1
|
Cho FH, Park J, Oh S, Yu J, Jeong Y, Colazzo L, Spree L, Hommel C, Ardavan A, Boero G, Donati F. A continuous-wave and pulsed X-band electron spin resonance spectrometer operating in ultra-high vacuum for the study of low dimensional spin ensembles. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:063904. [PMID: 38864723 DOI: 10.1063/5.0189974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
Abstract
We report the development of a continuous-wave and pulsed X-band electron spin resonance (ESR) spectrometer for the study of spins on ordered surfaces down to cryogenic temperatures. The spectrometer operates in ultra-high vacuum and utilizes a half-wavelength microstrip line resonator realized using epitaxially grown copper films on single crystal Al2O3 substrates. The one-dimensional microstrip line resonator exhibits a quality factor of more than 200 at room temperature, close to the upper limit determined by radiation losses. The surface characterizations of the copper strip of the resonator by atomic force microscopy, low-energy electron diffraction, and scanning tunneling microscopy show that the surface is atomically clean, flat, and single crystalline. Measuring the ESR spectrum at 15 K from a few nm thick molecular film of YPc2, we find a continuous-wave ESR sensitivity of 2.6 × 1011 spins/G · Hz1/2, indicating that a signal-to-noise ratio of 3.9 G · Hz1/2 is expected from a monolayer of YPc2 molecules. Advanced pulsed ESR experimental capabilities, including dynamical decoupling and electron-nuclear double resonance, are demonstrated using free radicals diluted in a glassy matrix.
Collapse
Affiliation(s)
- Franklin H Cho
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Ewha Womans University, Seoul 03760, South Korea
| | - Juyoung Park
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Department of Physics, Ewha Womans University, Seoul 03760, South Korea
| | - Soyoung Oh
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Department of Physics, Ewha Womans University, Seoul 03760, South Korea
| | - Jisoo Yu
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Department of Physics, Ewha Womans University, Seoul 03760, South Korea
| | - Yejin Jeong
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Department of Physics, Ewha Womans University, Seoul 03760, South Korea
| | - Luciano Colazzo
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Ewha Womans University, Seoul 03760, South Korea
| | - Lukas Spree
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Ewha Womans University, Seoul 03760, South Korea
| | - Caroline Hommel
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Ewha Womans University, Seoul 03760, South Korea
| | - Arzhang Ardavan
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Giovanni Boero
- Microsystems Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Fabio Donati
- Center for Quantum Nanoscience, Institute for Basic Science, Seoul 03760, South Korea
- Department of Physics, Ewha Womans University, Seoul 03760, South Korea
| |
Collapse
|
2
|
Nevzorov AA, Marek A, Milikisiyants S, Smirnov AI. High-frequency high-power DNP/EPR spectrometer operating at 7 T magnetic field. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 362:107677. [PMID: 38631171 PMCID: PMC11102838 DOI: 10.1016/j.jmr.2024.107677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
One of the most essential prerequisites for the development of pulse Dynamic Nuclear Polarization (DNP) is the ability to generate high-power coherent mm-wave pulses at the electron precession frequencies corresponding to the magnetic fields of modern high-resolution NMR spectrometers. As a major step towards achieving this goal, an Extended Interaction Klystron (EIK) pulse amplifier custom-built by the Communications and Power Industries, Inc. and producing up to 140 W at 197.8 GHz, was integrated with in-house built NMR/DNP/EPR spectrometer operating at 7 T magnetic field. The spectrometer employs a Thomas Keating, Ltd. quasioptical bridge to direct mm-waves into a homebuilt DNP probe incorporating photonic bandgap (PBG) resonators to further boost electronic B1e fields. Three-pulse electron spin echo nutation experiments were employed to characterize the B1e fields at the sample by operating the homodyne 198 GHz bridge in an induction mode. Room-temperature experiments with a single-crystal high-pressure, high-temperature (HPHT) diamond and a polystyrene film doped with BDPA radical yielded < 9 ns π/2 pulses at ca. 50 W specified EIK output at the corresponding resonance frequencies and the PBG resonator quality factor of Q≈300. DNP experiments carried out in a "gated" mode by supplying 20 μs mm-wave pulses every 1 ms yielded 13C solid-effect DNP with gains up to 20 for the polystyrene-BDPA sample at natural 13C abundance. For a single-crystal HPHT diamond, the gated DNP mode yielded almost the same 13C enhancement as a low-power continuous wave (CW) mode at 0.4 W, whereas no DNP effect was observed for the BDPA/polystyrene sample in the latter case. To illustrate the versatility of our upgraded DNP spectrometer, room-temperature Overhauser DNP enhancements of 7-14 for 31P NMR signal were demonstrated using a liquid droplet of 1 M tri-phenyl phosphine co-dissolved with 100 mM of BDPA in toluene‑d8.
