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Famulari A, Correddu D, Di Nardo G, Gilardi G, Mitrikas G, Chiesa M, García-Rubio I. Heme Spin Distribution in the Substrate-Free and Inhibited Novel CYP116B5hd: A Multifrequency Hyperfine Sublevel Correlation ( HYSCORE) Study. Molecules 2024; 29:518. [PMID: 38276601 PMCID: PMC10819608 DOI: 10.3390/molecules29020518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The cytochrome P450 family consists of ubiquitous monooxygenases with the potential to perform a wide variety of catalytic applications. Among the members of this family, CYP116B5hd shows a very prominent resistance to peracid damage, a property that makes it a promising tool for fine chemical synthesis using the peroxide shunt. In this meticulous study, we use hyperfine spectroscopy with a multifrequency approach (X- and Q-band) to characterize in detail the electronic structure of the heme iron of CYP116B5hd in the resting state, which provides structural details about its active site. The hyperfine dipole-dipole interaction between the electron and proton nuclear spins allows for the locating of two different protons from the coordinated water and a beta proton from the cysteine axial ligand of heme iron with respect to the magnetic axes centered on the iron. Additionally, since new anti-cancer therapies target the inhibition of P450s, here we use the CYP116B5hd system-imidazole as a model for studying cytochrome P450 inhibition by an azo compound. The effects of the inhibition of protein by imidazole in the active-site geometry and electron spin distribution are presented. The binding of imidazole to CYP116B5hd results in an imidazole-nitrogen axial coordination and a low-spin heme FeIII. HYSCORE experiments were used to detect the hyperfine interactions. The combined interpretation of the gyromagnetic tensor and the hyperfine and quadrupole tensors of magnetic nuclei coupled to the iron electron spin allowed us to obtain a precise picture of the active-site geometry, including the orientation of the semi-occupied orbitals and magnetic axes, which coincide with the porphyrin N-Fe-N axes. The electronic structure of the iron does not seem to be affected by imidazole binding. Two different possible coordination geometries of the axial imidazole were observed. The angles between gx (coinciding with one of the N-Fe-N axes) and the projection of the imidazole plane on the heme were determined to be -60° and -25° for each of the two possibilities via measurement of the hyperfine structure of the axially coordinated 14N.
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Affiliation(s)
- Antonino Famulari
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Danilo Correddu
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - George Mitrikas
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, 15341 Athens, Greece;
| | - Mario Chiesa
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Inés García-Rubio
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
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Carvalho MA, Merahi K, Haumesser J, Pereira AMVM, Parizel N, Weiss J, Orio M, Maurel V, Ruhlmann L, Choua S, Ruppert R. Syntheses and Electrochemical and EPR Studies of Porphyrins Functionalized with Bulky Aromatic Amine Donors. Molecules 2023; 28:molecules28114405. [PMID: 37298881 DOI: 10.3390/molecules28114405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
A series of nickel(II) porphyrins bearing one or two bulky nitrogen donors at the meso positions were prepared by using Ullmann methodology or more classical Buchwald-Hartwig amination reactions to create the new C-N bonds. For several new compounds, single crystals were obtained, and the X-ray structures were solved. The electrochemical data of these compounds are reported. For a few representative examples, spectroelectrochemical measurements were used to clarify the electron exchange process. In addition, a detailed electron paramagnetic resonance (EPR) study was performed to estimate the extent of delocalization of the generated radical cations. In particular, electron nuclear double resonance spectroscopy (ENDOR) was used to determine the coupling constants. DFT calculations were conducted to corroborate the EPR spectroscopic data.
