1
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Morales-Urrea D, López-Córdoba A, Contreras EM. Inactivation kinetics of horseradish peroxidase (HRP) by hydrogen peroxide. Sci Rep 2023; 13:13363. [PMID: 37591893 PMCID: PMC10435507 DOI: 10.1038/s41598-023-39687-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/29/2023] [Indexed: 08/19/2023] Open
Abstract
In recent years, the peroxidase enzymes have generated wide interest in several industrial processes, such as wastewater treatments, food processing, pharmaceuticals, and the production of fine chemicals. However, the low stability of the peroxidases in the presence of hydrogen peroxide (H2O2) has limited its commercial use. In the present work, the effect of H2O2 on the inactivation of horseradish peroxidase (HRP) was evaluated. Three states of HRP (E0, E2, and E3) were identified. While in the absence of H2O2, the resting state E0 was observed, in the presence of low and high concentrations of H2O2, E2, and E3 were found, respectively. The results showed that HRP catalyzed the H2O2 decomposition, forming the species Ex, which was catalytically inactive. Results suggest that this loss of enzymatic activity is an intrinsic characteristic of the studied HRP. A model from a modified version of the Dunford mechanism of peroxidases was developed, which was validated against experimental data and findings reported by the literature.
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Affiliation(s)
- Diego Morales-Urrea
- Grupo de Investigación en Bioeconomía y Sostenibilidad Agroalimentaria, Escuela de Administración de Empresas Agropecuarias, Facultad Seccional Duitama, Universidad Pedagógica y Tecnológica de Colombia, Duitama, Colombia
- Instituto de Investigaciones en Ciencia y Tecnología de Materiales (INTEMA), CCT - Mar del Plata. CONICET, Mar del Plata, Argentina
| | - Alex López-Córdoba
- Grupo de Investigación en Bioeconomía y Sostenibilidad Agroalimentaria, Escuela de Administración de Empresas Agropecuarias, Facultad Seccional Duitama, Universidad Pedagógica y Tecnológica de Colombia, Duitama, Colombia
| | - Edgardo M Contreras
- Instituto de Investigaciones en Ciencia y Tecnología de Materiales (INTEMA), CCT - Mar del Plata. CONICET, Mar del Plata, Argentina.
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2
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Kumar N, He J, Rusling JF. Electrochemical transformations catalyzed by cytochrome P450s and peroxidases. Chem Soc Rev 2023; 52:5135-5171. [PMID: 37458261 DOI: 10.1039/d3cs00461a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Cytochrome P450s (Cyt P450s) and peroxidases are enzymes featuring iron heme cofactors that have wide applicability as biocatalysts in chemical syntheses. Cyt P450s are a family of monooxygenases that oxidize fatty acids, steroids, and xenobiotics, synthesize hormones, and convert drugs and other chemicals to metabolites. Peroxidases are involved in breaking down hydrogen peroxide and can oxidize organic compounds during this process. Both heme-containing enzymes utilize active FeIVO intermediates to oxidize reactants. By incorporating these enzymes in stable thin films on electrodes, Cyt P450s and peroxidases can accept electrons from an electrode, albeit by different mechanisms, and catalyze organic transformations in a feasible and cost-effective way. This is an advantageous approach, often called bioelectrocatalysis, compared to their biological pathways in solution that require expensive biochemical reductants such as NADPH or additional enzymes to recycle NADPH for Cyt P450s. Bioelectrocatalysis also serves as an ex situ platform to investigate metabolism of drugs and bio-relevant chemicals. In this paper we review biocatalytic electrochemical reactions using Cyt P450s including C-H activation, S-oxidation, epoxidation, N-hydroxylation, and oxidative N-, and O-dealkylation; as well as reactions catalyzed by peroxidases including synthetically important oxidations of organic compounds. Design aspects of these bioelectrocatalytic reactions are presented and discussed, including enzyme film formation on electrodes, temperature, pH, solvents, and activation of the enzymes. Finally, we discuss challenges and future perspective of these two important bioelectrocatalytic systems.
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Affiliation(s)
- Neeraj Kumar
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
| | - Jie He
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
| | - James F Rusling
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
- Department of Surgery and Neag Cancer Center, Uconn Health, Farmington, CT 06030, USA
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
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3
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Zhou W, Lai R, Cheng Y, Bao Y, Miao W, Cao X, Jia G, Li G, Li C. Insights into How NH 4+ Ions Enhance the Activity of Dimeric G-Quadruplex/Hemin DNAzyme. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Wenqin Zhou
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Rui Lai
- State Key Laboratory of Molecular Reaction Dynamics, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Cheng
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Bao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Wenhui Miao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Xupeng Cao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Can Li
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
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4
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Kobayashi K, Ito YT, Kasu Y, Horitani M, Kozawa T. Intramolecular electron transfer from biopterin to Fe II-O 2 complex in nitric oxide synthases occurs at very different rates between bacterial and mammalian enzymes: Direct observation of a catalytically active intermediate. J Inorg Biochem 2023; 238:112035. [PMID: 36327499 DOI: 10.1016/j.jinorgbio.2022.112035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/05/2022] [Accepted: 10/17/2022] [Indexed: 11/21/2022]
Abstract
Nitric oxide synthase (NOS) is a cytochrome P450-type mono‑oxygenase that catalyzes the oxidation of L-arginine to nitric oxide. We previously observed that intramolecular electron transfer from biopterin to Fe2+-O2 in Deinococcus radiodurans NOS (DrNOS) using pulse radiolysis. However, the rate of electron transfer in DrNOS (2.2 × 103 s-1) contrasts with a reported corresponding rate (11 s-1) in a mammalian NOS determined using rapid freeze-quench (RFQ) EPR. We applied pulse radiolysis to Bacillus subtilis NOS (bsNOS) and to rat neural NOS oxygenase domain NOS (mNOS). Concurrently, RFQ EPR was used to trap a pterin radical during single-turnover enzyme reactions of the enzymes. By using the pulse radiolysis method, hydrated electrons (eaq-) reduced the heme iron of NOS enzymes. Subsequently, ferrous heme reacted with O2 to form a Fe2+-O2 intermediate. In the presence of pterin, the intermediate of bsNOS was found to convert to other intermediate in the time range of milliseconds. A similar process was determined to have occurred after pulse radiolysis of the pterin-bound mNOS, though the rate was much slower. The intermediates of all of the NOS enzymes further converted to the original ferric form in the time range of seconds. When using the RFQ method, pterin radicals were formed very rapidly in both DrNOS and bsNOS in the time range of milliseconds. In contrast, the pterin radical in mNOS was observed to form slowly, at a rate of ∼20 s-1.
