1
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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. J Magn Reson 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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2
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Cui C, Song DY, Drennan CL, Stubbe J, Nocera DG. Radical Transport Facilitated by a Proton Transfer Network at the Subunit Interface of Ribonucleotide Reductase. J Am Chem Soc 2023; 145:5145-5154. [PMID: 36812162 PMCID: PMC10561588 DOI: 10.1021/jacs.2c11483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Ribonucleotide reductases (RNRs) play an essential role in the conversion of nucleotides to deoxynucleotides in all organisms. The Escherichia coli class Ia RNR requires two homodimeric subunits, α and β. The active form is an asymmetric αα'ββ' complex. The α subunit houses the site for nucleotide reduction initiated by a thiyl radical (C439•), and the β subunit houses the diferric-tyrosyl radical (Y122•) that is essential for C439• formation. The reactions require a highly regulated and reversible long-range proton-coupled electron transfer pathway involving Y122•[β] ↔ W48?[β] ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]. In a recent cryo-EM structure, Y356[β] was revealed for the first time and it, along with Y731[α], spans the asymmetric α/β interface. An E52[β] residue, which is essential for Y356 oxidation, allows access to the interface and resides at the head of a polar region comprising R331[α], E326[α], and E326[α'] residues. Mutagenesis studies with canonical and unnatural amino acid substitutions now suggest that these ionizable residues are important in enzyme activity. To gain further insights into the roles of these residues, Y356• was photochemically generated using a photosensitizer covalently attached adjacent to Y356[β]. Mutagenesis studies, transient absorption spectroscopy, and photochemical assays monitoring deoxynucleotide formation collectively indicate that the E52[β], R331[α], E326[α], and E326[α'] network plays the essential role of shuttling protons associated with Y356 oxidation from the interface to bulk solvent.
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Affiliation(s)
- Chang Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - David Y. Song
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Catherine L. Drennan
- Department of Chemistr, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - JoAnne Stubbe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Chemistr, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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3
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Zhong J, Reinhardt CR, Hammes-Schiffer S. Direct Proton-Coupled Electron Transfer between Interfacial Tyrosines in Ribonucleotide Reductase. J Am Chem Soc 2023; 145:4784-4790. [PMID: 36802630 PMCID: PMC10344599 DOI: 10.1021/jacs.2c13615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Ribonucleotide reductase (RNR) regulates DNA synthesis and repair in all organisms. The mechanism of Escherichia coli RNR requires radical transfer over a proton-coupled electron transfer (PCET) pathway spanning ∼32 Å across two protein subunits. A key step along this pathway is the interfacial PCET reaction between Y356 in the β subunit and Y731 in the α subunit. Herein, this PCET reaction between two tyrosines across an aqueous interface is explored with classical molecular dynamics and quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The simulations suggest that the water-mediated mechanism involving double proton transfer through an intervening water molecule is thermodynamically and kinetically unfavorable. The direct PCET mechanism between Y356 and Y731 becomes feasible when Y731 is flipped toward the interface and is predicted to be approximately isoergic with a relatively low free energy barrier. This direct mechanism is facilitated by the hydrogen bonding of water to both Y356 and Y731. These simulations provide fundamental insights into radical transfer across aqueous interfaces.
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Affiliation(s)
- Jiayun Zhong
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Clorice R. Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
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4
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Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA Advances 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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5
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Reinhardt CR, Konstantinovsky D, Soudackov AV, Hammes-Schiffer S. Kinetic model for reversible radical transfer in ribonucleotide reductase. Proc Natl Acad Sci U S A 2022; 119:e2202022119. [PMID: 35714287 DOI: 10.1073/pnas.2202022119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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7
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Zhong J, Reinhardt CR, Hammes-Schiffer S. Role of Water in Proton-Coupled Electron Transfer between Tyrosine and Cysteine in Ribonucleotide Reductase. J Am Chem Soc 2022; 144:7208-7214. [PMID: 35426309 PMCID: PMC9197590 DOI: 10.1021/jacs.1c13455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides and is critical for DNA synthesis and repair in all organisms. Its mechanism requires radical transfer along a ∼32 Å pathway through a series of proton-coupled electron transfer (PCET) steps. Previous simulations suggested that a glutamate residue (E623) mediates the PCET reaction between two stacked tyrosine residues (Y730 and Y731) through a proton relay mechanism. This work focuses on the adjacent PCET reaction between Y730 and a cysteine residue (C439). Quantum mechanical/molecular mechanical free energy simulations illustrate that when Y730 and Y731 are stacked, E623 stabilizes the radical on C439 through hydrogen bonding with the Y730 hydroxyl group. When Y731 is flipped away from Y730, a water molecule stabilizes the radical on C439 through hydrogen bonding with Y730 and lowers the free energy barrier for radical transfer from Y730 to C439 through electrostatic interactions with the transferring hydrogen but does not directly accept the proton. These simulations indicate that the conformational motions and electrostatic interactions of the tyrosines, cysteine, glutamate, and water strongly impact the thermodynamics and kinetics of these two coupled PCET reactions. Such insights are important for protein engineering efforts aimed at altering radical transfer in RNR.
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Affiliation(s)
- Jiayun Zhong
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Clorice R. Reinhardt
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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8
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Banerjee R, Srinivas V, Lebrette H. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Subcell Biochem 2022; 99:109-153. [PMID: 36151375 DOI: 10.1007/978-3-031-00793-4_4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France.
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9
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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] [What about the content of this article? (0)] [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...
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10
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Lee C, Ha SC, Rao Z, Hwang Y, Kim DS, Kim SY, Yoo H, Yoon C, Na JG, Park JH, Lee SJ. Elucidation of the electron transfer environment in the MMOR FAD-binding domain from Methylosinus sporium 5. Dalton Trans 2021; 50:16493-16498. [PMID: 34734616 DOI: 10.1039/d1dt03273a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
By facilitating electron transfer to the hydroxylase diiron center, MMOR-a reductase-serves as an essential component of the catalytic cycle of soluble methane monooxygenase. Here, the X-ray structure analysis of the FAD-binding domain of MMOR identified crucial residues and its influence on the catalytic cycle.
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Affiliation(s)
- Chaemin Lee
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
| | - Sung Chul Ha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Zhili Rao
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea.
| | - Yunha Hwang
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
| | - Da Som Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea.
| | - So Young Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea.
| | - Heeseon Yoo
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
| | - Chungwoon Yoon
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Republic of Korea.
| | - Jung Hee Park
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea. .,Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Seung Jae Lee
- Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54796, Republic of Korea.