Collapse
Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC 27695, US.
| | - Antonin Marek
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC 27695, US
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC 27695, US
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC 27695, US.
| |
Collapse
|
3
|
Bogdanov A, Frydman V, Seal M, Rapatskiy L, Schnegg A, Zhu W, Iron M, Gronenborn AM, Goldfarb D. Extending the Range of Distances Accessible by 19F Electron-Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels. J Am Chem Soc 2024; 146:6157-6167. [PMID: 38393979 PMCID: PMC10921402 DOI: 10.1021/jacs.3c13745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024]
Abstract
Fluorine electron-nuclear double resonance (19F ENDOR) has recently emerged as a valuable tool in structural biology for distance determination between F atoms and a paramagnetic center, either intrinsic or conjugated to a biomolecule via spin labeling. Such measurements allow access to distances too short to be measured by double electron-electron resonance (DEER). To further extend the accessible distance range, we exploit the high-spin properties of Gd(III) and focus on transitions other than the central transition (|-1/2⟩ ↔ |+1/2⟩), that become more populated at high magnetic fields and low temperatures. This increases the spectral resolution up to ca. 7 times, thus raising the long-distance limit of 19F ENDOR almost 2-fold. We first demonstrate this on a model fluorine-containing Gd(III) complex with a well-resolved 19F spectrum in conventional central transition measurements and show quantitative agreement between the experimental spectra and theoretical predictions. We then validate our approach on two proteins labeled with 19F and Gd(III), in which the Gd-F distance is too long to produce a well-resolved 19F ENDOR doublet when measured at the central transition. By focusing on the |-5/2⟩ ↔ |-3/2⟩ and |-7/2⟩ ↔ |-5/2⟩ EPR transitions, a resolution enhancement of 4.5- and 7-fold was obtained, respectively. We also present data analysis strategies to handle contributions of different electron spin manifolds to the ENDOR spectrum. Our new extended 19F ENDOR approach may be applicable to Gd-F distances as large as 20 Å, widening the current ENDOR distance window.
Collapse
Affiliation(s)
- Alexey Bogdanov
- Department
of Chemical and Biological Physics, The
Weizmann Institute of Science, P.O. Box 26, Rehovot, 7610001, Israel
| | - Veronica Frydman
- Department
of Chemical Research Support, The Weizmann
Institute of Science, P.O. Box 26, Rehovot, 7610001, Israel
| | - Manas Seal
- Department
of Chemical and Biological Physics, The
Weizmann Institute of Science, P.O. Box 26, Rehovot, 7610001, Israel
| | - Leonid Rapatskiy
- Max
Planck Institute for Chemical Energy Conversion, 34-36 Stiftstraße, Mülheim an der Ruhr, 45470, Germany
| | - Alexander Schnegg
- Max
Planck Institute for Chemical Energy Conversion, 34-36 Stiftstraße, Mülheim an der Ruhr, 45470, Germany
| | - Wenkai Zhu
- Department
of Structural Biology, University of Pittsburgh, 4200 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Mark Iron
- Department
of Chemical Research Support, The Weizmann
Institute of Science, P.O. Box 26, Rehovot, 7610001, Israel
| | - Angela M. Gronenborn
- Department
of Structural Biology, University of Pittsburgh, 4200 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Daniella Goldfarb
- Department
of Chemical and Biological Physics, The
Weizmann Institute of Science, P.O. Box 26, Rehovot, 7610001, Israel
| |
Collapse
|
4
|
Grazia Concilio M, Frydman L. Steady state effects introduced by local relaxation modes on J-driven DNP-enhanced NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 355:107542. [PMID: 37672989 DOI: 10.1016/j.jmr.2023.107542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/03/2023] [Accepted: 08/26/2023] [Indexed: 09/08/2023]
Abstract
