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Nguyen RC, Davis I, Dasgupta M, Wang Y, Simon PS, Butryn A, Makita H, Bogacz I, Dornevil K, Aller P, Bhowmick A, Chatterjee R, Kim IS, Zhou T, Mendez D, Paley D, Fuller F, Alonso-Mori R, Batyuk A, Sauter NK, Brewster AS, Orville AM, Yachandra VK, Yano J, Kern JF, Liu A. In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121. J Am Chem Soc 2023; 145:25120-25133. [PMID: 37939223 PMCID: PMC10799213 DOI: 10.1021/jacs.3c04991] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon-carbon (C-C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. We show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme-substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C-C bond coupling chemistry.
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Affiliation(s)
- Romie C. Nguyen
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Yifan Wang
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Kednerlin Dornevil
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Tiankun Zhou
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Daniel Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Franklin Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jan F. Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
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Nolan K, Wang Y. Combined spectroscopic and structural approaches to explore the mechanism of histidine-ligated heme-dependent aromatic oxygenases. Methods Enzymol 2023; 685:405-432. [PMID: 37245909 PMCID: PMC11057917 DOI: 10.1016/bs.mie.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The emergence of histidine-ligated heme-dependent aromatic oxygenases (HDAOs) has greatly enriched heme chemistry, and more studies are required to appreciate the diversity found in His-ligated heme proteins. This chapter describes recent methods in probing the HDAO mechanisms in detail, along with the discussion on how they can benefit structure-function studies of other heme systems. The experimental details are centered on studies of TyrHs, followed by explanation of how the results obtained would advance the understanding of the specific enzyme and also HDAOs. Spectroscopic methods, namely, electronic absorption and EPR spectroscopies, and X-ray crystallography are valuable techniques commonly used to characterize the properties of the heme center and the nature of heme-based intermediate. Herein, we show that the combination of these tools are extremely powerful, not only because one can acquire electronic, magnetic, and conformational information from different phases, but also because of the advantages brought by spectroscopic characterization on crystal samples.
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Affiliation(s)
- Katie Nolan
- Department of Chemistry, University of Georgia, Athens, GA, United States
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, GA, United States.
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3
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Pal I, Dey SG. The Role of Heme and Copper in Alzheimer's Disease and Type 2 Diabetes Mellitus. JACS AU 2023; 3:657-681. [PMID: 37006768 PMCID: PMC10052274 DOI: 10.1021/jacsau.2c00572] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/19/2023]
Abstract
Beyond the well-explored proposition of protein aggregation or amyloidosis as the central event in amyloidogenic diseases like Alzheimer's Disease (AD), and Type 2 Diabetes Mellitus (T2Dm); there are alternative hypotheses, now becoming increasingly evident, which suggest that the small biomolecules like redox noninnocent metals (Fe, Cu, Zn, etc.) and cofactors (Heme) have a definite influence in the onset and extent of such degenerative maladies. Dyshomeostasis of these components remains as one of the common features in both AD and T2Dm etiology. Recent advances in this course reveal that the metal/cofactor-peptide interactions and covalent binding can alarmingly enhance and modify the toxic reactivities, oxidize vital biomolecules, significantly contribute to the oxidative stress leading to cell apoptosis, and may precede the amyloid fibrils formation by altering their native folds. This perspective highlights this aspect of amyloidogenic pathology which revolves around the impact of the metals and cofactors in the pathogenic courses of AD and T2Dm including the active site environments, altered reactivities, and the probable mechanisms involving some highly reactive intermediates as well. It also discusses some in vitro metal chelation or heme sequestration strategies which might serve as a possible remedy. These findings might open up a new paradigm in our conventional understanding of amyloidogenic diseases. Moreover, the interaction of the active sites with small molecules elucidates potential biochemical reactivities that can inspire designing of drug candidates for such pathologies.
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Affiliation(s)
- Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick
Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick
Road, Jadavpur, Kolkata 700032, India
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4
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Nath AK, Roy M, Dey C, Dey A, Dey SG. Spin state dependent peroxidase activity of heme bound amyloid β peptides relevant to Alzheimer's disease. Chem Sci 2022; 13:14305-14319. [PMID: 36545147 PMCID: PMC9749105 DOI: 10.1039/d2sc05008k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
The colocalization of heme rich deposits in the senile plaque of Aβ in the cerebral cortex of the Alzheimer's disease (AD) brain along with altered heme homeostasis and heme deficiency symptoms in AD patients has invoked the association of heme in AD pathology. Heme bound Aβ complexes, depending on the concentration of the complex or peptide to heme ratio, exhibit an equilibrium between a high-spin mono-His bound peroxidase-type active site and a low-spin bis-His bound cytochrome b type active site. The high-spin heme-Aβ complex shows higher peroxidase activity than free heme, where compound I is the reactive oxidant. It is also capable of oxidizing neurotransmitters like serotonin in the presence of peroxide, owing to the formation of compound I. The low-spin bis-His heme-Aβ complex on the other hand shows enhanced peroxidase activity relative to high-spin heme-Aβ. It reacts with H2O2 to produce two stable intermediates, compound 0 and compound I, which are characterized by absorption, EPR and resonance Raman spectroscopy. The stability of compound I of low-spin heme-Aβ is accountable for its enhanced peroxidase activity and oxidation of the neurotransmitter serotonin. The effect of the second sphere Tyr10 residue of Aβ on the formation and stability of the intermediates of low-spin heme-Aβ has also been investigated. The higher stability of compound I for low-spin heme-Aβ is likely due to H-bonding interactions involving Tyr10 in the distal pocket.
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Affiliation(s)
- Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Chinmay Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
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Gunatilake U, Garcia-Rey S, Ojeda E, Basabe-Desmonts L, Benito-Lopez F. TiO 2 Nanotubes Alginate Hydrogel Scaffold for Rapid Sensing of Sweat Biomarkers: Lactate and Glucose. ACS APPLIED MATERIALS & INTERFACES 2021; 13:37734-37745. [PMID: 34340308 PMCID: PMC8397235 DOI: 10.1021/acsami.1c11446] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Versatile sensing matrixes are essential for the development of enzyme-immobilized optical biosensors. A novel three-dimensional titanium dioxide nanotubes/alginate hydrogel scaffold is proposed for the detection of sweat biomarkers, lactate, and glucose in artificial sweat. Hydrothermally synthesized titanium dioxide nanotubes were introduced to the alginate polymeric matrix, followed by cross-linking nanocomposite with dicationic calcium ions to fabricate the scaffold platform. Rapid colorimetric detection (blue color optical signal) was carried out for both lactate and glucose biomarkers in artificial sweat at 4 and 6 min, respectively. The superhydrophilicity and the capillarity of the synthesized titanium dioxide nanotubes, when incorporated into the alginate matrix, facilitate the rapid transfer of the artificial sweat components throughout the sensor scaffold, decreasing the detection times. Moreover, the scaffold was integrated on a cellulose paper to demonstrate the adaptability of the material to other matrixes, obtaining fast and homogeneous colorimetric detection of lactate and glucose in the paper substrate when image analysis was performed. The properties of this new composite provide new avenues in the development of paper-based sensor devices. The biocompatibility, the efficient immobilization of biological enzymes/colorimetric assays, and the quick optical signal readout behavior of the titanium dioxide nanotubes/alginate hydrogel scaffolds provide a prospective opportunity for integration into wearable devices.
