1
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Dai L, Zhou X, Yang Y, Hu P, Ci L. Ordered porous Mn - Co spinel oxide (CoMn 2O 4) with vacancies modulation as efficient electrocatalyst for Li - O 2 battery. J Colloid Interface Sci 2024; 670:719-728. [PMID: 38788439 DOI: 10.1016/j.jcis.2024.05.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/12/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
Nonaqueous Li - O2 battery (LOB) is considered one of the most promising energy storage system due to its ultrahigh theoretical specific capacity (3500 Wh kg-1). Introducing vacancies in CoMn2O4 catalysts is regarded as an effective strategy to enhance the electrochemical performances of LOB. However, the relation between vacancy types in CoMn2O4 and catalytic performances in the LOB remains ambiguous. Herein, ordered porous CoMn2O4 with oxygen and metal vacancies is obtained via solvothermal reaction followed by temperature-controlled calcination using polystyrene spheres as templates. The increase in treatment temperature reduces the content of oxygen vacancies while increasing that of the metal vacancies. Notably, experimental results and theoretical calculations show that oxygen vacancies in CoMn2O4 have a greater influence than metal vacancies in modulating the LiO2 adsorption during the reaction processes and reducing the overpotential. CoMn2O4 synthesized at 500 ℃ (CoMnO-500) with higher oxygen vacancies exhibits stronger adsorption onto the LiO2, facilitating the formation of film-like Li2O2. Therefore, an LOB with the CoMnO-500 catalyst presents the lowest overpotential of 1.2 V and longest cycle lifespan of 286 cycles at a current density of 200 mA g-1. This study offers insights into the effect of CoMn2O4 vacancies on the formation pathway of Li2O2 discharge products.
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Affiliation(s)
- Linna Dai
- School of Science, Hubei University of Technology, Nanli Road #28, Wuhan, Hubei Province 430068, China
| | - Xin Zhou
- School of Science, Hubei University of Technology, Nanli Road #28, Wuhan, Hubei Province 430068, China
| | - Yuan Yang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Pei Hu
- School of Science, Hubei University of Technology, Nanli Road #28, Wuhan, Hubei Province 430068, China.
| | - Lijie Ci
- Research Center for Carbon Nanomaterials, Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials (Ministry of Education), School of Materials Science and Engineering, Shandong University, Jinan 250061, China.
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2
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Switala J, Donald L, Ivancich A. A remarkable peroxidase-like behavior of the catalase KatA from the pathogenic bacteria Helicobacter pylori: The oxidation reaction with formate as substrate and the stabilization of an [Fe(IV) = O Trp •] intermediate assessed by multifrequency EPR spectroscopy. J Inorg Biochem 2024; 257:112594. [PMID: 38749080 DOI: 10.1016/j.jinorgbio.2024.112594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/15/2024] [Accepted: 05/04/2024] [Indexed: 06/09/2024]
Abstract
We have characterized the catalytic cycle of the Helicobacter pylori KatA catalase (HPC). H. pylori is a human and animal pathogen responsible for gastrointestinal infections. Multifrequency (9-285 GHz) EPR spectroscopy was applied to identify the high-valent intermediates (5 ≤ pH ≤ 8.5). The broad (2000 G) 9-GHz EPR spectrum consistent with the [Fe(IV) = O Por•+] intermediate was detected, and showed a clear pH dependence on the exchange-coupling of the radical (delocalized over the porphyrin moiety) due to the magnetic interaction with the ferryl iron. In addition, Trp• (for pH ≤ 6) and Tyr• (for 5 ≤ pH ≤ 8.5) species were distinguished by the advantageous resolution of their g-values in the 285-GHz EPR spectrum. The unequivocal identification of the high-valent intermediates in HPC by their distinct EPR spectra allowed us to address their reactivity towards substrates. The stabilization of an [Fe(IV) = O Trp•] species in HPC, unprecedented in monofunctional catalases and possibly involved in the oxidation of formate to the formyloxyl radical at pH ≤ 6, is reminiscent of intermediates previously identified in the catalytic cycle of bifunctional catalase-peroxidases. The 2e- oxidation of formate by the [Fe(IV) = O Por•+] species, both at basic and acidic pH conditions, involving a 1H+/2e- oxidation in a cytochrome P450 peroxygenase-like reaction is proposed. Our findings demonstrate that moonlighting by the H. pylori catalase includes formate oxidation, an enzymatic reaction possibly related to the unique strategy of the neutrophile bacterium for gastric colonization, that is the release of CO2 to regulate the pH in the acidic environment.