One of solution-state Nuclear Magnetic Resonance (NMR)'s main weaknesses, is its relative insensitivity. J-driven Dynamic Nuclear Polarization (JDNP) was recently proposed for enhancing solution-state NMR's sensitivity, by bypassing the limitations faced by conventional Overhauser DNP (ODNP), at the high magnetic fields where most analytical research is performed. By relying on biradicals with inter-electron exchange couplings Jex on the order of the electron Larmor frequency ωE, JDNP was predicted to introduce a transient enhancement in NMR's nuclear polarization at high magnetic fields, and for a wide range of rotational correlation times of medium-sized molecules in conventional solvents. This communication revisits the JDNP proposal, including additional effects and conditions that were not considered in the original treatment. These include relaxation mechanisms arising from local vibrational modes that often dominate electron relaxation in organic radicals, as well as the possibility of using biradicals with Jex of the order of the nuclear Larmor frequency ωN as potential polarizing agents. The presence of these new relaxation effects lead to variations in the JDNP polarization mechanism originally proposed, and indicate that triplet-to-singlet cross-relaxation processes may lead to a nuclear polarization enhancement that persists even at steady states. The physics and potential limitations of the ensuing theoretical derivations, are briefly discussed.
Collapse
Affiliation(s)
- Maria Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
5
|
Wiechers H, Kehl A, Hiller M, Eltzner B, Huckemann SF, Meyer A, Tkach I, Bennati M, Pokern Y. Bayesian optimization to estimate hyperfine couplings from 19F ENDOR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107491. [PMID: 37301045 DOI: 10.1016/j.jmr.2023.107491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
ENDOR spectroscopy is a fundamental method to detect nuclear spins in the vicinity of paramagnetic centers and their mutual hyperfine interaction. Recently, site-selective introduction of 19F as nuclear labels has been proposed as a tool for ENDOR-based distance determination in biomolecules, complementing pulsed dipolar spectroscopy in the range of angstrom to nanometer. Nevertheless, one main challenge of ENDOR still consists of its spectral analysis, which is aggravated by a large parameter space and broad resonances from hyperfine interactions. Additionally, at high EPR frequencies and fields (⩾94 GHz/3.4 Tesla), chemical shift anisotropy might contribute to broadening and asymmetry in the spectra. Here, we use two nitroxide-fluorine model systems to examine a statistical approach to finding the best parameter fit to experimental 263 GHz 19F ENDOR spectra. We propose Bayesian optimization for a rapid, global parameter search with little prior knowledge, followed by a refinement by more standard gradient-based fitting procedures. Indeed, the latter suffer from finding local rather than global minima of a suitably defined loss function. Using a new and accelerated simulation procedure, results for the semi-rigid nitroxide-fluorine two and three spin systems lead to physically reasonable solutions, if minima of similar loss can be distinguished by DFT predictions. The approach also delivers the stochastic error of the obtained parameter estimates. Future developments and perspectives are discussed.
Collapse
Affiliation(s)
- H Wiechers
- Felix-Bernstein-Institute for Mathematical Statistics in the Biosciences, Georgia-Augusta-University, Goldschmidtstr. 7, D-37077 Göttingen, Germany
| | - A Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - M Hiller
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - B Eltzner
- Research Group Computational Biomolecular Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - S F Huckemann
- Felix-Bernstein-Institute for Mathematical Statistics in the Biosciences, Georgia-Augusta-University, Goldschmidtstr. 7, D-37077 Göttingen, Germany
| | - A Meyer
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany; Institute of Physical Chemistry, Georgia-Augusta-University, Tammanstr. 6, D-37077 Göttingen, Germany
| | - I Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - M Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany; Institute of Physical Chemistry, Georgia-Augusta-University, Tammanstr. 6, D-37077 Göttingen, Germany.
| | - Y Pokern
- Department of Statistical Science, University College London, WC1E 6BT, United Kingdom.