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Affiliation(s)
- Udara
Bimendra Gunatilake
- Microfluidics
Cluster UPV/EHU, Analytical Microsystems & Materials for Lab-on-a-Chip
(AMMa-LOAC) Group, Analytical Chemistry Department, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- Microfluidics
Cluster UPV/EHU, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avenida Miguel de Unamuno, 3, 01006 Vitoria-Gasteiz, Spain
| | - Sandra Garcia-Rey
- Microfluidics
Cluster UPV/EHU, Analytical Microsystems & Materials for Lab-on-a-Chip
(AMMa-LOAC) Group, Analytical Chemistry Department, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- Microfluidics
Cluster UPV/EHU, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avenida Miguel de Unamuno, 3, 01006 Vitoria-Gasteiz, Spain
| | - Edilberto Ojeda
- Microfluidics
Cluster UPV/EHU, Analytical Microsystems & Materials for Lab-on-a-Chip
(AMMa-LOAC) Group, Analytical Chemistry Department, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- Microfluidics
Cluster UPV/EHU, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avenida Miguel de Unamuno, 3, 01006 Vitoria-Gasteiz, Spain
| | - Lourdes Basabe-Desmonts
- Microfluidics
Cluster UPV/EHU, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avenida Miguel de Unamuno, 3, 01006 Vitoria-Gasteiz, Spain
- Bioaraba
Health Research Institute, Microfluidics Cluster UPV/EHU, Avenida Miguel de Unamuno, 3, 01006 Vitoria-Gasteiz, Spain
- BCMaterials,
Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, 48949 Leioa, Spain
- Basque
Foundation of Science, IKERBASQUE, María Díaz Haroko Kalea, 3, 48013 Bilbao, Spain
| | - Fernando Benito-Lopez
- Microfluidics
Cluster UPV/EHU, Analytical Microsystems & Materials for Lab-on-a-Chip
(AMMa-LOAC) Group, Analytical Chemistry Department, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- Bioaraba
Health Research Institute, Microfluidics Cluster UPV/EHU, Avenida Miguel de Unamuno, 3, 01006 Vitoria-Gasteiz, Spain
- BCMaterials,
Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, 48949 Leioa, Spain
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6
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Wang Y, Davis I, Shin I, Xu H, Liu A. Molecular Rationale for Partitioning between C-H and C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase. J Am Chem Soc 2021; 143:4680-4693. [PMID: 33734681 DOI: 10.1021/jacs.1c00175] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The heme-dependent l-tyrosine hydroxylases (TyrHs) in natural product biosynthesis constitute a new enzyme family in contrast to the nonheme iron enzymes for DOPA production. A representative TyrH exhibits dual reactivity of C-H and C-F bond cleavage when challenged with 3-fluoro-l-tyrosine (3-F-Tyr) as a substrate. However, little is known about how the enzyme mediates two distinct reactions. Herein, a new TyrH from the thermophilic bacterium Streptomyces sclerotialus (SsTyrH) was functionally and structurally characterized. A de novo crystal structure of the enzyme-substrate complex at 1.89-Å resolution provides the first comprehensive structural study of this hydroxylase. The binding conformation of l-tyrosine indicates that C-H bond hydroxylation is initiated by electron transfer. Mutagenesis studies confirmed that an active site histidine, His88, participates in catalysis. We also obtained a 1.68-Å resolution crystal structure in complex with the monofluorinated substrate, 3-F-Tyr, which shows one binding conformation but two orientations of the fluorine atom with a ratio of 7:3, revealing that the primary factor of product distribution is the substrate orientation. During in crystallo reaction, a ferric-hydroperoxo intermediate (compound 0, Fe3+-OOH) was observed with 3-F-Tyr as a substrate based on characteristic spectroscopic features. We determined the crystal structure of this compound 0-type intermediate and refined it to 1.58-Å resolution. Collectively, this study provided the first molecular details of the heme-dependent TyrH and determined the primary factor that dictates the partitioning between the dual reactivities of C-H and C-F bond activation.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Inchul Shin
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Hui Xu
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
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Kim H, Rogler PJ, Sharma SK, Schaefer AW, Solomon EI, Karlin KD. Heme-Fe III Superoxide, Peroxide and Hydroperoxide Thermodynamic Relationships: Fe III-O 2•- Complex H-Atom Abstraction Reactivity. J Am Chem Soc 2020; 142:3104-3116. [PMID: 31913628 PMCID: PMC7034651 DOI: 10.1021/jacs.9b12571] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Establishing redox and thermodynamic relationships between metal-ion-bound O2 and its reduced (and protonated) derivatives is critically important for a full understanding of (bio)chemical processes involving dioxygen processing. Here, a ferric heme peroxide complex, [(F8)FeIII-(O22-)]- (P) (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a superoxide complex, [(F8)FeIII-(O2•-)] (S), are shown to be redox interconvertible. Using Cr(η-C6H6)2, an equilibrium state where S and P are present is established in tetrahydrofuran (THF) at -80 °C, allowing determination of the reduction potential of S as -1.17 V vs Fc+/0. P could be protonated with 2,6-lutidinium triflate, yielding the low-spin ferric hydroperoxide species, [(F8)FeIII-(OOH)] (HP). Partial conversion of HP back to P using a derivatized phosphazene base gave a P/HP equilibrium mixture, leading to the determination of pKa = 28.8 for HP (THF, -80 °C). With the measured reduction potential and pKa, the O-H bond dissociation free energy (BDFE) of hydroperoxide species HP was calculated to be 73.5 kcal/mol, employing the thermodynamic square scheme and Bordwell relationship. This calculated O-H BDFE of HP, in fact, lines up with an experimental demonstration of the oxidizing ability of S via hydrogen atom transfer (HAT) from TEMPO-H (2,2,6,6-tetramethylpiperdine-N-hydroxide, BDFE = 66.5 kcal/mol in THF), forming the hydroperoxide species HP and TEMPO radical. Kinetic studies carried out with TEMPO-H(D) reveal second-order behavior, kH = 0.5, kD = 0.08 M-1 s-1 (THF, -80 °C); thus, the hydrogen/deuterium kinetic isotope effect (KIE) = 6, consistent with H-atom abstraction by S being the rate-determining step. This appears to be the first case where experimentally derived thermodynamics lead to a ferric heme hydroperoxide OO-H BDFE determination, that FeIII-OOH species being formed via HAT reactivity of the partner ferric heme superoxide complex.
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Affiliation(s)
- Hyun Kim
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Patrick J Rogler
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Savita K Sharma
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Andrew W Schaefer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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Pal I, Nath AK, Roy M, Seal M, Ghosh C, Dey A, Dey SG. Formation of compound I in heme bound Aβ-peptides relevant to Alzheimer's disease. Chem Sci 2019; 10:8405-8410. [PMID: 31803419 PMCID: PMC6844219 DOI: 10.1039/c9sc01679a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/22/2019] [Indexed: 12/02/2022] Open
Abstract
Proteolysis of Amyloid Precursor Protein, APP, results in the formation of amyloid β (Aβ) peptides, which have been associated with Alzheimer's disease (AD). Recently the failure of therapeutic agents that prohibit Aβ aggregation and sequester Cu/Zn in providing symptomatic relief to AD patients has questioned the amyloid and metal ion hypothesis. Alternatively, abnormal heme homeostasis and reduced levels of neurotransmitters in the brain are hallmark features of AD. Heme can bind Aβ peptides forming a peroxidase type active site which can oxidatively degrade neurotransmitters like serotonin. To date the reactive species responsible for this activity has not been identified. Using rapid kinetics and freeze quenching, we show that heme bound Aβ forms a highly reactive intermediate, compound I. Thus, compound I provides a basis for elucidating the oxidative degradation of neurotransmitters like serotonin, resulting in abnormal neurotransmission, a key pathological feature of AD. Site directed mutants indicate that the Arg5 and Tyr10 residues, unique to human Aβ, affect the rates of formation and decay of compound I providing insight into their roles in the oxidative degradation of neurotransmitters. Tyr10 can potentially play a natural protective role against the highly reactive oxidant, compound I, in AD.
