1
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Gong Z, Wang L, Xu Y, Xie D, Qi X, Nam W, Guo M. Enhanced Reactivities of Iron(IV)-Oxo Porphyrin Species in Oxidation Reactions Promoted by Intramolecular Hydrogen-Bonding. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310333. [PMID: 38477431 PMCID: PMC11109629 DOI: 10.1002/advs.202310333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/19/2024] [Indexed: 03/14/2024]
Abstract
High-valent iron-oxo species are one of the common intermediates in both biological and biomimetic catalytic oxidation reactions. Recently, hydrogen-bonding (H-bonding) has been proved to be critical in determining the selectivity and reactivity. However, few examples have been established for mechanistic insights into the H-bonding effect. Moreover, intramolecular H-bonding effect on both C-H activation and oxygen atom transfer (OAT) reactions in synthetic porphyrin model system has not been investigated yet. In this study, a series of heme-containing iron(IV)-oxo porphyrin species with or without intramolecular H-bonding are synthesized and characterized. Kinetic studies revealed that intramolecular H-bonding can significantly enhance the reactivity of iron(IV)-oxo species in OAT, C-H activation, and electron-transfer reactions. This unprecedented unified H-bonding effect is elucidated by theoretical calculations, which showed that intramolecular H-bonding interactions lower the energy of the anti-bonding orbital of iron(IV)-oxo porphyrin species, resulting in the enhanced reactivities in oxidation reactions irrespective of the reaction type. To the best of the knowledge, this is the first extensive investigation on the intramolecular H-bonding effect in heme system. The results show that H-bonding interactions have a unified effect with iron(IV)-oxo porphyrin species in all three investigated reactions.
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Affiliation(s)
- Zhe Gong
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Liwei Wang
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Yiran Xu
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Duanfeng Xie
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Xiaotian Qi
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Wonwoo Nam
- Department of Chemistry and Nano ScienceEwha Womans UniversitySeoul03760South Korea
| | - Mian Guo
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
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2
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Ansari M, Bhattacharjee S, Pantazis DA. Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II. J Am Chem Soc 2024; 146:9640-9656. [PMID: 38530124 PMCID: PMC11009960 DOI: 10.1021/jacs.3c13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024]
Abstract
Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.
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Affiliation(s)
- Mursaleem Ansari
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Sinjini Bhattacharjee
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
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3
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Barreiro DS, Oliveira RN, Pauleta SR. Bacterial peroxidases – Multivalent enzymes that enable the use of hydrogen peroxide for microaerobic and anaerobic proliferation. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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4
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Ramos DR, Furtmüller PG, Obinger C, Peña-Gallego Á, Pérez-Juste I, Santaballa JA. Common Reactivity and Properties of Heme Peroxidases: A DFT Study of Their Origin. Antioxidants (Basel) 2023; 12:antiox12020303. [PMID: 36829861 PMCID: PMC9952403 DOI: 10.3390/antiox12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Electronic structure calculations using the density-functional theory (DFT) have been performed to analyse the effect of water molecules and protonation on the heme group of peroxidases in different redox (ferric, ferrous, compounds I and II) and spin states. Shared geometries, spectroscopic properties at the Soret region, and the thermodynamics of peroxidases are discussed. B3LYP and M06-2X density functionals with different basis sets were employed on a common molecular model of the active site (Fe-centred porphine and proximal imidazole). Computed Gibbs free energies indicate that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) centre in native ferric peroxidases, with a water molecule located at a non-bonding distance. Protonation of the ferryl oxygen of compound II is discussed in terms of thermodynamics, Fe-O bond distances, and redox properties. It is demonstrated that this protonation is necessary to account for the experimental data, and computed Gibbs free energies reveal pKa values of compound II about 8.5-9.0. Computation indicates that the general oxidative properties of peroxidase intermediates, as well as their reactivity towards water and protons and Soret bands, are mainly controlled by the iron porphyrin and its proximal histidine ligand.
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Affiliation(s)
- Daniel R. Ramos
- Chemical Reactivity & Photoreactivity Group (React!), Department of Chemistry, CICA & Faculty of Sciences, Universidade da Coruña, Campus da Zapateira, E-15071 A Coruña, Spain
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
- Correspondence: (D.R.R.); (J.A.S.)
| | - Paul G. Furtmüller
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Ángeles Peña-Gallego
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
| | - Ignacio Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
| | - J. Arturo Santaballa
- Chemical Reactivity & Photoreactivity Group (React!), Department of Chemistry, CICA & Faculty of Sciences, Universidade da Coruña, Campus da Zapateira, E-15071 A Coruña, Spain
- Correspondence: (D.R.R.); (J.A.S.)
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5
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Schröder GC, O'Dell WB, Webb SP, Agarwal PK, Meilleur F. Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. Chem Sci 2022; 13:13303-13320. [PMID: 36507176 PMCID: PMC9683017 DOI: 10.1039/d2sc05031e] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022] Open
Abstract
Metalloproteins perform a diverse array of redox-related reactions facilitated by the increased chemical functionality afforded by their metallocofactors. Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes that are responsible for the breakdown of recalcitrant polysaccharides via oxidative cleavage at the glycosidic bond. The activated copper-oxygen intermediates and their mechanism of formation remains to be established. Neutron protein crystallography which permits direct visualization of protonation states was used to investigate the initial steps of oxygen activation directly following active site copper reduction in Neurospora crassa LPMO9D. Herein, we cryo-trap an activated dioxygen intermediate in a mixture of superoxo and hydroperoxo states, and we identify the conserved second coordination shell residue His157 as the proton donor. Density functional theory calculations indicate that both superoxo and hydroperoxo active site states are stable. The hydroperoxo formed is potentially an early LPMO catalytic reaction intermediate or the first step in the mechanism of hydrogen peroxide formation in the absence of substrate. We observe that the N-terminal amino group of the copper coordinating His1 remains doubly protonated directly following molecular oxygen reduction by copper. Aided by molecular dynamics and mining minima free energy calculations we establish that the conserved second-shell His161 in MtPMO3* displays conformational flexibility in solution and that this flexibility is also observed, though to a lesser extent, in His157 of NcLPMO9D. The imidazolate form of His157 observed in our structure following oxygen intermediate protonation can be attributed to abolished His157 flexibility due steric hindrance in the crystal as well as the solvent-occluded active site environment due to crystal packing. A neutron crystal structure of NcLPMO9D at low pH further supports occlusion of the active site since His157 remains singly protonated even at acidic conditions.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Simon P. Webb
- VeraChem LLC12850 Middlebrook Rd. Ste 205GermantownMD 20874-5244USA
| | - Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterOK 74078USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
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6
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Lee J, Yang M, Song WJ. The expanded landscape of metalloproteins by genetic incorporation of noncanonical amino acids. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jaehee Lee
- Department of Chemistry Seoul National University Seoul South Korea
| | - Minwoo Yang
- Department of Chemistry Seoul National University Seoul South Korea
| | - Woon Ju Song
- Department of Chemistry Seoul National University Seoul South Korea
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7
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Lučić M, Wilson MT, Tosha T, Sugimoto H, Shilova A, Axford D, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB. ACS Catal 2022; 12:13349-13359. [PMID: 36366763 PMCID: PMC9638988 DOI: 10.1021/acscatal.2c03754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/05/2022] [Indexed: 11/30/2022]
Abstract
![]()
Controlling the reactivity
of high-valent Fe(IV)–O
catalytic
intermediates, Compounds I and II, generated in heme enzymes upon
reaction with dioxygen or hydrogen peroxide, is important for function.
