bonds. The information presented in this paper is complemented with the X-ray emission spectra of the same compounds published in an accompanying paper. Taken together, the two studies provide the foundation for a better understanding of the X-ray spectroscopic data of the oxygen evolving complex (OEC) in photosystem II.
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Affiliation(s)
- Vera Krewald
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Benedikt Lassalle-Kaiser
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Thaddeus T. Boron
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christopher J. Pollock
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Jan Kern
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Martha A. Beckwith
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Vittal K. Yachandra
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Junko Yano
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Frank Neese
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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Yosca TH, Rittle J, Krest CM, Onderko EL, Silakov A, Calixto JC, Behan RK, Green MT. Iron(IV)hydroxide pK(a) and the role of thiolate ligation in C-H bond activation by cytochrome P450. Science 2013; 342:825-9. [PMID: 24233717 PMCID: PMC4299822 DOI: 10.1126/science.1244373] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cytochrome P450 enzymes activate oxygen at heme iron centers to oxidize relatively inert substrate carbon-hydrogen bonds. Cysteine thiolate coordination to iron is posited to increase the pK(a) (where K(a) is the acid dissociation constant) of compound II, an iron(IV)hydroxide complex, correspondingly lowering the one-electron reduction potential of compound I, the active catalytic intermediate, and decreasing the driving force for deleterious auto-oxidation of tyrosine and tryptophan residues in the enzyme's framework. Here, we report on the preparation of an iron(IV)hydroxide complex in a P450 enzyme (CYP158) in ≥90% yield. Using rapid mixing technologies in conjunction with Mössbauer, ultraviolet/visible, and x-ray absorption spectroscopies, we determine a pK(a) value for this compound of 11.9. Marcus theory analysis indicates that this elevated pK(a) results in a >10,000-fold reduction in the rate constant for oxidations of the protein framework, making these processes noncompetitive with substrate oxidation.
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Affiliation(s)
- Timothy H Yosca
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
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Coggins MK, Brines LM, Kovacs JA. Synthesis and structural characterization of a series of Mn(III)OR complexes, including a water-soluble Mn(III)OH that promotes aerobic hydrogen-atom transfer. Inorg Chem 2013; 52:12383-93. [PMID: 24156315 DOI: 10.1021/ic401234t] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hydrogen-atom-transfer (HAT) reactions are a class of proton-coupled electron-transfer (PCET) reactions used in biology to promote substrate oxidation. The driving force for such reactions depends on both the oxidation potential of the catalyst and the pKa value of the proton-acceptor site. Both high-valent transition-metal oxo M(IV)═O (M = Fe, Mn) and lower-valent transition-metal hydroxo compounds M(III)OH (M = Fe, Mn) have been shown to promote these reactions. Herein we describe the synthesis, structure, and reactivity properties of a series of Mn(III)OR compounds [R = (p)NO2Ph (5), Ph (6), Me (7), H (8)], some of which abstract H atoms. The Mn(III)OH complex 8 is water-soluble and represents a rare example of a stable mononuclear Mn(III)OH. In water, the redox potential of 8 was found to be pH-dependent and the Pourbaix (E(p,c) vs pH) diagram has a slope (52 mV pH(-1)) that is indicative of the transfer a single proton with each electron (i.e., PCET). The two compounds with the lowest oxidation potential, hydroxide- and methoxide-bound 7 and 8, are found to oxidize 2,2',6,6'-tetramethylpiperidin-1-ol (TEMPOH), whereas the compounds with the highest oxidation potential, phenol-ligated 5 and 6, are shown to be unreactive. Hydroxide-bound 8 reacts with TEMPOH an order of magnitude faster than methoxide-bound 7. Kinetic data [kH/kD = 3.1 (8); kH/kD = 2.1 (7)] are consistent with concerted H-atom abstraction. The reactive species 8 can be aerobically regenerated in H2O, and at least 10 turnovers can be achieved without significant degradation of the "catalyst". The linear correlation between the redox potential and pH, obtained from the Pourbaix diagram, was used to calculate the bond dissociation free energy (BDFE) = 74.0 ± 0.5 kcal mol(-1) for Mn(II)OH2 in water, and in MeCN, its BDFE was estimated to be 70.1 kcal mol(-1). The reduced protonated derivative of 8, [Mn(II)(S(Me2)N4(tren))(H2O)](+) (9), was estimated to have a pKa of 21.2 in MeCN. The ability (7) and inability (5 and 6) of the other members of the series to abstract a H atom from TEMPOH was used to estimate either an upper or lower limit to the Mn(II)O(H)R pKa based on their experimentally determined redox potentials. The trend in pKa [21.2 (R = H) > 16.2 (R = Me) > 13.5 (R = Ph) > 12.2 (R = (p)NO2Ph)] is shown to oppose that of the oxidation potential E(p,c) [-220 (R = (p)NO2Ph) > -300 (R = Ph) > -410 (R = Me) > -600 (R = H) mV vs Fc(+/0)] for this particular series.