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Abstract
Radicals in biology, once thought to all be bad actors, are now known to play a central role in many enzymatic reactions. Of the known radical-based enzymes, ribonucleotide reductases (RNRs) are pre-eminent as they are essential in the biology of all organisms by providing the building blocks and controlling the fidelity of DNA replication and repair. Intense examination of RNRs has led to the development of new tools and a guiding framework for the study of radicals in biology, pointing the way to future frontiers in radical enzymology.
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Affiliation(s)
- JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 20139 USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 20139 USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138 USA
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138 USA
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
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13
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Pokern Y, Eltzner B, Huckemann SF, Beeken C, Stubbe J, Tkach I, Bennati M, Hiller M. Statistical analysis of ENDOR spectra. Proc Natl Acad Sci U S A 2021; 118:e2023615118. [PMID: 34215694 DOI: 10.1073/pnas.2023615118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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.
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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16
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Caldas Nogueira ML, Pastore AJ, Davidson VL. Diversity of structures and functions of oxo-bridged non-heme diiron proteins. Arch Biochem Biophys 2021; 705:108917. [PMID: 33991497 DOI: 10.1016/j.abb.2021.108917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023]
Abstract
Oxo-bridged diiron proteins are a distinct class of non-heme iron proteins. Their active sites are composed of two irons that are coordinated by amino acid side chains, and a bridging oxygen that interacts with each iron. These proteins are members of the ferritin superfamily and share the structural feature of a four α-helix bundle that provides the residues that coordinate the irons. The different proteins also display a wide range of structures and functions. A prototype of this family is hemerythrin, which functions as an oxygen transporter. Several other hemerythrin-like proteins have been described with a diversity of functions including oxygen and iron sensing, and catalytic activities. Rubrerythrins react with hydrogen peroxide and rubrerythrin-like proteins possess a rubredoxin domain, in addition to the oxo-bridged diiron center. Other redox enzymes with oxo-bridged irons include flavodiiron proteins that act as O2 or NO reductases, ribonucleotide reductase and methane monooxygenase. Ferritins have an oxo-bridged diiron in the ferroxidase center of the protein, which plays a role in the iron storage function of these proteins. There are also bacterial ferritins that exhibit catalytic activities. The structures and functions of this broad class of oxo-bridged diiron proteins are described and compared in this review.
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Affiliation(s)
- Maria Luiza Caldas Nogueira
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Anthony J Pastore
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States.
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17
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Reinhardt CR, Sayfutyarova ER, Zhong J, Hammes-Schiffer S. Glutamate Mediates Proton-Coupled Electron Transfer Between Tyrosines 730 and 731 in Escherichia coli Ribonucleotide Reductase. J Am Chem Soc 2021; 143:6054-6059. [DOI: 10.1021/jacs.1c02152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Clorice R. Reinhardt
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Elvira R. Sayfutyarova
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Jiayun Zhong
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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18
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Abstract
The hyperfine coupling between an electron spin and a nuclear spin depends on the Fermi contact coupling aiso and, through dipolar coupling, the distance r between the electron and the nucleus. It is measured with electron-nuclear double resonance (ENDOR) spectroscopy and provides insight into the electronic and spatial structure of paramagnetic centers. The analysis and interpretation of ENDOR spectra is commonly done by ordinary least-squares fitting. As this is an ill-posed, inverse mathematical problem, this is challenging, in particular for spectra that show features from several nuclei or where the hyperfine coupling parameters are distributed. We introduce a novel Tikhonov-type regularization approach that analyzes an experimental ENDOR spectrum in terms of a complete non-parametric distribution over r and aiso. The approach uses a penalty function similar to the cross entropy between the fitted distribution and a Bayesian prior distribution that is derived from density functional theory calculations. Additionally, we show that smoothness regularization, commonly used for a similar purpose in double electron-electron resonance (DEER) spectroscopy, is not suited for ENDOR. We demonstrate that the novel approach is able to identify and quantitate ligand protons with electron-nucleus distances between 4 and 9 Å in a series of vanadyl porphyrin compounds.
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Affiliation(s)
- Stephan Pribitzer
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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19
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Cui C, Greene BL, Kang G, Drennan CL, Stubbe J, Nocera DG. Gated Proton Release during Radical Transfer at the Subunit Interface of Ribonucleotide Reductase. J Am Chem Soc 2020; 143:176-183. [PMID: 33353307 DOI: 10.1021/jacs.0c07879] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The class Ia ribonucleotide reductase of Escherichia coli requires strict regulation of long-range radical transfer between two subunits, α and β, through a series of redox-active amino acids (Y122•[β] ↔ W48?[β] ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]). Nowhere is this more precarious than at the subunit interface. Here, we show that the oxidation of Y356 is regulated by proton release involving a specific residue, E52[β], which is part of a water channel at the subunit interface for rapid proton transfer to the bulk solvent. An E52Q variant is incapable of Y356 oxidation via the native radical transfer pathway or non-native photochemical oxidation, following photosensitization by covalent attachment of a photo-oxidant at position 355[β]. Substitution of Y356 for various FnY analogues in an E52Q-photoβ2, where the side chain remains deprotonated, recovered photochemical enzymatic turnover. Transient absorption and emission data support the conclusion that Y356 oxidation requires E52 for proton management, suggesting its essential role in gating radical transport across the protein-protein interface.
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Affiliation(s)
- Chang Cui
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Brandon L Greene
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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20
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Kang G, Taguchi AT, Stubbe J, Drennan CL. Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex. Science 2020; 368:424-427. [PMID: 32217749 DOI: 10.1126/science.aba6794] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/16/2020] [Indexed: 12/27/2022]
Abstract
Ribonucleotide reductases (RNRs) are a diverse family of enzymes that are alone capable of generating 2'-deoxynucleotides de novo and are thus critical in DNA biosynthesis and repair. The nucleotide reduction reaction in all RNRs requires the generation of a transient active site thiyl radical, and in class I RNRs, this process involves a long-range radical transfer between two subunits, α and β. Because of the transient subunit association, an atomic resolution structure of an active α2β2 RNR complex has been elusive. We used a doubly substituted β2, E52Q/(2,3,5)-trifluorotyrosine122-β2, to trap wild-type α2 in a long-lived α2β2 complex. We report the structure of this complex by means of cryo-electron microscopy to 3.6-angstrom resolution, allowing for structural visualization of a 32-angstrom-long radical transfer pathway that affords RNR activity.