It has been hypothesized that the presence (wet) or absence (dry)
of distal heme pocket water molecules can influence whether Compound
I undergoes sequential one-electron additions or a concerted two-electron
reduction. To test this hypothesis, we investigate the role of water
in the heme distal pocket of a dye-decolorizing peroxidase utilizing
a combination of serial femtosecond crystallography and rapid kinetic
studies. In a dry distal heme site, Compound I reduction proceeds
through a mechanism in which Compound II concentration is low. This
reaction shows a strong deuterium isotope effect, indicating that
reduction is coupled to proton uptake. The resulting protonated Compound
II (Fe(IV)–OH) rapidly reduces to the ferric state, giving
the appearance of a two-electron transfer process. In a wet site,
reduction of Compound I is faster, has no deuterium effect, and yields
highly populated Compound II, which is subsequently reduced to the
ferric form. This work provides a definitive experimental test of
the hypothesis advanced in the literature that relates sequential
or concerted electron transfer to Compound I in wet or dry distal
heme sites.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park,
Essex, ColchesterCO4 3SQ, U.K
| | - Michael T. Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park,
Essex, ColchesterCO4 3SQ, U.K
| | - Takehiko Tosha
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo, Hyogo679-5148Japan
| | | | - Anastasya Shilova
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, DidcotOX11 0DE, U.K
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, DidcotOX11 0DE, U.K
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, DidcotOX11 0DE, U.K
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park,
Essex, ColchesterCO4 3SQ, U.K
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, DidcotOX11 0DE, U.K
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park,
Essex, ColchesterCO4 3SQ, U.K
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8
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Moreno-Chicano T, Carey LM, Axford D, Beale JH, Doak RB, Duyvesteyn HME, Ebrahim A, Henning RW, Monteiro DCF, Myles DA, Owada S, Sherrell DA, Straw ML, Šrajer V, Sugimoto H, Tono K, Tosha T, Tews I, Trebbin M, Strange RW, Weiss KL, Worrall JAR, Meilleur F, Owen RL, Ghiladi RA, Hough MA. Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature. IUCRJ 2022; 9:610-624. [PMID: 36071813 PMCID: PMC9438502 DOI: 10.1107/s2052252522006418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.
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Affiliation(s)
- Tadeo Moreno-Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Leiah M. Carey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Helen M. E. Duyvesteyn
- Division of Structural Biology (STRUBI), University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ali Ebrahim
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Robert W. Henning
- BioCARS, University of Chicago, Building 434B, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Diana C. F. Monteiro
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203-1102, USA
| | - Dean A. Myles
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Darren A. Sherrell
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Megan L. Straw
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Vukica Šrajer
- BioCARS, University of Chicago, Building 434B, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | | | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ivo Tews
- Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, United Kingdom
| | - Martin Trebbin
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203-1102, USA
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Kevin L. Weiss
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Flora Meilleur
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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9
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Freeman SL, Skafar V, Kwon H, Fielding AJ, Moody PCE, Martínez A, Issoglio FM, Inchausti L, Smircich P, Zeida A, Piacenza L, Radi R, Raven EL. Crystal structure of Trypanosoma cruzi heme peroxidase and characterization of its substrate specificity and compound I intermediate. J Biol Chem 2022; 298:102204. [PMID: 35772495 PMCID: PMC9358470 DOI: 10.1016/j.jbc.2022.102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/26/2022] Open
Abstract
The protozoan parasite Trypanosoma cruzi is the causative agent of American trypanosomiasis, otherwise known as Chagas disease. To survive in the host, the T. cruzi parasite needs antioxidant defense systems. One of these is a hybrid heme peroxidase, the T. cruzi ascorbate peroxidase-cytochrome c peroxidase enzyme (TcAPx-CcP). TcAPx-CcP has high sequence identity to members of the class I peroxidase family, notably ascorbate peroxidase (APX) and cytochrome c peroxidase (CcP), as well as a mitochondrial peroxidase from Leishmania major (LmP). The aim of this work was to solve the structure and examine the reactivity of the TcAPx-CcP enzyme. Low temperature electron paramagnetic resonance spectra support the formation of an exchange-coupled [Fe(IV)=O Trp233•+] compound I radical species, analogous to that used in CcP and LmP. We demonstrate that TcAPx-CcP is similar in overall structure to APX and CcP, but there are differences in the substrate-binding regions. Furthermore, the electron transfer pathway from cytochrome c to the heme in CcP and LmP is preserved in the TcAPx-CcP structure. Integration of steady state kinetic experiments, molecular dynamic simulations, and bioinformatic analyses indicates that TcAPx-CcP preferentially oxidizes cytochrome c but is still competent for oxidization of ascorbate. The results reveal that TcAPx-CcP is a credible cytochrome c peroxidase, which can also bind and use ascorbate in host cells, where concentrations are in the millimolar range. Thus, kinetically and functionally TcAPx-CcP can be considered a hybrid peroxidase.
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Affiliation(s)
- Samuel L Freeman
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Vera Skafar
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Hanna Kwon
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| | - Alistair J Fielding
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moore University, Liverpool, United Kingdom
| | - Peter C E Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| | - Alejandra Martínez
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Federico M Issoglio
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Lucas Inchausti
- Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay; Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay; Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Lucía Piacenza
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad of Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol, United Kingdom.
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10
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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11
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Borgstahl GEO, O'Dell WB, Egli M, Kern JF, Kovalevsky A, Lin JYY, Myles D, Wilson MA, Zhang W, Zwart P, Coates L. EWALD: A macromolecular diffractometer for the second target station. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:064103. [PMID: 35778015 DOI: 10.1063/5.0090810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Revealing the positions of all the atoms in large macromolecules is powerful but only possible with neutron macromolecular crystallography (NMC). Neutrons provide a sensitive and gentle probe for the direct detection of protonation states at near-physiological temperatures and clean of artifacts caused by x rays or electrons. Currently, NMC use is restricted by the requirement for large crystal volumes even at state-of-the-art instruments such as the macromolecular neutron diffractometer at the Spallation Neutron Source. EWALD's design will break the crystal volume barrier and, thus, open the door for new types of experiments, the study of grand challenge systems, and the more routine use of NMC in biology. EWALD is a single crystal diffractometer capable of collecting data from macromolecular crystals on orders of magnitude smaller than what is currently feasible. The construction of EWALD at the Second Target Station will cause a revolution in NMC by enabling key discoveries in the biological, biomedical, and bioenergy sciences.
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Affiliation(s)
- Gloria E O Borgstahl
- Eppley Institute for Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, Nebraska 68198-6805, USA
| | - William B O'Dell
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA and Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Jiao Y Y Lin
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Dean Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Mark A Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Petrus Zwart
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
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12
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Aboelnga MM. Mechanistic insights into the chemistry of compound I formation in heme peroxidases: quantum chemical investigations of cytochrome c peroxidase. RSC Adv 2022; 12:15543-15554. [PMID: 35685178 PMCID: PMC9125774 DOI: 10.1039/d2ra01073a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peroxidases are heme containing enzymes that catalyze peroxide-dependant oxidation of a variety of substrates through forming key ferryl intermediates, compounds I and II. Cytochrome c peroxidase (Ccp1) has served for decades as a chemical model toward understanding the chemical biology of this heme family of enzymes. It is known to feature a distinctive electronic behaviour for its compound I despite significant structural similarity to other peroxidases. A water-assisted mechanism has been proposed over a dry one for the formation of compound I in similar peroxidases. To better identify the viability of these mechanisms, we employed quantum chemistry calculations for the heme pocket of Ccp1 in three different spin states. We provided comparative energetic and structural results for the six possible pathways that suggest the preference of the dry mechanism energetically and structurally. The doublet state is found to be the most preferable spin state for the mechanism to proceed and for the formation of the Cpd I ferryl-intermediate irrespective of the considered dielectric constant used to represent the solvent environment. The nature of the spin state has negligible effects on the calculated structures but great impact on the energetics. Our analysis was also expanded to explain the major contribution of key residues to the peroxidase activity of Ccp1 through exploring the mechanism at various in silico generated Ccp1 variants. Overall, we provide valuable findings toward solving the current ambiguity of the exact mechanism in Ccp1, which could be applied to peroxidases with similar heme pockets. Discerning the feasibility of a no-water peroxidase mechanism in the doublet spin state irrespective of the environment surrounding the heme pocket.![]()
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Affiliation(s)
- Mohamed M Aboelnga
- Chemistry Department, Faculty of Science, Damietta University New Damietta 34517 Egypt
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13
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Onoda H, Tanaka S, Watanabe Y, Shoji O. Exploring hitherto uninvestigated reactions of the fatty acid peroxygenase CYP152A1: catalase reaction and Compound I formation. Faraday Discuss 2022; 234:304-314. [PMID: 35179151 DOI: 10.1039/d1fd00065a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CYP152A1 (cytochrome P450BSβ) is a fatty acid peroxygenase, which specifically catalyses the oxidation of long-chain fatty acids using hydrogen peroxide as an oxidant. We have found that CYP152A1 possesses catalase activity, which competes with the hydroxylation of long-chain fatty acids, the oxidation of non-native substrates, and haem degradation. Using hydrogen peroxide, Compound I of CYP152A1 could not be observed, due to its swift decomposition via catalase activity, where Compound I reacts with another molecule of hydrogen peroxide to form O2. In contrast, a clear spectral change indicative of Compound I formation was observed when mCPBA was employed as the oxidant. This work presents valuable insights into an important role for the catalase activity of CYP152A1 in avoiding enzyme deactivation when no substrate is available for oxidation.