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Affiliation(s)
- Ishita Pal
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Arnab Kumar Nath
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Madhuparna Roy
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Manas Seal
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Chandradeep Ghosh
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Abhishek Dey
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Somdatta Ghosh Dey
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
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9
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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11
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Wise CE, Hsieh CH, Poplin NL, Makris TM. Dioxygen Activation by the Biofuel-Generating Cytochrome P450 OleT. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02631] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Courtney E. Wise
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Chun H. Hsieh
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Nathan L. Poplin
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Thomas M. Makris
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
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12
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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: 591] [Impact Index Per Article: 98.5] [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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13
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Brissos V, Tavares D, Sousa AC, Robalo MP, Martins LO. Engineering a Bacterial DyP-Type Peroxidase for Enhanced Oxidation of Lignin-Related Phenolics at Alkaline pH. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03331] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vânia Brissos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Diogo Tavares
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Ana Catarina Sousa
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Maria Paula Robalo
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Lígia O. Martins
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
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14
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Davydov R, Fleischhacker AS, Bagai I, Hoffman BM, Ragsdale SW. Comparison of the Mechanisms of Heme Hydroxylation by Heme Oxygenases-1 and -2: Kinetic and Cryoreduction Studies. Biochemistry 2015; 55:62-8. [PMID: 26652036 DOI: 10.1021/acs.biochem.5b00943] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The two isoforms of human heme oxygenase (HO1 and HO2) catalyze oxidative degradation of heme to biliverdin, Fe, and CO. Unlike HO1, HO2 contains two C-terminal heme regulatory motifs (HRMs) centered at Cys265 and Cys282 that act as redox switches and, in their reduced dithiolate state, bind heme (Fleischhacker et al., Biochemistry , 2015 , 54 , 2693 - 2708 ). Here, we describe cryoreduction/annealing and electron paramagnetic resonance spectroscopic experiments to study the structural features of the oxyheme moiety in HO2 and to elucidate the initial steps in heme degradation. We conclude that the same mechanism of heme hydroxylation to α-meso-hydroxyheme is employed by both isoforms and that the HRMs do not affect the physicochemical properties of the oxy-Fe(II) and HOO-Fe(III) states of HO2. However, the absorption spectrum of oxy-Fe(II)-HO2 is slightly blue-shifted relative to that of HO1. Furthermore, heme hydroxylation proceeds three times more slowly, and the oxy-Fe(II) state is 100-fold less stable in HO2 than in HO1. These distinctions are attributed to slight structural variances in the two proteins, including differences in equilibrium between open versus closed conformations. Kinetic studies revealed that heme oxygenation by HO2 occurs solely at the catalytic core in that a variant of HO2 lacking the C-terminal HRM domain exhibits the same specific activity as one containing both the catalytic core and HRM domain; furthermore, a truncated variant containing only the HRM region binds but cannot oxidize heme. In summary, HO1 and HO2 share similar catalytic mechanisms, and the HRMs do not play a direct role in the HO2 catalytic cycle.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Angela S Fleischhacker
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Ireena Bagai
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
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15
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Structure and bonding analysis of intermediate model heme-imidazole and heme-thiolate enzymes complexed with formate, acetate and nitrate: A theoretical study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Mendes S, Catarino T, Silveira C, Todorovic S, Martins LO. The catalytic mechanism of A-type dye-decolourising peroxidase BsDyP: neither aspartate nor arginine is individually essential for peroxidase activity. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00478k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BsDyP from Bacillus subtilis belongs to the new dye-decolourising peroxidase (DyP) family. Here, we use transient kinetics to provide details on the catalytic cycle of BsDyP.
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Affiliation(s)
- S. Mendes
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - T. Catarino
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
- Departamento de Química
- Faculdade de Ciências e Tecnologia
| | - C. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - S. Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - L. O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
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17
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Mak PJ, Thammawichai W, Wiedenhoeft D, Kincaid JR. Resonance Raman Spectroscopy Reveals pH-Dependent Active Site Structural Changes of Lactoperoxidase Compound 0 and Its Ferryl Heme O–O Bond Cleavage Products. J Am Chem Soc 2014; 137:349-61. [DOI: 10.1021/ja5107833] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Piotr J. Mak
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Warut Thammawichai
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Dennis Wiedenhoeft
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - James R. Kincaid
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
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18
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Davydov R, Laryukhin M, Ledbetter-Rogers A, Sono M, Dawson JH, Hoffman BM. Electron paramagnetic resonance and electron-nuclear double resonance studies of the reactions of cryogenerated hydroperoxoferric-hemoprotein intermediates. Biochemistry 2014; 53:4894-903. [PMID: 25046203 PMCID: PMC4144713 DOI: 10.1021/bi500296d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The fleeting ferric peroxo and hydroperoxo
intermediates of dioxygen
activation by hemoproteins can be readily trapped and characterized
during cryoradiolytic reduction of ferrous hemoprotein–O2 complexes at 77 K. Previous cryoannealing studies suggested
that the relaxation of cryogenerated hydroperoxoferric intermediates
of myoglobin (Mb), hemoglobin, and horseradish peroxidase (HRP), either
trapped directly at 77 K or generated by cryoannealing of a trapped
peroxo-ferric state, proceeds through dissociation of bound H2O2 and formation of the ferric heme without formation
of the ferryl porphyrin π-cation radical intermediate, compound
I (Cpd I). Herein we have reinvestigated the mechanism of decays of
the cryogenerated hydroperoxyferric intermediates of α- and
β-chains of human hemoglobin, HRP, and chloroperoxidase (CPO).