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Affiliation(s)
- Mary-Ambre Carvalho
- Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Khalissa Merahi
- Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Julien Haumesser
- Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | | | - Nathalie Parizel
- Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Jean Weiss
- Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Maylis Orio
- Campus of St Jérôme, Aix-Marseille University, CNRS, Centrale Marseille, iSm2, CEDEX 20, 13397 Marseille, France
| | - Vincent Maurel
- SyMMES, UMR 5819 CEA Grenoble/CNRS/Université Grenoble-Alpes, CEA Grenoble, 17 rue des Martyrs, CEDEX 9, 38054 Grenoble, France
| | - Laurent Ruhlmann
- Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Sylvie Choua
- Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Romain Ruppert
- Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, France
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York NJ, Lockart MM, Schmittou AN, Pierce BS. Cyanide replaces substrate in obligate-ordered addition of nitric oxide to the non-heme mononuclear iron AvMDO active site. J Biol Inorg Chem 2023; 28:285-299. [PMID: 36809458 PMCID: PMC10075186 DOI: 10.1007/s00775-023-01990-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/12/2023] [Indexed: 02/23/2023]
Abstract
Thiol dioxygenases are a subset of non-heme mononuclear iron oxygenases that catalyze the O2-dependent oxidation of thiol-bearing substrates to yield sulfinic acid products. Cysteine dioxygenase (CDO) and 3-mercaptopropionic acid (3MPA) dioxygenase (MDO) are the most extensively characterized members of this enzyme family. As with many non-heme mononuclear iron oxidase/oxygenases, CDO and MDO exhibit an obligate-ordered addition of organic substrate before dioxygen. As this substrate-gated O2-reactivity extends to the oxygen-surrogate, nitric oxide (NO), EPR spectroscopy has long been used to interrogate the [substrate:NO:enzyme] ternary complex. In principle, these studies can be extrapolated to provide information about transient iron-oxo intermediates produced during catalytic turnover with dioxygen. In this work, we demonstrate that cyanide mimics the native thiol-substrate in ordered-addition experiments with MDO cloned from Azotobacter vinelandii (AvMDO). Following treatment of the catalytically active Fe(II)-AvMDO with excess cyanide, addition of NO yields a low-spin (S = 1/2) (CN/NO)-Fe-complex. Continuous wave and pulsed X-band EPR characterization of this complex produced in wild-type and H157N variant AvMDO reveal multiple nuclear hyperfine features diagnostic of interactions within the first- and outer-coordination sphere of the enzymatic Fe-site. Spectroscopically validated computational models indicate simultaneous coordination of two cyanide ligands replaces the bidentate (thiol and carboxylate) coordination of 3MPA allowing for NO-binding at the catalytically relevant O2-binding site. This promiscuous substrate-gated reactivity of AvMDO with NO provides an instructive counterpoint to the high substrate-specificity exhibited by mammalian CDO for L-cysteine.
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Affiliation(s)
- Nicholas J York
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA
| | - Molly M Lockart
- Department of Chemistry and Biochemistry, Samford University, 800 Lakeshore Drive, Homewood, AL, 35229, USA
| | - Allison N Schmittou
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA
| | - Brad S Pierce
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA.
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Šimėnas M, O'Sullivan J, Zollitsch CW, Kennedy O, Seif-Eddine M, Ritsch I, Hülsmann M, Qi M, Godt A, Roessler MM, Jeschke G, Morton JJL. A sensitivity leap for X-band EPR using a probehead with a cryogenic preamplifier. J Magn Reson 2021; 322:106876. [PMID: 33264732 DOI: 10.1016/j.jmr.2020.106876] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Inspired by the considerable success of cryogenically cooled NMR cryoprobes, we present an upgraded X-band EPR probehead, equipped with a cryogenic low-noise preamplifier. Our setup suppresses source noise, can handle the high microwave powers typical in X-band pulsed EPR, and is compatible with the convenient resonator coupling and sample access found on commercially available spectrometers. Our approach allows standard pulsed and continuous-wave EPR experiments to be performed at X-band frequency with significantly increased sensitivity compared to the unmodified setup. The probehead demonstrates a voltage signal-to-noise ratio (SNR) enhancement by a factor close to 8× at a temperature of 6 K, and remains close to 2× at room temperature. By further suppressing room-temperature noise at the expense of reduced microwave power (and thus minimum π-pulse length), the factor of SNR improvement approaches 15 at 6 K, corresponding to an impressive 200-fold reduction in EPR measurement time. We reveal the full potential of this probehead by demonstrating such SNR improvements using a suite of typical hyperfine and dipolar spectroscopy experiments on exemplary samples.
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Affiliation(s)
- Mantas Šimėnas
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK.
| | - James O'Sullivan
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
| | | | - Oscar Kennedy
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
| | - Maryam Seif-Eddine
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London W12 0BZ, UK
| | - Irina Ritsch
- ETH Zürich, Department of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Miriam Hülsmann
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, Bielefeld 33615, Germany
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, Bielefeld 33615, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, Bielefeld 33615, Germany
| | - Maxie M Roessler
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London W12 0BZ, UK
| | - Gunnar Jeschke
- ETH Zürich, Department of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - John J L Morton
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Electronic & Electrical Engineering, UCL, London WC1E 7JE, UK.
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5
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York NJ, Lockart MM, Sardar S, Khadka N, Shi W, Stenkamp RE, Zhang J, Kiser PD, Pierce BS. Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center. J Biol Chem 2021; 296:100492. [PMID: 33662397 PMCID: PMC8050391 DOI: 10.1016/j.jbc.2021.100492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022] Open
Abstract
Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O2-binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme-substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen.