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Affiliation(s)
- Hiroki Onoda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan. .,Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shota Tanaka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan.
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan.
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan.
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14
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Cao F, Sang Y, Liu C, Bai F, Zheng L, Ren J, Qu X. Self-Adaptive Single-Atom Catalyst Boosting Selective Ferroptosis in Tumor Cells. ACS NANO 2022; 16:855-868. [PMID: 35025200 DOI: 10.1021/acsnano.1c08464] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Ferroptosis, resulting from the catastrophic accumulation of lipid reactive oxygen species (ROS) and the inactivation of glutathione (GSH)-dependent peroxidase 4 (GPX4), has emerged as a form of regulated cell death for cancer therapy. Despite progress made with current ferroptosis inducers, efficient systems to trigger ferroptosis remain challenging, owing largely to their low activity, uncontrollable behavior, and even nonselective interactions. Here, we report a self-adaptive ferroptosis platform by engineering a DNA modulator onto the surface of single-atom nanozymes (SAzymes). The modulator could not only specifically intensify the ROS-generating activity but also endow the SAzymes with on-demand GSH-consuming ability in tumor cells, accelerating selective and safe ferroptosis. The self-adaptive antitumor response has been demonstrated in colon cancer and breast cancer, promoting the development of selective cancer therapy.
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Affiliation(s)
- Fangfang Cao
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Yanjuan Sang
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Chaoying Liu
- Department of Respiratory Medicine, First Affiliated Hospital, Jilin University, Jilin 130021, P. R. China
| | - Fuquan Bai
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University, Jilin, Changchun 130021, P. R. China
| | - Lirong Zheng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Ren
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
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15
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Kelpšas V, von Wachenfeldt C. Enhancing protein perdeuteration by experimental evolution of Escherichia coli K-12 for rapid growth in deuterium-based media. Protein Sci 2021; 30:2457-2473. [PMID: 34655136 PMCID: PMC8605374 DOI: 10.1002/pro.4206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/07/2022]
Abstract
Deuterium is a natural low abundance stable hydrogen isotope that in high concentrations negatively affects growth of cells. Here, we have studied growth of Escherichia coli MG1655, a wild-type laboratory strain of E. coli K-12, in deuterated glycerol minimal medium. The growth rate and final biomass in deuterated medium is substantially reduced compared to cells grown in ordinary medium. By using a multi-generation adaptive laboratory evolution-based approach, we have isolated strains that show increased fitness in deuterium-based growth media. Whole-genome sequencing identified the genomic changes in the obtained strains and show that there are multiple routes to genetic adaptation to growth in deuterium-based media. By screening a collection of single-gene knockouts of nonessential genes, no specific gene was found to be essential for growth in deuterated minimal medium. Deuteration of proteins is of importance for NMR spectroscopy, neutron protein crystallography, neutron reflectometry, and small angle neutron scattering. The laboratory evolved strains, with substantially improved growth rate, were adapted for recombinant protein production by T7 RNA polymerase overexpression systems and shown to be suitable for efficient production of perdeuterated soluble and membrane proteins for structural biology applications.
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Affiliation(s)
- Vinardas Kelpšas
- The Microbiology Group, Department of Biology, Lund University, Lund, Sweden
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16
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Zippilli C, Bizzarri BM, Gabellone S, Botta L, Saladino R. Oxidative Coupling of Coumarins by Blue‐LED‐Driven
in situ
Activation of Horseradish Peroxidase in a Two‐Liquid‐Phase System. ChemCatChem 2021. [DOI: 10.1002/cctc.202100753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Claudio Zippilli
- Department of Biological and Ecological Sciences University of Tuscia Via S.C. De Lellis s.n.c. 01100 Viterbo Italy
| | - Bruno Mattia Bizzarri
- Department of Biological and Ecological Sciences University of Tuscia Via S.C. De Lellis s.n.c. 01100 Viterbo Italy
| | - Sofia Gabellone
- Department of Biological and Ecological Sciences University of Tuscia Via S.C. De Lellis s.n.c. 01100 Viterbo Italy
| | - Lorenzo Botta
- Department of Biological and Ecological Sciences University of Tuscia Via S.C. De Lellis s.n.c. 01100 Viterbo Italy
| | - Raffaele Saladino
- Department of Biological and Ecological Sciences University of Tuscia Via S.C. De Lellis s.n.c. 01100 Viterbo Italy
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17
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Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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18
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Lee JL, Ross DL, Barman SK, Ziller JW, Borovik AS. C-H Bond Cleavage by Bioinspired Nonheme Metal Complexes. Inorg Chem 2021; 60:13759-13783. [PMID: 34491738 DOI: 10.1021/acs.inorgchem.1c01754] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The functionalization of C-H bonds is one of the most challenging transformations in synthetic chemistry. In biology, these processes are well-known and are achieved with a variety of metalloenzymes, many of which contain a single metal center within their active sites. The most well studied are those with Fe centers, and the emerging experimental data show that high-valent iron oxido species are the intermediates responsible for cleaving the C-H bond. This Forum Article describes the state of this field with an emphasis on nonheme Fe enzymes and current experimental results that provide insights into the properties that make these species capable of C-H bond cleavage. These parameters are also briefly considered in regard to manganese oxido complexes and Cu-containing metalloenzymes. Synthetic iron oxido complexes are discussed to highlight their utility as spectroscopic and mechanistic probes and reagents for C-H bond functionalization. Avenues for future research are also examined.