The latter two proteins are well-known to form spectroscopically detectable
quasistable Cpds I. Peroxoferric intermediates are trapped during
77 K cryoreduction of oxy Mb, α-chains, and β-chains of
human hemoglobin and CPO. They convert into hydroperoxoferric intermediates
during annealing at temperatures above 160 K. The hydroperoxoferric
intermediate of HRP is trapped directly at 77 K. All studied hydroperoxoferric
intermediates decay with measurable rates at temperatures above 170
K with appreciable solvent kinetic isotope effects. The hydroperoxoferric
intermediate of β-chains converts to the S =
3/2 Cpd I, which in turn decays to an electron paramagnetic resonance
(EPR)-silent product at temperature above 220 K. For all the other
hemoproteins studied, cryoannealing of the hydroperoxo intermediate
directly yields an EPR-silent majority product. In each case, a second
follow-up 77 K γ-irradiation of the annealed samples yields
low-spin EPR signals characteristic of cryoreduced ferrylheme (compound
II, Cpd II). This indicates that in general the hydroperoxoferric
intermediates relax to Cpd I during cryoanealing at low temperatures,
but when this state is not captured by reaction with a bound substrate,
it is reduced to Cpd II by redox-active products of radiolysis.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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19
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Gelalcha FG. Biomimetic Iron-Catalyzed Asymmetric Epoxidations: Fundamental Concepts, Challenges and Opportunities. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300716] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Zhao J, Franzen S. Kinetic Study of the Inhibition Mechanism of Dehaloperoxidase-Hemoglobin A by 4-Bromophenol. J Phys Chem B 2013; 117:8301-9. [DOI: 10.1021/jp3116353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
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21
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DiFranco SA, Staples RJ, Odom AL. Single-site N-N bond cleavage by Mo(IV): possible mechanisms of hydrazido(1-) to nitrido conversion. Dalton Trans 2013; 42:2530-9. [PMID: 23212118 DOI: 10.1039/c2dt32643d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mo(NMe(2))(4) and the tridentate, dipyrrolyl ligand H(2)dpma(mes) were found to form 5-coordinate Mo(NMe(2))(2)(dpma(mes)) (1), which exhibits spin-crossover behaviour in solution. The complex is a ground state singlet with a barrier of 1150 cm(-1) for production of the triplet in d(8)-toluene. The complex reacts with 1,1-disubstituted hydrazines or O-benzylhydroxylamine to produce nitrido MoN(NMe(2))(dpma(mes)). The mechanism of the 1,1-dimethylhydrazine reaction with 1 was examined along with the mechanism of substitution of NMe(2) with H(2)NNMe(2) in a diamagnetic zirconium analogue. The proposed mechanism involves production of a hydrazido(1-) intermediate, Mo(NMe(2))(NHNMe(2))(dpma(mes)), which undergoes an α,β-proton shift and N-N bond cleavage with metal oxidation to form the nitrido. The rate law for the reaction was found to be -d[1]/dt = k(obs)[1][hydrazine] by initial rate experiments and examination of the full reaction profile. This conversion from hydrazido(1-) to nitrido is somewhat analogous to the proposed mechanism for O-O bond cleavage in some peroxidases.
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Affiliation(s)
- Stephen A DiFranco
- Michigan State University, Department of Chemistry, 578 S. Shaw Ln, East Lansing, MI 48824, USA
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22
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Ibrahim M, Kincaid JR. Spectroscopic studies of peroxo/hydroperoxo derivatives of heme proteins and model compounds. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424604000209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The spectroscopic characterization of peroxo- and hydroperoxo- intermediates of heme proteins and enzymes has long interested scientists studying the structure and function of these important biochemical systems. Until very recently, little progress had been made in studying these fleeting intermediates by vibrational spectroscopic methods. In this brief review, recent studies reporting the Resonance Raman and Infrared spectra of such intermediates and pertinent model compounds are reviewed and compared to corresponding studies utilizing electronic absorption and electron paramagnetic resonance spectrometric methods.
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Affiliation(s)
- Mohammed Ibrahim
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - James R. Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
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23
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Cryoradiolysis and cryospectroscopy for studies of heme-oxygen intermediates in cytochromes p450. Methods Mol Biol 2012; 875:375-91. [PMID: 22573452 DOI: 10.1007/978-1-61779-806-1_20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryogenic radiolytic reduction is one of the most straightforward and convenient methods of generation and stabilization of reactive iron-oxygen intermediates for mechanistic studies in chemistry and biochemistry. The method is based on one-electron reduction of the precursor complex in frozen solution via exposure to the ionizing radiation at cryogenic temperatures. Such approach allows for accumulation of the fleeting reactive complexes which otherwise could not be generated at sufficient amount for structural and mechanistic studies. Application of this method allowed for characterizing of peroxo-ferric and hydroperoxo-ferric intermediates, which are common for the oxygen activation mechanism in cytochromes P450, heme oxygenases, and nitric oxide synthases, as well as for the peroxide metabolism by peroxidases and catalases.
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24
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D'Antonio J, Ghiladi RA. Reactivity of deoxy- and oxyferrous dehaloperoxidase B from Amphitrite ornata: identification of compound II and its ferrous-hydroperoxide precursor. Biochemistry 2011; 50:5999-6011. [PMID: 21619067 DOI: 10.1021/bi200311u] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a bifunctional enzyme that possesses both hemoglobin and peroxidase activities. The bifunctional nature of DHP as a globin peroxidase appears to be at odds with the traditional starting oxidation state for each individual activity. Namely, reversible oxygen binding is only mediated via a ferrous heme in globins, and peroxidase activity is initiated from ferric centers and to the exclusion of the oxyferrous oxidation state from the peroxidase cycle. Thus, to address what appears to be a paradox, herein we report the details of our investigations into the DHP catalytic cycle when initiated from the deoxy- and oxyferrous states using biochemical assays, stopped-flow UV-visible, and rapid-freeze-quench electron paramagnetic resonance spectroscopies, and anaerobic methods. We demonstrate the formation of Compound II directly from deoxyferrous DHP B upon its reaction with hydrogen peroxide and show that this occurs both in the presence and in the absence of trihalophenol. Prior to the formation of Compound II, we have identified a new species that we have preliminarily attributed to a ferrous-hydroperoxide precursor that undergoes heterolysis to generate the aforementioned ferryl intermediate. Taken together, the results demonstrate that the oxyferrous state in DHP is a peroxidase competent starting species, and an updated catalytic cycle for DHP is proposed in which the ferric oxidation state is not an obligatory starting point for the peroxidase catalytic cycle of dehaloperoxidase. The data presented herein provide a link between the peroxidase and oxygen transport activities, which furthers our understanding of how this bifunctional enzyme is able to unite its two inherent functions in one system.