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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.
| | - Yuko Tsutsui Ito
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Yuri Kasu
- Department of Applied Biochemistry and Food Science, Saga University, Honjo-machi Saga, 840-8502, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry and Food Science, Saga University, Honjo-machi Saga, 840-8502, Japan; The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Takahiro Kozawa
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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5
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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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
The colocalization of heme rich deposits in the senile plaque of Aβ in the cerebral cortex of the Alzheimer's disease (AD) brain along with altered heme homeostasis and heme deficiency symptoms in AD patients has invoked the association of heme in AD pathology. Heme bound Aβ complexes, depending on the concentration of the complex or peptide to heme ratio, exhibit an equilibrium between a high-spin mono-His bound peroxidase-type active site and a low-spin bis-His bound cytochrome b type active site. The high-spin heme-Aβ complex shows higher peroxidase activity than free heme, where compound I is the reactive oxidant. It is also capable of oxidizing neurotransmitters like serotonin in the presence of peroxide, owing to the formation of compound I. The low-spin bis-His heme-Aβ complex on the other hand shows enhanced peroxidase activity relative to high-spin heme-Aβ. It reacts with H2O2 to produce two stable intermediates, compound 0 and compound I, which are characterized by absorption, EPR and resonance Raman spectroscopy. The stability of compound I of low-spin heme-Aβ is accountable for its enhanced peroxidase activity and oxidation of the neurotransmitter serotonin. The effect of the second sphere Tyr10 residue of Aβ on the formation and stability of the intermediates of low-spin heme-Aβ has also been investigated. The higher stability of compound I for low-spin heme-Aβ is likely due to H-bonding interactions involving Tyr10 in the distal pocket.
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Affiliation(s)
- Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
| | - Chinmay Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 India
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6
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Clinger JA, Moreau DW, McLeod MJ, Holyoak T, Thorne RE. Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection. IUCRJ 2021; 8:784-792. [PMID: 34584739 PMCID: PMC8420759 DOI: 10.1107/s2052252521007053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/08/2021] [Indexed: 05/28/2023]
Abstract
Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and the complex experimental infrastructure that are required remain serious obstacles to its widespread application. Here, millisecond mix-and-quench crystallography (MMQX) has been developed, which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxy-kinase (PEPCK) is observed with a time resolution of 40 ms. By lowering the entry barrier to time-resolved crystallography, MMQX should enable a broad expansion in structural studies of protein dynamics.
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Affiliation(s)
- Jonathan A. Clinger
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
| | - David W. Moreau
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
| | - Matthew J. McLeod
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Todd Holyoak
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Robert E. Thorne
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
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7
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Sharma GS, Bhattacharya R, Singh LR. Functional inhibition of redox regulated heme proteins: A novel mechanism towards oxidative stress induced by homocysteine. Redox Biol 2021; 46:102080. [PMID: 34325357 PMCID: PMC8334742 DOI: 10.1016/j.redox.2021.102080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 11/19/2022] Open
Abstract
Homocysteine (Hcy) is a sulfur containing non-protein toxic amino acid synthesized from methionine. Elevated level of Hcy is associated with cardiovascular complications and neurodegeneration. Hcy is believed to induce organ damage and apoptosis via oxidative stress. The pro-oxidant nature of Hcy is considered to originate from the metal-induced oxidation of thiol group-containing molecules forming disulfides (Hcy-Hcy, Hcy-cysteine, Hcy-glutathione, etc) or with free cysteine residues of proteins (a process called protein S-homocysteinylation). Formation of such disulfides indeed results in the generation of reactive oxygen species (ROS) which eventually leads to loss of cellular integrity. In the present manuscript, we performed systematic investigation of the effect of Hcy on iron containing proteins. We discover a novel mechanism of Hcy toxicity wherein Hcy oxidation is linked with the functional loss of the protein with iron as cofactors. Our results indicate that redox regulated heme proteins might be primarily involved in the Hcy toxicity and associated oxidative stress.
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Affiliation(s)
- Gurumayum Suraj Sharma
- Department of Botany, Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, 110075, India
| | - Reshmee Bhattacharya
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
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8
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Calvey GD, Katz AM, Zielinski KA, Dzikovski B, Pollack L. Characterizing Enzyme Reactions in Microcrystals for Effective Mix-and-Inject Experiments using X-ray Free-Electron Lasers. Anal Chem 2020; 92:13864-13870. [PMID: 32955854 PMCID: PMC8367009 DOI: 10.1021/acs.analchem.0c02569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mix-and-inject serial crystallography is an emerging technique that utilizes X-ray free-electron lasers (XFELs) and microcrystalline samples to capture atomically detailed snapshots of biomolecules as they function. Early experiments have yielded exciting results; however, there are limited options to characterize reactions in crystallo in advance of the beamtime. Complementary measurements are needed to identify the best conditions and timescales for observing structural intermediates. Here, we describe the interface of XFEL compatible mixing injectors with rapid freeze-quenching and X-band EPR spectroscopy, permitting characterization of reactions in crystals under the same conditions as an XFEL experiment. We demonstrate this technology by tracking the reaction of azide with microcrystalline myoglobin, using only a fraction of the sample required for a mix-and-inject experiment. This spectroscopic method enables optimization of sample and mixer conditions to maximize the populations of intermediate states, eliminating the guesswork of current mix-and-inject experiments.
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Affiliation(s)
- George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Kara A Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, United States
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
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9
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Influence of Varying Functionalization on the Peroxidase Activity of Nickel(II)–Pyridine Macrocycle Catalysts: Mechanistic Insights from Density Functional Theory. COMPUTATION 2020. [DOI: 10.3390/computation8020052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nickel(II) complexes of mono-functionalized pyridine-tetraazamacrocycles (PyMACs) are a new class of catalysts that possess promising activity similar to biological peroxidases. Experimental studies with ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), substrate) and H2O2 (oxidant) proposed that hydrogen-bonding and proton-transfer reactions facilitated by their pendant arm were responsible for their catalytic activity. In this work, density functional theory calculations were performed to unravel the influence of pendant arm functionalization on the catalytic performance of Ni(II)–PyMACs. Generated frontier orbitals suggested that Ni(II)–PyMACs activate H2O2 by satisfying two requirements: (1) the deprotonation of H2O2 to form the highly nucleophilic HOO−, and (2) the generation of low-spin, singlet state Ni(II)–PyMACs to allow the binding of HOO−. COSMO solvation-based energies revealed that the O–O Ni(II)–hydroperoxo bond, regardless of pendant arm type, ruptures favorably via heterolysis to produce high-spin (S = 1) [(L)Ni3+–O·]2+ and HO−. Aqueous solvation was found crucial in the stabilization of charged species, thereby favoring the heterolytic process over homolytic. The redox reaction of [(L)Ni3+–O·]2+ with ABTS obeyed a 1:2 stoichiometric ratio, followed by proton transfer to produce the final intermediate. The regeneration of Ni(II)–PyMACs at the final step involved the liberation of HO−, which was highly favorable when protons were readily available or when the pKa of the pendant arm was low.