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Affiliation(s)
- Gyunghoon Kang
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge MA, USA
| | - Alexander T Taguchi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA, USA
| | - JoAnne Stubbe
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA, USA. .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA, USA
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge MA, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA, USA
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
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22
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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] [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: 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.
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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
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23
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Abstract
Ribonucleotide reductases (RNRs) employ a complex radical-based mechanism during nucleotide reduction involving multiple active site cysteines that both activate the substrate and reduce it. Using an engineered allo-tRNA, we substituted two active site cysteines with distinct function in the class Ia RNR of Escherichia coli for selenocysteine (U) via amber codon suppression, with efficiency and selectivity enabling biochemical and biophysical studies. Examination of the interactions of the C439U α2 mutant protein with nucleotide substrates and the cognate β2 subunit demonstrates that the endogenous Y122• of β2 is reduced under turnover conditions, presumably through radical transfer to form a transient U439• species. This putative U439• species is formed in a kinetically competent fashion but is incapable of initiating nucleotide reduction via 3'-H abstraction. An analogous C225U α2 protein is also capable of radical transfer from Y122•, but the radical-based substrate chemistry partitions between turnover and stalled reduction akin to the reactivity of mechanism-based inhibitors of RNR. The results collectively demonstrate the essential role of cysteine redox chemistry in the class I RNRs and establish a new tool for investigating thiyl radical reactivity in biology.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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24
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Abstract
Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase, and many other proteins. However, Tyr and Trp are not functionally interchangeable, and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191•+ radical to oxidize reduced cytochrome c (Cc). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc. Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191• (via Leu232His or Glu) substantially alters activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191• by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191• formal potential of ∼200 mV in the presence of E232. Hence, Y191 inactivity results from a potential drop owing to Y191•+ deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr• potential into a range where it can effectively oxidize Cc. These findings have implications for the YZ/YD radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.
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Affiliation(s)
- Estella F Yee
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States.,National Biomedical Center for Advanced ESR Technologies (ACERT) , Cornell University , Ithaca , New York 14850 , United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
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25
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Li H, Wang Z, Jiang J, Luo Y. Competition between dispersion interactions and conventional hydrogen bonding: insights from a theoretical study on Z-Arg-OH. Phys Chem Chem Phys 2019; 21:17893-17900. [PMID: 31380529 DOI: 10.1039/c9cp03130h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dispersion interaction was reported to play a critical role in the stabilization of model dipeptide Z-Arg-OH, even greater than the conventional hydrogen bond (HB), which is opposite to the traditional opinion. Here the conformation of Z-Arg-OH has been systematically searched by the effective fragment based step-by-step strategy. All the newly-found low-energy conformers determined at the advanced DSD-PBEP86-D3(BJ)/aug-cc-pVTZ level are clearly in the stretched form with strong conventional HBs, rather than the reported folded structures with emphasis on the dispersion interactions. The simulated IR spectra of the stretched conformers fit better than those of the folded ones compared with the previous experimental observations. Near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges have also been simulated to unambiguously identify different isomers. This work thus provides valuable insight into the competitions between the conventional HB and the dispersion interactions and demonstrates that the conventional hydrogen bonding is still more important for such small peptides.
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Affiliation(s)
- Hongbao Li
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui University, Hefei, Anhui 230601, China
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26
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Tkach I, Bejenke I, Hecker F, Kehl A, Kasanmascheff M, Gromov I, Prisecaru I, Höfer P, Hiller M, Bennati M. 1H high field electron-nuclear double resonance spectroscopy at 263 GHz/9.4 T. J Magn Reson 2019; 303:17-27. [PMID: 30991287 DOI: 10.1016/j.jmr.2019.04.001] [Citation(s) in RCA: 10] [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: 12/03/2018] [Revised: 03/18/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
We present and discuss the performance of 1H electron-nuclear double resonance (ENDOR) at 263 GHz/9.4 T by employing a prototype, commercial quasi optical spectrometer. Basic instrumental features of the setup are described alongside a comprehensive characterization of the new ENDOR probe head design. The performance of three different ENDOR pulse sequences (Davies, Mims and CP-ENDOR) is evaluated using the 1H BDPA radical. A key feature of 263 GHz spectroscopy - the increase in orientation selectivity in comparison with 94 GHz experiments - is discussed in detail. For this purpose, the resolution of 1H ENDOR spectra at 263 GHz is verified using a representative protein sample containing approximately 15 picomoles of a tyrosyl radical. Davies ENDOR spectra recorded at 5 K reveal previously obscured spectral features, which are interpreted by spectral simulations aided by DFT calculations. Our analysis shows that seven internal proton couplings are detectable for this specific radical if sufficient orientation selectivity is achieved. The results prove the fidelity of 263 GHz experiments in reporting orientation-selected 1H ENDOR spectra and demonstrate that new significant information can be uncovered in complex molecular systems, owing to the enhanced resolution combined with high absolute sensitivity and no compromise in acquisition time.
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Affiliation(s)
- Igor Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Isabel Bejenke
- 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
| | - Annemarie Kehl
- 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. 2, Göttingen, Germany
| | - Müge Kasanmascheff
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Igor Gromov
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Ion Prisecaru
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Peter Höfer
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Markus Hiller
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 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. 2, Göttingen, Germany.
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27
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Hetzke T, Bowen AM, Vogel M, Gauger M, Suess B, Prisner TF. Binding of tetracycline to its aptamer determined by 2D-correlated Mn 2+ hyperfine spectroscopy. J Magn Reson 2019; 303:105-114. [PMID: 31039520 DOI: 10.1016/j.jmr.2019.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/13/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
The tetracycline-binding RNA aptamer (TC-aptamer) binds its cognate ligand the antibiotic tetracycline (TC) via a Mg2+ or Mn2+ ion with high affinity at high divalent metal ion concentrations (KD=800pM, ⩾10 mM). These concentrations lie above the physiological divalent metal ion concentration of ca. 1 mM and it is known from literature, that the binding affinity decreases upon decreasing the divalent metal ion concentration. This work uses a Mn2+ concentration of 1 mM and 1D-hyperfine experiments reveal two pronounced 31P couplings from the RNA besides the 13C signal of 13C-labeled TC. From these 1D-hyperfine data alone, however, no conclusions can be drawn on the binding of TC. Either TC may bind via Mn2+ to the aptamer or TC may form a free Mn-TC complex and some Mn2+ also binds to the aptamer. In this work, we show using 2D-correlated hyperfine spectroscopy at Q-band frequencies (34 GHz), that the 13C and 31P signals can be correlated; thus arising from a single species. We use THYCOS (triple hyperfine correlation spectroscopy) and 2D ELDOR-detected NMR (2D electron electron double resonance detected NMR) for this purpose showing that they are suitable techniques to correlate two different nuclear spin species (13C and 31P) on two different molecules (RNA and TC) to the same electron spin (Mn2+). Out of the two observed 31P-hyperfine couplings, only one shows a clear correlation to 13C. Although THYCOS and 2D EDNMR yield identical results, 2D EDNMR is far more sensitive. THYCOS spectra needed a time factor of ×20 in comparison to 2D EDNMR to achieve a comparable signal-to-noise.