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Affiliation(s)
- Justin L Lee
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Dolores L Ross
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Suman K Barman
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Joseph W Ziller
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - A S Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
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19
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Tian G, Hao G, Chen X, Liu Y. Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET: Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC. Inorg Chem 2021; 60:13539-13549. [PMID: 34382397 DOI: 10.1021/acs.inorgchem.1c01864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peroxide-dependent coproheme decarboxylase ChdC from Geobacillus stearothermophilus catalyzes two key steps in the synthesis of heme b, i.e., two sequential oxidative decarboxylations of coproporphyrinogen III (coproheme III) at propionate groups P2 and P4. In the binding site of coproheme III, P2 and P4 are anchored by different residues (Tyr144, Arg217, and Ser222 for P2 and Tyr113, Lys148, and Trp156 for P4); however, strong experimental evidence supports that the generated Tyr144 radical acts as an unique intermediary for hydrogen atom transfer (HAT) from both reactive propionates. So far, the reaction details are still unclear. Herein, we carried out quantum mechanics/molecular mechanics calculations to explore the decarboxylation mechanism of coproheme III. In our calculations, the coproheme Cpd I, Fe(IV) = O coupled to a porphyrin radical cation (por•+) with four propionate groups, was used as a reactant model. Our calculations reveal that Tyr144 is directly involved in the decarboxylation of propionate group P2. First, the proton-coupled electron transfer (PCET) occurs from Tyr144 to P2, generating a Tyr144 radical, which then abstracts a hydrogen atom from the Cβ of P2. The β-H extraction was calculated to be the rate-limiting step of decarboxylation. It is the porphyrin radical cation (por•+) that makes the PCET from Tyr144 to P2 to be quite easy to initiate the decarboxylation. Finally, the electron transfers from the Cβ• through the porphyrin to the iron center, leading to the decarboxylation of P2. Importantly, the decarboxylation of P4 mediated by Lys148 was calculated to be very difficult, which suggests that after the P2 decarboxylation, the generated harderoheme III intermediate should rebind or rotate in the active site so that the propionate P4 occupies the binding site of P2, and Tyr144 again mediates the decarboxylation of P4. Thus, our calculations support the fact that Tyr144 is responsible for the decarboxylation of both P2 and P4.
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Affiliation(s)
- Ge Tian
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China.,School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Gangping Hao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China
| | - Xiaohua Chen
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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20
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Lučić M, Wilson MT, Svistunenko DA, Owen RL, Hough MA, Worrall JAR. Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of Fe IV = O formation in bacterial dye-decolorizing peroxidases. J Biol Inorg Chem 2021; 26:743-761. [PMID: 34477969 PMCID: PMC8463360 DOI: 10.1007/s00775-021-01896-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, Oxfordshire, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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21
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Ortmayer M, Hardy FJ, Quesne MG, Fisher K, Levy C, Heyes DJ, Catlow CRA, de Visser SP, Rigby SEJ, Hay S, Green AP. A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase. JACS AU 2021; 1:913-918. [PMID: 34337604 PMCID: PMC8317151 DOI: 10.1021/jacsau.1c00145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nature employs high-energy metal-oxo intermediates embedded within enzyme active sites to perform challenging oxidative transformations with remarkable selectivity. Understanding how different local metal-oxo coordination environments control intermediate reactivity and catalytic function is a long-standing objective. However, conducting structure-activity relationships directly in active sites has proven challenging due to the limited range of amino acid substitutions achievable within the constraints of the genetic code. Here, we use an expanded genetic code to examine the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, by replacing the N-H group of the active site Trp51 of cytochrome c peroxidase by an S atom. Removal of a single hydrogen bond stabilizes the porphyrin π-cation radical state of CcP W191F compound I. In contrast, this modification leads to more basic and reactive neutral ferryl heme states, as found in CcP W191F compound II and the wild-type ferryl heme-Trp191 radical pair of compound I. This increased reactivity manifests in a >60-fold activity increase toward phenolic substrates but remarkably has negligible effects on oxidation of the biological redox partner cytc. Our data highlight how Trp51 tunes the lifetimes of key ferryl intermediates and works in synergy with the redox active Trp191 and a well-defined substrate binding site to regulate catalytic function. More broadly, this work shows how noncanonical substitutions can advance our understanding of active site features governing metal-oxo structure and reactivity.
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Affiliation(s)
- Mary Ortmayer
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Florence J. Hardy
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Matthew G. Quesne
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon OX11 0FA, United
Kingdom
- Cardiff
University, School of Chemistry, Main Building, Park Place, Cardiff CF10
3AT, United Kingdom
| | - Karl Fisher
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Colin Levy
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Derren J. Heyes
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - C. Richard A. Catlow
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon OX11 0FA, United
Kingdom
- Cardiff
University, School of Chemistry, Main Building, Park Place, Cardiff CF10
3AT, United Kingdom
- Kathleen
Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, Western Central 1H 0AJ, United Kingdom
| | - Sam P. de Visser
- Department
of Chemical Engineering and Analytical Science & Manchester Institute
of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Stephen E. J. Rigby
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Anthony P. Green
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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22
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Kono F, Tamada T. Neutron crystallography for the elucidation of enzyme catalysis. Curr Opin Struct Biol 2021; 71:36-42. [PMID: 34214927 DOI: 10.1016/j.sbi.2021.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/08/2021] [Accepted: 05/22/2021] [Indexed: 11/26/2022]
Abstract
Hydrogen atoms and hydration water molecules in proteins are indispensable for many biochemical processes, especially enzymatic catalysis. The locations of hydrogen atoms in proteins are usually predicted based on X-ray structures, but it is still very difficult to know the ionization states of the catalytic residues, the hydration structure of the protein, and the characteristics of hydrogen-bonding interactions. Neutron crystallography allows the direct observation of hydrogen atoms that play crucial roles in molecular recognition and the catalytic reactions of enzymes. In this review, we present the current status of neutron crystallography in structural biology and recent neutron structural analyses of three enzymes: ascorbate peroxidase, the main protease of severe acute respiratory syndrome coronavirus 2, and copper-containing nitrite reductase.
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Affiliation(s)
- Fumiaki Kono
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan.
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23
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Kwon H, Basran J, Pathak C, Hussain M, Freeman SL, Fielding AJ, Bailey AJ, Stefanou N, Sparkes HA, Tosha T, Yamashita K, Hirata K, Murakami H, Ueno G, Ago H, Tono K, Yamamoto M, Sawai H, Shiro Y, Sugimoto H, Raven EL, Moody PCE. XFEL Crystal Structures of Peroxidase Compound II. Angew Chem Int Ed Engl 2021; 60:14578-14585. [PMID: 33826799 PMCID: PMC8251747 DOI: 10.1002/anie.202103010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 01/07/2023]
Abstract
Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an FeIV =O or FeIV -OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated FeIV =O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme.
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Affiliation(s)
- Hanna Kwon
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Chinar Pathak
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Mahdi Hussain
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Samuel L. Freeman
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Alistair J. Fielding
- Centre for Natural Products Discovery, Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityJames Parsons Building, Byrom StreetLiverpoolL3 3AFUK
| | - Anna J. Bailey
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Natalia Stefanou
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Hazel A. Sparkes
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | - Keitaro Yamashita
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Present address: MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB1 0QHUK
| | - Kunio Hirata
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hironori Murakami
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | - Go Ueno
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hideo Ago
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Hitomi Sawai
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | - Yoshitsugu Shiro
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | | | - Emma L. Raven
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Peter C. E. Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
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24
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Kwon H, Basran J, Pathak C, Hussain M, Freeman SL, Fielding AJ, Bailey AJ, Stefanou N, Sparkes HA, Tosha T, Yamashita K, Hirata K, Murakami H, Ueno G, Ago H, Tono K, Yamamoto M, Sawai H, Shiro Y, Sugimoto H, Raven EL, Moody PCE. XFEL Crystal Structures of Peroxidase Compound II. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:14699-14706. [PMID: 38505375 PMCID: PMC10947387 DOI: 10.1002/ange.202103010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 03/21/2024]
Abstract
Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an FeIV=O or FeIV-OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated FeIV=O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme.