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Affiliation(s)
- Jennifer D'Antonio
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
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25
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Kitagishi H, Tamaki M, Ueda T, Hirota S, Ohta T, Naruta Y, Kano K. Oxoferryl Porphyrin/Hydrogen Peroxide System Whose Behavior is Equivalent to Hydroperoxoferric Porphyrin. J Am Chem Soc 2010; 132:16730-2. [DOI: 10.1021/ja106798a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Mariko Tamaki
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Takunori Ueda
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Shun Hirota
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Takehiro Ohta
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yoshinori Naruta
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Koji Kano
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan, Graduate School of Materials Science, Nara Institute Science and Technology, Ikoma, Nara 630-0192, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
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26
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Davydov R, Osborne RL, Shanmugam M, Du J, Dawson JH, Hoffman BM. Probing the oxyferrous and catalytically active ferryl states of Amphitrite ornata dehaloperoxidase by cryoreduction and EPR/ENDOR spectroscopy. Detection of compound I. J Am Chem Soc 2010; 132:14995-5004. [PMID: 20925340 PMCID: PMC2978736 DOI: 10.1021/ja1059747] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehaloperoxidase (DHP) from Amphitrite ornata is a heme protein that can function both as a hemoglobin and as a peroxidase. This report describes the use of 77 K cryoreduction EPR/ENDOR techniques to study both functions of DHP. Cryoreduced oxyferrous [Fe(II)-O(2)] DHP exhibits two EPR signals characteristic of a peroxoferric [Fe(III)-O(2)(2-)] heme species, reflecting the presence of conformational substates in the oxyferrous precursor. (1)H ENDOR spectroscopy of the cryogenerated substates shows that H-bonding interactions between His N(ε)H and heme-bound O(2) in these conformers are similar to those in the β-chain of oxyferrous hemoglobin A (HbA) and oxyferrous myoglobin, respectively. Decay of cryogenerated peroxoferric heme DHP intermediates upon annealing at temperatures above 180 K is accompanied by the appearance of a new paramagnetic species with an axial EPR signal with g(⊥) = 3.75 and g(∥) = 1.96, characteristic of an S = 3/2 spin state. This species is assigned to Compound I (Cpd I), in which a porphyrin π-cation radical is ferromagnetically coupled with an S = 1 ferryl [Fe(IV)═O] ion. This species was also trapped by rapid freeze-quench of the ambient-temperature reaction mixture of ferric [Fe(III)] DHP and H(2)O(2). However, in the latter case Cpd I is reduced very rapidly by a nearby tyrosine to form Cpd ES [(Fe(IV)═O)(porphyrin)/Tyr(•)]. Addition of the substrate analogue 2,4,6-trifluorophenol (F(3)PhOH) suppresses formation of the Cpd I intermediate during annealing of cryoreduced oxyferrous DHP at 190 K but has no effect on the spectroscopic properties of the remaining cryoreduced oxyferrous DHP intermediates and kinetics of their decay. These observations indicate that substrate (i) binds to oxyferrous DHP outside of the distal pocket and (ii) can reduce Cpd I to Cpd II [Fe(IV)═O]. These assumptions are also supported by the observation that F(3)PhOH has only a small effect on the EPR properties of radiolytically cryooxidized and cryoreduced ferrous [Fe(II)] DHP. EPR spectra of cryoreduced ferrous DHP disclose the multiconformational nature of the ferrous DHP precursor. The observation and characterization of Cpds I, II, and ES in the absence and in the presence of F(3)PhOH provides definitive evidence of a mechanism involving consecutive one-electron steps and clarifies the role of all intermediates formed during turnover.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Robert L. Osborne
- Department of Chemistry and Biochemistry University of South Carolina, Columbia, South Carolina 29208
| | | | - Jing Du
- Department of Chemistry and Biochemistry University of South Carolina, Columbia, South Carolina 29208
| | - John H. Dawson
- Department of Chemistry and Biochemistry University of South Carolina, Columbia, South Carolina 29208
- School of Medicine University of South Carolina, Columbia, South Carolina 29208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
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27
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Active intermediates in heme monooxygenase reactions as revealed by cryoreduction/annealing, EPR/ENDOR studies. Arch Biochem Biophys 2010; 507:36-43. [PMID: 20854788 DOI: 10.1016/j.abb.2010.09.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 09/13/2010] [Accepted: 09/14/2010] [Indexed: 11/21/2022]
Abstract
This review describes the use of cryoreduction/annealing EPR/ENDOR techniques for determining the active oxidizing species in reactions catalyzed by heme monooxygenases. The three candidate heme states are: ferric peroxo, ferric hydroperoxo and compound I intermediates. The enzymes discussed include cytochromes P450, nitric oxide synthase and heme oxygenase.
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28
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Liu JG, Ohta T, Yamaguchi S, Ogura T, Sakamoto S, Maeda Y, Naruta Y. Spectroscopic characterization of a hydroperoxo-heme intermediate: conversion of a side-on peroxo to an end-on hydroperoxo complex. Angew Chem Int Ed Engl 2010; 48:9262-7. [PMID: 19882613 DOI: 10.1002/anie.200904572] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jin-Gang Liu
- Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka, 812-8581, Japan
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Liu JG, Ohta T, Yamaguchi S, Ogura T, Sakamoto S, Maeda Y, Naruta Y. Spectroscopic Characterization of a HydroperoxoâHeme Intermediate: Conversion of a Side-On Peroxo to an End-On Hydroperoxo Complex. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904572] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Gantt SL, Denisov IG, Grinkova YV, Sligar SG. The critical iron-oxygen intermediate in human aromatase. Biochem Biophys Res Commun 2009; 387:169-73. [PMID: 19591804 DOI: 10.1016/j.bbrc.2009.06.154] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 06/26/2009] [Indexed: 10/20/2022]
Abstract
Aromatase (CYP19) is the target of several therapeutics used for breast cancer treatment and catalyzes the three-step conversion of androgens to estrogens, with an unusual C-C cleavage reaction in the third step. To better understand the CYP19 reaction, the oxy-ferrous complex of CYP19 with androstenedione substrate was cryotrapped, characterized by UV-vis spectroscopy, and cryoreduced to generate the next reaction cycle intermediate. EPR analysis revealed that the initial intermediate observed following cryoreduction is the unprotonated g(1)=2.254 peroxo-ferric intermediate, which is stable up to 180K. Upon gradual cryoannealing, the low-spin (g(1)=2.39) product complex is formed, with no evidence for accumulation of the g(1)=2.30 hydroperoxo-ferric intermediate. The relative stabilization of the peroxo-ferric heme and the lack of observed hydroperoxo-ferric heme distinguish CYP19 from other P450s, suggesting that the proton delivery pathway is more hindered in CYP19 than in most other P450s.
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Affiliation(s)
- Stephanie L Gantt
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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31
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Tatoli S, Zazza C, Sanna N, Palma A, Aschi M. The role of Arginine 38 in horseradish peroxidase enzyme revisited: A computational investigation. Biophys Chem 2009; 141:87-93. [DOI: 10.1016/j.bpc.2008.12.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/29/2008] [Accepted: 12/30/2008] [Indexed: 11/25/2022]
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32
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Suarez J, Ranguelova K, Jarzecki AA, Manzerova J, Krymov V, Zhao X, Yu S, Metlitsky L, Gerfen GJ, Magliozzo RS. An oxyferrous heme/protein-based radical intermediate is catalytically competent in the catalase reaction of Mycobacterium tuberculosis catalase-peroxidase (KatG). J Biol Chem 2009; 284:7017-29. [PMID: 19139099 DOI: 10.1074/jbc.m808106200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A mechanism accounting for the robust catalase activity in catalase-peroxidases (KatG) presents a new challenge in heme protein enzymology. In Mycobacterium tuberculosis, KatG is the sole catalase and is also responsible for peroxidative activation of isoniazid, an anti-tuberculosis pro-drug. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy both at the X-band and at the D-band, and mutagenesis are used to identify catalase reaction intermediates in M. tuberculosis KatG. In the presence of millimolar H2O2 at neutral pH, oxyferrous heme is formed within milliseconds from ferric (resting) KatG, whereas at pH 8.5, low spin ferric heme is formed. Using rapid freeze-quench EPR at X-band under both of these conditions, a narrow doublet radical signal with an 11 G principal hyperfine splitting was detected within the first milliseconds of turnover. The radical and the unique heme intermediates persist in wild-type KatG only during the time course of turnover of excess H2O2 (1000-fold or more). Mutation of Met255, Tyr229, or Trp107, which have covalently linked side chains in a unique distal side adduct (MYW) in wild-type KatG, abolishes this radical and the catalase activity. The D-band EPR spectrum of the radical exhibits a rhombic g tensor with dual gx values (2.00550 and 2.00606) and unique gy (2.00344) and gz values (2.00186) similar to but not typical of native tyrosyl radicals. Density functional theory calculations based on a model of an MYW adduct radical built from x-ray coordinates predict experimentally observed hyperfine interactions and a shift in g values away from the native tyrosyl radical. A catalytic role for an MYW adduct radical in the catalase mechanism of KatG is proposed.