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10
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Schmidt T, Jeon J, Okuno Y, Chiliveri SC, Clore GM. Submillisecond Freezing Permits Cryoprotectant-Free EPR Double Electron-Electron Resonance Spectroscopy. Chemphyschem 2020; 21:1224-1229. [PMID: 32383308 DOI: 10.1002/cphc.202000312] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/06/2020] [Indexed: 01/22/2023]
Abstract
Double electron-electron resonance (DEER) EPR spectroscopy is a powerful method for obtaining distance distributions between pairs of engineered nitroxide spin-labels in proteins and other biological macromolecules. These measurements require the use of cryogenic temperatures (77 K or less) to prolong the phase memory relaxation time (Tm ) sufficiently to enable detection of a DEER echo curve. Generally, a cryoprotectant such as glycerol is added to protein samples to facilitate glass formation and avoid protein clustering (which can result in a large decrease in Tm ) during relatively slow flash freezing in liquid N2 . However, cryoprotectants are osmolytes and can influence protein folding/unfolding equilibria, as well as species populations in weak multimeric systems. Here we show that submillisecond rapid freezing, achieved by high velocity spraying of the sample onto a rapidly spinning, liquid nitrogen cooled copper disc obviates the requirement for cryoprotectants and permits high quality DEER data to be obtained in absence of glycerol. We demonstrate this approach on five different protein systems: protein A, the metastable drkN SH3 domain, urea-unfolded drkN SH3, HIV-1 reverse transcriptase, and the transmembrane domain of HIV-1 gp41 in lipid bicelles.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Jaekyun Jeon
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Yusuke Okuno
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Sai C Chiliveri
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
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11
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Shinomiya R, Araki H, Momotake A, Kotani H, Kojima T, Yamamoto Y. Identification of Intermediates in Peroxidase Catalytic Cycle of a DNAzyme Possessing Heme. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190157] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ryosuke Shinomiya
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Haruka Araki
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Hiroaki Kotani
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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12
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Sun Han Chang R, Lee JCW, Pedron S, Harley BAC, Rogers SA. Rheological Analysis of the Gelation Kinetics of an Enzyme Cross-linked PEG Hydrogel. Biomacromolecules 2019; 20:2198-2206. [PMID: 31046247 PMCID: PMC6765384 DOI: 10.1021/acs.biomac.9b00116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diverse requirements of hydrogels for tissue engineering motivate the development of cross-linking reactions to fabricate hydrogel networks with specific features, particularly those amenable to the activity of biological materials (e.g., cells, proteins) that do not require exposure to UV light. We describe gelation kinetics for a library of thiolated poly(ethylene glycol) sulfhydryl hydrogels undergoing enzymatic cross-linking via horseradish peroxidase, a catalyst-driven reaction activated by hydrogen peroxide. We report the use of small-amplitude oscillatory shear (SAOS) to quantify gelation kinetics as a function of reaction conditions (hydrogen peroxide and polymer concentrations). We employ a novel approach to monitor the change of viscoelastic properties of hydrogels over the course of gelation (Δ tgel) via the time derivative of the storage modulus (d G'/d t). This approach, fundamentally distinct from traditional methods for defining a gel point, quantifies the time interval over which gelation events occur. We report that gelation depends on peroxide and polymer concentrations as well as system temperature, where the effects of hydrogen peroxide tend to saturate over a critical concentration. Further, this cross-linking reaction can be reversed using l-cysteine for rapid cell isolation, and the rate of hydrogel dissolution can be monitored using SAOS.
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Affiliation(s)
- Raul Sun Han Chang
- Department Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Johnny Ching-Wei Lee
- Department Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sara Pedron
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brendan A. C. Harley
- Department Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Simon A. Rogers
- Department Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, 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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Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III) Reaction Intermediate Models of Peroxidase Enzymes. Molecules 2016; 21:molecules21070804. [PMID: 27355940 PMCID: PMC6273987 DOI: 10.3390/molecules21070804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/01/2016] [Accepted: 06/13/2016] [Indexed: 11/17/2022] Open
Abstract
The spectroscopic and kinetic characterization of two intermediates from the H₂O₂ oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1-3 + guaiacol + H₂O₂ → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H₂O₂, resulting in only two types of kinetics that were developed during the first 0-4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N'-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, ¹H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity.
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15
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Fehr N, García-Rubio I, Jeschke G, Paulsen H. Early folding events during light harvesting complex II assembly in vitro monitored by pulsed electron paramagnetic resonance. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:695-704. [PMID: 27063475 DOI: 10.1016/j.bbabio.2016.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/16/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022]
Abstract
Efficient energy transfer in the major light harvesting complex II (LHCII) of green plants is facilitated by the precise alignment of pigments due to the protein matrix they are bound to. Much is known about the import of the LHCII apoprotein into the chloroplast via the TOC/TIC system and its targeting to the thylakoid membrane but information is sparse about when and where the pigments are bound and how this is coordinated with protein folding. In vitro, the LHCII apoprotein spontaneously folds and binds its pigments if the detergent-solubilized protein is combined with a mixture of chlorophylls a and b and carotenoids. In the present work, we employed this approach to study apoprotein folding and pigment binding in a time-resolved manner by using pulsed electron paramagnetic resonance (EPR). Intra-molecular distances were measured before folding, after 255 ms and 40 s folding time in the absence of cryoprotectant, and in the fully folded and assembled LHCII. In accordance with earlier results, the most of the folding of the three membrane-spanning alpha helices precedes their apposition into the final tertiary structure. However, their formation follows different kinetics, partially extending into the final phase of LHCII formation during which much of the condensation of the pigment-protein structure occurs, presumably governed by the binding of chlorophyll b. A rough timetable is proposed to sort partial events into the LHCII formation process.
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Affiliation(s)
- Niklas Fehr
- Department of General Botany, Johannes Gutenberg-University, 55128 Mainz, Germany
| | - Inés García-Rubio
- Department of Physical Chemistry, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Gunnar Jeschke
- Department of Physical Chemistry, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Harald Paulsen
- Department of General Botany, Johannes Gutenberg-University, 55128 Mainz, Germany.