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Affiliation(s)
- Hanna Kwon
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Chinar Pathak
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Mahdi Hussain
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
| | - Samuel L. Freeman
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Alistair J. Fielding
- Centre for Natural Products Discovery, Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityJames Parsons Building, Byrom StreetLiverpoolL3 3AFUK
| | - Anna J. Bailey
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Natalia Stefanou
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Hazel A. Sparkes
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | - Keitaro Yamashita
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Present address: MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB1 0QHUK
| | - Kunio Hirata
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hironori Murakami
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | - Go Ueno
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Hideo Ago
- RIKEN SPring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Hitomi Sawai
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | - Yoshitsugu Shiro
- Graduate School of Life ScienceUniversity of Hyogo3-2-1 Kouto, Kamigori-choAko-gunHyogo678-1297Japan
| | | | - Emma L. Raven
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Peter C. E. Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLancaster RoadLeicesterLE1 7RHUK
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25
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Harp JM, Coates L, Sullivan B, Egli M. Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography. Nucleic Acids Res 2021; 49:4782-4792. [PMID: 33872377 PMCID: PMC8096259 DOI: 10.1093/nar/gkab264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/28/2021] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)]2. The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
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26
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Wang J, Wang X, Ouyang Q, Liu W, Shan J, Tan H, Li X, Chen G. N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement. Inorg Chem 2021; 60:7719-7731. [PMID: 34004115 DOI: 10.1021/acs.inorgchem.1c00057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the FeII-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent FeIV═O species. In the catalytic reaction pathway, the O2 binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the Cε-Nω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.
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Affiliation(s)
- Junkai Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xixi Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiankai Shan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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27
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Abstract
In addition to heme's role as the prosthetic group buried inside many different proteins that are ubiquitous in biology, there is new evidence that heme has substantive roles in cellular signaling and regulation. This means that heme must be available in locations distant from its place of synthesis (mitochondria) in response to transient cellular demands. A longstanding question has been to establish the mechanisms that control the supply and demand for cellular heme. By fusing a monomeric heme-binding peroxidase (ascorbate peroxidase, mAPX) to a monomeric form of green-fluorescent protein (mEGFP), we have developed a heme sensor (mAPXmEGFP) that can respond to heme availability. By means of fluorescence lifetime imaging, this heme sensor can be used to quantify heme concentrations; values of the mean fluorescence lifetime (τMean) for mAPX-mEGFP are shown to be responsive to changes in free (unbound) heme concentration in cells. The results demonstrate that concentrations are typically limited to one molecule or less within cellular compartments. These miniscule amounts of free heme are consistent with a system that sequesters the heme and is able to buffer changes in heme availability while retaining the capability to mobilize heme when and where it is needed. We propose that this exchangeable supply of heme can operate using mechanisms for heme transfer that are analogous to classical ligand-exchange mechanisms. This exquisite control, in which heme is made available for transfer one molecule at a time, protects the cell against the toxic effect of excess heme and offers a simple mechanism for heme-dependent regulation in single-molecule steps.
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28
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Ravanfar R, Abbaspourrad A. Monitoring the heme iron state in horseradish peroxidase to detect ultratrace amounts of hydrogen peroxide in alcohols. RSC Adv 2021; 11:9901-9910. [PMID: 35423493 PMCID: PMC8695524 DOI: 10.1039/d1ra00733e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/26/2021] [Indexed: 11/21/2022] Open
Abstract
Despite the importance of hydrogen peroxide (H2O2) in initiating oxidative damage and its connection to various diseases, the detection of low concentrations of H2O2 (<10 μM) is still limited using current methods, particularly in non-aqueous systems. One of the most common methods is based on examining the color change of a reducing substrate upon oxidation using UV/Vis spectrophotometry, fluorophotometry and/or paper test strips. In this study, we show that this method encounters low efficiency and sensitivity for detection of ultratrace amounts of H2O2 in non-aqueous media. Thus, we have developed a simple, fast, accurate and inexpensive method based on UV/Vis spectrophotometry to detect H2O2 in non-aqueous systems, such as alcohols. In this regard, we demonstrate that monitoring the Soret and Q-band regions of high-valent iron-oxo (ferryl heme) intermediates in horseradish peroxidase (HRP) is well suited to detect ultratrace amounts of H2O2 impurities in alcohols in the range of 0.001-1000 μM using UV/Vis spectrophotometry. We monitor the optical spectra of HRP solution for the red shift in the Soret and Q-band regions upon the addition of alcohols with H2O2 impurity. We also monitor the reversibility of this shift to the original wavelength over time to check the spontaneous decay of ferryl intermediates to the ferric state. Thus, we have found that the ferryl intermediates of HRP can be used for the detection of H2O2 in alcohols at μg L-1 levels through via UV/Vis spectrophotometric method.
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29
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation. Angew Chem Int Ed Engl 2020; 59:21656-21662. [PMID: 32780931 PMCID: PMC7756461 DOI: 10.1002/anie.202008622] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 01/06/2023]
Abstract
Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (FeIV =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the FeIII and FeIV =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | | | - Michael T. Wilson
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Amanda K. Chaplin
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Bradley Davy
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Ali Ebrahim
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Danny Axford
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | | | | | - Shigeki Owada
- RIKEN Spring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Ivo Tews
- Biological SciencesInstitute for Life SciencesUniversity of SouthamptonUniversity RoadSouthamptonSO17 1BJUK
| | - Robin L. Owen
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Michael A. Hough
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
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30
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water‐Free Distal Heme Site in a Dye‐Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe
IV
=O Formation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marina Lučić
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | | | - Michael T. Wilson
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Amanda K. Chaplin
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Bradley Davy
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Ali Ebrahim
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Danny Axford
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Takehiko Tosha
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Shigeki Owada
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
- Japan Synchrotron Radiation Research Institute 1-1-1 Kouto Sayo Hyogo 679-5198 Japan
| | | | - Ivo Tews
- Biological Sciences Institute for Life Sciences University of Southampton University Road Southampton SO17 1BJ UK
| | - Robin L. Owen
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Michael A. Hough
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
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31
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Hiromoto T, Nishikawa K, Inoue S, Matsuura H, Hirano Y, Kurihara K, Kusaka K, Cuneo M, Coates L, Tamada T, Higuchi Y. Towards cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:946-953. [PMID: 33021496 DOI: 10.1107/s2059798320011365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/19/2020] [Indexed: 11/10/2022]
Abstract
A membrane-bound hydrogenase from Desulfovibrio vulgaris Miyazaki F is a metalloenzyme that contains a binuclear Ni-Fe complex in its active site and mainly catalyzes the oxidation of molecular hydrogen to generate a proton gradient in the bacterium. The active-site Ni-Fe complex of the aerobically purified enzyme shows its inactive oxidized form, which can be reactivated through reduction by hydrogen. Here, in order to understand how the oxidized form is reactivated by hydrogen and further to directly evaluate the bridging of a hydride ligand in the reduced form of the Ni-Fe complex, a neutron structure determination was undertaken on single crystals grown in a hydrogen atmosphere. Cryogenic crystallography is being introduced into the neutron diffraction research field as it enables the trapping of short-lived intermediates and the collection of diffraction data to higher resolution. To optimize the cooling of large crystals under anaerobic conditions, the effects on crystal quality were evaluated by X-rays using two typical methods, the use of a cold nitrogen-gas stream and plunge-cooling into liquid nitrogen, and the former was found to be more effective in cooling the crystals uniformly than the latter. Neutron diffraction data for the reactivated enzyme were collected at the Japan Photon Accelerator Research Complex under cryogenic conditions, where the crystal diffracted to a resolution of 2.0 Å. A neutron diffraction experiment on the reduced form was carried out at Oak Ridge National Laboratory under cryogenic conditions and showed diffraction peaks to a resolution of 2.4 Å.
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Affiliation(s)
- Takeshi Hiromoto
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Koji Nishikawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
| | - Seiya Inoue
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
| | - Hiroaki Matsuura
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
| | - Yu Hirano
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Kazuo Kurihara
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Matthew Cuneo
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
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32
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Abstract
Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.