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Affiliation(s)
- Thilo Hetzke
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alice M Bowen
- Center for Advanced Electron Spin Resonance (CAESR), Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Maximilian Gauger
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany.
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28
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Sirohiwal A, Neese F, Pantazis DA. Microsolvation of the Redox-Active Tyrosine-D in Photosystem II: Correlation of Energetics with EPR Spectroscopy and Oxidation-Induced Proton Transfer. J Am Chem Soc 2019; 141:3217-3231. [PMID: 30666866 PMCID: PMC6728127 DOI: 10.1021/jacs.8b13123] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Photosystem
II (PSII) of oxygenic photosynthesis captures sunlight
to drive the catalytic oxidation of water and the reduction of plastoquinone.
Among the several redox-active cofactors that participate in intricate
electron transfer pathways there are two tyrosine residues, YZ and YD. They are situated in symmetry-related
electron transfer branches but have different environments and play
distinct roles. YZ is the immediate oxidant of the oxygen-evolving
Mn4CaO5 cluster, whereas YD serves
regulatory and protective functions. The protonation states and hydrogen-bond
network in the environment of YD remain debated, while
the role of microsolvation in stabilizing different redox states of
YD and facilitating oxidation or mediating deprotonation,
as well the fate of the phenolic proton, is unclear. Here we present
detailed structural models of YD and its environment using
large-scale quantum mechanical models and all-atom molecular dynamics
of a complete PSII monomer. The energetics of water distribution within
a hydrophobic cavity adjacent to YD are shown to correlate
directly with electron paramagnetic resonance (EPR) parameters such
as the tyrosyl g-tensor, allowing us to map the correspondence
between specific structural models and available experimental observations.
EPR spectra obtained under different conditions are explained with
respect to the mode of interaction of the proximal water with the
tyrosyl radical and the position of the phenolic proton within the
cavity. Our results revise previous models of the energetics and build
a detailed view of the role of confined water in the oxidation and
deprotonation of YD. Finally, the model of microsolvation
developed in the present work rationalizes in a straightforward way
the biphasic oxidation kinetics of YD, offering new structural
insights regarding the function of the radical in biological photosynthesis.
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Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany.,Fakultät für Chemie und Biochemie , Ruhr-Universität Bochum , 44780 Bochum , Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
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29
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Abstract
Class Ia ribonucleotide reductase (RNR) of Escherichia coli contains an unusually stable tyrosyl radical cofactor in the β2 subunit (Y122•) necessary for nucleotide reductase activity. Upon binding the cognate α2 subunit, loaded with nucleoside diphosphate substrate and an allosteric/activity effector, a rate determining conformational change(s) enables rapid radical transfer (RT) within the active α2β2 complex from the Y122• site in β2 to the substrate activating cysteine residue (C439) in α2 via a pathway of redox active amino acids (Y122[β] ↔ W48[β]? ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]) spanning >35 Å. Ionizable residues at the α2β2 interface are essential in mediating RT, and therefore control activity. One of these mutations, E350X (where X = A, D, Q) in β2, obviates all RT, though the mechanism of control by which E350 mediates RT remains unclear. Herein, we utilize an E350Q-photoβ2 construct to photochemically rescue RNR activity from an otherwise inactive construct, wherein the initial RT event (Y122• → Y356) is replaced by direct photochemical radical generation of Y356•. These data present compelling evidence that E350 conveys allosteric information between the α2 and β2 subunits facilitating conformational gating of RT that specifically targets Y122• reduction, while the fidelity of the remainder of the RT pathway is retained.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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30
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Rahmani A, Zabardasti A, Kakanejadifard A. Intermolecular complexes of [B6H6]2− with nH2 (n = 1-8) molecules: a theoretical study. Struct Chem 2019; 30:669-80. [DOI: 10.1007/s11224-018-1208-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Lee W, Kasanmascheff M, Huynh M, Quartararo A, Costentin C, Bejenke I, Nocera DG, Bennati M, Tommos C, Stubbe J. Properties of Site-Specifically Incorporated 3-Aminotyrosine in Proteins To Study Redox-Active Tyrosines: Escherichia coli Ribonucleotide Reductase as a Paradigm. Biochemistry 2018; 57:3402-3415. [PMID: 29630358 DOI: 10.1021/acs.biochem.8b00160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3-Aminotyrosine (NH2Y) has been a useful probe to study the role of redox active tyrosines in enzymes. This report describes properties of NH2Y of key importance for its application in mechanistic studies. By combining the tRNA/NH2Y-RS suppression technology with a model protein tailored for amino acid redox studies (α3X, X = NH2Y), the formal reduction potential of NH2Y32(O•/OH) ( E°' = 395 ± 7 mV at pH 7.08 ± 0.05) could be determined using protein film voltammetry. We find that the Δ E°' between NH2Y32(O•/OH) and Y32(O•/OH) when measured under reversible conditions is ∼300-400 mV larger than earlier estimates based on irreversible voltammograms obtained on aqueous NH2Y and Y. We have also generated D6-NH2Y731-α2 of ribonucleotide reductase (RNR), which when incubated with β2/CDP/ATP generates the D6-NH2Y731•-α2/β2 complex. By multifrequency electron paramagnetic resonance (35, 94, and 263 GHz) and 34 GHz 1H ENDOR spectroscopies, we determined the hyperfine coupling (hfc) constants of the amino protons that establish RNH2• planarity and thus minimal perturbation of the reduction potential by the protein environment. The amount of Y in the isolated NH2Y-RNR incorporated by infidelity of the tRNA/NH2Y-RS pair was determined by a generally useful LC-MS method. This information is essential to the utility of this NH2Y probe to study any protein of interest and is employed to address our previously reported activity associated with NH2Y-substituted RNRs.