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Affiliation(s)
- Javier Suarez
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, USA
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33
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Hersleth HP, Hsiao YW, Ryde U, Görbitz CH, Andersson KK. The influence of X-rays on the structural studies of peroxide-derived myoglobin intermediates. Chem Biodivers 2008; 5:2067-2089. [PMID: 18972498 DOI: 10.1002/cbdv.200890189] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In recent years, the awareness of potential radiation damage of metal centers in protein crystals during crystallographic data collection has received increasing attention. The radiation damage can lead to radiation-induced changes and reduction of the metal sites. One of the research fields where these concerns have been comprehensively addressed is the study of the reaction intermediates of the heme peroxidase and oxygenase reaction cycles. For both the resting states and the high-valent intermediates, the X-rays used in the structure determination have given undesired side effects through radiation-induced changes to the trapped intermediates. However, X-rays have been used to generate and trap the peroxy/hydroperoxy state in crystals. In this review, the structural work and the influence of X-rays on these intermediates in myoglobin are summarized and viewed in light of analogous studies on similar intermediates in peroxidases and oxygenases.
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Affiliation(s)
- Hans-Petter Hersleth
- University of Oslo, Department of Molecular Biosciences, P. O. Box 1041 Blindern, N-0316 Oslo
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34
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The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection. Biochem J 2008; 412:257-64. [DOI: 10.1042/bj20070921] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 01/22/2008] [Accepted: 01/23/2008] [Indexed: 11/17/2022]
Abstract
Myoglobin has the ability to react with hydrogen peroxide, generating high-valent complexes similar to peroxidases (compounds I and II), and in the presence of excess hydrogen peroxide a third intermediate, compound III, with an oxymyoglobin-type structure is generated from compound II. The compound III is, however, easily one-electron reduced to peroxymyoglobin by synchrotron radiation during crystallographic data collection. We have generated and solved the 1.30 Å (1 Å=0.1 nm) resolution crystal structure of the peroxymyoglobin intermediate, which is isoelectric to compound 0 and has a Fe–O distance of 1.8 Å and O–O bond of 1.3 Å in accordance with a FeII–O–O− (or FeIII–O–O2−) structure. The generation of the peroxy intermediate through reduction of compound III by X-rays shows the importance of using single-crystal microspectrophotometry when doing crystallography on metalloproteins. After having collected crystallographic data on a peroxy-generated myoglobin crystal, we were able (by a short annealing) to break the O–O bond leading to formation of compound II. These results indicate that the cryoradiolytic-generated peroxymyoglobin is biologically relevant through its conversion into compound II upon heating. Additionally, we have observed that the Xe1 site is occupied by a water molecule, which might be the leaving group in the compound II to compound III reaction.
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Davydov R, Osborne RL, Kim SH, Dawson JH, Hoffman BM. EPR and ENDOR studies of cryoreduced compounds II of peroxidases and myoglobin. Proton-coupled electron transfer and protonation status of ferryl hemes. Biochemistry 2008; 47:5147-55. [PMID: 18407661 DOI: 10.1021/bi702514d] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nature of the [Fe(IV)-O] center in hemoprotein Compounds II has recently received considerable attention, as several experimental and theoretical investigations have suggested that this group is not necessarily the traditionally assumed ferryl ion, [Fe(IV)=O]2+, but can be the protonated ferryl, [Fe(IV)-OH]3+. We show here that cryoreduction of the EPR-silent Compound II by gamma-irradiation at 77 K produces Fe(III) species retaining the structure of the precursor [Fe(IV)=O]2+ or [Fe(IV)-OH]3+, and that the properties of the cryogenerated species provide a report on structural features and the protonation state of the parent Compound II when studied by EPR and 1H and 14N ENDOR spectroscopies. To give the broadest view of the properties of Compounds II we have carried out such measurements on cryoreduced Compounds II of HRP, Mb, DHP and CPO and on CCP Compound ES. EPR and ENDOR spectra of cryoreduced HRP II, CPO II and CCP ES are characteristic of low-spin hydroxy-Fe(III) heme species. In contrast, cryoreduced "globins", Mb II, Hb II, and DHP II, show EPR spectra having lower rhombicity. In addition the cryogenerated ferric "globin" species display strongly coupled exchangeable (1)H ENDOR signals, with A max approximately 20 MHz and a iso approximately 14 MHz, both substantially greater than for hydroxide/water ligand protons. Upon annealing at T > 180 K the cryoreduced globin compounds II relax to the low-spin hydroxy-ferric form with a solvent kinetic isotope effect, KIE > 6. The results presented here together with published resonance Raman and Mossbauer data suggest that the high-valent iron center of globin and HRP compounds II, as well as of CCP ES, is [Fe(IV)=O]2+, and that its cryoreduction produces [Fe(III)-O]+. Instead, as proposed by Green and co-workers, CPO II contains [Fe(IV)-OH]3+ which forms [Fe(III)-OH]2+ upon radiolysis. The [Fe(III)-O]+ generated by cryoreduction of HRP II and CCP ES protonate at 77 K, presumably because the heme is linked to a distal-pocket hydrogen bonding/proton-delivery network through an H-bond to the "oxide" ligand. The data also indicate that Mb and HRP compounds II exist as two major conformational substates.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Tech K148, Evanston, Illinois 60208-3113, USA
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36
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Hersleth HP, Varnier A, Harbitz E, Røhr ÅK, Schmidt PP, Sørlie M, Cederkvist FH, Marchal S, Gorren AC, Mayer B, Uchida T, Schünemann V, Kitagawa T, Trautwein AX, Shimizu T, Lange R, Görbitz CH, Andersson KK. Reactive complexes in myoglobin and nitric oxide synthase. Inorganica Chim Acta 2008. [DOI: 10.1016/j.ica.2007.09.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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37
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Zazza C, Amadei A, Palma A, Sanna N, Tatoli S, Aschi M. Theoretical Modeling of Enzyme Reactions: The Thermodynamics of Formation of Compound 0 in Horseradish Peroxidase. J Phys Chem B 2008; 112:3184-92. [DOI: 10.1021/jp0774692] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Costantino Zazza
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Andrea Amadei
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Amedeo Palma
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Nico Sanna
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Simone Tatoli
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Massimiliano Aschi
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
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38
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Nicholls P. The oxygenase-peroxidase theory of Bach and Chodat and its modern equivalents: change and permanence in scientific thinking as shown by our understanding of the roles of water, peroxide, and oxygen in the functioning of redox enzymes. BIOCHEMISTRY (MOSCOW) 2008; 72:1039-46. [PMID: 18021062 DOI: 10.1134/s0006297907100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Alexander Bach was both revolutionary politician and biochemist. His earliest significant publication, "Tsar-golod" ("The Tsar of Hunger"), introduced Marxist thought to Russian workers. In exile for 30 years, he moved to study the dialectic of the oxidases. When his theory of oxidases as combinations of oxygenases and peroxidases was developed (circa 1900) the enzyme concept was not fully formulated, and the enzyme/substrate distinction not yet made. Peroxides however were then and remain now significant intermediates, when either free or bound, in oxidase catalyses. The aerobic dehydrogenase/peroxidase/catalase coupled systems which were studied slightly later clarified the Bach model and briefly became an oxidase paradigm. Identification of peroxidase as a metalloprotein, a key step in understanding oxidase and peroxidase mechanisms, postdated Bach's major work. Currently we recognize catalytic organic peroxides in flavoprotein oxygenases; such organic peroxides are also involved in lipid oxidation and tryptophan radical decay. But most physiologically important peroxides are now known to be bound to transition metals (either Fe or Cu) and formed both directly and indirectly (from oxygen). The typical stable metalloprotein peroxide product is the ferryl state. When both peroxide oxidizing equivalents are retained the second equivalent is held as a protein or porphyrin radical. True metal peroxide complexes are unstable. But often water molecules mark the spot where the original peroxide decayed. The cytochrome c oxidase Fe-Cu center can react with either peroxide or oxygen to form the intermediate higher oxidation states P and F. In its resting state water molecules and hydroxyl ions can be seen marking the original location of the oxygen or peroxide molecule.
