1
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Kisgeropoulos EC, Gan YJ, Greer SM, Hazel JM, Shafaat HS. Pulsed Multifrequency Electron Paramagnetic Resonance Spectroscopy Reveals Key Branch Points for One- vs Two-Electron Reactivity in Mn/Fe Proteins. J Am Chem Soc 2022; 144:11991-12006. [PMID: 35786920 DOI: 10.1021/jacs.1c13738] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Traditionally, the ferritin-like superfamily of proteins was thought to exclusively use a diiron active site in catalyzing a diverse array of oxygen-dependent reactions. In recent years, novel redox-active cofactors featuring heterobimetallic Mn/Fe active sites have been discovered in both the radical-generating R2 subunit of class Ic (R2c) ribonucleotide reductases (RNRs) and the related R2-like ligand-binding oxidases (R2lox). However, the protein-specific factors that differentiate the radical reactivity of R2c from the C-H activation reactions of R2lox remain unknown. In this work, multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy and ligand hyperfine techniques in conjunction with broken-symmetry density functional theory calculations are used to characterize the molecular and electronic structures of two EPR-active intermediates trapped during aerobic assembly of the R2lox Mn/Fe cofactor. A MnIII(μ-O)(μ-OH)FeIII species is identified as the first EPR-active species and represents a common state between the two classes of redox-active Mn/Fe proteins. The species downstream from the MnIII(μ-O)(μ-OH)FeIII state exhibits unique EPR properties, including unprecedented spectral breadth and isotope-dependent g-tensors, which are attributed to a weakly coupled, hydrogen-bonded MnIII(μ-OH)FeIII species. This final intermediate precedes formation of the MnIII/FeIII resting state and is suggested to be relevant to understanding the endogenous reactivity of R2lox.
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Affiliation(s)
- Effie C Kisgeropoulos
- The Ohio State Biochemistry Program, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Yunqiao J Gan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Samuel M Greer
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Joseph M Hazel
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State Biochemistry Program, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
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2
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Richardson KH, Seif-Eddine M, Sills A, Roessler MM. Controlling and exploiting intrinsic unpaired electrons in metalloproteins. Methods Enzymol 2022; 666:233-296. [PMID: 35465921 DOI: 10.1016/bs.mie.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Electron paramagnetic resonance spectroscopy encompasses a versatile set of techniques that allow detailed insight into intrinsically occurring paramagnetic centers in metalloproteins and enzymes that undergo oxidation-reduction reactions. In this chapter, we discuss the process from isolating the protein to acquiring and analyzing pulse EPR spectra, adopting a practical perspective. We start with considerations when preparing the protein sample, explain techniques and procedures available for determining the reduction potential of the redox-active center of interest and provide details on methodologies to trap a given paramagnetic state for detailed pulse EPR studies, with an emphasis on biochemical and spectroscopic tools available when multiple EPR-active species are present. We elaborate on some of the most commonly used pulse EPR techniques and the choices the user has to make, considering advantages and disadvantages and how to avoid pitfalls. Examples are provided throughout.
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Affiliation(s)
| | - Maryam Seif-Eddine
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Adam Sills
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Maxie M Roessler
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom.
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3
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Richardson KH, Wright JJ, Šimėnas M, Thiemann J, Esteves AM, McGuire G, Myers WK, Morton JJL, Hippler M, Nowaczyk MM, Hanke GT, Roessler MM. Functional basis of electron transport within photosynthetic complex I. Nat Commun 2021; 12:5387. [PMID: 34508071 PMCID: PMC8433477 DOI: 10.1038/s41467-021-25527-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023] Open
Abstract
Photosynthesis and respiration rely upon a proton gradient to produce ATP. In photosynthesis, the Respiratory Complex I homologue, Photosynthetic Complex I (PS-CI) is proposed to couple ferredoxin oxidation and plastoquinone reduction to proton pumping across thylakoid membranes. However, little is known about the PS-CI molecular mechanism and attempts to understand its function have previously been frustrated by its large size and high lability. Here, we overcome these challenges by pushing the limits in sample size and spectroscopic sensitivity, to determine arguably the most important property of any electron transport enzyme - the reduction potentials of its cofactors, in this case the iron-sulphur clusters of PS-CI (N0, N1 and N2), and unambiguously assign them to the structure using double electron-electron resonance. We have thus determined the bioenergetics of the electron transfer relay and provide insight into the mechanism of PS-CI, laying the foundations for understanding of how this important bioenergetic complex functions.