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Affiliation(s)
- Michael K Coggins
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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Krest CM, Onderko EL, Yosca TH, Calixto JC, Karp RF, Livada J, Rittle J, Green MT. Reactive intermediates in cytochrome p450 catalysis. J Biol Chem 2013; 288:17074-81. [PMID: 23632017 DOI: 10.1074/jbc.r113.473108] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, we reported the spectroscopic and kinetic characterizations of cytochrome P450 compound I in CYP119A1, effectively closing the catalytic cycle of cytochrome P450-mediated hydroxylations. In this minireview, we focus on the developments that made this breakthrough possible. We examine the importance of enzyme purification in the quest for reactive intermediates and report the preparation of compound I in a second P450 (P450ST). In an effort to bring clarity to the field, we also examine the validity of controversial reports claiming the production of P450 compound I through the use of peroxynitrite and laser flash photolysis.
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Affiliation(s)
- Courtney M Krest
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Collins DP, Isaac IS, Coulter ED, Hager PW, Ballou DP, Dawson JH. Reaction of ferric Caldariomyces fumago chloroperoxidase with meta-chloroperoxybenzoic acid: sequential formation of compound I, compound II and regeneration of the ferric state using one reactant. J PORPHYR PHTHALOCYA 2013. [DOI: 10.1142/s1088424612501234] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The mechanism of the reaction between ferric Caldariomyces fumago chloroperoxidase (CCPO) and meta-chloroperoxybenzoic acid (mCPBA) has been examined. It has previously been established that an Fe(IV) -oxo porphyrin radical species known as Compound I (Cpd I) is formed by two-electron oxidation of the native ferric enzyme by a variety of oxidants including organic peracids and hydroperoxides. Cpd I can return to the ferric state either by direct oxygen insertion into an organic substrate (e.g. a P450 oxygenase-like reaction), or by two consecutive one-electron additions, the first resulting in an intermediate Fe(IV) -oxo species known as Compound II (Cpd II). There has been much debate over the role of Cpd II and the details of its structure. In the present study, both CCPO Fe(IV) -oxo intermediates are formed, but unlike most CCPO reactions, Cpd I and Cpd II are formed using the same reactant, mCPBA. Thus, the peracid is used as an oxo donor to produce Cpd I and then as a reductant to reduce Cpd I to Cpd II, and finally, Cpd II to the ferric state. The observation of saturation kinetics with respect to mCPBA concentration for each step is consistent with the formation of CCPO-mCPBA complexes in each phase of the reaction. The original reaction mechanism for ferric CCPO with mCPBA was hypothesized to involve a scrambling mechanism with a unique Fe -OOO-C(O)R intermediate formed with no observed Cpd II intermediate. The data reported herein clearly demonstrate the formation of Cpd II in returning the oxidized enzyme back to its native ferric state.
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Affiliation(s)
- Daniel P. Collins
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Issa S. Isaac
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Eric D. Coulter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Paul W. Hager
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - David P. Ballou
- Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
- School of Medicine, University of South Carolina, Columbia, SC 29208, USA
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Intrinsic properties and reactivities of mononuclear nonheme iron–oxygen complexes bearing the tetramethylcyclam ligand. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Mak PJ, Yang Y, Im S, Waskell LA, Kincaid JR. Experimental Documentation of the Structural Consequences of Hydrogen-Bonding Interactions to the Proximal Cysteine of a Cytochrome P450. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205912] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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48
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Mak PJ, Yang Y, Im S, Waskell LA, Kincaid JR. Experimental documentation of the structural consequences of hydrogen-bonding interactions to the proximal cysteine of a cytochrome P450. Angew Chem Int Ed Engl 2012; 51:10403-7. [PMID: 22968976 DOI: 10.1002/anie.201205912] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
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Abstract
Selective functionalization of unactivated C-H bonds and ammonia production are extremely important industrial processes. A range of metalloenyzmes achieve these challenging tasks in biology by activating dioxygen and dinitrogen using cheap and abundant transition metals, such as iron, copper and manganese. High-valent iron-oxo and -nitrido complexes act as active intermediates in many of these processes. The generation of well-described model compounds can provide vital insights into the mechanism of such enzymatic reactions. Advances in the chemistry of model high-valent iron-oxo and -nitrido systems can be related to our understanding of the biological systems.
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Manner VW, Lindsay AD, Mader EA, Harvey JN, Mayer JM. Spin-forbidden hydrogen atom transfer reactions in a cobalt biimidazoline system. Chem Sci 2012. [DOI: 10.1039/c1sc00387a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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