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33
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Oswald VF, Lee JL, Biswas S, Weitz AC, Mittra K, Fan R, Li J, Zhao J, Hu MY, Alp EE, Bominaar EL, Guo Y, Green MT, Hendrich MP, Borovik AS. Effects of Noncovalent Interactions on High-Spin Fe(IV)-Oxido Complexes. J Am Chem Soc 2020; 142:11804-11817. [PMID: 32489096 DOI: 10.1021/jacs.0c03085] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
High-valent nonheme FeIV-oxido species are key intermediates in biological oxidation, and their properties are proposed to be influenced by the unique microenvironments present in protein active sites. Microenvironments are regulated by noncovalent interactions, such as hydrogen bonds (H-bonds) and electrostatic interactions; however, there is little quantitative information about how these interactions affect crucial properties of high valent metal-oxido complexes. To address this knowledge gap, we introduced a series of FeIV-oxido complexes that have the same S = 2 spin ground state as those found in nature and then systematically probed the effects of noncovalent interactions on their electronic, structural, and vibrational properties. The key design feature that provides access to these complexes is the new tripodal ligand [poat]3-, which contains phosphinic amido groups. An important structural aspect of [FeIVpoat(O)]- is the inclusion of an auxiliary site capable of binding a Lewis acid (LAII); we used this unique feature to further modulate the electrostatic environment around the Fe-oxido unit. Experimentally, studies confirmed that H-bonds and LAII s can interact directly with the oxido ligand in FeIV-oxido complexes, which weakens the Fe═O bond and has an impact on the electronic structure. We found that relatively large vibrational changes in the Fe-oxido unit correlate with small structural changes that could be difficult to measure, especially within a protein active site. Our work demonstrates the important role of noncovalent interactions on the properties of metal complexes, and that these interactions need to be considered when developing effective oxidants.
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Affiliation(s)
- Victoria F Oswald
- Department of Chemistry, 1102 Natural Sciences II, University of California at Irvine, Irvine, California 92697, United States
| | - Justin L Lee
- Department of Chemistry, 1102 Natural Sciences II, University of California at Irvine, Irvine, California 92697, United States
| | - Saborni Biswas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Andrew C Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kaustuv Mittra
- Department of Molecular Biosciences and Biochemistry, University of California at Irvine, Irvine, California 92697, United States
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jikun Li
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Esen E Alp
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael T Green
- Department of Chemistry, 1102 Natural Sciences II, University of California at Irvine, Irvine, California 92697, United States.,Department of Molecular Biosciences and Biochemistry, University of California at Irvine, Irvine, California 92697, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - A S Borovik
- Department of Chemistry, 1102 Natural Sciences II, University of California at Irvine, Irvine, California 92697, United States
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Kwon H, Basran J, Devos JM, Suardíaz R, van der Kamp MW, Mulholland AJ, Schrader TE, Ostermann A, Blakeley MP, Moody PCE, Raven EL. Visualizing the protons in a metalloenzyme electron proton transfer pathway. Proc Natl Acad Sci U S A 2020; 117:6484-6490. [PMID: 32152099 PMCID: PMC7104402 DOI: 10.1073/pnas.1918936117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In redox metalloenzymes, the process of electron transfer often involves the concerted movement of a proton. These processes are referred to as proton-coupled electron transfer, and they underpin a wide variety of biological processes, including respiration, energy conversion, photosynthesis, and metalloenzyme catalysis. The mechanisms of proton delivery are incompletely understood, in part due to an absence of information on exact proton locations and hydrogen bonding structures in a bona fide metalloenzyme proton pathway. Here, we present a 2.1-Å neutron crystal structure of the complex formed between a redox metalloenzyme (ascorbate peroxidase) and its reducing substrate (ascorbate). In the neutron structure of the complex, the protonation states of the electron/proton donor (ascorbate) and all of the residues involved in the electron/proton transfer pathway are directly observed. This information sheds light on possible proton movements during heme-catalyzed oxygen activation, as well as on ascorbate oxidation.
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Affiliation(s)
- Hanna Kwon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Juliette M Devos
- Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Reynier Suardíaz
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | | | - Tobias E Schrader
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85748 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, D-85748 Garching, Germany
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Peter C E Moody
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom;
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
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35
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Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals. Methods Enzymol 2020. [PMID: 32093831 DOI: 10.1016/bs.mie.2019.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Dynamic nuclear polarization (DNP) can provide a powerful means to amplify neutron diffraction from biological crystals by 10-100-fold, while simultaneously enhancing the visibility of hydrogen by an order of magnitude. Polarizing the neutron beam and aligning the proton spins in a polarized sample modulates the coherent and incoherent neutron scattering cross-sections of hydrogen, in ideal cases amplifying the coherent scattering by almost an order of magnitude and suppressing the incoherent background to zero. This chapter describes current efforts to develop and apply DNP techniques for spin polarized neutron protein crystallography, highlighting concepts, experimental design, labeling strategies and recent results, as well as considering new strategies for data collection and analysis that these techniques could enable.
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36
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Ortmayer M, Fisher K, Basran J, Wolde-Michael EM, Heyes DJ, Levy C, Lovelock SL, Anderson JLR, Raven EL, Hay S, Rigby SEJ, Green AP. Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code. ACS Catal 2020; 10:2735-2746. [PMID: 32550044 PMCID: PMC7273622 DOI: 10.1021/acscatal.9b05129] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/22/2020] [Indexed: 01/14/2023]
Abstract
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Nature
employs a limited number of genetically encoded axial ligands
to control diverse heme enzyme activities. Deciphering the functional
significance of these ligands requires a quantitative understanding of how their electron-donating
capabilities modulate the structures and reactivities of the iconic
ferryl intermediates compounds I and II. However, probing these relationships
experimentally has proven to be challenging as ligand substitutions
accessible via conventional mutagenesis do not allow fine tuning of
electron donation and typically abolish catalytic function. Here,
we exploit engineered translation components to replace the histidine
ligand of cytochrome c peroxidase (CcP) by a less electron-donating Nδ-methyl histidine (Me-His) with little effect on the enzyme structure.
The rate of formation (k1) and the reactivity
(k2) of compound I are unaffected by ligand
substitution. In contrast, proton-coupled electron transfer to compound
II (k3) is 10-fold slower in CcP Me-His, providing a direct link between electron donation
and compound II reactivity, which can be explained by weaker electron
donation from the Me-His ligand (“the push”) affording
an electron-deficient ferryl oxygen with reduced proton affinity (“the
pull”). The deleterious effects of the Me-His ligand can be
fully compensated by introducing a W51F mutation designed to increase
“the pull” by removing a hydrogen bond to the ferryl
oxygen. Analogous substitutions in ascorbate peroxidase lead to similar
activity trends to those observed in CcP, suggesting
that a common mechanistic strategy is employed by enzymes using distinct
electron transfer pathways. Our study highlights how noncanonical
active site substitutions can be used to directly probe and deconstruct
highly evolved bioinorganic mechanisms.
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Affiliation(s)
- Mary Ortmayer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Karl Fisher
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Emmanuel M. Wolde-Michael
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Colin Levy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Sarah L. Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - J. L. Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Emma L. Raven
- School of Chemistry, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Stephen E. J. Rigby
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Anthony P. Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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37
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Kwon H, Schrader TE, Ostermann A, Blakeley MP, Raven EL, Moody PCE. Heme peroxidase-Trapping intermediates by cryo neutron crystallography. Methods Enzymol 2020; 634:379-389. [PMID: 32093841 DOI: 10.1016/bs.mie.2020.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
By combining the normal practice for X-ray crystallography of collecting diffraction data at 100K with neutron crystallography the structures of cryo-trapped enzyme intermediates have been determined, revealing the positions of the previously hidden hydrogens that are essential to a better understanding of the involved mechanism.