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Affiliation(s)
- Nicholas J York
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Molly M Lockart
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Sinjinee Sardar
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Nimesh Khadka
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Wuxian Shi
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Ronald E Stenkamp
- Departments of Biological Structure and Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jianye Zhang
- Department of Ophthalmology, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Philip D Kiser
- Department of Ophthalmology, School of Medicine, University of California, Irvine, Irvine, California, USA; Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA; Research Service, VA Long Beach Healthcare System, Long Beach, California, USA.
| | - Brad S Pierce
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA.
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6
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Seif Eddine M, Biaso F, Rendon J, Pilet E, Guigliarelli B, Magalon A, Grimaldi S. 1,2H hyperfine spectroscopy and DFT modeling unveil the demethylmenasemiquinone binding mode to E. coli nitrate reductase A (NarGHI). Biochim Biophys Acta Bioenerg 2020; 1861:148203. [PMID: 32305411 DOI: 10.1016/j.bbabio.2020.148203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 11/23/2022]
Abstract
The quinol oxidation site QD in E. coli respiratory nitrate reductase A (EcNarGHI) reacts with the three isoprenoid quinones naturally synthesized by the bacterium, i.e. ubiquinones (UQ), menaquinones (MK) and demethylmenaquinones (DMK). The binding mode of the demethylmenasemiquinone (DMSK) intermediate to the EcNarGHI QD quinol oxidation site is analyzed in detail using 1,2H hyperfine (hf) spectroscopy in combination with H2O/D2O exchange experiments and DFT modeling, and compared to the menasemiquinone one bound to the QD site (MSKD) previously studied by us. DMSKD and MSKD are shown to bind in a similar and strongly asymmetric manner through a short (~1.7 Å) H-bond. The origin of the specific hf pattern resolved on the DMSKD field-swept EPR spectrum is unambiguously ascribed to slightly inequivalent contributions from two β-methylene protons of the isoprenoid side chain. DFT calculations show that their large isotropic hf coupling constants (Aiso ~12 and 15 MHz) are consistent with both (i) a specific highly asymmetric binding mode of DMSKD and (ii) a near in-plane orientation of its isoprenyl chain at Cβ relative to the aromatic ring, which differs by ~90° to that predicted for free or NarGHI-bound MSK. Our results provide new insights into how the conformation and the redox properties of different natural quinones are selectively fine-tuned by the protein environment at a single Q site. Such a fine-tuning most likely contributes to render NarGHI as an efficient and flexible respiratory enzyme to be used upon rapid variations of the Q-pool content.
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Lockart MM, Butler JT, Mize CJ, Fair MN, Cruce AA, Conner KP, Atkins WM, Bowman MK. Multiple drug binding modes in Mycobacterium tuberculosis CYP51B1. J Inorg Biochem 2020; 205:110994. [PMID: 31982812 DOI: 10.1016/j.jinorgbio.2020.110994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/08/2023]
Abstract
The Mycobacterium tuberculosis (Mtb) genome encodes 20 different cytochrome P450 enzymes (CYPs), many of which serve essential biosynthetic roles. CYP51B1, the Mtb version of eukaryotic sterol demethylase, remains a potential therapeutic target. The binding of three drug fragments containing nitrogen heterocycles to CYP51B1 is studied here by continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) techniques to determine how each drug fragment binds to the heme active-site. All three drug fragments form a mixture of complexes, some of which retain the axial water ligand from the resting state. Hyperfine sublevel correlation spectroscopy (HYSCORE) and electron-nuclear double resonance spectroscopy (ENDOR) observe protons of the axial water and on the drug fragments that reveal drug binding modes. Binding in CYP51B1 is complicated by the presence of multiple binding modes that coexist in the same solution. These results aid our understanding of CYP-inhibitor interactions and will help guide future inhibitor design.
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Fábregas Ibáñez L, Soetbeer J, Klose D, Tinzl M, Hilvert D, Jeschke G. Non-uniform HYSCORE: Measurement, processing and analysis with Hyscorean. J Magn Reson 2019; 307:106576. [PMID: 31450188 DOI: 10.1016/j.jmr.2019.106576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Non-uniform sampling (NUS) provides a considerable reduction of measurement time especially for multi-dimensional experiments. This comes at the cost of additional signal processing steps to reconstruct the complete signal from the experimental data points. Despite being routinely employed in NMR for many experiments, EPR applications have not benefited from NUS due to the lack of a straightforward implementation to perform NUS in common commercial spectrometers. In this work we present a novel method to perform NUS HYSCORE experiments on commercial Bruker EPR spectrometers, along with a benchmark of modern reconstruction methods, and new processing software tools for NUS HYSCORE signals. All of this comes in the form of a free-software package: Hyscorean. Experimental NUS spectra are measured and processed with this package using different reconstruction methods and compared to their uniform sampled counterparts, thereby showcasing the method's potential for EPR spectroscopy.