| |
Collapse
|
6
|
Fu PX, Zhou S, Liu Z, Wu CH, Fang YH, Wu ZR, Tao XQ, Yuan JY, Wang YX, Gao S, Jiang SD. Multiprocessing Quantum Computing through Hyperfine Couplings in Endohedral Fullerene Derivatives. Angew Chem Int Ed Engl 2022; 61:e202212939. [PMID: 36310119 DOI: 10.1002/anie.202212939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 11/06/2022]
Abstract
Magnetic molecules have shown great potential in quantum information processing due to the chemical tunablity of their quantum behaviors. Chemical derivatives of endohedral nitrogen fullerenes with long coherence time and rich energy levels were synthesized and studied to demonstrate the ability of multiprocessing in quantum information using electron magnetic resonance. After initialization of the 12-levelled spin system, subgroups of spin energy levels coursed by the hyperfine couplings can be selectively manipulated. The cooperatively combining of the parallel calculations enabled quantum error correction, increasing the correct rate by up to 17.82 %. Also, different subgroups of transitions divided by hyperfine coupling can be treated as independent qubits, and multi-task quantum computing were realized by performing Z-gate and X-gate simultaneously, which accelerates the overall gating speed.
Collapse
Affiliation(s)
- Peng-Xiang Fu
- Beijing National Laboratory of Molecular Science, Beijing Key Laboratory of Magnetoelectric Materials and Devices, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shen Zhou
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China.,Institute for Quantum Information Science and technology, College of Science, National University of Defense Technology, Changsha, China
| | - Zheng Liu
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China
| | - Cong-Hui Wu
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China
| | - Yu-Hui Fang
- Beijing National Laboratory of Molecular Science, Beijing Key Laboratory of Magnetoelectric Materials and Devices, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Zhi-Rong Wu
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China
| | - Xing-Quan Tao
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China
| | - Jia-Yue Yuan
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China.,Institute for Quantum Information Science and technology, College of Science, National University of Defense Technology, Changsha, China
| | - Ye-Xin Wang
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China
| | - Song Gao
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China.,Beijing National Laboratory of Molecular Science, Beijing Key Laboratory of Magnetoelectric Materials and Devices, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shang-Da Jiang
- Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology, Guangzhou, China
| |
Collapse
|
7
|
Meyer A, Kehl A, Cui C, Reichardt FAK, Hecker F, Funk LM, Pan KT, Urlaub H, Tittmann K, Stubbe J, Bennati M. 19F Electron-Nuclear Double Resonance Reveals Interaction between Redox-Active Tyrosines across the α/β Interface of E. coli Ribonucleotide Reductase. J Am Chem Soc 2022; 144:11270-11282. [PMID: 35652913 PMCID: PMC9248007 DOI: 10.1021/jacs.2c02906] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Ribonucleotide reductases
(RNRs) catalyze the reduction of ribonucleotides
to deoxyribonucleotides, thereby playing a key role in DNA replication
and repair. Escherichia coli class
Ia RNR is an α2β2 enzyme complex
that uses a reversible multistep radical transfer (RT) over 32 Å
across its two subunits, α and β, to initiate, using its
metallo-cofactor in β2, nucleotide reduction in α2. Each step is proposed to involve a distinct proton-coupled
electron-transfer (PCET) process. An unresolved step is the RT involving
Y356(β) and Y731(α) across the α/β
interface. Using 2,3,5-F3Y122-β2 with 3,5-F2Y731-α2, GDP (substrate) and TTP (allosteric effector), a Y356• intermediate was trapped and its identity was
verified by 263 GHz electron paramagnetic resonance (EPR) and 34 GHz
pulse electron–electron double resonance spectroscopies. 94
GHz 19F electron-nuclear double resonance spectroscopy
allowed measuring the interspin distances between Y356• and the 19F nuclei of 3,5-F2Y731 in this RNR mutant. Similar experiments with the
double mutant E52Q/F3Y122-β2 were carried out for comparison to the recently published
cryo-EM structure of a holo RNR complex. For both mutant combinations,
the distance measurements reveal two conformations of 3,5-F2Y731. Remarkably, one conformation is consistent with
3,5-F2Y731 within the H-bond distance to Y356•, whereas the second one is consistent
with the conformation observed in the cryo-EM structure. The observations
unexpectedly suggest the possibility of a colinear PCET, in which
electron and proton are transferred from the same donor to the same
acceptor between Y356 and Y731. The results
highlight the important role of state-of-the-art EPR spectroscopy
to decipher this mechanism.