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Affiliation(s)
| | - Müge Kasanmascheff
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 Germany
| | - Michael Huynh
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 United States
| | | | - Cyrille Costentin
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 United States.,Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université - CNRS No 7591 , Université Paris Diderot, Sorbonne Paris Cité , Bâtiment Lavoisier, 15 rue Jean de Baïf , 75205 Paris Cedex 13 , France
| | - Isabel Bejenke
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 Germany
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 United States
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 Germany
| | - Cecilia Tommos
- Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania 19104 , United States
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32
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Ayyadevara S, Balasubramaniam M, Kakraba S, Alla R, Mehta JL, Shmookler Reis RJ. Aspirin-Mediated Acetylation Protects Against Multiple Neurodegenerative Pathologies by Impeding Protein Aggregation. Antioxid Redox Signal 2017; 27:1383-1396. [PMID: 28537433 PMCID: PMC5661865 DOI: 10.1089/ars.2016.6978] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AIMS Many progressive neurological disorders, including Alzheimer's disease (AD), Huntington's disease, and Parkinson's disease (PD), are characterized by accumulation of insoluble protein aggregates. In prospective trials, the cyclooxygenase inhibitor aspirin (acetylsalicylic acid) reduced the risk of AD and PD, as well as cardiovascular events and many late-onset cancers. Considering the role played by protein hyperphosphorylation in aggregation and neurodegenerative diseases, and aspirin's known ability to donate acetyl groups, we asked whether aspirin might reduce both phosphorylation and aggregation by acetylating protein targets. RESULTS Aspirin was substantially more effective than salicylate in reducing or delaying aggregation in human neuroblastoma cells grown in vitro, and in Caenorhabditis elegans models of human neurodegenerative diseases in vivo. Aspirin acetylates many proteins, while reducing phosphorylation, suggesting that acetylation may oppose phosphorylation. Surprisingly, acetylated proteins were largely excluded from compact aggregates. Molecular-dynamic simulations indicate that acetylation of amyloid peptide energetically disfavors its association into dimers and octamers, and oligomers that do form are less compact and stable than those comprising unacetylated peptides. INNOVATION Hyperphosphorylation predisposes certain proteins to aggregate (e.g., tau, α-synuclein, and transactive response DNA-binding protein 43 [TDP-43]), and it is a critical pathogenic marker in both cardiovascular and neurodegenerative diseases. We present novel evidence that acetylated proteins are underrepresented in protein aggregates, and that aggregation varies inversely with acetylation propensity after diverse genetic and pharmacologic interventions. CONCLUSIONS These results are consistent with the hypothesis that aspirin inhibits protein aggregation and the ensuing toxicity of aggregates through its acetyl-donating activity. This mechanism may contribute to the neuro-protective, cardio-protective, and life-prolonging effects of aspirin. Antioxid. Redox Signal. 27, 1383-1396.
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Affiliation(s)
- Srinivas Ayyadevara
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,2 Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Meenakshisundaram Balasubramaniam
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,2 Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Samuel Kakraba
- 3 Bioinformatics Program, University of Arkansas for Medical Sciences, and University of Arkansas at Little Rock , Little Rock, Arkansas
| | - Ramani Alla
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,2 Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Jawahar L Mehta
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,4 Divison of Cardiology, Department of Medicine, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Robert J Shmookler Reis
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,2 Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences , Little Rock, Arkansas.,3 Bioinformatics Program, University of Arkansas for Medical Sciences, and University of Arkansas at Little Rock , Little Rock, Arkansas
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33
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Greene BL, Taguchi AT, Stubbe J, Nocera DG. Conformationally Dynamic Radical Transfer within Ribonucleotide Reductase. J Am Chem Soc 2017; 139:16657-16665. [PMID: 29037038 DOI: 10.1021/jacs.7b08192] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNR) catalyze the reduction of nucleotides to deoxynucleotides through a mechanism involving an essential cysteine based thiyl radical. In the E. coli class 1a RNR the thiyl radical (C439•) is a transient species generated by radical transfer (RT) from a stable diferric-tyrosyl radical cofactor located >35 Å away across the α2:β2 subunit interface. RT is facilitated by sequential proton-coupled electron transfer (PCET) steps along a pathway of redox active amino acids (Y122β ↔ [W48β?] ↔ Y356β ↔ Y731α ↔ Y730α ↔ C439α). The mutant R411A(α) disrupts the H-bonding environment and conformation of Y731, ostensibly breaking the RT pathway in α2. However, the R411A protein retains significant enzymatic activity, suggesting Y731 is conformationally dynamic on the time scale of turnover. Installation of the radical trap 3-amino tyrosine (NH2Y) by amber codon suppression at positions Y731 or Y730 and investigation of the NH2Y• trapped state in the active α2:β2 complex by HYSCORE spectroscopy validate that the perturbed conformation of Y731 in R411A-α2 is dynamic, reforming the H-bond between Y731 and Y730 to allow RT to propagate to Y730. Kinetic studies facilitated by photochemical radical generation reveal that Y731 changes conformation on the ns-μs time scale, significantly faster than the enzymatic kcat. Furthermore, the kinetics of RT across the subunit interface were directly assessed for the first time, demonstrating conformationally dependent RT rates that increase from 0.6 to 1.6 × 104 s-1 when comparing wild type to R411A-α2, respectively. These results illustrate the role of conformational flexibility in modulating RT kinetics by targeting the PCET pathway of radical transport.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Alexander T Taguchi
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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34
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Taguchi AT, O’Malley PJ, Wraight CA, Dikanov SA. Determination of the Complete Spin Density Distribution in 13C-Labeled Protein-Bound Radical Intermediates Using Advanced 2D Electron Paramagnetic Resonance Spectroscopy and Density Functional Theory. J Phys Chem B 2017; 121:10256-10268. [DOI: 10.1021/acs.jpcb.7b10036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander T. Taguchi
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Veterinary Clinical Medicine, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | - Colin A. Wraight
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sergei A. Dikanov
- Department
of Veterinary Clinical Medicine, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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35
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Affiliation(s)
- Frank Neese
- Max Planck Institute for Chemical Energy Conversion; Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
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36
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Affiliation(s)
- Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion; Stiftstraße 34-36 45470 Mülheim an der Ruhr Deutschland
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37
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Nick TU, Ravichandran KR, Stubbe J, Kasanmascheff M, Bennati M. Spectroscopic Evidence for a H Bond Network at Y 356 Located at the Subunit Interface of Active E. coli Ribonucleotide Reductase. Biochemistry 2017. [PMID: 28640584 DOI: 10.1021/acs.biochem.7b00462] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction catalyzed by E. coli ribonucleotide reductase (RNR) composed of α and β subunits that form an active α2β2 complex is a paradigm for proton-coupled electron transfer (PCET) processes in biological transformations. β2 contains the diferric tyrosyl radical (Y122·) cofactor that initiates radical transfer (RT) over 35 Å via a specific pathway of amino acids (Y122· ⇆ [W48] ⇆ Y356 in β2 to Y731 ⇆ Y730 ⇆ C439 in α2). Experimental evidence exists for colinear and orthogonal PCET in α2 and β2, respectively. No mechanistic model yet exists for the PCET across the subunit (α/β) interface. Here, we report unique EPR spectroscopic features of Y356·-β, the pathway intermediate generated by the reaction of 2,3,5-F3Y122·-β2/CDP/ATP with wt-α2, Y731F-α2, or Y730F-α2. High field EPR (94 and 263 GHz) reveals a dramatically perturbed g tensor. [1H] and [2H]-ENDOR reveal two exchangeable H bonds to Y356·: a moderate one almost in-plane with the π-system and a weak one. DFT calculation on small models of Y· indicates that two in-plane, moderate H bonds (rO-H ∼1.8-1.9 Å) are required to reproduce the gx value of Y356· (wt-α2). The results are consistent with a model, in which a cluster of two, almost symmetrically oriented, water molecules provide the two moderate H bonds to Y356· that likely form a hydrogen bond network of water molecules involved in either the reversible PCET across the subunit interface or in H+ release to the solvent during Y356 oxidation.