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Affiliation(s)
- Luis Fábregas Ibáñez
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Janne Soetbeer
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Daniel Klose
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Matthias Tinzl
- ETH Zurich Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Donald Hilvert
- ETH Zurich Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Gunnar Jeschke
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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9
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Drover MW, Schild DJ, Oyala PH, Peters JC. Snapshots of a Migrating H-Atom: Characterization of a Reactive Iron(III) Indenide Hydride and its Nearly Isoenergetic Ring-Protonated Iron(I) Isomer. Angew Chem Int Ed Engl 2019; 58:15504-15511. [PMID: 31465624 DOI: 10.1002/anie.201909050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 12/22/2022]
Abstract
We report the characterization of an S= 1 / 2 iron π-complex, [Fe(η6 -IndH)(depe)]+ (Ind=Indenide (C9 H7 - ), depe=1,2-bis(diethylphosphino)ethane), which results via C-H elimination from a transient FeIII hydride, [Fe(η3 :η2 -Ind)(depe)H]+ . Owing to weak M-H/C-H bonds, these species appear to undergo proton-coupled electron transfer (PCET) to release H2 through bimolecular recombination. Mechanistic information, gained from stoichiometric as well as computational studies, reveal the open-shell π-arene complex to have a BDFEC-H value of ≈50 kcal mol-1 , roughly equal to the BDFEFe-H of its FeIII -H precursor (ΔG°≈0 between them). Markedly, this reactivity differs from related Fe(η5 -Cp/Cp*) compounds, for which terminal FeIII -H cations are isolable and have been structurally characterized, highlighting the effect of a benzannulated ring (indene). Overall, this study provides a structural, thermochemical, and mechanistic foundation for the characterization of indenide/indene PCET precursors and outlines a valuable approach for the differentiation of a ring- versus a metal-bound H-atom by way of continuous-wave (CW) and pulse EPR (HYSCORE) spectroscopic measurements.
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Affiliation(s)
- Marcus W Drover
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Dirk J Schild
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jonas C Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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10
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Morra E, Signorile M, Salvadori E, Bordiga S, Giamello E, Chiesa M. Nature and Topology of Metal-Oxygen Binding Sites in Zeolite Materials: 17 O High-Resolution EPR Spectroscopy of Metal-Loaded ZSM-5. Angew Chem Int Ed Engl 2019; 58:12398-12403. [PMID: 31294524 DOI: 10.1002/anie.201906488] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Indexed: 11/05/2022]
Abstract
Determining structural models is pivotal to the rational understanding and development of heterogeneous catalytic systems. A paradigmatic case is represented by open-shell metals supported on oxides, where the catalytic properties crucially depend on the nature of the metal-oxygen bonds and the extent of charge and spin transfer. Through a combination of selective 17 O isotopic enrichment and the unique properties of open-shell s-state monovalent Group 12 cations, we derive a site-specific topological description of active sites in an MFI zeolite. We show that just a few selected sites out of all possible are populated and that the relative occupancies depend on the specific properties of the metal, and we provide maps of charge and spin transfer at the metal-oxygen interface. This approach is not restricted to zeotype materials, rather it is applicable to any catalysts supported on oxygen-containing materials.
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Affiliation(s)
- Elena Morra
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Matteo Signorile
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Enrico Salvadori
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Silvia Bordiga
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Elio Giamello
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria, 7, 10125, Torino, Italy
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11
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Motygullina AE, Mobli M, Harmer JR. Optimizing the transformation of HYSCORE data using the maximum entropy algorithm. J Magn Reson 2019; 301:30-39. [PMID: 30844691 DOI: 10.1016/j.jmr.2019.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Non-uniform sampling (NUS) in combination with the Maximum Entropy (MaxEnt) algorithm as applied to multi-dimensional NMR data has been thoroughly investigated and the NUS approach shown to provide significant sensitivity improvements as compared to methods using uniformly sampled (US) data and the discrete Fourier transform (DFT). Hyperfine sublevel correlation (HYSCORE) is a standard pulse EPR experiment that can potentially benefit greatly from this approach, but the data present unique challenges as compared to NMR. HYSCORE data typically exhibit a very large range of peak intensities, signals are in the form of irregularly shaped ridges with variable intensities, and time traces are generally truncated to save measurement time. MaxEnt has the advantageous properties that it does not require US data, dampens weak signals (noise) and does not suffer from windowing artifacts due to truncation of the time traces. Critical to the success of the MaxEnt algorithm is the choice of the two input parameters aim and def which describe the data noise and contribution of entropy in the optimization, respectively. In this paper we expand our preliminary study on the application of MaxEnt to the reconstruction of HYSCORE spectra to include a detailed analysis on sensitivity to detect weak peaks, investigate the non-linearity of the transformation and ascertain if it can be characterized by the introduction of synthetic peaks, and define a general range for the choice of aim and def. Furthermore, the ability of the MaxEnt method to remove windowing artefacts in uniformly sampled truncated HYSCORE data is described.