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16
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Aitha M, Moller AJ, Sahu ID, Horitani M, Tierney DL, Crowder MW. Investigating the position of the hairpin loop in New Delhi metallo-β-lactamase, NDM-1, during catalysis and inhibitor binding. J Inorg Biochem 2016; 156:35-9. [PMID: 26717260 PMCID: PMC4843777 DOI: 10.1016/j.jinorgbio.2015.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/07/2015] [Accepted: 10/19/2015] [Indexed: 12/29/2022]
Abstract
In an effort to examine the relative position of a hairpin loop in New Delhi metallo-β-lactamase, NDM-1, during catalysis, rapid freeze quench double electron electron resonance (RFQ-DEER) spectroscopy was used. A doubly-labeled mutant of NDM-1, which had one spin label on the invariant loop at position 69 and another label at position 235, was prepared and characterized. The reaction of the doubly spin labeled mutant with chromacef was freeze quenched at 500μs and 10ms. DEER results showed that the average distance between labels decreased by 4Å in the 500μs quenched sample and by 2Å in the 10ms quenched sample, as compared to the distance in the unreacted enzyme, although the peaks corresponding to distance distributions were very broad. DEER spectra with the doubly spin labeled enzyme with two inhibitors showed that the distance between the loop residue at position 69 and the spin label at position 235 does not change upon inhibitor binding. This study suggests that the hairpin loop in NDM-1 moves over the metal ion during the catalysis and then moves back to its original position after hydrolysis, which is consistent with a previous hypothesis based on NMR solution studies on a related metallo-β-lactamase. This study also demonstrates that this loop motion occurs in the millisecond time domain.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Abraham J Moller
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Masaki Horitani
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA.
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17
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Matsumura H, Moënne-Loccoz P. Characterizing millisecond intermediates in hemoproteins using rapid-freeze-quench resonance Raman spectroscopy. Methods Mol Biol 2015; 1122:107-23. [PMID: 24639256 DOI: 10.1007/978-1-62703-794-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The combination of rapid freeze quenching (RFQ) with resonance Raman (RR) spectroscopy represents a unique tool with which to investigate the nature of short-lived intermediates formed during the enzymatic reactions of metalloproteins. Commercially available equipment allows trapping of intermediates within a millisecond to second time scale for low-temperature RR analysis resulting in the direct detection of metal-ligand vibrations and porphyrin skeletal vibrations in hemoproteins. This chapter briefly discusses RFQ-RR studies carried out previously in our laboratory and presents, as a practical example, protocols for the preparation of RFQ samples of the reaction of metmyoglobin with nitric oxide (NO) under anaerobic conditions. Also described are important controls and practical procedures for the analysis of these samples by low-temperature RR spectroscopy.
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Affiliation(s)
- Hirotoshi Matsumura
- Oregon Health & Science University, Institute of Environmental Health, Mail code: HRC3, 3181 SW Sam Jackson Park Road, Portland, OR97239, USA
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18
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Hudson DA, Gannon SA, Thorpe C. Oxidative protein folding: from thiol-disulfide exchange reactions to the redox poise of the endoplasmic reticulum. Free Radic Biol Med 2015; 80:171-82. [PMID: 25091901 PMCID: PMC4312752 DOI: 10.1016/j.freeradbiomed.2014.07.037] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 07/23/2014] [Indexed: 12/21/2022]
Abstract
This review examines oxidative protein folding within the mammalian endoplasmic reticulum (ER) from an enzymological perspective. In protein disulfide isomerase-first (PDI-first) pathways of oxidative protein folding, PDI is the immediate oxidant of reduced client proteins and then addresses disulfide mispairings in a second isomerization phase. In PDI-second pathways the initial oxidation is PDI-independent. Evidence for the rapid reduction of PDI by reduced glutathione is presented in the context of PDI-first pathways. Strategies and challenges are discussed for determination of the concentrations of reduced and oxidized glutathione and of the ratios of PDI(red):PDI(ox). The preponderance of evidence suggests that the mammalian ER is more reducing than first envisaged. The average redox state of major PDI-family members is largely to almost totally reduced. These observations are consistent with model studies showing that oxidative protein folding proceeds most efficiently at a reducing redox poise consistent with a stoichiometric insertion of disulfides into client proteins. After a discussion of the use of natively encoded fluorescent probes to report the glutathione redox poise of the ER, this review concludes with an elaboration of a complementary strategy to discontinuously survey the redox state of as many redox-active disulfides as can be identified by ratiometric LC-MS-MS methods. Consortia of oxidoreductases that are in redox equilibrium can then be identified and compared to the glutathione redox poise of the ER to gain a more detailed understanding of the factors that influence oxidative protein folding within the secretory compartment.
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Affiliation(s)
- Devin A Hudson
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Shawn A Gannon
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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19
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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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20
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Pievo R, Angerstein B, Fielding AJ, Koch C, Feussner I, Bennati M. A rapid freeze-quench setup for multi-frequency EPR spectroscopy of enzymatic reactions. Chemphyschem 2013; 14:4094-101. [PMID: 24323853 DOI: 10.1002/cphc.201300714] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/22/2013] [Indexed: 11/11/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy in combination with the rapid freeze-quench (RFQ) technique is a well-established method to trap and characterize intermediates in chemical or enzymatic reactions at the millisecond or even shorter time scales. The method is particularly powerful for mechanistic studies of enzymatic reactions when combined with high-frequency EPR (ν≥90 GHz), which permits the identification of substrate or protein radical intermediates by their electronic g values. In this work, we describe a new custom-designed micro-mix rapid freeze-quench apparatus, for which reagent volumes for biological samples as small as 20 μL are required. The apparatus was implemented with homemade sample collectors appropriate for 9, 34, and 94 GHz EPR capillaries (4, 2, and 0.87 mm outer diameter, respectively) and the performance was evaluated. We demonstrate the application potential of the RFQ apparatus by following the enzymatic reaction of PpoA, a fungal dioxygenase producing hydro(pero)xylated fatty acids. The larger spectral resolution at 94 GHz allows the discernment of structural changes in the EPR spectra, which are not detectable in the same samples at the standard 9 GHz frequency.
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Affiliation(s)
- Roberta Pievo
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen (Germany).