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Affiliation(s)
- Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Lynda Donald
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Anabella Ivancich
- Bioénergétique et Ingénierie des Protéines, UMR 7281 and IMM FR3479, CNRS, Aix-Marseille Univ., 31 chemin Joseph Aiguier, 13009 Marseille, France.
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3
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Daniel DT, Mitra S, Eichel RA, Diddens D, Granwehr J. Machine Learning Isotropic g Values of Radical Polymers. J Chem Theory Comput 2024; 20:2592-2604. [PMID: 38456629 DOI: 10.1021/acs.jctc.3c01252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Methods for electronic structure computations, such as density functional theory (DFT), are routinely used for the calculation of spectroscopic parameters to establish and validate structure-parameter correlations. DFT calculations, however, are computationally expensive for large systems such as polymers. This work explores the machine learning (ML) of isotropic g values, giso, obtained from electron paramagnetic resonance (EPR) experiments of an organic radical polymer. An ML model based on regression trees is trained on DFT-calculated g values of poly(2,2,6,6-tetramethylpiperidinyloxy-4-yl methacrylate) (PTMA) polymer structures extracted from different time frames of a molecular dynamics trajectory. The DFT-derived g values, gisocalc, for different radical densities of PTMA, are compared against experimentally derived g values obtained from in operando EPR measurements of a PTMA-based organic radical battery. The ML-predicted giso values, gisopred, were compared with gisocalc to evaluate the performance of the model. Mean deviations of gisopred from gisocalc were found to be on the order of 0.0001. Furthermore, a performance evaluation on test structures from a separate MD trajectory indicated that the model is sensitive to the radical density and efficiently learns to predict giso values even for radical densities that were not part of the training data set. Since our trained model can reproduce the changes in giso along the MD trajectory and is sensitive to the extent of equilibration of the polymer structure, it is a promising alternative to computationally more expensive DFT methods, particularly for large systems that cannot be easily represented by a smaller model system.
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Affiliation(s)
- Davis Thomas Daniel
- Institute of Energy and Climate Research (IEK-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52056 Aachen, Germany
| | - Souvik Mitra
- Institute of Physical Chemistry, University of Münster, 48149 Münster, Germany
| | - Rüdiger-A Eichel
- Institute of Energy and Climate Research (IEK-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Aachen 52056, Germany
| | - Diddo Diddens
- Helmholtz Institute Münster (IEK-12), Forschungszentrum Jülich GmbH, 48149 Münster, Germany
| | - Josef Granwehr
- Institute of Energy and Climate Research (IEK-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52056 Aachen, Germany
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4
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Katarzyna Lesiów M, Witwicki M, Tan NK, Graziotto ME, New EJ. Unravelling the Mystery of COVID-19 Pathogenesis: Spike Protein and Cu Can Synergize to Trigger ROS Production. Chemistry 2023; 29:e202301530. [PMID: 37414735 DOI: 10.1002/chem.202301530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
The COVID-19 pandemic has had a devastating impact on global health, highlighting the need to understand how the SARS-CoV-2 virus damages the lungs in order to develop effective treatments. Recent research has shown that patients with COVID-19 experience severe oxidative damage to various biomolecules. We propose that the overproduction of reactive oxygen species (ROS) in SARS-CoV-2 infection involves an interaction between copper ions and the virus's spike protein. We tested two peptide fragments, Ac-ELDKYFKNH-NH2 (L1) and Ac-WSHPQFEK-NH2 (L2), derived from the spike protein of the Wuhan strain and the β variant, respectively, and found that they bind Cu(II) ions and form a three-nitrogen complexes at lung pH. Our research demonstrates that these complexes trigger the overproduction of ROS, which can break both DNA strands and transform DNA into its linear form. Using A549 cells, we demonstrated that ROS overproduction occurs in the mitochondria, not in the cytoplasm. Our findings highlight the importance of the interaction between copper ions and the virus's spike protein in the development of lung damage and may aid in the development of therapeutic procedures.