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Affiliation(s)
- Katherine H. Richardson
- grid.4868.20000 0001 2171 1133School of Biological and Chemical Sciences, Queen Mary University of London, London, UK ,grid.7445.20000 0001 2113 8111Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
| | - John J. Wright
- grid.4868.20000 0001 2171 1133School of Biological and Chemical Sciences, Queen Mary University of London, London, UK ,grid.14105.310000000122478951Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge, UK
| | - Mantas Šimėnas
- grid.83440.3b0000000121901201London Centre for Nanotechnology, University College London, London, UK
| | - Jacqueline Thiemann
- grid.5570.70000 0004 0490 981XPlant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Ana M. Esteves
- grid.4868.20000 0001 2171 1133School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Gemma McGuire
- grid.4868.20000 0001 2171 1133School of Biological and Chemical Sciences, Queen Mary University of London, London, UK ,grid.7445.20000 0001 2113 8111Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
| | - William K. Myers
- grid.4991.50000 0004 1936 8948Inorganic Chemistry, University of Oxford, Oxford, UK
| | - John J. L. Morton
- grid.83440.3b0000000121901201London Centre for Nanotechnology, University College London, London, UK ,grid.83440.3b0000000121901201Department of Electronic & Electrical Engineering, UCL, London, UK
| | - Michael Hippler
- grid.5949.10000 0001 2172 9288Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany ,grid.261356.50000 0001 1302 4472Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Marc M. Nowaczyk
- grid.5570.70000 0004 0490 981XPlant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Guy T. Hanke
- grid.4868.20000 0001 2171 1133School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Maxie M. Roessler
- grid.7445.20000 0001 2113 8111Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
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4
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Haeri HH, Duraisamy R, Harmgarth N, Liebing P, Lorenz V, Hinderberger D, Edelmann FT. Electronic and Geometric Structures of Paramagnetic Diazadiene Complexes of Lithium and Sodium. ChemistryOpen 2018; 7:701-708. [PMID: 30202705 PMCID: PMC6123648 DOI: 10.1002/open.201800114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Indexed: 11/08/2022] Open
Abstract
The electronic and molecular structures of the lithium and sodium complexes of 1,4-bis(2,6-diisopropylphenyl)-2,3-dimethyl-1,4-diazabutadiene (Me2DADDipp) were fully characterized by using a multi-frequency electron paramagnetic resonance (EPR) spectroscopy approach and crystallography, together with density functional theory (DFT) calculations. EPR measurements, using T1 relaxation-time-filtered pulse EPR spectroscopy, revealed the diagonal elements of the A and g tensors for the metal and ligand sites. It was found that the central metals in the lithium complexes had sizable contributions to the SOMO, whereas this contribution was less strongly observed for the sodium complex. Such strong contributions were attributed to structural specifications (e.g. geometrical data and atomic size) rather than electronic effects.
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Affiliation(s)
- Haleh H. Haeri
- Institute of ChemistryMartin Luther University Halle-WittenbergVon-Danckelmann-Platz 406120HalleGermany
| | - Ramesh Duraisamy
- Institute of ChemistryOtto-von-Guericke UniversityMagdeburg39106Germany
| | - Nicole Harmgarth
- Institute of ChemistryOtto-von-Guericke UniversityMagdeburg39106Germany
| | - Phil Liebing
- Laboratory for Inorganic ChemistryETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Volker Lorenz
- Institute of ChemistryOtto-von-Guericke UniversityMagdeburg39106Germany
| | - Dariush Hinderberger
- Institute of ChemistryMartin Luther University Halle-WittenbergVon-Danckelmann-Platz 406120HalleGermany
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5
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Chabbra S, Smith DM, Bode BE. Isolation of EPR spectra and estimation of spin-states in two-component mixtures of paramagnets. Dalton Trans 2018; 47:10473-10479. [PMID: 29697132 DOI: 10.1039/c8dt00977e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of multiple paramagnetic species can lead to overlapping electron paramagnetic resonance (EPR) signals. This complication can be a critical obstacle for the use of EPR to unravel mechanisms and aid the understanding of earth abundant metal catalysis. Furthermore, redox or spin-crossover processes can result in the simultaneous presence of metal centres in different oxidation or spin states. In this contribution, pulse EPR experiments on model systems containing discrete mixtures of Cr(i) and Cr(iii) or Cu(ii) and Mn(ii) complexes demonstrate the feasibility of the separation of the EPR spectra of these species by inversion recovery filters and the identification of the relevant spin states by transient nutation experiments. We demonstrate the isolation of component spectra and identification of spin states in a mixture of catalyst precursors. The usefulness of the approach is emphasised by monitoring the fate of the chromium species upon activation of an industrially used precatalyst system.