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Affiliation(s)
- Alina E Motygullina
- The Centre for Advanced Imaging, University of Queensland, St Lucia, QLD 4072, Australia
| | - Mehdi Mobli
- The Centre for Advanced Imaging, University of Queensland, St Lucia, QLD 4072, Australia
| | - Jeffrey R Harmer
- The Centre for Advanced Imaging, University of Queensland, St Lucia, QLD 4072, Australia.
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12
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Eaton SS, Ngendahimana T, Eaton GR, Jupp AR, Stephan DW. Electron paramagnetic resonance of a 10B-containing heterocyclic radical. J Magn Reson 2018; 290:76-84. [PMID: 29579535 DOI: 10.1016/j.jmr.2018.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 06/08/2023]
Abstract
Electron paramagnetic resonance measurements for a 10B-containing heterocyclic phenanthrenedione radical, (C6F5)2B(O2C14H8), were made at X-band in 9:1 toluene:dichloromethane from 10 to 293 K and in toluene from 180 to 293 K. In well-deoxygenated 0.1 mM toluene solution at room temperature hyperfine couplings to 10B, four pairs of protons and five pairs of fluorines contribute to a continuous wave spectrum with many resolved lines. Hyperfine couplings were adjusted to provide the best fit for spectra of the radical enriched in 10B and the analogous radical synthesized with 10,11B in natural abundance, resulting in small refinements of the hyperfine coupling constants previously reported for the natural abundance sample. Electron spin relaxation rates at temperatures between 15 and 293 K were similar for samples containing 10B and natural isotope abundance. Analysis of electron spin echo envelope modulation and hyperfine correlation spectroscopy data at 80 K found Axx = -7.5 ± 0.3, Ayy = -8.5 ± 0.3, and Azz = -10.8 ± 0.3 MHz for 11B, which indicates small spin density on the boron. The spin echo and hyperfine spectroscopy data for the 10B -containing radical are consistent with the factor of 2.99 smaller hyperfine values for 10B than for 11B.
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Affiliation(s)
- Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA.
| | - Andrew R Jupp
- University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada
| | - Douglas W Stephan
- University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada
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13
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Abstract
Cytochrome P450 (CYP) monoxygenses utilize heme cofactors to catalyze oxidation reactions. They play a critical role in metabolism of many classes of drugs, are an attractive target for drug development, and mediate several prominent drug interactions. Many substrates and inhibitors alter the spin state of the ferric heme by displacing the heme's axial water ligand in the resting enzyme to yield a five-coordinate iron complex, or they replace the axial water to yield a nitrogen-ligated six-coordinate iron complex, which are traditionally assigned by UV-vis spectroscopy. However, crystal structures and recent pulsed electron paramagnetic resonance (EPR) studies find a few cases where molecules hydrogen bond to the axial water. The water-bridged drug-H2O-heme has UV-vis spectra similar to nitrogen-ligated, six-coordinate complexes, but are closer to "reverse type I" complexes described in older liteature. Here, pulsed and continuous wave (CW) EPR demonstrate that water-bridged complexes are remarkably common among a range of nitrogenous drugs or drug fragments that bind to CYP3A4 or CYP2C9. Principal component analysis reveals a distinct clustering of CW EPR spectral parameters for water-bridged complexes. CW EPR reveals heterogeneous mixtures of ligated states, including multiple directly-coordinated complexes and water-bridged complexes. These results suggest that water-bridged complexes are under-represented in CYP structural databases and can have energies similar to other ligation modes. The data indicates that water-bridged binding modes can be identified and distinguished from directly-coordinated binding by CW EPR.
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Affiliation(s)
- Molly M Lockart
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States
| | - Carlo A Rodriguez
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States
| | - William M Atkins
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, WA 98195-7610, United States
| | - Michael K Bowman
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States.