Collapse
Affiliation(s)
- Andreas Meyer
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Annemarie Kehl
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Chang Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Fehmke A K Reichardt
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Fabian Hecker
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Lisa-Marie Funk
- Department of structural dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Molecular Enzymology, Georg-August University, 37077 Göttingen, Germany
| | - Kuan-Ting Pan
- Research group bioanalytical mass spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Bioanalytics, University Medical Center, 37075 Göttingen, Germany
| | - Henning Urlaub
- Research group bioanalytical mass spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Bioanalytics, University Medical Center, 37075 Göttingen, Germany
| | - Kai Tittmann
- Department of structural dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Molecular Enzymology, Georg-August University, 37077 Göttingen, Germany
| | - JoAnne Stubbe
- Department of Chemistry and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States
| | - Marina Bennati
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Chemistry, Georg-August University, 37077 Göttingen, Germany
| |
Collapse
|
8
|
Asanbaeva N, Sukhanov A, Diveikina AA, Rogozhnikova O, Trukhin DV, Tormyshev VM, Chubarov AS, Maryasov AG, Genaev A, Shernyukov AV, Salnikov GE, Lomzov AA, Pyshnyi DV, Bagryanskaya E. Application of W-band 19F electron nuclear double resonance (ENDOR) spectroscopy to distance measurement using a trityl spin probe and a fluorine label. Phys Chem Chem Phys 2022; 24:5982-6001. [DOI: 10.1039/d1cp05445g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, Marina Bennati and coworkers (Angew. Chemie - Int. Ed., 2020, 59, 373–379., A. J. Magn. Reson., 2021, 333, 107091) proposed to use electron nuclear double resonance (ENDOR) spectroscopy in...
Collapse
|
9
|
Kehl A, Hiller M, Hecker F, Tkach I, Dechert S, Bennati M, Meyer A. Resolution of chemical shift anisotropy in 19F ENDOR spectroscopy at 263 GHz/9.4 T. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 333:107091. [PMID: 34749036 DOI: 10.1016/j.jmr.2021.107091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Pulsed 19F ENDOR spectroscopy provides a selective method for measuring angstrom to nanometer distances in structural biology. Here, the performance of 19F ENDOR at fields of 3.4 T and 9.4 T is compared using model compounds containing one to three 19F atoms. CF3 groups are included in two compounds, for which the possible occurrence of uniaxial rotation might affect the distance distribution. At 9.4 T, pronounced asymmetric features are observed in many of the presented 19F ENDOR spectra. Data analysis by spectral simulations shows that these features arise from the chemical shift anisotropy (CSA) of the 19F nuclei. This asymmetry is also observed at 3.4 T, albeit to a much smaller extent, confirming the physical origin of the effect. The CSA parameters are well consistent with DFT predicted values and can be extracted from simulation of the experimental data in favourable cases, thereby providing additional information about the geometrical and electronic structure of the spin system. The feasibility of resolving the CSA at 9.4 T provides important information for the interpretation of line broadening in ENDOR spectra also at lower fields, which is relevant for developing methods to extract distance distributions from 19F ENDOR spectra.
Collapse
Affiliation(s)
- Annemarie Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Markus Hiller
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Fabian Hecker
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Igor Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sebastian Dechert
- Department of Chemistry, Georg August University of Göttingen, Tammannstr. 4, Göttingen, Germany
| | - Marina Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Department of Chemistry, Georg August University of Göttingen, Tammannstr. 4, Göttingen, Germany.