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21
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Heidari Torkabadi H, Che T, Shou J, Shanmugam S, Crowder MW, Bonomo RA, Pusztai-Carey M, Carey PR. Raman spectra of interchanging β-lactamase inhibitor intermediates on the millisecond time scale. J Am Chem Soc 2013; 135:2895-8. [PMID: 23406484 DOI: 10.1021/ja311440p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid mix-rapid freeze is a powerful method to study the mechanisms of enzyme-substrate reactions in solution. Here we report a protocol that combines this method with normal (non-resonance) Raman microscopy to enable us to define molecular details of intermediates at early time points. With this combined method, SHV-1, a class A β-lactamase, and tazobactam, a commercially available β-lactamase inhibitor, were rapidly mixed on the millisecond time scale and then were flash-frozen by injection into an isopentane solution surrounded by liquid nitrogen. The "ice" was finally freeze-dried and characterized by Raman microscopy. We found that the reaction is almost complete in solution at 25 ms, giving rise to a major population composed of the trans-enamine intermediate. Between 25 and 500 ms, minor populations of protonated imine are detected that have previously been postulated to precede enamine intermediates. However, within 1 s, the imines are converted entirely to enamines. Interestingly, with this method, we can measure directly the turnover number of SHV-1 and tazobactam. The enzyme is completely inhibited at 1:4 ratio (enzyme:inhibitor) or greater, a number that agrees with the turnover number derived from steady-state kinetic methods. This application, employing non-intensity-enhanced Raman spectroscopy, provides a general and effective route to study the early events in enzyme-substrate reactions.
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22
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Jahn A, Lucas F, Wepf RA, Dittrich PS. Freezing continuous-flow self-assembly in a microfluidic device: toward imaging of liposome formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:1717-1723. [PMID: 23289615 DOI: 10.1021/la303675g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A new method is described that combines a microfluidic device for the controlled formation of liposomes with instantaneous immobilization by means of ultrarapid cooling. The microfluidic device is composed of capillaries to hydrodynamically focus a stream of lipids dissolved in 2-propanol by two adjacent aqueous buffer streams before rapidly cooling by propane jet-freezing. The capillary containing the frozen sheath-flow is subsequently separated from the flow-focusing unit and trimmed with cryo-ultramicrotomy for imaging with cryo-scanning electron microscopy (SEM). The emergence of liposomes could be visualized by cryo-SEM without the need for chemical fixation or labeling. We demonstrate that the method is capable of revealing in more detail the formation of nonequilibrium liposomes. Partially and completely formed liposomes were observed at the miscible alcohol-buffer interface. The number density of lipid vesicles varied along the focused interface, and we frequently found clusters of liposomes. Additionally, evidence for the formation of disclike transient intermediates is presented. The method is not limited to studying self-assembly processes only. It can be extended to other biochemical reactions, crystallization processes, and even systematic interfacial mixing studies between different solvents.
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Affiliation(s)
- Andreas Jahn
- Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
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23
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Manzerova J, Krymov V, Gerfen GJ. Investigating the intermediates in the reaction of ribonucleoside triphosphate reductase from Lactobacillus leichmannii: An application of HF EPR-RFQ technology. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:32-45. [PMID: 21944735 DOI: 10.1016/j.jmr.2011.08.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 08/23/2011] [Indexed: 05/31/2023]
Abstract
In this investigation high-frequency electron paramagnetic resonance spectroscopy (HFEPR) in conjunction with innovative rapid freeze-quench (RFQ) technology is employed to study the exchange-coupled thiyl radical-cob(II)alamin system in ribonucleotide reductase from a prokaryote Lactobacillus leichmannii. The size of the exchange coupling (Jex) and the values of the thiyl radical g tensor are refined, while confirming the previously determined (Gerfen et al. (1996) [20]) distance between the paramagnets. Conclusions relevant to ribonucleotide reductase catalysis and the architecture of the active site are presented. A key part of this work has been the development of a unique RFQ apparatus for the preparation of millisecond quench time RFQ samples which can be packed into small (0.5 mm ID) sample tubes used for CW and pulsed HFEPR--lack of this ability has heretofore precluded such studies. The technology is compatible with a broad range of spectroscopic techniques and can be readily adopted by other laboratories.
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Affiliation(s)
- Julia Manzerova
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, United States
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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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Jung C, Vries SD, Schünemann V. Spectroscopic characterization of cytochrome P450 Compound I. Arch Biochem Biophys 2011; 507:44-55. [DOI: 10.1016/j.abb.2010.12.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 11/25/2022]
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Schmidt B, Mahmud G, Soh S, Kim SH, Page T, O’Halloran TV, Grzybowski BA, Hoffman BM. Design, Implementation, Simulation, and Visualization of a Highly Efficient RIM Microfluidic Mixer for Rapid Freeze-Quench of Biological Samples. APPLIED MAGNETIC RESONANCE 2011; 40:415-425. [PMID: 22180701 PMCID: PMC3237052 DOI: 10.1007/s00723-011-0195-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rapid freeze-quench (RFQ) trapping of short-lived reaction intermediates for spectroscopic study plays an important role in the characterization of biological reactions. Recently there has been considerable effort to achieve submillisecond reaction deadtimes. We present here a new, robust, high-velocity microfluidic mixer that enables such rapid freeze-quenching. It is a based on the mixing method of two impinging jets commonly used in reaction injection molding (RIM) of plastics. This method achieves efficient mixing by inducing chaotic flow at relatively low Reynolds numbers (Re =140). We present the first mathematical simulation and microscopic visualization of mixing in such RFQ micromixers, the results of which show that the impinging solutions efficiently mix within the mixing chamber. These tests, along with a practical demonstration in a RFQ setup that involves copper wheels, show this new mixer can in practice provide reaction deadtimes as low as 100 microseconds.
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Affiliation(s)
- Bryan Schmidt
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Goher Mahmud
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208
| | - Siowling Soh
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208
| | - Sun Hee Kim
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Taylor Page
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | | | - Bartosz A. Grzybowski
- Department of Chemistry, Northwestern University, Evanston, IL 60208
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
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Krebs C, Bollinger JM. Freeze-quench (57)Fe-Mössbauer spectroscopy: trapping reactive intermediates. PHOTOSYNTHESIS RESEARCH 2009; 102:295-304. [PMID: 19238577 DOI: 10.1007/s11120-009-9406-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 01/15/2009] [Indexed: 05/24/2023]
Abstract
(57)Fe-Mössbauer spectroscopy is a method that probes transitions between the nuclear ground state (I=1/2) and the first nuclear excited state (I=3/2). This technique provides detailed information about the chemical environment and electronic structure of iron. Therefore, it has played an important role in studies of the numerous iron-containing proteins and enzymes. In conjunction with the freeze-quench method, (57)Fe-Mössbauer spectroscopy allows for monitoring changes of the iron site(s) during a biochemical reaction. This approach is particularly powerful for detection and characterization of reactive intermediates. Comparison of experimentally determined Mössbauer parameters to those predicted by density functional theory for hypothetical model structures can then provide detailed insight into the structures of reactive intermediates. We have recently used this methodology to study the reactions of various mononuclear non-heme-iron enzymes by trapping and characterizing several Fe(IV)-oxo reaction intermediates. In this article, we summarize these findings and demonstrate the potential of the method.