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14
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Kraffert F, Bahro D, Meier C, Denne M, Colsmann A, Behrends J. Transport-related triplet states and hyperfine couplings in organic tandem solar cells probed by pulsed electrically detected magnetic resonance spectroscopy. J Magn Reson 2017; 282:10-17. [PMID: 28686953 DOI: 10.1016/j.jmr.2017.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/16/2017] [Accepted: 06/24/2017] [Indexed: 06/07/2023]
Abstract
Tandem solar cells constitute the most successful organic photovoltaic devices with power conversion efficiencies comparable to thin-film silicon solar cells. Especially their high open-circuit voltage - only achievable by a well-adjusted layer stacking - leads to their high efficiencies. Nevertheless, the microscopic processes causing the lossless recombination of charge carriers within the recombination zone are not well understood yet. We show that advanced pulsed electrically detected magnetic resonance techniques such as electrically detected (ED)-Rabi nutation measurements and electrically detected hyperfine sublevel correlation (ED-HYSCORE) spectroscopy help to understand the role of triplet excitons in these microscopic processes. We investigate fully working miniaturised organic tandem solar cells and detect current-influencing doublet states in different layers as well as triplet excitons located on the fullerene-based acceptor. We apply ED-HYSCORE in order to study the nuclear spin environment of the relevant electron/hole spins and detect a significant amount of the low abundant 13C nuclei coupled to the observer spins.
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Affiliation(s)
- Felix Kraffert
- Berlin Joint EPR Lab, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Daniel Bahro
- Light Technology Institute, Karlsruhe Institute of Technology, Engesserstrasse 13, 76131 Karlsruhe, Germany
| | - Christoph Meier
- Berlin Joint EPR Lab, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Maximilian Denne
- Light Technology Institute, Karlsruhe Institute of Technology, Engesserstrasse 13, 76131 Karlsruhe, Germany
| | - Alexander Colsmann
- Light Technology Institute, Karlsruhe Institute of Technology, Engesserstrasse 13, 76131 Karlsruhe, Germany
| | - Jan Behrends
- Berlin Joint EPR Lab, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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15
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Morra E, Giamello E, Chiesa M. EPR approaches to heterogeneous catalysis. The chemistry of titanium in heterogeneous catalysts and photocatalysts. J Magn Reson 2017; 280:89-102. [PMID: 28579105 DOI: 10.1016/j.jmr.2017.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 06/07/2023]
Abstract
Paramagnetic species are often involved in catalytic or photocatalytic reactions occurring at the solid-gas interface of heterogeneous catalysts. In this contribution we will provide an overview of the wealth and breadth of information that can be obtained from EPR in the characterization of paramagnetic species in such systems, illustrating the advantages that modern pulsed EPR methodologies can offer in monitoring the elementary processes occurring within the coordination sphere of surface transition-metal ions. To do so we selected three representative systems, where titanium ions in low oxidation states act as active catalytic sites, trying to outline the methodological approaches which characterize the application of EPR techniques and the questions that can be answered and addressed relative to the characterization of heterogeneous catalytic materials.
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Affiliation(s)
- Elena Morra
- Dipartimento di Chimica, Università di Torino, Via Giuria, 7, 10125 Torino, Italy
| | - Elio Giamello
- Dipartimento di Chimica, Università di Torino, Via Giuria, 7, 10125 Torino, Italy
| | - Mario Chiesa
- Dipartimento di Chimica, Università di Torino, Via Giuria, 7, 10125 Torino, Italy.
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16
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Van Doorslaer S. Understanding heme proteins with hyperfine spectroscopy. J Magn Reson 2017; 280:79-88. [PMID: 28579104 DOI: 10.1016/j.jmr.2017.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 06/07/2023]
Abstract
Heme proteins are versatile proteins that are involved in a large number of biological processes. Many spectroscopic methods are used to gain insight into the different mechanistic processes governing heme-protein functions. Since many (intermediate) states of heme proteins are paramagnetic, electron paramagnetic resonance (EPR) methods, such as hyperfine spectroscopy, offer unique tools for these investigations. This perspective gives an overview of the use of state-of-the-art hyperfine spectroscopy in heme research, focusing on the advantages, limits and challenges of the different techniques.
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Affiliation(s)
- Sabine Van Doorslaer
- BIMEF Laboratory, Department of Physics, University of Antwerp, B-2610 Antwerp, Belgium.