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Affiliation(s)
- P Nicholls
- Department of Biological Sciences, Essex University, Colchester, Essex, CO 4 3SQ, UK.
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39
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Makris TM, von Koenig K, Schlichting I, Sligar SG. Alteration of P450 distal pocket solvent leads to impaired proton delivery and changes in heme geometry. Biochemistry 2007; 46:14129-40. [PMID: 18001135 DOI: 10.1021/bi7013695] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Distal pocket water molecules have been widely implicated in the delivery of protons required in O-O bond heterolysis in the P450 reaction cycle. Targeted dehydration of the cytochrome P450cam (CYP101) distal pocket through mutagenesis of a distal pocket glycine to either valine or threonine results in the alteration of spin state equilibria, and has dramatic consequences on the catalytic rate, coupling efficiency, and kinetic solvent isotope effect parameters, highlighting an important role of the active-site hydration level on P450 catalysis. Cryoradiolysis of the mutant CYP101 oxyferrous complexes further indicates a specific perturbation of proton-transfer events required for the transformation of ferric-peroxo to ferric-hydroperoxo states. Finally, crystallography of the 248Val and 248Thr mutants in both the ferric camphor bound resting state and ferric-cyano adducts shows both the alteration of hydrogen-bonding networks and the alteration of heme geometry parameters. Taken together, these results indicate that the distal pocket microenvironment governs the transformation of reactive heme-oxygen intermediates in P450 cytochromes.
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Affiliation(s)
- Thomas M Makris
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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40
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Unno M, Chen H, Kusama S, Shaik S, Ikeda-Saito M. Structural characterization of the fleeting ferric peroxo species in myoglobin: experiment and theory. J Am Chem Soc 2007; 129:13394-5. [PMID: 17929929 DOI: 10.1021/ja076108x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Masaki Unno
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
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41
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Denisov IG, Dawson JH, Hager LP, Sligar SG. The ferric-hydroperoxo complex of chloroperoxidase. Biochem Biophys Res Commun 2007; 363:954-8. [PMID: 17920039 DOI: 10.1016/j.bbrc.2007.09.085] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Accepted: 09/19/2007] [Indexed: 10/22/2022]
Abstract
The hydroperoxo-ferric complex, or Compound 0 (Cpd 0), is an unstable transient intermediate common for oxygen activating heme enzymes such as the cytochromes P450, nitric oxide synthases, and heme oxygenases, as well as the peroxidases and catalases which utilize hydrogen peroxide as a source of oxygen and reducing equivalents. Detailed understanding of the mechanism of oxygen activation and formation of the higher valent catalytically active intermediates in heme enzyme catalysis requires the structural and spectroscopic characterization of this immediate precursor, Cpd 0. Using the method of cryoradiolytic reduction of the oxy-ferrous heme complex, we have prepared and characterized hydroperoxo-ferric complex in chloroperoxidase (CPO) and compared this to the same intermediate generated in cytochrome P450 CYP101. Optical absorption spectrum of Cpd 0 in CPO has a Soret band at 449 nm and poorly resolved alpha, beta bands at 576 and 546 nm.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, 116 Morrill Hall, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801, USA
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42
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Hersleth HP, Uchida T, Røhr AK, Teschner T, Schünemann V, Kitagawa T, Trautwein AX, Görbitz CH, Andersson KK. Crystallographic and Spectroscopic Studies of Peroxide-derived Myoglobin Compound II and Occurrence of Protonated FeIV–O. J Biol Chem 2007; 282:23372-86. [PMID: 17565988 DOI: 10.1074/jbc.m701948200] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (<1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe-O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an Fe(IV)-O species with a single bond. The presence of Fe(IV) is indicated by a small isomer shift of delta = 0.07 mm/s from Mössbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.
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Affiliation(s)
- Hans-Petter Hersleth
- Department of Chemistry, University of Oslo, PO Box 1033, Blindern, Oslo N-0315, Norway
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43
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Watanabe Y, Nakajima H, Ueno T. Reactivities of oxo and peroxo intermediates studied by hemoprotein mutants. Acc Chem Res 2007; 40:554-62. [PMID: 17567089 DOI: 10.1021/ar600046a] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of myoglobin mutants, in which distal sites are modified by site-directed mutagenesis, are able to catalyze peroxidase, catalase, and P450 reactions even though their proximal histidine ligands are intact. More importantly, reactions of P450, catalase, and peroxidase substrates and compound I of myoglobin mutants can be observed spectroscopically. Thus, detailed oxidation mechanisms were examined. On the basis of these results, we suggest that the different reactivities of P450, catalase, and peroxidase are mainly caused by their active site structures, but not the axial ligand. We have also prepared compound 0 under physiological conditions by employing a mutant of cytochrome c 552. Compound 0 is not able to oxidize ascorbic acid.
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Affiliation(s)
- Yoshihito Watanabe
- Research Center for Materials Science and Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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44
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Ichikawa Y, Nakajima H, Watanabe Y. Characterization of peroxide-bound heme species generated in the reaction of thermally tolerant cytochrome c552 with hydrogen peroxide. Chembiochem 2007; 7:1582-9. [PMID: 16921577 DOI: 10.1002/cbic.200600135] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Peroxide-bound heme species have been considered difficult to detect under physiological conditions because of their intrinsically transient properties. Cytochrome c552 (cyt c552), from Thermus thermophirus HB8, bearing a mutation to an alanine at Met69 (M69A) reacts with hydrogen peroxide (H(2)O(2)) to generate a detectable hydroperoxo-ferric heme ([Fe(3+)--OOH]) species at ambient temperature. EPR measurements during appropriate reaction periods reveal that the [Fe(3+)--OOH] species is in a preequilibrium state between the resting form of the cyt c552 variant and a subsequent intermediate, compound II with a protein radical. Addition of ascorbic acid to the reaction mixture of the cyt c552 variant and H(2)O(2) does not affect the formation of the [Fe(3+)--OOH] species,a result suggesting that the species is incompetent for the oxidation of even an oxidatively fragile substrate such as ascorbic acid. Another variant bearing an additional mutation to aspartic acid at Val49 (V49D/M69A) reveals that a highly hydrophobic heme cavity in cyt c552 accounts for the generation of the durable [Fe(3+)--OOH] species. The less polar environment inside the cavity is expected to prevent H(2)O from approaching the cavity. This would suppress protonation of the distal oxygen atom of the [Fe(3+)--OOH] species and retard subsequent dissociation of H(2)O from the OOH moiety.