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Affiliation(s)
- Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, 332 Chemistry Building, Pennsylvania, PA 16802, USA.
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28
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Chandrasekaran A, Packirisamy M. Experimental investigation of evanescence-based infrared biodetection technique for micro-total-analysis systems. JOURNAL OF BIOMEDICAL OPTICS 2009; 14:054050. [PMID: 19895151 DOI: 10.1117/1.3210766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The advent of microoptoelectromechanical systems (MOEMS) and its integration with other technologies such as microfluidics, microthermal, immunoproteomics, etc. has led to the concept of an integrated micro-total-analysis systems (microTAS) or Lab-on-a-Chip for chemical and biological applications. Recently, research and development of microTAS have attained a significant growth rate over several biodetection sciences, in situ medical diagnoses, and point-of-care testing applications. However, it is essential to develop suitable biophysical label-free detection methods for the success, reliability, and ease of use of the microTAS. We proposed an infrared (IR)-based evanescence wave detection system on the silicon-on-insulator platform for biodetection with microTAS. The system operates on the principle of bio-optical interaction that occurs due to the evanescence of light from the waveguide device. The feasibility of biodetection has been experimentally investigated by the detection of horse radish peroxidase upon its reaction with hydrogen peroxide.
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Affiliation(s)
- Arvind Chandrasekaran
- Concordia University, Department of Mechanical Engineering, Optical-Bio Microsystems Laboratory, 1515 Street Catherine Ouest, Montreal, Quebec H3G 2W1, Canada.
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29
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Abstract
Based on explicit definitions of biomolecular EPR spectroscopy and of the metallome, this tutorial review positions EPR in the field of metallomics as a unique method to study native, integrated systems of metallobiomolecular coordination complexes subject to external stimuli. The specific techniques of whole-system bioEPR spectroscopy are described and their historic, recent, and anticipated applications are discussed.
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Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands.
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30
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Egawa T, Durand JL, Hayden EY, Rousseau DL, Yeh SR. Design and evaluation of a passive alcove-based microfluidic mixer. Anal Chem 2009; 81:1622-7. [PMID: 19140669 DOI: 10.1021/ac802410g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel passive microfluidic silicon mixer has been designed, optimized and fabricated. The architecture of the mixer consists of a simple "T" junction, made up by a 20 microm wide by 82 microm deep channel, followed by three repeats of an alcove, each with a triangular obstruction, arranged in a zigzag fashion. Numerical simulations were employed to optimize the geometry, particularly the dimensions of the alcoves, the relative orientation and the spacing between them, and the degree of intrusion associated with them. The simulation results demonstrate that chaotic flow due to recirculation within the alcoves results in transverse velocity that promotes effective fluid mixing. The microfluidic mixer with the simulation-optimized geometry was fabricated with photolithographic techniques and characterized by optical imaging, fluorescence, and Raman microscope spectroscopy. At a sample flow rate of 20 microL/s, the mixer exhibits a short mixing deadtime of approximately 22 micros and a high mixing efficiency under both low and high viscosity conditions. The alcove-based microfluidic silicon mixer offers unique advantages for its short deadtime and slow sample consumption rate. In addition, it provides a valuable component for laboratory-on-a-chip applications for its ease of development into multiple networks for massively parallel analytical processes.
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Affiliation(s)
- Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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Bogachev AV, Belevich NP, Bertsova YV, Verkhovsky MI. Primary steps of the Na+-translocating NADH:ubiquinone oxidoreductase catalytic cycle resolved by the ultrafast freeze-quench approach. J Biol Chem 2008; 284:5533-8. [PMID: 19117949 DOI: 10.1074/jbc.m808984200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+)-translocating NADH:ubiquinone oxidoreductase (Na(+)-NQR) is a component of respiratory chain of various bacteria, and it generates a redox-driven transmembrane electrochemical Na(+) potential. Primary steps of the catalytic cycle of Na(+)-NQR from Vibrio harveyi were followed by the ultrafast freeze-quench approach in combination with conventional stopped-flow technique. The obtained sequence of events includes NADH binding ( approximately 1.5 x 10(7) m(-1) s(-1)), hydride ion transfer from NADH to FAD ( approximately 3.5 x 10(3) s(-1)), and partial electron separation and formation of equivalent fractions of reduced 2Fe-2S cluster and neutral semiquinone of FAD ( approximately 0.97 x 10(3) s(-1)). In the last step, a quasi-equilibrium is approached between the two states of FAD: two-electron reduced (50%) and one-electron reduced (the other 50%) species. The latter, neutral semiquinone of FAD, shares the second electron with the 2Fe-2S center. The transient midpoint redox potentials for the cofactors obtained during the fast kinetics measurements are very different from ones achieved during equilibrium redox titration and show that the functional states of the enzyme realized during its turning over cannot be modeled by the equilibrium approach.
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Affiliation(s)
- Alexander V Bogachev
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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Parker CO, Tothill IE. Development of an electrochemical immunosensor for aflatoxin M1 in milk with focus on matrix interference. Biosens Bioelectron 2008; 24:2452-7. [PMID: 19167207 DOI: 10.1016/j.bios.2008.12.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 12/15/2008] [Accepted: 12/16/2008] [Indexed: 11/17/2022]
Abstract
A simple sensor method was developed for aflatoxin M(1) analysis to be applied directly with milk by using antibody modified screen-printed carbon working electrode with carbon counter and silver-silver chloride pseudo-reference electrode. A competitive ELISA assay format was constructed on the surface of the working electrode using 3,3,5',5'-tetramethylbenzidine dihyrochloride (TMB)/H(2)O(2) electrochemical detection scheme with horseradish peroxidase (HRP) as the enzyme label. The performance of the assay and the sensor was optimised and characterised in pure buffer conditions before applying to milk samples. Extensive interference to the electroanalytical signal was observed upon the analysis of milk. Through a series of chemical fractionations of the milk, and testing the electrochemical properties of the fractions, the interference was attributed to whey proteins with focus towards alpha-lactalbumin. A simple pre-treatment technique of incorporating 18 mM calcium chloride, in the form of Dulbucco's PBS, in a 1:1 ratio to the milk sample or standards and also to the washing buffer stabilised the whey proteins in solution and eliminate the interfering signal. The resulting immunosensor was interference free and achieved a limit of detection of 39 ng l(-1) with a linear dynamic detection range up to 1000 ng l(-1). The developed immunosensor method was compared to a commercial ELISA kit and an in-house HPLC method. The immunsensor was comparable, in term of sensitivity, but vastly superior in term of portability and cost therefore a key instrument for the detection of aflatoxin M(1) at the source of the contamination.