| | - Andreas Meyer
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| |
Collapse
|
10
|
Meichsner SL, Kutin Y, Kasanmascheff M. In‐Cell Characterization of the Stable Tyrosyl Radical in
E. coli
Ribonucleotide Reductase Using Advanced EPR Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shari L. Meichsner
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Yury Kutin
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
| |
Collapse
|
11
|
Abstract
Electron-nuclear double resonance (ENDOR) measures the hyperfine interaction of magnetic nuclei with paramagnetic centers and is hence a powerful tool for spectroscopic investigations extending from biophysics to material science. Progress in microwave technology and the recent availability of commercial electron paramagnetic resonance (EPR) spectrometers up to an electron Larmor frequency of 263 GHz now open the opportunity for a more quantitative spectral analysis. Using representative spectra of a prototype amino acid radical in a biologically relevant enzyme, the [Formula: see text] in Escherichia coli ribonucleotide reductase, we developed a statistical model for ENDOR data and conducted statistical inference on the spectra including uncertainty estimation and hypothesis testing. Our approach in conjunction with 1H/2H isotopic labeling of [Formula: see text] in the protein unambiguously established new unexpected spectral contributions. Density functional theory (DFT) calculations and ENDOR spectral simulations indicated that these features result from the beta-methylene hyperfine coupling and are caused by a distribution of molecular conformations, likely important for the biological function of this essential radical. The results demonstrate that model-based statistical analysis in combination with state-of-the-art spectroscopy accesses information hitherto beyond standard approaches.
Collapse
|
12
|
Meichsner SL, Kutin Y, Kasanmascheff M. In-Cell Characterization of the Stable Tyrosyl Radical in E. coli Ribonucleotide Reductase Using Advanced EPR Spectroscopy. Angew Chem Int Ed Engl 2021; 60:19155-19161. [PMID: 33844392 PMCID: PMC8453577 DOI: 10.1002/anie.202102914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/11/2021] [Indexed: 12/21/2022]
Abstract
The E. coli ribonucleotide reductase (RNR), a paradigm for class Ia enzymes including human RNR, catalyzes the biosynthesis of DNA building blocks and requires a di‐iron tyrosyl radical (Y122.) cofactor for activity. The knowledge on the in vitro Y122. structure and its radical distribution within the β2 subunit has accumulated over the years; yet little information exists on the in vivo Y122.. Here, we characterize this essential radical in whole cells. Multi‐frequency EPR and electron‐nuclear double resonance (ENDOR) demonstrate that the structure and electrostatic environment of Y122. are identical under in vivo and in vitro conditions. Pulsed dipolar EPR experiments shed light on a distinct in vivo Y122. per β2 distribution, supporting the key role of Y. concentrations in regulating RNR activity. Additionally, we spectroscopically verify the generation of an unnatural amino acid radical, F3Y122., in whole cells, providing a crucial step towards unique insights into the RNR catalysis under physiological conditions.
Collapse
Affiliation(s)
- Shari L Meichsner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Yury Kutin
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| |
Collapse
|
13
|
Hecker F, Stubbe J, Bennati M. Detection of Water Molecules on the Radical Transfer Pathway of Ribonucleotide Reductase by 17O Electron-Nuclear Double Resonance Spectroscopy. J Am Chem Soc 2021; 143:7237-7241. [PMID: 33957040 PMCID: PMC8154519 DOI: 10.1021/jacs.1c01359] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 12/19/2022]
Abstract
The role of water in biological proton-coupled electron transfer (PCET) is emerging as a key for understanding mechanistic details at atomic resolution. Here we demonstrate 17O high-frequency electron-nuclear double resonance (ENDOR) in conjunction with H217O-labeled protein buffer to establish the presence of ordered water molecules at three radical intermediates in an active enzyme complex, the α2β2 E. coli ribonucleotide reductase. Our data give unambiguous evidence that all three, individually trapped, intermediates are hyperfine coupled to one water molecule with Tyr-O···17O distances in the range 2.8-3.1 Å. The availability of this structural information will allow for quantitative models of PCET in this prototype enzyme. The results also provide a spectroscopic signature for water H-bonded to a tyrosyl radical.