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17
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O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors. Chembiochem 2017; 18:914-920. [PMID: 28253432 PMCID: PMC5445010 DOI: 10.1002/cbic.201700052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 11/11/2022]
Abstract
Isoprenoid biosynthesis is an important area for anti-infective drug development. One isoprenoid target is (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) reductase (IspH), which forms isopentenyl diphosphate and dimethylallyl diphosphate from HMBPP in a 2H+ /2e- reduction. IspH contains a 4 Fe-4 S cluster, and in this work, we first investigated how small molecules bound to the cluster by using HYSCORE and NRVS spectroscopies. The results of these, as well as other structural and spectroscopic investigations, led to the conclusion that, in most cases, ligands bound to IspH 4 Fe-4 S clusters by η1 coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2 O, O2 ) binding. Based on these ideas, we used in silico methods to find drug-like inhibitors that might occupy the HMBPP substrate binding pocket and bind to Fe, leading to the discovery of a barbituric acid analogue with a Ki value of ≈500 nm against Pseudomonas aeruginosa IspH.
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Affiliation(s)
- Bing O'Dowd
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Sarah Williams
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Hongxin Wang
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Joo Hwan No
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Weixue Wang
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093, USA
- National Biomedical Computation Resource, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Stephen P Cramer
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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18
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Van Doorslaer S, Beirinckx Q, Nys K, Mangiameli MF, Cuypers B, Callens F, Vrielinck H, González JC. EPR and DFT analysis of biologically relevant chromium(V) complexes with d-glucitol and d-glucose. J Inorg Biochem 2016; 162:216-226. [PMID: 27460210 DOI: 10.1016/j.jinorgbio.2016.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
1,2-diolato ligands, such as carbohydrates and glycoproteins, tend to stabilize chromium(V), thus forming important intermediates that have been implicated in the genotoxicity of Cr(VI). Since many years, room-temperature continuous-wave electron paramagnetic resonance (EPR) at X-band microwave frequencies has been used as a standard characterization tool to study chromium(V) intermediates formed during the reduction of Cr(VI) in the presence of biomolecules. In this work, the added value is tested of using a combination of pulsed and high-field EPR techniques with density functional theory computations to unravel the nature of Cr(V) complexes with biologically relevant chelators, such as carbohydrates. The study focuses on the oxidochromium(V) complexes formed during reduction of potassium dichromate with glutathione in the presence of the monosaccharide d-glucose or the polyalcohol d-glucitol. It is shown that although the presence of a multitude of Cr(V) intermediates may hamper a complete structural determination, the combined EPR and DFT approach reveals unambiguously the effect of freezing on the location of the counterions, the gradual replacement of water ligands by the diols, and the preference of Cr(V) to bind certain conformers.
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Affiliation(s)
- Sabine Van Doorslaer
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Quinten Beirinckx
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Kevin Nys
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - María Florencia Mangiameli
- Universidad National de Rosario, Departamento de Químico Física - Área Química General, Facultad de Ciencias Bioquímicas y Farmacéuticas, IQUIR-CONICET, Suipacha 531, Rosario, Santa Fe, Argentina.
| | - Bert Cuypers
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Freddy Callens
- Ghent University, Dept. of Solid State Sciences, Krijgslaan 281-S1, B-9000 Ghent, Belgium.
| | - Henk Vrielinck
- Ghent University, Dept. of Solid State Sciences, Krijgslaan 281-S1, B-9000 Ghent, Belgium.
| | - Juan Carlos González
- University of Antwerp, Department of Physics, Universiteitsplein 1, B-2610 Antwerp, Belgium; Universidad National de Rosario, Departamento de Químico Física - Área Química General, Facultad de Ciencias Bioquímicas y Farmacéuticas, IQUIR-CONICET, Suipacha 531, Rosario, Santa Fe, Argentina.