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Affiliation(s)
| | - Maciej Witwicki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Nian Kee Tan
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for, Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Elizabeth Joy New
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for, Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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5
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Dubroca T, Wang X, Mentink-Vigier F, Trociewitz B, Starck M, Parker D, Sherwin MS, Hill S, Krzystek J. Terahertz EPR spectroscopy using a 36-tesla high-homogeneity series-connected hybrid magnet. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107480. [PMID: 37331305 DOI: 10.1016/j.jmr.2023.107480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/24/2023] [Accepted: 05/13/2023] [Indexed: 06/20/2023]
Abstract
Electron Paramagnetic Resonance (EPR) is a powerful technique to study materials and biological samples on an atomic scale. High-field EPR in particular enables extracting very small g-anisotropies in organic radicals and half-filled 3d and 4f metal ions such as MnII (3d5) or GdIII (4f7), and resolving EPR signals from unpaired spins with very close g-values, both of which provide high-resolution details of the local atomic environment. Before the recent commissioning of the high-homogeneity Series Connected Hybrid magnet (SCH, superconducting + resistive) at the National High Magnetic Field Laboratory (NHMFL), the highest-field, high-resolution EPR spectrometer available was limited to 25 T using a purely resistive "Keck" magnet at the NHMFL. Herein, we report the first EPR experiments performed using the SCH magnet capable of reaching the field of 36 T, corresponding to an EPR frequency of 1 THz for g = 2. The magnet's intrinsic homogeneity (25 ppm, that is 0.9 mT at 36 T over 1 cm diameter, 1 cm length cylinder) was previously established by NMR. We characterized the magnet's temporal stability (5 ppm, which is 0.2 mT at 36 T over one-minute, the typical acquisition time) using 2,2-diphenyl-1-picrylhydrazyl (DPPH). This high resolution enables resolving the weak g-anisotropy of 1,3-bis(diphenylene)-2-phenylallyl (BDPA), Δg = 2.5 × 10-4 obtained from measurements at 932 GHz and 33 T. Subsequently, we recorded EPR spectra at multiple frequencies for two GdIII complexes with potential applications as spin labels. We demonstrated a significant reduction in line broadening in Gd[DTPA], attributed to second order zero field splitting, and a resolution enhancement of g-tensor anisotropy for Gd[sTPATCN]-SL.
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Affiliation(s)
- Thierry Dubroca
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA.
| | - Xiaoling Wang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Center for Molecular Magnetic Quantum Materials, University of Florida, Gainesville, FL 32611, USA
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Bianca Trociewitz
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Matthieu Starck
- Department of Chemistry, University of Durham, Durham DH13LE, UK
| | - David Parker
- Department of Chemistry, University of Durham, Durham DH13LE, UK
| | - Mark S Sherwin
- Department of Physics, University of California Santa Barbara, CA 93106, USA
| | - Stephen Hill
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Center for Molecular Magnetic Quantum Materials, University of Florida, Gainesville, FL 32611, USA; Department of Physics, Florida State University, Tallahassee FL 32306, USA
| | - J Krzystek
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA.
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6
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Gibbs C, Fedoretz-Maxwell BP, MacNeil GA, Walsby CJ, Warren JJ. Proximal Methionine Amino Acid Residue Affects the Properties of Redox-Active Tryptophan in an Artificial Model Protein. ACS OMEGA 2023; 8:19798-19806. [PMID: 37305310 PMCID: PMC10249128 DOI: 10.1021/acsomega.3c01589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/11/2023] [Indexed: 06/13/2023]
Abstract
Redox-active amino acid residues are at the heart of biological electron-transfer reactions. They play important roles in natural protein functions and are implicated in disease states (e.g., oxidative-stress-associated disorders). Tryptophan (Trp) is one such redox-active amino acid residue, and it has long been known to serve a functional role in proteins. Broadly speaking, there is still much to learn about the local features that make some Trp redox active and others inactive. Herein, we describe a new protein model system where we investigate how a methionine (Met) residue proximal to a redox-active Trp affects its reactivity and spectroscopy. We use an artificial variant of azurin from Pseudomonas aeruginosa to produce these models. We employ a series of UV-visible spectroscopy, electrochemistry, electron paramagnetic resonance, and density functional theory experiments to demonstrate the effect that placing Met near Trp radicals has in the context of redox proteins. The introduction of Met proximal to Trp lowers its reduction potential by ca. 30 mV and causes clear shifts in the optical spectra of the corresponding radicals. While the effect may be small, it is significant enough to be a way for natural systems to tune Trp reactivity.
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7
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Ledray AP, Dwaraknath S, Chakarawet K, Sponholtz MR, Merchen C, Van Stappen C, Rao G, Britt RD, Lu Y. Tryptophan Can Promote Oxygen Reduction to Water in a Biosynthetic Model of Heme Copper Oxidases. Biochemistry 2023; 62:388-395. [PMID: 36215733 DOI: 10.1021/acs.biochem.2c00300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Heme-copper oxidases (HCOs) utilize tyrosine (Tyr) to donate one of the four electrons required for the reduction of O2 to water in biological respiration, while tryptophan (Trp) is speculated to fulfill the same role in cyt bd oxidases. We previously engineered myoglobin into a biosynthetic model of HCOs and demonstrated the critical role that Tyr serves in the oxygen reduction reaction (ORR). To address the roles of Tyr and Trp in these oxidases, we herein report the preparation of the same biosynthetic model with the Tyr replaced by Trp and further demonstrate that Trp can also promote the ORR, albeit with lower activity. An X-ray crystal structure of the Trp variant shows a hydrogen-bonding network involving two water molecules that are organized by Trp, similar to that in the Tyr variant, which is absent in the crystal structure with the native Phe residue. Additional electron paramagnetic resonance measurements are consistent with the formation of a Trp radical species upon reacting with H2O2. We attribute the lower activity of the Trp variant to Trp's higher reduction potential relative to Tyr. Together, these findings demonstrate, for the first time, that Trp can indeed promote the ORR and provides a structural basis for the observation of varying activities. The results support a redox role for the conserved Trp in bd oxidase while suggesting that HCOs use Tyr instead of Trp to achieve higher reactivity.