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Affiliation(s)
- Hanna Kwon
- School of Chemistry, University of Bristol, Bristol, United Kingdom.
| | - Tobias E Schrader
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Garching, Germany
| | | | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Peter C E Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
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38
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High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase. Proc Natl Acad Sci U S A 2020; 117:4071-4077. [PMID: 32041886 PMCID: PMC7049163 DOI: 10.1073/pnas.1918125117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
X-ray crystallography often fails to determine the positions of hydrogen atoms, which play crucial roles in enzymatic reactions. Despite many X-ray crystallographic studies, the reaction mechanism of copper-containing nitrite reductases (CuNIRs), which reduce nitrite using two protons, has been controversial. The high-resolution neutron structure of a CuNIR reveals the protonation states of catalytic residues and key water molecules, thus providing insights into the catalytic mechanism. The catalytic Cu is shown to be coordinated by a hydroxide ion and not water. Furthermore, the hydrogen-deuterium exchange ratio suggests that intramolecular electron transfer is involved in a hydrogen-bond jump. These observations are consistent with previous computational chemistry; therefore, our study forms a bridge between the structural biology and quantum chemistry of CuNIRs. Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide, which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from the failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 Å resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of ∼106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation states of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels.
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Abstract
The use of neutron protein crystallography (NPX) is expanding rapidly, with most structures determined in the last decade. This growth is stimulated by a number of developments, spanning from the building of new NPX beamlines to the availability of improved software for structure refinement. The main bottleneck preventing structural biologists from adding NPX to the suite of methods commonly used is the large volume of the individual crystals required for a successful experiment. A survey of deposited NPX structures in the Protein Data Bank shows that about two-thirds came from crystals prepared using vapor diffusion, while batch and dialysis-based methods all-together contribute to most of the remaining one-third. This chapter explains the underlying principles of these protein crystallization methods and provides practical examples that may help others to successfully prepare large crystals for NPX.
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40
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Meilleur F, Kovalevsky A, Myles DAA. IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor. Methods Enzymol 2020; 634:69-85. [PMID: 32093843 DOI: 10.1016/bs.mie.2019.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
IMAGINE is a high intensity, quasi-Laue neutron crystallography beamline developed at the 85MW High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). This state-of-the-art facility for neutron-diffraction enables neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of <1mm3 and unit cell edges of <150Å. The beamline features include elliptical focusing mirrors that deliver neutrons into a 2.0×3.2mm2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations. The beamline is equipped with a single-axis goniometer, neutron-sensitive cylindrical image plate detector and room temperature and cryogenic sample environments. This article describes the beamline components, the diffractometer and the data collection and data analysis protocols that are used, and outlines the protein deuteration, crystallization and conventional crystallography capabilities that are available to users at ORNL's neutron facilities. We also present examples of the scientific questions being addressed at this beamline and highlight important findings in enzyme chemistry that have been made possible by IMAGINE.
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Affiliation(s)
- Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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41
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Lučić M, Chaplin AK, Moreno-Chicano T, Dworkowski FSN, Wilson MT, Svistunenko DA, Hough MA, Worrall JAR. A subtle structural change in the distal haem pocket has a remarkable effect on tuning hydrogen peroxide reactivity in dye decolourising peroxidases fromStreptomyces lividans. Dalton Trans 2020; 49:1620-1636. [DOI: 10.1039/c9dt04583j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A subtle positional shift of the distal haem pocket aspartate in two dye decolourising peroxidase homologs has a remarkable effect on their reactivity with H2O2.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences
- University of Essex
- Colchester
- UK
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42
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Hoogerheide DP, Forsyth VT, Brown KA. Neutron scattering for STRUCTURAL BIOLOGY: Modern neutron sources illuminate the complex functions of living systems. PHYSICS TODAY 2020; 73:10.1063/pt.3.4498. [PMID: 38487716 PMCID: PMC10938470 DOI: 10.1063/pt.3.4498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Modern neutron sources illuminate the complex functions of living systems.
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Affiliation(s)
- David P Hoogerheide
- National Institute of Standards and Technology Center for Neutron Research in Gaithersburg, Maryland
| | - V Trevor Forsyth
- Institut Laue-Langevin in Grenoble, France; he also holds a chair in biophysics at Keele University in the UK
| | - Katherine A Brown
- Cavendish Laboratory at Cambridge University in the UK and at the University of Texas at Austin
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43
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Osawa K, Kossowska D, Park K, Kwak K, Cho M. Two-dimensional infrared spectroscopic study of cytochrome c peroxidase activity in deep eutectic solvent. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:064703. [PMID: 31867407 PMCID: PMC6920052 DOI: 10.1063/1.5130940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Deep eutectic solvents (DESs) prepared by mixing hydrogen-bond donor and acceptor molecules have been found to be of use in several applications. Recently, it was shown that DESs can enhance the peroxidation activity of cytochrome c. Here, to elucidate the effects of DESs on the peroxidase activity of cytochrome c, we carried out linear and nonlinear infrared spectroscopic studies of the CO stretch mode of carbon monoxide cytochrome c (COCytc) in ethylammonium chloride (EAC)/urea DES. The FTIR spectrum of COCytc shows a significant spectral shift upon addition of the DES. The broadening and red-shifting of the CO band are observed in both urea and DES solutions, which are induced by the change of the distal ligands around the heme. Although the FTIR study is sensitive to structural changes in the active site, it does not provide quantitative information about structural dynamics related to the catalytic activity itself. Thus, we carried out two-dimensional IR spectroscopy of the CO mode, which suggests that there is a different conformer that could be related to the enhanced catalytic activity in DES. In particular, the spectral diffusion dynamics of that conformer exhibits quite different behavior. The experimental results lead us to propose a hypothesis that the DES increases the population of the conformer with distal ligand lysines close to the reaction center through the combining effect of urea and EAC, which results in the enhancement of the peroxidase activity of cytochrome c. We anticipate that the present experimental work stimulates future investigations of the effects of DES on biocatalysis.
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Affiliation(s)
- Koji Osawa
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | | | - Kwanghee Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
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44
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Suga M, Shimada A, Akita F, Shen JR, Tosha T, Sugimoto H. Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA. Biochim Biophys Acta Gen Subj 2019; 1864:129466. [PMID: 31678142 DOI: 10.1016/j.bbagen.2019.129466] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach. SCOPE OF REVIEW Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described. MAJOR CONCLUSIONS XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data. GENERAL SIGNIFICANCE XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.
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Affiliation(s)
- Michihiro Suga
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan..
| | - Atsuhiro Shimada
- Graduate School of Applied Biological Sciences and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan..
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Takehiko Tosha
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hiroshi Sugimoto
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan..
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45
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Laurynėnas A, Butkevičius M, Dagys M, Shleev S, Kulys J. Consecutive Marcus Electron and Proton Transfer in Heme Peroxidase Compound II-Catalysed Oxidation Revealed by Arrhenius Plots. Sci Rep 2019; 9:14092. [PMID: 31575893 PMCID: PMC6773748 DOI: 10.1038/s41598-019-50466-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/12/2019] [Indexed: 11/16/2022] Open
Abstract
Electron and proton transfer reactions in enzymes are enigmatic and have attracted a great deal of theoretical, experimental, and practical attention. The oxidoreductases provide model systems for testing theoretical predictions, applying experimental techniques to gain insight into catalytic mechanisms, and creating industrially important bio(electro)conversion processes. Most previous and ongoing research on enzymatic electron transfer has exploited a theoretically and practically sound but limited approach that uses a series of structurally similar ("homologous") substrates, measures reaction rate constants and Gibbs free energies of reactions, and analyses trends predicted by electron transfer theory. This approach, proposed half a century ago, is based on a hitherto unproved hypothesis that pre-exponential factors of rate constants are similar for homologous substrates. Here, we propose a novel approach to investigating electron and proton transfer catalysed by oxidoreductases. We demonstrate the validity of this new approach for elucidating the kinetics of oxidation of "non-homologous" substrates catalysed by compound II of Coprinopsis cinerea and Armoracia rusticana peroxidases. This study - using the Marcus theory - demonstrates that reactions are not only limited by electron transfer, but a proton is transferred after the electron transfer event and thus both events control the reaction rate of peroxidase-catalysed oxidation of substrates.