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Affiliation(s)
- Yusuke Ichikawa
- Department of Chemistry, Graduate School of Science Nagoya University, 464-8602 Nagoya, Japan
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45
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Denisov IG, Victoria DC, Sligar SG. Cryoradiolytic reduction of heme proteins: Maximizing dose dependent yield. Radiat Phys Chem Oxf Engl 1993 2007; 76:714-721. [PMID: 18379640 DOI: 10.1016/j.radphyschem.2006.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Radiolytic reduction in frozen solutions and crystals is a useful method for generation of trapped intermediates in protein based radical reactions. In this communication we define the conditions which provide the maximum yield of one electron reduced myoglobin at 77 K using (60)Co γ-irradiation in aqueous glycerol glass. The yield reached 50% after 20 kGy, was almost complete at ∼160 kGy total dose, and does not depend on the protein concentration in the range 0.01 - 5 mM.
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Affiliation(s)
- Ilia G Denisov
- University of Illinois Urbana-Champaign, Department of Biochemistry, Urbana IL, 61801
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46
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Svistunenko DA, Reeder BJ, Wankasi MM, Silaghi-Dumitrescu RL, Cooper CE, Rinaldo S, Cutruzzolà F, Wilson MT. Reaction of Aplysia limacina metmyoglobin with hydrogen peroxide. Dalton Trans 2007:840-50. [PMID: 17297511 DOI: 10.1039/b615770j] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Myoglobin (Mb) from gastropod mollusc Aplysia limacina shows only 20% sequence homology to the 'prototype' sperm whale Mb but exhibits a typical Mb fold and can reversibly bind oxygen. An intriguing feature of aplysia Mb is that it lacks the distal histidine and displays a ligand stabilisation based on an arginine. Here we report the reaction of aplysia metMb with hydrogen peroxide studied by optical and electron paramagnetic resonance (EPR) spectroscopies. Two electron oxidation of the protein by H2O2 results in formation of two intermediates typical for this class of reactions, the oxoferryl haem state and a globin-bound free radical. An unusual characteristic of the aplysia Mb reaction is formation, prior to haem oxidation, of an optically distinct compound with an EPR spectrum typical of the low spin Fe3+ haem state. This compound is interpreted as the complex between H2O2 and the ferric haem state (Compound), formed prior to cleavage of the dioxygen bond. We conclude that H2O2 is singly deprotonated in Compound which can thus be notated as [Fe3+--OOH]. A new low spin ferric haem state has been observed over the period of Compound decay, and hypotheses have been formulated as to its identity and role. The location of the protein bound radical observed in aplysia Mb is discussed in light of the fact that the protein does not have any tyrosine residues, the most common site of free radical formation in the haem protein/peroxide systems. All intermediates of the reaction are kinetically characterised.
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Affiliation(s)
- Dimitri A Svistunenko
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom.
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Kühnel K, Derat E, Terner J, Shaik S, Schlichting I. Structure and quantum chemical characterization of chloroperoxidase compound 0, a common reaction intermediate of diverse heme enzymes. Proc Natl Acad Sci U S A 2006; 104:99-104. [PMID: 17190816 PMCID: PMC1765485 DOI: 10.1073/pnas.0606285103] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have determined the crystal structure of the chloroperoxidase (CPO) hydroperoxo reaction intermediate (CPO compound 0) at 1.75-A resolution. The intermediate was generated through controlled photoreduction of the CPO oxygen complex during x-ray data collection, which was monitored by recording of the crystal absorption spectra. Initially, the peroxo-anion species was formed and then protonated to yield compound 0. Quantum chemical calculations indicate that the peroxo-anion species is not stable and collapses instantaneously to compound 0. Compound 0 is present in the ferric low-spin doublet ground state and is characterized by a long O O bond length of 1.5 A and a Fe O bond distance of 1.8 A, which is also observed in the crystal structure.
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Affiliation(s)
- Karin Kühnel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Etienne Derat
- Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University, 91904 Jerusalem, Israel; and
| | - James Terner
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006
| | - Sason Shaik
- Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University, 91904 Jerusalem, Israel; and
- To whom correspondence may be addressed. E-mail:
or
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- To whom correspondence may be addressed. E-mail:
or
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48
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Bakac A. Kinetic and mechanistic studies of the reactions of transition metal-activated oxygen with inorganic substrates. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.02.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Makris TM, von Koenig K, Schlichting I, Sligar SG. The status of high-valent metal oxo complexes in the P450 cytochromes. J Inorg Biochem 2006; 100:507-18. [PMID: 16510191 DOI: 10.1016/j.jinorgbio.2006.01.025] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 01/17/2006] [Accepted: 01/17/2006] [Indexed: 11/24/2022]
Abstract
The oxidative prowess of the P450 cytochromes in physiological reactions is attributed to the production of a high-valent iron-oxo complex, or Compound I intermediate, in the reaction cycle. Despite many years of study, however, the full electronic description of this fleeting intermediate still remains an active area of study. In this manuscript, the current status of the isolation and characterization of the P450 oxo-Fe(IV) is examined and compared to analogous states in related heme enzymes. In addition, the utilization of cofactor exchange to stabilize high-valent oxo-states in the P450 is addressed. Structural and spectroscopic studies on manganese reconstituted P450, and its corresponding oxo-complex, are presented.
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Affiliation(s)
- Thomas M Makris
- Department of Biochemistry, University of Illinois Urbana-Champaign, 116 Morrill Hall, Urbana, IL 61801, USA.
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50
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Sudhamsu J, Crane BR. Structure and reactivity of a thermostable prokaryotic nitric-oxide synthase that forms a long-lived oxy-heme complex. J Biol Chem 2006; 281:9623-32. [PMID: 16407211 DOI: 10.1074/jbc.m510062200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In an effort to generate more stable reaction intermediates involved in substrate oxidation by nitric-oxide synthases (NOSs), we have cloned, expressed, and characterized a thermostable NOS homolog from the thermophilic bacterium Geobacillus stearothermophilus (gsNOS). As expected, gsNOS forms nitric oxide (NO) from l-arginine via the stable intermediate N-hydroxy l-arginine (NOHA). The addition of oxygen to ferrous gsNOS results in long-lived heme-oxy complexes in the presence (Soret peak 427 nm) and absence (Soret peak 413 nm) of substrates l-arginine and NOHA. The substrate-induced red shift correlates with hydrogen bonding between substrate and heme-bound oxygen resulting in conversion to a ferric heme-superoxy species. In single turnover experiments with NOHA, NO forms only in the presence of H(4)B. The crystal structure of gsNOS at 3.2 AA of resolution reveals great similarity to other known bacterial NOS structures, with the exception of differences in the distal heme pocket, close to the oxygen binding site. In particular, a Lys-356 (Bacillus subtilis NOS) to Arg-365 (gsNOS) substitution alters the conformation of a conserved Asp carboxylate, resulting in movement of an Ile residue toward the heme. Thus, a more constrained heme pocket may slow ligand dissociation and increase the lifetime of heme-bound oxygen to seconds at 4 degrees C. Similarly, the ferric-heme NO complex is also stabilized in gsNOS. The slow kinetics of gsNOS offer promise for studying downstream intermediates involved in substrate oxidation.
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Affiliation(s)
- Jawahar Sudhamsu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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