Collapse
Affiliation(s)
- Fabian Hecker
- Max
Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - JoAnne Stubbe
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 20139, United States
| | - Marina Bennati
- Max
Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Department
of Chemistry, Georg-August-University, 37077 Göttingen, Germany
| |
Collapse
|
14
|
Nys K, Furtmüller PG, Obinger C, Van Doorslaer S, Pfanzagl V. On the Track of Long-Range Electron Transfer in B-Type Dye-Decolorizing Peroxidases: Identification of a Tyrosyl Radical by Computational Prediction and Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2021; 60:1226-1241. [PMID: 33784066 PMCID: PMC8154254 DOI: 10.1021/acs.biochem.1c00129] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic activity of dye-decolorizing peroxidases (DyPs) toward bulky substrates, including anthraquinone dyes, phenolic lignin model compounds, or 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), is in strong contrast to their sterically restrictive active site. In two of the three known subfamilies (A- and C/D-type DyPs), catalytic protein radicals at surface-exposed sites, which are connected to the heme cofactor by electron transfer path(s), have been identified. So far in B-type DyPs, there has been no evidence for protein radical formation after activation by hydrogen peroxide. Interestingly, B-type Klebsiella pneumoniae dye-decolorizing peroxidase (KpDyP) displays a persistent organic radical in the resting state composed of two species that can be distinguished by W-band electron spin echo electron paramagnetic resonance (EPR) spectroscopy. Here, on the basis of a comprehensive mutational and EPR study of computationally predicted tyrosine and tryptophan variants of KpDyP, we demonstrate the formation of tyrosyl radicals (Y247 and Y92) and a radical-stabilizing Y-W dyad between Y247 and W18 in KpDyP, which are unique to enterobacterial B-type DyPs. Y247 is connected to Y92 by a hydrogen bonding network, is solvent accessible in simulations, and is involved in ABTS oxidation. This suggests the existence of long-range electron path(s) in B-type DyPs. The mechanistic and physiological relevance of the reaction mechanism of B-type DyPs is discussed.
Collapse
Affiliation(s)
- Kevin Nys
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Paul Georg Furtmüller
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Vera Pfanzagl
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| |
Collapse
|
15
|
Meyer A, Dechert S, Dey S, Höbartner C, Bennati M. Measurement of Angstrom to Nanometer Molecular Distances with
19
F Nuclear Spins by EPR/ENDOR Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201908584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Andreas Meyer
- Research Group EPR Spectroscopy Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
| | - Sebastian Dechert
- Department of Chemistry Georg-August-University Tammannstr 37077 Göttingen Germany
| | - Surjendu Dey
- Institute of Organic Chemistry Julius-Maximilians-University Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry Julius-Maximilians-University Würzburg Am Hubland 97074 Würzburg Germany
| | - Marina Bennati
- Research Group EPR Spectroscopy Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Department of Chemistry Georg-August-University Tammannstr 37077 Göttingen Germany
| |
Collapse
|
16
|
Meyer A, Dechert S, Dey S, Höbartner C, Bennati M. Measurement of Angstrom to Nanometer Molecular Distances with 19 F Nuclear Spins by EPR/ENDOR Spectroscopy. Angew Chem Int Ed Engl 2020; 59:373-379. [PMID: 31539187 PMCID: PMC6973229 DOI: 10.1002/anie.201908584] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/02/2019] [Indexed: 12/22/2022]
Abstract
Spectroscopic and biophysical methods for structural determination at atomic resolution are fundamental in studies of biological function. Here we introduce an approach to measure molecular distances in bio-macromolecules using 19 F nuclear spins and nitroxide radicals in combination with high-frequency (94 GHz/3.4 T) electron-nuclear double resonance (ENDOR). The small size and large gyromagnetic ratio of the 19 F label enables to access distances up to about 1.5 nm with an accuracy of 0.1-1 Å. The experiment is not limited by the size of the bio-macromolecule. Performance is illustrated on synthesized fluorinated model compounds as well as spin-labelled RNA duplexes. The results demonstrate that our simple but strategic spin-labelling procedure combined with state-of-the-art spectroscopy accesses a distance range crucial to elucidate active sites of nucleic acids or proteins in the solution state.
Collapse
Affiliation(s)
- Andreas Meyer
- Research Group EPR SpectroscopyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Sebastian Dechert
- Department of ChemistryGeorg-August-UniversityTammannstr37077GöttingenGermany
| | - Surjendu Dey
- Institute of Organic ChemistryJulius-Maximilians-University WürzburgAm Hubland97074WürzburgGermany
| | - Claudia Höbartner
- Institute of Organic ChemistryJulius-Maximilians-University WürzburgAm Hubland97074WürzburgGermany
| | - Marina Bennati
- Research Group EPR SpectroscopyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
- Department of ChemistryGeorg-August-UniversityTammannstr37077GöttingenGermany
| |
Collapse
|