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Affiliation(s)
- Charlie O Parker
- Cranfield Health, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
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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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Chandrasekaran A, Packirisamy M. Absorption detection of enzymatic reaction using optical microfluidics based intermittent flow microreactor system. IEE PROCEEDINGS. NANOBIOTECHNOLOGY 2006; 153:137-43. [PMID: 17187445 DOI: 10.1049/ip-nbt:20060012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The advantages of integrating microfluidics into photonics-based biosensing for fabricating microreactor type lab-on-a-chip devices carries a lot of advantages, such as smaller sample volume handling, controlled drug delivery and high throughput diagnosis, which is useful for in situ medical diagnosis and point-of-care (POC) testing. A hybrid integrated optical microfluidic system has been developed for the study of single molecules and enzymatic reactions. The method of optical absorption has been employed for biosensing and the feasibility of absorption-based detection on the microfluidic platform has been demonstrated using horseradish peroxidase and hydrogen peroxide, as an example. The results show that the device is useful for the analysis of both the individual chemical specimen and also the study of chemical and biological reaction between two reacting species. The hybrid integration of microfluidics and optical ensembles thus forms the basis for developing the microreactor type lab-on-a-chip device, which would have several important applications in the area of nanobiotechnology.
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Affiliation(s)
- A Chandrasekaran
- Optical Microsystems Laboratory, Department of Mechanical and Industrial Engineering, Concordia University, Montréal, Canada.
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36
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Bollinger JM, Krebs C. Stalking intermediates in oxygen activation by iron enzymes: motivation and method. J Inorg Biochem 2006; 100:586-605. [PMID: 16513177 DOI: 10.1016/j.jinorgbio.2006.01.022] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Accepted: 01/16/2006] [Indexed: 11/16/2022]
Abstract
The study of high-valent-iron enzyme intermediates began in the mid-1900s with the discovery of compounds I (or ES) and II in the heme peroxidases, progressed to non-heme-diiron enzymes in the 1990s with the detection and characterization of the Fe(III)-Fe(IV) complex, X, and the Fe(IV)-Fe(IV) complex, Q, in O(2) activation by ribonucleotide reductase R2 (RNR-R2) and soluble methane monooxygenase (sMMO), respectively, and was most recently extended to mononuclear non-heme-iron oxygenases with the trapping and spectroscopic characterization of the Fe(IV)-oxo intermediate, J, in the reaction of taurine:alpha-ketoglutarate dioxygenase (TauD). Individually, each of these landmark studies helped reveal the chemical logic of that particular enzyme system. Collectively, they have significantly advanced our understanding of Nature's strategies for oxidative transformation of biomolecules (both natural and "xenobiotic"). With high-valent complexes now having been described in representatives of three major classes of iron enzymes, it is an appropriate time to ask whether and what additional insights might be gleaned from further stalking of related intermediates in other systems. In this review, we advocate that there is still much to be learned from this pursuit and summarize the insight provided by two of the landmark discoveries mentioned above (the latter two) and the subsequent studies that they spurred to support our contention. In addition, we attempt to provide, to the extent that it is possible to do so, a "how-to" guide for detection and characterization of such intermediates, focusing primarily on enzymes in which they form by activation of molecular oxygen. In this latter objective, we have drawn from an earlier review by Johnson (Enzymes, third ed. vol. 20, 1992, pp. 1-61) covering, more generally, dissection of enzyme reaction pathways by transient-state kinetic methods. That work elegantly illustrated that, although it may be impossible to develop a true algorithm for the process, a synthesis of guidelines and general principles can be of considerable value.
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Affiliation(s)
- J Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 306 South Frear Building, University Park, PA 16802, USA.
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Shintaku M, Matsuura K, Yoshioka S, Takahashi S, Ishimori K, Morishima I. Absence of a detectable intermediate in the compound I formation of horseradish peroxidase at ambient temperature. J Biol Chem 2005; 280:40934-8. [PMID: 16221678 DOI: 10.1074/jbc.m503472200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A microsecond-resolved absorption spectrometer was developed to investigate the elementary steps in hydrogen peroxide (H(2)O(2)) activation reaction of horseradish peroxidase (HRP) at ambient temperature. The kinetic absorption spectra of HRP upon the mixing with various concentrations of H(2)O(2) (0.5-3 mm) were monitored in the time range from 50 to 300 mus. The time-resolved spectra in the Soret region possessed isosbestic points that were close to those between the resting state and compound I. The kinetic changes in the Soret absorbance could be well fitted by a single exponential function. Accordingly, no distinct spectrum of the putative intermediate between the resting state and compound I was identified. These results were consistent with the proposal that the O-O bond activation in heme peroxidases is promoted by the imidazolium form of the distal histidine that exists only transiently. It was estimated that the rate constant for the breakage of the O-O bond in H(2)O(2) by HRP is significantly faster than 1 x 10(4) s(-1).
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Affiliation(s)
- Masato Shintaku
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
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38
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Kumita H, Matsuura K, Hino T, Takahashi S, Hori H, Fukumori Y, Morishima I, Shiro Y. NO Reduction by Nitric-oxide Reductase from Denitrifying Bacterium Pseudomonas aeruginosa. J Biol Chem 2004; 279:55247-54. [PMID: 15504726 DOI: 10.1074/jbc.m409996200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitric-oxide reductase (NOR) of a denitrifying bacterium catalyzes NO reduction to N(2)O at the binuclear catalytic center consisting of high spin heme b(3) and non-heme Fe(B). The structures of the reaction intermediates in the single turnover of the NO reduction by NOR from Pseudomonas aeruginosa were investigated using optical absorption and EPR spectroscopies combined with an originally designed freeze-quench device. In the EPR spectrum of the sample, in which the fully reduced NOR was mixed with an NO solution and quenched at 0.5 ms after the mixing, two characteristic signals for the ferrous Fe(B)-NO and the penta-coordinated ferrous heme b(3)-NO species were observed. The CO inhibition of its formation indicated that two NO molecules were simultaneously distributed into the two irons of the same binuclear center of the enzyme in this state. The time- and temperature-dependent EPR spectral changes indicated that the species that appeared at 0.5 ms is a transient reaction intermediate prior to the N(2)O formation, in good agreement with the so-called "trans" mechanism. It was also found that the final state of the enzyme in the single turnover cycle is the fully oxidized state, in which the mu-oxo-bridged ligand is absent between the two irons of its binuclear center, unlike the resting form of NOR as isolated. On the basis of these present findings, we propose a newly developed mechanism for the NO reduction reaction conducted by NOR.