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Affiliation(s)
- Sonia Chabbra
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK.
| | - David M Smith
- Sasol UK Ltd, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK.
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6
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Van Landeghem M, Maes W, Goovaerts E, Van Doorslaer S. Disentangling overlapping high-field EPR spectra of organic radicals: Identification of light-induced polarons in the record fullerene-free solar cell blend PBDB-T:ITIC. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 288:1-10. [PMID: 29367021 DOI: 10.1016/j.jmr.2018.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 06/07/2023]
Abstract
We present a combined high-field EPR and DFT study of light-induced radicals in the bulk heterojunction blend of PBDB-T:ITIC, currently one of the highest efficiency non-fullerene donor:acceptor combinations in organic photovoltaics. We demonstrate two different approaches for disentangling the strongly overlapping high-field EPR spectra of the positive and negative polarons after charge separation: (1) relaxation-filtered field-swept EPR based on the difference in T1 spin-relaxation times and (2) field-swept EDNMR-induced EPR by exploiting the presence of 14N hyperfine couplings in only one of the radical species, the small molecule acceptor radical. The approach is validated by light-induced EPR spectra on related blends and the spectral assignment is underpinned by DFT computations. The broader applicability of the spectral disentangling methods is discussed.
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Affiliation(s)
- Melissa Van Landeghem
- Department of Physics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.
| | - Wouter Maes
- Institute for Materials Research, Design & Synthesis of Organic Semiconductors, Hasselt University, Agoralaan 1, 3590 Diepenbeek, Belgium.
| | - Etienne Goovaerts
- Department of Physics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.
| | - Sabine Van Doorslaer
- Department of Physics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.
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7
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Le Breton N, Wright JJ, Jones AJY, Salvadori E, Bridges HR, Hirst J, Roessler MM. Using Hyperfine Electron Paramagnetic Resonance Spectroscopy to Define the Proton-Coupled Electron Transfer Reaction at Fe-S Cluster N2 in Respiratory Complex I. J Am Chem Soc 2017; 139:16319-16326. [PMID: 29039928 DOI: 10.1021/jacs.7b09261] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Energy-transducing respiratory complex I (NADH:ubiquinone oxidoreductase) is one of the largest and most complicated enzymes in mammalian cells. Here, we used hyperfine electron paramagnetic resonance (EPR) spectroscopic methods, combined with site-directed mutagenesis, to determine the mechanism of a single proton-coupled electron transfer reaction at one of eight iron-sulfur clusters in complex I, [4Fe-4S] cluster N2. N2 is the terminal cluster of the enzyme's intramolecular electron-transfer chain and the electron donor to ubiquinone. Because of its position and pH-dependent reduction potential, N2 has long been considered a candidate for the elusive "energy-coupling" site in complex I at which energy generated by the redox reaction is used to initiate proton translocation. Here, we used hyperfine sublevel correlation (HYSCORE) spectroscopy, including relaxation-filtered hyperfine and single-matched resonance transfer (SMART) HYSCORE, to detect two weakly coupled exchangeable protons near N2. We assign the larger coupling with A(1H) = [-3.0, -3.0, 8.7] MHz to the exchangeable proton of a conserved histidine and conclude that the histidine is hydrogen-bonded to N2, tuning its reduction potential. The histidine protonation state responds to the cluster oxidation state, but the two are not coupled sufficiently strongly to catalyze a stoichiometric and efficient energy transduction reaction. We thus exclude cluster N2, despite its proton-coupled electron transfer chemistry, as the energy-coupling site in complex I. Our work demonstrates the capability of pulse EPR methods for providing detailed information on the properties of individual protons in even the most challenging of energy-converting enzymes.