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Affiliation(s)
- Audrius Laurynėnas
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania.
| | - Marius Butkevičius
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania
| | - Marius Dagys
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania
| | - Sergey Shleev
- Malmö University, Jan Waldenströmsgata 25, SE-214 28, Malmö, Sweden
| | - Juozas Kulys
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania
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46
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Ehudin MA, Quist DA, Karlin KD. Enhanced Rates of C-H Bond Cleavage by a Hydrogen-Bonded Synthetic Heme High-Valent Iron(IV) Oxo Complex. J Am Chem Soc 2019; 141:12558-12569. [PMID: 31318198 PMCID: PMC6734939 DOI: 10.1021/jacs.9b01253] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Secondary coordination sphere interactions are critical in facilitating the formation, stabilization, and enhanced reactivity of high-valent oxidants required for essential biochemical processes. Herein, we compare the C-H bond oxidizing capabilities of spectroscopically characterized synthetic heme iron(IV) oxo complexes, F8Cmpd-II (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a 2,6-lutidinium triflate (LutH+) Lewis acid adduct involving ferryl O-atom hydrogen-bonding, F8Cmpd-II(LutH+). Second-order rate constants utilizing C-H and C-D substrates were obtained by UV-vis spectroscopic monitoring, while products were characterized and quantified by EPR spectroscopy and gas chromatography (GC). With xanthene, F8Cmpd-II(LutH+) reacts 40 times faster (k2 = 14.2 M-1 s-1; -90 °C) than does F8Cmpd-II, giving bixanthene plus xanthone and the heme product [F8FeIIIOH2]+. For substrates with greater C-H bond dissociation energies (BDEs) F8Cmpd-II(LutH+) reacts with the second order rate constants k2(9,10-dihydroanthracene; DHA) = 0.485 M-1 s-1 and k2(fluorene) = 0.102 M-1 s-1 (-90 °C); by contrast, F8Cmpd-II is unreactive toward these substrates. For xanthene vs xanthene-(d2), large, nonclassical deuterium kinetic isotope effects are roughly estimated for both F8Cmpd-II and F8Cmpd-II(LutH+). The deuterated H-bonded analog, F8Cmpd-II(LutD+), was also prepared; for the reaction with DHA, an inverse KIE (compared to F8Cmpd-II(LutH+)) was observed. This work originates/inaugurates experimental investigation of the reactivity of authentic H-bonded heme-based FeIV═O compounds, critically establishing the importance of oxo H-bonding (or protonation) in heme complexes and enzyme active sites.
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Affiliation(s)
- Melanie A. Ehudin
- 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
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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47
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Ebrahim A, Moreno-Chicano T, Appleby MV, Chaplin AK, Beale JH, Sherrell DA, Duyvesteyn HME, Owada S, Tono K, Sugimoto H, Strange RW, Worrall JAR, Axford D, Owen RL, Hough MA. Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins. IUCRJ 2019; 6:543-551. [PMID: 31316799 PMCID: PMC6608622 DOI: 10.1107/s2052252519003956] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/22/2019] [Indexed: 05/18/2023]
Abstract
An approach is demonstrated to obtain, in a sample- and time-efficient manner, multiple dose-resolved crystal structures from room-temperature protein microcrystals using identical fixed-target supports at both synchrotrons and X-ray free-electron lasers (XFELs). This approach allows direct comparison of dose-resolved serial synchrotron and damage-free XFEL serial femtosecond crystallography structures of radiation-sensitive proteins. Specifically, serial synchrotron structures of a heme peroxidase enzyme reveal that X-ray induced changes occur at far lower doses than those at which diffraction quality is compromised (the Garman limit), consistent with previous studies on the reduction of heme proteins by low X-ray doses. In these structures, a functionally relevant bond length is shown to vary rapidly as a function of absorbed dose, with all room-temperature synchrotron structures exhibiting linear deformation of the active site compared with the XFEL structure. It is demonstrated that extrapolation of dose-dependent synchrotron structures to zero dose can closely approximate the damage-free XFEL structure. This approach is widely applicable to any protein where the crystal structure is altered by the synchrotron X-ray beam and provides a solution to the urgent requirement to determine intact structures of such proteins in a high-throughput and accessible manner.
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Affiliation(s)
- Ali Ebrahim
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Amanda K. Chaplin
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Helen M. E. Duyvesteyn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- Division of Structural Biology (STRUBI), The Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Hiroshi Sugimoto
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Jonathan A. R. Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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48
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Nóbrega CS, Pauleta SR. Reduction of hydrogen peroxide in gram-negative bacteria - bacterial peroxidases. Adv Microb Physiol 2019; 74:415-464. [PMID: 31126534 DOI: 10.1016/bs.ampbs.2019.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacteria display an array of enzymes to detoxify reactive oxygen species that cause damage to DNA and to other biomolecules leading to cell death. Hydrogen peroxide is one of these species, with endogenous and exogenous sources, such as lactic acid bacteria, oxidative burst of the immune system or chemical reactions at oxic-anoxic interfaces. The enzymes that detoxify hydrogen peroxide will be the focus of this review, with special emphasis on bacterial peroxidases that reduce hydrogen peroxide to water. Bacterial peroxidases are periplasmic cytochromes with either two or three c-type haems, which have been classified as classical and non-classical bacterial peroxidases, respectively. Most of the studies have been focus on the classical bacterial peroxidases, showing the presence of a reductive activation in the presence of calcium ions. Mutagenesis studies have clarified the catalytic mechanism of this enzyme and were used to propose an intramolecular electron transfer pathway, with far less being known about the intermolecular electron transfer that occurs between reduced electron donors and the enzyme. The physiological function of these enzymes was not very clear until it was shown, for the non-classical bacterial peroxidase, that this enzyme is required for the bacteria to use hydrogen peroxide as terminal electron acceptor under anoxic conditions. These non-classical bacterial peroxidases are quinol peroxidases that do not require reductive activation but need calcium ions to attain maximum activity and share similar catalytic intermediates with the classical bacterial peroxidases.
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Affiliation(s)
- Cláudia S Nóbrega
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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49
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Chaplin AK, Chicano TM, Hampshire BV, Wilson MT, Hough MA, Svistunenko DA, Worrall JAR. An Aromatic Dyad Motif in Dye Decolourising Peroxidases Has Implications for Free Radical Formation and Catalysis. Chemistry 2019; 25:6141-6153. [PMID: 30945782 DOI: 10.1002/chem.201806290] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 01/27/2023]
Abstract
Dye decolouring peroxidases (DyPs) are the most recent class of heme peroxidase to be discovered. On reacting with H2 O2 , DyPs form a high-valent iron(IV)-oxo species and a porphyrin radical (Compound I) followed by stepwise oxidation of an organic substrate. In the absence of substrate, the ferryl species decays to form transient protein-bound radicals on redox active amino acids. Identification of radical sites in DyPs has implications for their oxidative mechanism with substrate. Using a DyP from Streptomyces lividans, referred to as DtpA, which displays low reactivity towards synthetic dyes, activation with H2 O2 was explored. A Compound I EPR spectrum was detected, which in the absence of substrate decays to a protein-bound radical EPR signal. Using a newly developed version of the Tyrosyl Radical Spectra Simulation Algorithm, the radical EPR signal was shown to arise from a pristine tyrosyl radical and not a mixed Trp/Tyr radical that has been widely reported in DyP members exhibiting high activity with synthetic dyes. The radical site was identified as Tyr374, with kinetic studies inferring that although Tyr374 is not on the electron-transfer pathway from the dye RB19, its replacement with a Phe does severely compromise activity with other organic substrates. These findings hint at the possibility that alternative electron-transfer pathways for substrate oxidation are operative within the DyP family. In this context, a role for a highly conserved aromatic dyad motif is discussed.
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Affiliation(s)
- Amanda K Chaplin
- Present address: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Tadeo Moreno Chicano
- Present address: Department of Molecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Bethany V Hampshire
- Present address: Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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50
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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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