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Affiliation(s)
- Thomas U Nick
- Research Group Electron-Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | - Kanchana R Ravichandran
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Müge Kasanmascheff
- Research Group Electron-Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | - Marina Bennati
- Research Group Electron-Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany.,Department of Chemistry, University of Göttingen , 37077 Göttingen, Germany
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38
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Reece SY, Seyedsayamdost MR. Long-range proton-coupled electron transfer in the Escherichia coli class Ia ribonucleotide reductase. Essays Biochem 2017; 61:281-92. [PMID: 28487404 DOI: 10.1042/EBC20160072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 11/17/2022]
Abstract
Escherichia coli class Ia ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to 2'-deoxynucleotides using a radical mechanism. Each turnover requires radical transfer from an assembled diferric tyrosyl radical (Y•) cofactor to the enzyme active site over 35 Å away. This unprecedented reaction occurs via an amino acid radical hopping pathway spanning two protein subunits. To study the mechanism of radical transport in RNR, a suite of biochemical approaches have been developed, such as site-directed incorporation of unnatural amino acids with altered electronic properties and photochemical generation of radical intermediates. The resulting variant RNRs have been investigated using a variety of time-resolved physical techniques, including transient absorption and stopped-flow UV-Vis spectroscopy, as well as rapid freeze-quench EPR, ENDOR, and PELDOR spectroscopic methods. The data suggest that radical transport occurs via proton-coupled electron transfer (PCET) and that the protein structure has evolved to manage the proton and electron transfer co-ordinates in order to prevent 'off-pathway' reactivity and build-up of oxidised intermediates. Thus, precise design and control over the factors that govern PCET is key to enabling reversible and long-range charge transport by amino acid radicals in RNR.
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39
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Lin Q, Parker MJ, Taguchi AT, Ravichandran K, Kim A, Kang G, Shao J, Drennan CL, Stubbe J. Glutamate 52-β at the α/β subunit interface of Escherichia coli class Ia ribonucleotide reductase is essential for conformational gating of radical transfer. J Biol Chem 2017; 292:9229-9239. [PMID: 28377505 DOI: 10.1074/jbc.m117.783092] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 02/23/2017] [Revised: 04/02/2017] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of nucleoside diphosphate substrates (S) to deoxynucleotides with allosteric effectors (e) controlling their relative ratios and amounts, crucial for fidelity of DNA replication and repair. Escherichia coli class Ia RNR is composed of α and β subunits that form a transient, active α2β2 complex. The E. coli RNR is rate-limited by S/e-dependent conformational change(s) that trigger the radical initiation step through a pathway of 35 Å across the subunit (α/β) interface. The weak subunit affinity and complex nucleotide-dependent quaternary structures have precluded a molecular understanding of the kinetic gating mechanism(s) of the RNR machinery. Using a docking model of α2β2 created from X-ray structures of α and β and conserved residues from a new subclassification of the E. coli Ia RNR (Iag), we identified and investigated four residues at the α/β interface (Glu350 and Glu52 in β2 and Arg329 and Arg639 in α2) of potential interest in kinetic gating. Mutation of each residue resulted in loss of activity and with the exception of E52Q-β2, weakened subunit affinity. An RNR mutant with 2,3,5-trifluorotyrosine radical (F3Y122•) replacing the stable Tyr122• in WT-β2, a mutation that partly overcomes conformational gating, was placed in the E52Q background. Incubation of this double mutant with His6-α2/S/e resulted in an RNR capable of catalyzing pathway-radical formation (Tyr356•-β2), 0.5 eq of dCDP/F3Y122•, and formation of an α2β2 complex that is isolable in pulldown assays over 2 h. Negative stain EM images with S/e (GDP/TTP) revealed the uniformity of the α2β2 complex formed.