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Affiliation(s)
- Nolwenn Le Breton
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London, E1 4NS, United Kingdom
| | - John J Wright
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London, E1 4NS, United Kingdom
| | - Andrew J Y Jones
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge , Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Enrico Salvadori
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London, E1 4NS, United Kingdom.,London Centre for Nanotechnology, University College London , 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Hannah R Bridges
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge , Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge , Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London, E1 4NS, United Kingdom
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8
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Spindler PE, Schöps P, Kallies W, Glaser SJ, Prisner TF. Perspectives of shaped pulses for EPR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 280:30-45. [PMID: 28579101 DOI: 10.1016/j.jmr.2017.02.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 06/07/2023]
Abstract
This article describes current uses of shaped pulses, generated by an arbitrary waveform generator, in the field of EPR spectroscopy. We show applications of sech/tanh and WURST pulses to dipolar spectroscopy, including new pulse schemes and procedures, and discuss the more general concept of optimum-control-based pulses for applications in EPR spectroscopy. The article also describes a procedure to correct for experimental imperfections, mostly introduced by the microwave resonator, and discusses further potential applications and limitations of such pulses.
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Affiliation(s)
- Philipp E Spindler
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany
| | - Philipp Schöps
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany
| | - Wolfgang Kallies
- Department of Chemistry, Technical University of Munich, Germany
| | - Steffen J Glaser
- Department of Chemistry, Technical University of Munich, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany.
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9
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Wright JJ, Salvadori E, Bridges HR, Hirst J, Roessler MM. Small-volume potentiometric titrations: EPR investigations of Fe-S cluster N2 in mitochondrial complex I. J Inorg Biochem 2016; 162:201-206. [DOI: 10.1016/j.jinorgbio.2016.04.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/19/2016] [Accepted: 04/18/2016] [Indexed: 11/17/2022]
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10
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Franck JM, Barnes RP, Keller TJ, Kaufmann T, Han S. Active cancellation - A means to zero dead-time pulse EPR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 261:199-204. [PMID: 26507308 PMCID: PMC4688155 DOI: 10.1016/j.jmr.2015.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/25/2015] [Accepted: 07/05/2015] [Indexed: 05/02/2023]
Abstract
The necessary resonator employed in pulse electron paramagnetic resonance (EPR) rings after the excitation pulse and creates a finite detector dead-time that ultimately prevents the detection of signal from fast relaxing spin systems, hindering the application of pulse EPR to room temperature measurements of interesting chemical or biological systems. We employ a recently available high bandwidth arbitrary waveform generator (AWG) to produce a cancellation pulse that precisely destructively interferes with the resonant cavity ring-down. We find that we can faithfully detect EPR signal at all times immediately after, as well as during, the excitation pulse. This is a proof of concept study showcasing the capability of AWG pulses to precisely cancel out the resonator ring-down, and allow for the detection of EPR signal during the pulse itself, as well as the dead-time of the resonator. However, the applicability of this approach to conventional EPR experiments is not immediate, as it hinges on either (1) the availability of low-noise microwave sources and amplifiers to produce the necessary power for pulse EPR experiment or (2) the availability of very high conversion factor micro coil resonators that allow for pulse EPR experiments at modest microwave power.