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Affiliation(s)
- Hideyuki Kumita
- RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
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Cherepanov AV, De Vries S. Microsecond freeze-hyperquenching: development of a new ultrafast micro-mixing and sampling technology and application to enzyme catalysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1656:1-31. [PMID: 15136155 DOI: 10.1016/j.bbabio.2004.02.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Revised: 02/17/2004] [Accepted: 02/17/2004] [Indexed: 11/21/2022]
Abstract
A novel freeze-quench instrument with a characteristic <<dead-time>> of 137 +/- 18 micros is reported. The prototype has several key features that distinguish it from conventional freeze-quench devices and provide a significant improvement in time resolution: (a) high operating pressures (up to 400 bar) result in a sample flow with high linear rates (up to 200 m s(-1)); (b) tangential micro-mixer with an operating volume of approximately 1 nl yields short mixing times (up to 20 micros); (c) fast transport between the mixer and the cryomedium results in short reaction times: the ageing solution exits the mixer as a free-flowing jet, and the chemical reaction occurs "in-flight" on the way to the cryomedium; (d) a small jet diameter (approximately 20 microm) and a high jet velocity (approximately 200 m s(-1)) provide high sample-cooling rates, resulting in a short cryofixation time (up to 30 micros). The dynamic range of the freeze-quench device is between 130 micros and 15 ms. The novel tangential micro-mixer efficiently mixes viscous aqueous solutions, showing more than 95% mixing at eta < or = 4 (equivalent to protein concentrations up to 250 mg ml(-1)), which makes it an excellent tool for the preparation of pre-steady state samples of concentrated protein solutions for spectroscopic structure analysis. The novel freeze-quench device is characterized using the reaction of binding of azide to metmyoglobin from horse heart. Reaction samples are analyzed using 77 K optical absorbance spectroscopy, and X-band EPR spectroscopy. A simple procedure of spectral analysis is reported that allows (a) to perform a quantitative analysis of the reaction kinetics and (b) to identify and characterize novel reaction intermediates. The reduction of dioxygen by the bo3-type quinol oxidase from Escherichia coli is assayed using the MHQ technique. In these pilot experiments, low-temperature optical absorbance measurements show the rapid oxidation of heme o3 in the first 137 micros of the reaction, accompanied by the formation of an oxo-ferryl species. X-band EPR spectroscopy shows that a short-living radical intermediate is formed during the oxidation of heme o3. The radical decays within approximately 1 ms concomitant with the oxidation of heme b, and can be attributed to the PM reaction intermediate converting to the oxoferryl intermediate F. The general field of application of the freeze-quench methodology is discussed.
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Affiliation(s)
- Alexey V Cherepanov
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Schünemann V, Lendzian F, Jung C, Contzen J, Barra AL, Sligar SG, Trautwein AX. Tyrosine radical formation in the reaction of wild type and mutant cytochrome P450cam with peroxy acids: a multifrequency EPR study of intermediates on the millisecond time scale. J Biol Chem 2003; 279:10919-30. [PMID: 14688245 DOI: 10.1074/jbc.m307884200] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report a multifrequency (9.6-, 94-, 190-, and 285-GHz) EPR study of a freeze-quenched intermediate obtained from reaction of substrate-free cytochrome P450cam (CYP101) and its Y96F and Y96F/Y75F mutants with peroxy acids. It is generally assumed that in such a shunt reaction an intermediate [Fe(IV)=O, porphyrin-pi-cation radical] is formed, which should be identical to the species in the natural reaction cycle. However, for the wild type as well as for the mutant proteins, a porphyrin-pi-cation radical is not detectable within 8 ms. Instead, EPR signals corresponding to tyrosine radicals are obtained for the wild type and the Y96F mutant. Replacement of both Tyr-96 and Tyr-75 by phenylalanine leads to the disappearance of the tyrosine EPR signals. EPR studies at 285 GHz on freeze-quenched wild type and Y96F samples reveal g tensor components for the radical (stretched g(x) values from 2.0078 to 2.0064, g(y) = 2.0043, and g(z) = 2.0022), which are fingerprints for tyrosine radicals in a heterogeneous polar environment. The measurements at 94 GHz using a fundamental mode microwave resonator setup confirm the 285-GHz study. From the simulation of the hyperfine structure in the 94-GHz EPR spectra the signals have been assigned to Tyr-96 in the wild type and to Tyr-75 in the Y96F mutant. We suggest that a transiently formed Fe(IV)=O porphyrin-pi-cation radical intermediate in P450cam is reduced by intramolecular electron transfer from these tyrosines within 8 ms.
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Egawa T, Yoshioka S, Takahashi S, Hori H, Nagano S, Shimada H, Ishimori K, Morishima I, Suematsu M, Ishimura Y. Kinetic and spectroscopic characterization of a hydroperoxy compound in the reaction of native myoglobin with hydrogen peroxide. J Biol Chem 2003; 278:41597-606. [PMID: 12902339 DOI: 10.1074/jbc.m210383200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The reaction of metmyoglobin with H2O2 was investigated in a pH range between 8.5 and 6.0 with the aid of stopped flow-rapid scan and rapid freezing-EPR techniques. Singular value decomposition analyses of the stopped flow data at pH 8.5 revealed that a spectral species previously unknown accumulated during the reaction and exhibited a Soret absorption maximum at >/=423 nm. In the EPR experiments, the new species exhibited a set of g values at 2.32, 2.19, and 1.94, indicating that the species was assignable to a ferric hydroperoxy (Fe(III)[O-O-H]-) compound. In contrast, the hydroperoxy compound scarcely accumulated in the reaction at pH 6.0, and the dominant intermediate species accumulated was compound I, which was derived from the oxygen-oxygen bond cleavage of the hydroperoxy compound. The accumulated amount of the hydroperoxy compound relative to compound I showed a pH dependence with an apparent pKa (pKaapp) from 6.95 to 7.27 depending on the metmyoglobins examined. This variation in pKaapp paralleled that in pKa of the acid-alkaline transition (pKaAB) of metmyoglobins, suggesting that the accumulation of hydroperoxy compound is controlled by the distal histidine. We propose that the H2O2 activation by metmyoglobin is promoted at the acidic condition due to the imidazolium form of the distal histidine, and we further propose that the controlled protonation state of the distal histidine is important for the facile O-O bond cleavage in heme peroxidases.
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Affiliation(s)
- Tsuyoshi Egawa
- Department of Biochemistry, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
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