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Affiliation(s)
- Qinghui Lin
- From the Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou 310058, China and
| | | | | | | | | | | | - Jimin Shao
- From the Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou 310058, China and
| | - Catherine L Drennan
- the Departments of Chemistry and .,Biology, and.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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40
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Ravichandran KR, Zong AB, Taguchi AT, Nocera DG, Stubbe J, Tommos C. Formal Reduction Potentials of Difluorotyrosine and Trifluorotyrosine Protein Residues: Defining the Thermodynamics of Multistep Radical Transfer. J Am Chem Soc 2017; 139:2994-3004. [PMID: 28171730 DOI: 10.1021/jacs.6b11011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Redox-active tyrosines (Ys) play essential roles in enzymes involved in primary metabolism including energy transduction and deoxynucleotide production catalyzed by ribonucleotide reductases (RNRs). Thermodynamic characterization of Ys in solution and in proteins remains a challenge due to the high reduction potentials involved and the reactive nature of the radical state. The structurally characterized α3Y model protein has allowed the first determination of formal reduction potentials (E°') for a Y residing within a protein (Berry, B. W.; Martı́nez-Rivera, M. C.; Tommos, C. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 9739-9743). Using Schultz's technology, a series of fluorotyrosines (FnY, n = 2 or 3) was site-specifically incorporated into α3Y. The global protein properties of the resulting α3(3,5)F2Y, α3(2,3,5)F3Y, α3(2,3)F2Y and α3(2,3,6)F3Y variants are essentially identical to those of α3Y. A protein film square-wave voltammetry approach was developed to successfully obtain reversible voltammograms and E°'s of the very high-potential α3FnY proteins. E°'(pH 5.5; α3FnY(O•/OH)) spans a range of 1040 ± 3 mV to 1200 ± 3 mV versus the normal hydrogen electrode. This is comparable to the potentials of the most oxidizing redox cofactors in nature. The FnY analogues, and the ability to site-specifically incorporate them into any protein of interest, provide new tools for mechanistic studies on redox-active Ys in proteins and on functional and aberrant hole-transfer reactions in metallo-enzymes. The former application is illustrated here by using the determined α3FnY ΔE°'s to model the thermodynamics of radical-transfer reactions in FnY-RNRs and to experimentally test and support the key prediction made.
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Affiliation(s)
| | - Allan B Zong
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | | | - Cecilia Tommos
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
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41
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Ravichandran K, Minnihan EC, Lin Q, Yokoyama K, Taguchi AT, Shao J, Nocera DG, Stubbe J. Glutamate 350 Plays an Essential Role in Conformational Gating of Long-Range Radical Transport in Escherichia coli Class Ia Ribonucleotide Reductase. Biochemistry 2017; 56:856-868. [PMID: 28103007 DOI: 10.1021/acs.biochem.6b01145] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli class Ia ribonucleotide reductase (RNR) is composed of two subunits that form an active α2β2 complex. The nucleoside diphosphate substrates (NDP) are reduced in α2, 35 Å from the essential diferric-tyrosyl radical (Y122•) cofactor in β2. The Y122•-mediated oxidation of C439 in α2 occurs by a pathway (Y122 ⇆ [W48] ⇆ Y356 in β2 to Y731 ⇆ Y730 ⇆ C439 in α2) across the α/β interface. The absence of an α2β2 structure precludes insight into the location of Y356 and Y731 at the subunit interface. The proximity in the primary sequence of the conserved E350 to Y356 in β2 suggested its importance in catalysis and/or conformational gating. To study its function, pH-rate profiles of wild-type β2/α2 and mutants in which 3,5-difluorotyrosine (F2Y) replaces residue 356, 731, or both are reported in the presence of E350 or E350X (X = A, D, or Q) mutants. With E350, activity is maintained at the pH extremes, suggesting that protonated and deprotonated states of F2Y356 and F2Y731 are active and that radical transport (RT) can occur across the interface by proton-coupled electron transfer at low pH or electron transfer at high pH. With E350X mutants, all RNRs were inactive, suggesting that E350 could be a proton acceptor during oxidation of the interface Ys. To determine if E350 plays a role in conformational gating, the strong oxidants, NO2Y122•-β2 and 2,3,5-F3Y122•-β2, were reacted with α2, CDP, and ATP in E350 and E350X backgrounds and the reactions were monitored for pathway radicals by rapid freeze-quench electron paramagnetic resonance spectroscopy. Pathway radicals are generated only when E350 is present, supporting its essential role in gating the conformational change(s) that initiates RT and masking its role as a proton acceptor.
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Affiliation(s)
| | | | - Qinghui Lin
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine , Hangzhou 310058, China
| | | | | | - Jimin Shao
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine , Hangzhou 310058, China
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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42
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Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Fariba Mohammadian-Sabet
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Esmail Vessally
- Department of Chemistry, Payame Noor University, Tehran, Iran
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43
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Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Esmail Vessally
- Department of Chemistry, Payame Noor University, Tehran, Iran
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44
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Ravichandran KR, Taguchi AT, Wei Y, Tommos C, Nocera DG, Stubbe J. A >200 meV Uphill Thermodynamic Landscape for Radical Transport in Escherichia coli Ribonucleotide Reductase Determined Using Fluorotyrosine-Substituted Enzymes. J Am Chem Soc 2016; 138:13706-13716. [PMID: 28068088 PMCID: PMC5224885 DOI: 10.1021/jacs.6b08200] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Escherichia coli class Ia ribonucleotide reductase
(RNR) converts ribonucleotides to deoxynucleotides. A diferric-tyrosyl
radical (Y122•) in one subunit (β2) generates
a transient thiyl radical in another subunit (α2) via long-range
radical transport (RT) through aromatic amino acid residues (Y122 ⇆ [W48] ⇆ Y356 in β2
to Y731 ⇆ Y730 ⇆ C439 in α2). Equilibration of Y356•, Y731•, and Y730• was recently observed using
site specifically incorporated unnatural tyrosine analogs; however,
equilibration between Y122• and Y356•
has not been detected. Our recent report of Y356•
formation in a kinetically and chemically competent fashion in the
reaction of β2 containing 2,3,5-trifluorotyrosine at Y122 (F3Y122•-β2) with α2, CDP
(substrate), and ATP (effector) has now afforded the opportunity to
investigate equilibration of F3Y122•
and Y356•. Incubation of F3Y122•-β2, Y731F-α2 (or Y730F-α2),
CDP, and ATP at different temperatures (2–37 °C) provides
ΔE°′(F3Y122•–Y356•) of 20 ± 10 mV at 25
°C. The pH dependence of the F3Y122•
⇆ Y356• interconversion (pH 6.8–8.0)
reveals that the proton from Y356 is in rapid exchange
with solvent, in contrast to the proton from Y122. Insertion
of 3,5-difluorotyrosine (F2Y) at Y356 and rapid
freeze-quench EPR analysis of its reaction with Y731F-α2,
CDP, and ATP at pH 8.2 and 25 °C shows F2Y356• generation by the native Y122•. FnY-RNRs (n = 2 and 3) together
provide a model for the thermodynamic landscape of the RT pathway
in which the reaction between Y122 and C439 is
∼200 meV uphill.