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11
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Kaufmann T, Keller TJ, Franck JM, Barnes RP, Glaser SJ, Martinis JM, Han S. DAC-board based X-band EPR spectrometer with arbitrary waveform control. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 235:95-108. [PMID: 23999530 PMCID: PMC3863685 DOI: 10.1016/j.jmr.2013.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/28/2013] [Accepted: 07/30/2013] [Indexed: 05/07/2023]
Abstract
We present arbitrary control over a homogenous spin system, demonstrated on a simple, home-built, electron paramagnetic resonance (EPR) spectrometer operating at 8-10 GHz (X-band) and controlled by a 1 GHz arbitrary waveform generator (AWG) with 42 dB (i.e. 14-bit) of dynamic range. Such a spectrometer can be relatively easily built from a single DAC (digital to analog converter) board with a modest number of stock components and offers powerful capabilities for automated digital calibration and correction routines that allow it to generate shaped X-band pulses with precise amplitude and phase control. It can precisely tailor the excitation profiles "seen" by the spins in the microwave resonator, based on feedback calibration with experimental input. We demonstrate the capability to generate a variety of pulse shapes, including rectangular, triangular, Gaussian, sinc, and adiabatic rapid passage waveforms. We then show how one can precisely compensate for the distortion and broadening caused by transmission into the microwave cavity in order to optimize corrected waveforms that are distinctly different from the initial, uncorrected waveforms. Specifically, we exploit a narrow EPR signal whose width is finer than the features of any distortions in order to map out the response to a short pulse, which, in turn, yields the precise transfer function of the spectrometer system. This transfer function is found to be consistent for all pulse shapes in the linear response regime. In addition to allowing precise waveform shaping capabilities, the spectrometer presented here offers complete digital control and calibration of the spectrometer that allows one to phase cycle the pulse phase with 0.007° resolution and to specify the inter-pulse delays and pulse durations to ≤ 250 ps resolution. The implications and potential applications of these capabilities will be discussed.
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Affiliation(s)
- Thomas Kaufmann
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Timothy J. Keller
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - John M. Franck
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Ryan P. Barnes
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - John M. Martinis
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Corresponding author. Address: Department of Chemistry and Biochemistry, 9510, University of California Santa Barbara, CA, USA. (S. Han)
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12
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van Wonderen JH, Kostrz DN, Dennison C, MacMillan F. Refined distances between paramagnetic centers of a multi-copper nitrite reductase determined by pulsed EPR (iDEER) spectroscopy. Angew Chem Int Ed Engl 2013; 52:1990-3. [PMID: 23296685 PMCID: PMC3596801 DOI: 10.1002/anie.201208166] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Jessica H van Wonderen
- Henry Wellcome Unit of Biological EPR, School of Chemistry, University of East Anglia, Norwich, UK
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13
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van Wonderen JH, Kostrz DN, Dennison C, MacMillan F. Refined Distances Between Paramagnetic Centers of a Multi-Copper Nitrite Reductase Determined by Pulsed EPR (iDEER) Spectroscopy. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Spindler PE, Zhang Y, Endeward B, Gershernzon N, Skinner TE, Glaser SJ, Prisner TF. Shaped optimal control pulses for increased excitation bandwidth in EPR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 218:49-58. [PMID: 22578555 DOI: 10.1016/j.jmr.2012.02.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 02/16/2012] [Accepted: 02/18/2012] [Indexed: 05/12/2023]
Abstract
A 1 ns resolution pulse shaping unit has been developed for pulsed EPR spectroscopy to enable 14-bit amplitude and phase modulation. Shaped broadband excitation pulses designed using optimal control theory (OCT) have been tested with this device at X-band frequency (9 GHz). FT-EPR experiments on organic radicals in solution have been performed with the new pulses, designed for uniform excitation over a significantly increased bandwidth compared to a classical rectangular π/2 pulse of the same B(1) amplitude. The concept of a dead-time compensated prefocused pulse has been introduced to EPR with a self-refocusing of 200 ns after the end of the pulse. Echo-like refocused signals have been recorded and compared to the performance of a classical Hahn-echo sequence. The impulse response function of the microwave setup has been measured and incorporated into the algorithm for designing OCT pulses, resulting in further significant improvements in performance. Experimental limitations and potential new applications of OCT pulses in EPR spectroscopy will be discussed.
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Affiliation(s)
- Philipp E Spindler
- Institut für physikalische und theoretische Chemie, Goethe Universität Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany.