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19
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Morra S, Maurelli S, Chiesa M, Mulder DW, Ratzloff MW, Giamello E, King PW, Gilardi G, Valetti F. The effect of a C298D mutation in CaHydA [FeFe]-hydrogenase: Insights into the protein-metal cluster interaction by EPR and FTIR spectroscopic investigation. Biochim Biophys Acta 2015; 1857:98-106. [PMID: 26482707 DOI: 10.1016/j.bbabio.2015.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/17/2023]
Abstract
A conserved cysteine located in the signature motif of the catalytic center (H-cluster) of [FeFe]-hydrogenases functions in proton transfer. This residue corresponds to C298 in Clostridium acetobutylicum CaHydA. Despite the chemical and structural difference, the mutant C298D retains fast catalytic activity, while replacement with any other amino acid causes significant activity loss. Given the proximity of C298 to the H-cluster, the effect of the C298D mutation on the catalytic center was studied by continuous wave (CW) and pulse electron paramagnetic resonance (EPR) and by Fourier transform infrared (FTIR) spectroscopies. Comparison of the C298D mutant with the wild type CaHydA by CW and pulse EPR showed that the electronic structure of the center is not altered. FTIR spectroscopy confirmed that absorption peak values observed in the mutant are virtually identical to those observed in the wild type, indicating that the H-cluster is not generally affected by the mutation. Significant differences were observed only in the inhibited state Hox-CO: the vibrational modes assigned to the COexo and Fed-CO in this state are shifted to lower values in C298D, suggesting different interaction of these ligands with the protein moiety when C298 is changed to D298. More relevant to the catalytic cycle, the redox equilibrium between the Hox and Hred states is modified by the mutation, causing a prevalence of the oxidized state. This work highlights how the interactions between the protein environment and the H-cluster, a dynamic closely interconnected system, can be engineered and studied in the perspective of designing bio-inspired catalysts and mimics.
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Affiliation(s)
- Simone Morra
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy
| | - Sara Maurelli
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W Ratzloff
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Elio Giamello
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy.
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20
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Kielmann U, Jeschke G, García-Rubio I. Structural Characterization of Polymer-Clay Nanocomposites Prepared by Co-Precipitation Using EPR Techniques. Materials (Basel) 2014; 7:1384-1408. [PMID: 28788520 PMCID: PMC5453077 DOI: 10.3390/ma7021384] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 02/16/2014] [Accepted: 02/17/2014] [Indexed: 11/16/2022]
Abstract
Polymer-clay nanocomposites (PCNCs) containing either a rubber or an acrylate polymer were prepared by drying or co-precipitating polymer latex and nanolayered clay (synthetic and natural) suspensions. The interface between the polymer and the clay nanoparticles was studied by electron paramagnetic resonance (EPR) techniques by selectively addressing spin probes either to the surfactant layer (labeled stearic acid) or the clay surface (labeled catamine). Continuous-wave (CW) EPR studies of the surfactant dynamics allow to define a transition temperature T* which was tentatively assigned to the order-disorder transition of the surfactant layer. CW EPR studies of PCNC showed that completely exfoliated nanoparticles coexist with agglomerates. HYSCORE spectroscopy in PCNCs showed couplings within the probe -assigned with DFT computations- and couplings with nuclei of the environment, ¹H and 23Na for the surfactant layer probe, and 29Si, ⁷Li, 19F and 23Na for the clay surface probe. Analysis of these couplings indicates that the integrity of the surfactant layer is conserved and that there are sizeable ionic regions containing sodium ions directly beyond the surfactant layer. Simulations of the very weak couplings demonstrated that the HYSCORE spectra are sensitive to the composition of the clay and whether or not clay platelets stack.
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Affiliation(s)
- Udo Kielmann
- Laboratory of Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Inés García-Rubio
- Laboratory of Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland.
- Centro Universitario de la Defensa, Ctra de Huesca s/n, 50090 Zaragoza, Spain.
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Winkler M, Esselborn J, Happe T. Molecular basis of [FeFe]-hydrogenase function: an insight into the complex interplay between protein and catalytic cofactor. Biochim Biophys Acta 2013; 1827:974-85. [PMID: 23507618 DOI: 10.1016/j.bbabio.2013.03.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/21/2013] [Accepted: 03/08/2013] [Indexed: 12/20/2022]
Abstract
The precise electrochemical features of metal cofactors that convey the functions of redox enzymes are essentially determined by the specific interaction pattern between cofactor and enclosing protein environment. However, while biophysical techniques allow a detailed understanding of the features characterizing the cofactor itself, knowledge about the contribution of the protein part is much harder to obtain. [FeFe]-hydrogenases are an interesting class of enzymes that catalyze both, H2 oxidation and the reduction of protons to molecular hydrogen with significant efficiency. The active site of these proteins consists of an unusual prosthetic group (H-cluster) with six iron and six sulfur atoms. While H-cluster architecture and catalytic states during the different steps of H2 turnover have been thoroughly investigated during the last 20 years, possible functional contributions from the polypeptide framework were only assumed according to the level of conservancy and X-ray structure analyses. Due to the recent development of simpler and more efficient expression systems the role of single amino acids can now be experimentally investigated. This article summarizes, compares and categorizes the results of recent investigations based on site directed and random mutagenesis according to their informative value about structure function relationships in [FeFe]-hydrogenases. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Martin Winkler
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Bochum, Germany
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