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Affiliation(s)
| | | | | | - Cecilia Tommos
- Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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45
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Affiliation(s)
- Mehdi D. Esrafili
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
| | - Zakiyeh Amiri
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
| | - Fatemeh Shankal
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
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Esrafili MD, Asadollahi S, Shahamat YD. The mutual influence of Y···N and H···H interactions in XHY···NCH···HM complexes (X = F, Cl, Br; Y = S, Se; M = Li, Na, BeH, MgH): tuning of the chalcogen bond by dihydrogen bond interaction. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The equilibrium structures, interaction energies, and bonding properties of ternary XHY···NCH···HM complexes are studied by ab initio calculations, where X = F, Cl, Br, Y = S, Se, and M = Li, Na, BeH, MgH. The ab initio calculations are carried out at the MP2/aug-cc-pVTZ level. The results indicate that all optimized Y···N and H···H binding distances in the ternary complexes are smaller than the corresponding values in the binary systems. The calculated cooperative energies (Ecoop) are between −0.20 kcal/mol in BrHS···NCH···HBeH and −3.29 kcal/mol in FHSe···NCH···HNa. For a given Y and M, the estimated Ecoop values increase as X = F > Cl > Br. In addition, the selenium-bonded complexes exibit larger Ecoop values than those of the sulfur-bonded counterparts. The cooperativity between Y···N and H···H interactions is further analyzed by quantum theory of atoms in molecules and natural bond orbital methods. Cooperative effects make an increase in the J(Y–N) and J(H–H) spin–spin coupling constants of the ternary complexes with respect to the binary systems.
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Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Soheila Asadollahi
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Yousef Dadban Shahamat
- Environmental Heath Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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Esrafili MD, Asadollahi S, Dadban Shahamat Y. Competition between chalcogen bond and halogen bond interactions in YOX4:NH3 (Y = S, Se; X = F, Cl, Br) complexes: An ab initio investigation. Struct Chem 2016; 27:1439-47. [DOI: 10.1007/s11224-016-0763-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Esrafili MD, Asadollahi S. Cationic P⋯N interaction in XH 3 P + ⋯NCY complexes (X = H, F, CN, NH 2 , OH; Y = H, Li, F, Cl) and its cooperativity with hydrogen/lithium/halogen bond. J Mol Graph Model 2016; 64:131-138. [DOI: 10.1016/j.jmgm.2016.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 12/27/2022]
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Kasanmascheff M, Lee W, Nick TU, Stubbe J, Bennati M. Radical transfer in E. coli ribonucleotide reductase: a NH 2Y 731/R 411A-α mutant unmasks a new conformation of the pathway residue 731. Chem Sci 2016; 7:2170-2178. [PMID: 29899944 PMCID: PMC5968753 DOI: 10.1039/c5sc03460d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/06/2015] [Indexed: 11/21/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all living organisms. The catalytic cycle of E. coli RNR involves a long-range proton-coupled electron transfer (PCET) from a tyrosyl radical (Y122˙) in subunit β2 to a cysteine (C439) in the active site of subunit α2, which subsequently initiates nucleotide reduction. This oxidation occurs over 35 Å and involves a specific pathway of redox active amino acids (Y122 ↔ [W48?] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2). The mechanisms of the PCET steps at the interface of the α2β2 complex remain puzzling due to a lack of structural information for this region. Recently, DFT calculations on the 3-aminotyrosyl radical (NH2Y731˙)-α2 trapped by incubation of NH2Y731-α2/β2/CDP(substrate)/ATP(allosteric effector) suggested that R411-α2, a residue close to the α2β2 interface, interacts with NH2Y731˙ and accounts in part for its perturbed EPR parameters. To examine its role, we further modified NH2Y731-α2 with a R411A substitution. NH2Y731˙/R411A generated upon incubation of NH2Y731/R411A-α2/β2/CDP/ATP was investigated using multi-frequency (34, 94 and 263 GHz) EPR, 34 GHz pulsed electron-electron double resonance (PELDOR) and electron-nuclear double resonance (ENDOR) spectroscopies. The data indicate a large conformational change in NH2Y731˙/R411A relative to the NH2Y731˙ single mutant. Particularly, the inter-spin distance from NH2Y731˙/R411A in one αβ pair to Y122˙ in a second αβ pair decreases by 3 Å in the presence of the R411A mutation. This is the first experimental evidence for the flexibility of pathway residue Y731-α2 in an α2β2 complex and suggests a role for R411 in the stacked Y731/Y730 conformation involved in collinear PCET. Furthermore, NH2Y731˙/R411A serves as a probe of the PCET process across the subunit interface.
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Affiliation(s)
- Müge Kasanmascheff
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- Department of Chemistry, University of Göttingen, 37077 Göttingen, Germany
| | - Wankyu Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Thomas U Nick
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- Department of Chemistry, University of Göttingen, 37077 Göttingen, Germany
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Abstract
Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides to provide the monomeric building blocks for DNA replication and repair. Nucleotide reduction occurs by way of multistep proton-coupled electron transfer (PCET) over a pathway of redox active amino acids spanning ∼35 Å and two subunits (α2 and β2). Despite the fact that PCET in RNR is rapid, slow conformational changes mask examination of the kinetics of these steps. As such, we have pioneered methodology in which site-specific incorporation of a [Re(I)] photooxidant on the surface of the β2 subunit (photoβ2) allows photochemical oxidation of the adjacent PCET pathway residue β-Y356 and time-resolved spectroscopic observation of the ensuing reactivity. A series of photoβ2s capable of performing photoinitiated substrate turnover have been prepared in which four different fluorotyrosines (FnYs) are incorporated in place of β-Y356. The FnYs are deprotonated under biological conditions, undergo oxidation by electron transfer (ET), and provide a means by which to vary the ET driving force (ΔG°) with minimal additional perturbations across the series. We have used these features to map the correlation between ΔG° and kET both with and without the fully assembled photoRNR complex. The photooxidation of FnY356 within the α/β subunit interface occurs within the Marcus inverted region with a reorganization energy of λ ≈ 1 eV. We also observe enhanced electronic coupling between donor and acceptor (HDA) in the presence of an intact PCET pathway. Additionally, we have investigated the dynamics of proton transfer (PT) by a variety of methods including dependencies on solvent isotopic composition, buffer concentration, and pH. We present evidence for the role of α2 in facilitating PT during β-Y356 photooxidation; PT occurs by way of readily exchangeable positions and within a relatively "tight" subunit interface. These findings show that RNR controls ET by lowering λ, raising HDA, and directing PT both within and between individual polypeptide subunits.
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Affiliation(s)
- Lisa Olshansky
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry and Chemical Biology, 12 Oxford St., Harvard University, Cambridge, Massachusetts 02138, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, 12 Oxford St., Harvard University, Cambridge, Massachusetts 02138, United States
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