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15
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Lyubenova S, Maly T, Zwicker K, Brandt U, Ludwig B, Prisner T. Multifrequency pulsed electron paramagnetic resonance on metalloproteins. Acc Chem Res 2010; 43:181-9. [PMID: 19842617 DOI: 10.1021/ar900050d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloproteins often contain metal centers that are paramagnetic in some functional state of the protein; hence electron paramagnetic resonance (EPR) spectroscopy can be a powerful tool for studying protein structure and function. Dipolar spectroscopy allows the determination of the dipole-dipole interactions between metal centers in protein complexes, revealing the structural arrangement of different paramagnetic centers at distances of up to 8 nm. Hyperfine spectroscopy can be used to measure the interaction between an unpaired electron spin and nuclear spins within a distance of 0.8 nm; it therefore permits the characterization of the local structure of the paramagnetic center's ligand sphere with very high precision. In this Account, we review our laboratory's recent applications of both dipolar and hyperfine pulsed EPR methods to metalloproteins. We used pulsed dipolar relaxation methods to investigate the complex of cytochrome c and cytochrome c oxidase, a noncovalent protein-protein complex involved in mitochondrial electron-transfer reactions. Hyperfine sublevel correlation spectroscopy (HYSCORE) was used to study the ligand sphere of iron-sulfur clusters in complex I of the mitochondrial respiratory chain and substrate binding to the molybdenum enzyme polysulfide reductase. These examples demonstrate the potential of the two techniques; however, they also highlight the difficulties of data interpretation when several paramagnetic species with overlapping spectra are present in the protein. In such cases, further approaches and data are very useful to enhance the information content. Relaxation filtered hyperfine spectroscopy (REFINE) can be used to separate the individual components of overlapping paramagnetic species on the basis of differences in their longitudinal relaxation rates; it is applicable to any kind of pulsed hyperfine or dipolar spectroscopy. Here, we show that the spectra of the iron-sulfur clusters in complex I can be separated by this method, allowing us to obtain hyperfine (and dipolar) information from the individual species. Furthermore, performing pulsed EPR experiments at different magnetic fields is another important tool to disentangle the spectral components in such complex systems. Despite the fact that high magnetic fields do not usually lead to better spectral separation for metal centers, they provide additional information about the relative orientation of different paramagnetic centers. Our high-field EPR studies on cytochrome c oxidase reveal essential information regarding the structural arrangement of the binuclear Cu(A) center with respect to both the manganese ion within the enzyme and the cytochrome in the protein-protein complex with cytochrome c.
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Affiliation(s)
- Sevdalina Lyubenova
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Thorsten Maly
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Klaus Zwicker
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Ulrich Brandt
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Bernd Ludwig
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Thomas Prisner
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
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Cammack R, MacMillan F. Electron Magnetic Resonance of Iron–Sulfur Proteins in Electron-Transfer Chains: Resolving Complexity. METALS IN BIOLOGY 2010. [DOI: 10.1007/978-1-4419-1139-1_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Maly T, Zwicker K, Cernescu A, Brandt U, Prisner TF. New pulsed EPR methods and their application to characterize mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:584-92. [PMID: 19366602 DOI: 10.1016/j.bbabio.2009.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 02/04/2009] [Accepted: 02/05/2009] [Indexed: 10/21/2022]
Abstract
Electron Paramagnetic Resonance (EPR) spectroscopy is the method of choice to study paramagnetic cofactors that often play an important role as active centers in electron transfer processes in biological systems. However, in many cases more than one paramagnetic species is contributing to the observed EPR spectrum, making the analysis of individual contributions difficult and in some cases impossible. With time-domain techniques it is possible to exploit differences in the relaxation behavior of different paramagnetic species to distinguish between them and separate their individual spectral contribution. Here we give an overview of the use of pulsed EPR spectroscopy to study the iron-sulfur clusters of NADH:ubiquinone oxidoreductase (complex I). While FeS cluster N1 can be studied individually at a temperature of 30 K, this is not possible for FeS cluster N2 due to its severe spectral overlap with cluster N1. In this case Relaxation Filtered Hyperfine (REFINE) spectroscopy can be used to separate the overlapping spectra based on differences in their relaxation behavior.
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Affiliation(s)
- Thorsten Maly
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Advanced Pulse EPR Methods for the Characterization of Metalloproteins. HIGH RESOLUTION EPR 2009. [DOI: 10.1007/978-0-387-84856-3_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Challenges in elucidating structure and mechanism of proton pumping NADH:ubiquinone oxidoreductase (complex I). J Bioenerg Biomembr 2008; 40:475-83. [PMID: 18982432 DOI: 10.1007/s10863-008-9171-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 08/01/2008] [Indexed: 12/11/2022]
Abstract
Proton pumping NADH:ubiquinone oxidoreductase (complex I) is the most complicated and least understood enzyme of the respiratory chain. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulfur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST- and 49-kDa subunits of complex I. An access path for ubiquinone and different partially overlapping inhibitor binding regions were defined within this pocket by site directed mutagenesis. A combination of biochemical and single particle analysis studies suggests that the ubiquinone reduction site is located well above the membrane domain. Therefore, direct coupling mechanisms seem unlikely and the redox energy must be converted into a conformational change that drives proton pumping across the membrane arm. It is not known which of the subunits and how many are involved in proton translocation. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. The physiological role of this phenomenon is yet unclear but it could contribute to the regulation of complex I activity in-vivo.
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Cernescu A, Maly T, Prisner TF. 2D-REFINE spectroscopy: separation of overlapping hyperfine spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 192:78-84. [PMID: 18343175 DOI: 10.1016/j.jmr.2008.02.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 02/04/2008] [Accepted: 02/04/2008] [Indexed: 05/26/2023]
Abstract
We show on a mixture of three spectrally overlapping paramagnetic compounds TEMPO, BDPA and CuHis that it is possible to separate their field-swept and hyperfine spectra based on the difference in their longitudinal relaxation times T1. This was achieved in a two-dimensional experiment, where one dimension corresponds to the spectral domain and the second dimension encodes the relaxation behavior of the individual compound. Inverse Laplace Transform with respect to this domain separates the field-swept and hyperfine spectra of the individual compounds in the relaxation rate domain. This extends our formerly proposed Relaxation Filtered Hyperfine (REFINE) method to be applicable to more than two spectrally overlapping spectra by adding a further dimension to the chosen EPR experiment.
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Affiliation(s)
- Adrian Cernescu
- Institute for Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University, Marie-Curie Str. 11, D-60439 Frankfurt am Main, Germany
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Ohnishi T, Nakamaru-Ogiso E. Were there any "misassignments" among iron-sulfur clusters N4, N5 and N6b in NADH-quinone oxidoreductase (complex I)? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:703-10. [PMID: 18486592 DOI: 10.1016/j.bbabio.2008.04.032] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 04/16/2008] [Accepted: 04/22/2008] [Indexed: 11/29/2022]
Abstract
NADH-quinone oxidoreductase (complex I) in bovine heart mitochondria has a molecular weight of approximately 1 million Da composed of 45 distinct subunits. It is the largest energy transducing complex so far known. Bacterial complex I is simpler and smaller, but the essential redox components and the basic mechanisms of electron and proton translocation are the same. Over the past three decades, Ohnishi et al. have pursued extensive EPR studies near liquid helium temperatures and characterized most of the iron-sulfur clusters in complex I. Recently, Yakovlev et al. [G. Yakovlev, T. Reda, J. Hirst, Reevaluating the relationship between EPR spectra and enzyme structure for the iron-sulfur clusters in NADH:quinone oxidoreductase, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 12720-12725] challenged Ohnishi's group by claiming that there were EPR "misassignments" among clusters N4, N5 and N6b (in order to prevent confusion, we used current consensus nomenclature, as the nickname). They claimed that we misassigned EPR signals arising from cluster N5 to cluster N4, and signals from cluster N6b to cluster N4. They also proposed that cluster N5 has (4Cys)-ligands. Based on the accumulated historical data and recent results of our site-specific mutagenesis experiments, we confirmed that cluster N5 has (1His+3Cys)-ligands as we had predicted. We revealed that E. coli cluster N5 signals could be clearly detected at the sample temperature around 3 K with microwave power higher than 5 mW. Thus Hirst's group could not detect N5 signals under any of their EPR conditions, reported in their PNAS paper. It seems that they misassigned the signals from cluster N4 to N5. As to the claim of "misassignment" between clusters N4 and N6b, that was not a possibility because our mutagenesis systems did not contain cluster N6b. Therefore, we believe that we have not made any "misassignment" in our work.
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Affiliation(s)
- Tomoko Ohnishi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA.
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Maly T, Grgic L, Zwicker K, Zickermann V, Brandt U, Prisner T. Cluster N1 of complex I from Yarrowia lipolytica studied by pulsed EPR spectroscopy. J Biol Inorg Chem 2006; 11:343-50. [PMID: 16502321 DOI: 10.1007/s00775-006-0081-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Accepted: 01/16/2006] [Indexed: 11/27/2022]
Abstract
After reduction with nicotinamide adenine dinucleotide (NADH), NADH:ubiquinone oxidoreductase (complex I) of the strictly aerobic yeast Yarrowia lipolytica shows clear signals from five different paramagnetic iron-sulfur (FeS) clusters (N1-N5) which can be detected using electron paramagnetic resonance (EPR) spectroscopy. The ligand environment and the assignment of several FeS clusters to specific binding motifs found in several subunits of the complex are still under debate. In order to characterize the hyperfine interaction of the surrounding nuclei with FeS cluster N1, one- and two-dimensional electron spin echo envelope modulation experiments were performed at a temperature of 30 K. At this temperature only cluster N1 contributes to the overall signal in a pulsed EPR experiment. The hyperfine and quadrupole tensors of a nitrogen nucleus and the isotropic and dipolar hyperfine couplings of two sets of protons could be determined by numerical simulation of the one- and two-dimensional spectra. The values obtained are in perfect agreement with a ferredoxin-like binding structure by four cysteine amino acid residues and allow the assignment of the nitrogen couplings to a backbone nitrogen nucleus and the proton couplings to the beta-protons of the bound cysteine residues.
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Affiliation(s)
- T Maly
- Institut für Physikalische und Theoretische Chemie and Center for Biological Magnetic Resonance, Johann-Wolfgang-Goethe-Universität Frankfurt, 60439, Frankfurt am Main, Germany
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Chattopadhyay M, Walter ED, Newell DJ, Jackson PJ, Aronoff-Spencer E, Peisach J, Gerfen GJ, Bennett B, Antholine WE, Millhauser GL. The octarepeat domain of the prion protein binds Cu(II) with three distinct coordination modes at pH 7.4. J Am Chem Soc 2005; 127:12647-56. [PMID: 16144413 PMCID: PMC2909831 DOI: 10.1021/ja053254z] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prion protein (PrP) binds Cu2+ in its N-terminal octarepeat domain. This unusual domain is comprised of four or more tandem repeats of the fundamental sequence PHGGGWGQ. Previous work from our laboratories demonstrates that at full copper occupancy, each HGGGW segment binds a single Cu2+. However, several recent studies suggest that low copper occupancy favors different coordination modes, possibly involving imidazoles from histidines in adjacent octapeptide segments. This is investigated here using a combination of X-band EPR, S-band EPR, and ESEEM, along with a library of modified peptides designed to favor different coordination interactions. At pH 7.4, three distinct coordination modes are identified. Each mode is fully characterized to reveal a series of copper-dependent octarepeat domain structures. Multiple His coordination is clearly identified at low copper stoichiometry. In addition, EPR detected copper-copper interactions at full occupancy suggest that the octarepeat domain partially collapses, perhaps stabilizing this specific binding mode and facilitating cooperative copper uptake. This work provides the first complete characterization of all dominant copper coordination modes at pH 7.4.
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Maly T, Prisner TF. Relaxation filtered hyperfine spectroscopy (REFINE). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 170:88-96. [PMID: 15324761 DOI: 10.1016/j.jmr.2004.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 06/04/2004] [Indexed: 05/24/2023]
Abstract
A simple and general applicable method to separate spectrally overlapping hyperfine spectra of two paramagnetic compounds is presented. Overlapping spectral contributions from different paramagnetic species are a common situation in electron paramagnetic resonance (EPR) spectroscopy, resulting in complicate EPR spectra of metal enzymes, organic radicals or in the field of material sciences. On the other hand, the longitudinal relaxation times T1 of these species contributing to the overall EPR signal can vary by several orders of magnitude, depending on the paramagnetic component under study. These differences can be used to selectively study individual species by using an inversion-recovery preparation sequence as a filter. Here, we demonstrate the possibility to separate hyperfine spectra of two spectrally overlapping paramagnetic species by combining an inversion-recovery based relaxation filter together with ESEEM or ENDOR hyperfine spectroscopy (REFINE). The feasibility of the presented method is demonstrated on model compounds and the necessary requirements are discussed.
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Affiliation(s)
- Th Maly
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, D-60439 Frankfurt am Main, Germany
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