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Affiliation(s)
- Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sudharsan Dwaraknath
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Khetpakorn Chakarawet
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Madeline R Sponholtz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Claire Merchen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Guodong Rao
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Department of Chemistry, 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
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8
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Pastore AJ, Montoya A, Kamat M, Basso KB, Italia JS, Chatterjee A, Drosou M, Pantazis DA, Angerhofer A. Selective incorporation of 5-hydroxytryptophan blocks long range electron transfer in oxalate decarboxylase. Protein Sci 2023; 32:e4537. [PMID: 36482787 PMCID: PMC9801070 DOI: 10.1002/pro.4537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Oxalate decarboxylase from Bacillus subtilis is a binuclear Mn-dependent acid stress response enzyme that converts the mono-anion of oxalic acid into formate and carbon dioxide in a redox neutral unimolecular disproportionation reaction. A π-stacked tryptophan dimer, W96 and W274, at the interface between two monomer subunits facilitates long-range electron transfer between the two Mn ions and plays an important role in the catalytic mechanism. Substitution of W96 with the unnatural amino acid 5-hydroxytryptophan leads to a persistent EPR signal which can be traced back to the neutral radical of 5-hydroxytryptophan with its hydroxyl proton removed. 5-Hydroxytryptophan acts as a hole sink preventing the formation of Mn(III) at the N-terminal active site and strongly suppresses enzymatic activity. The lower boundary of the standard reduction potential for the active site Mn(II)/Mn(III) couple can therefore be estimated as 740 mV against the normal hydrogen electrode at pH 4, the pH of maximum catalytic efficiency. Our results support the catalytic importance of long-range electron transfer in oxalate decarboxylase while at the same time highlighting the utility of unnatural amino acid incorporation and specifically the use of 5-hydroxytryptophan as an energetic sink for hole hopping to probe electron transfer in redox proteins.
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Affiliation(s)
| | - Alvaro Montoya
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - Manasi Kamat
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - Kari B. Basso
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - James S. Italia
- Department of ChemistryBoston CollegeChestnut HillMassachusettsUSA
| | | | - Maria Drosou
- Max‐Planck‐Institut für KohlenforschungMülheim an der RuhrGermany
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9
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Telser J. Linewidth, field, and frequency in electron paramagnetic resonance (EPR) spectroscopy. J Biol Inorg Chem 2022; 27:605-609. [DOI: 10.1007/s00775-022-01961-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/31/2022] [Indexed: 10/14/2022]
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10
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You X, Baiz CR. Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective. J Phys Chem A 2022; 126:5881-5889. [PMID: 35968816 DOI: 10.1021/acs.jpca.2c03803] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.
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Affiliation(s)
- Xiao You
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
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11
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Kisgeropoulos EC, Gan YJ, Greer SM, Hazel JM, Shafaat HS. Pulsed Multifrequency Electron Paramagnetic Resonance Spectroscopy Reveals Key Branch Points for One- vs Two-Electron Reactivity in Mn/Fe Proteins. J Am Chem Soc 2022; 144:11991-12006. [PMID: 35786920 DOI: 10.1021/jacs.1c13738] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Traditionally, the ferritin-like superfamily of proteins was thought to exclusively use a diiron active site in catalyzing a diverse array of oxygen-dependent reactions. In recent years, novel redox-active cofactors featuring heterobimetallic Mn/Fe active sites have been discovered in both the radical-generating R2 subunit of class Ic (R2c) ribonucleotide reductases (RNRs) and the related R2-like ligand-binding oxidases (R2lox). However, the protein-specific factors that differentiate the radical reactivity of R2c from the C-H activation reactions of R2lox remain unknown. In this work, multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy and ligand hyperfine techniques in conjunction with broken-symmetry density functional theory calculations are used to characterize the molecular and electronic structures of two EPR-active intermediates trapped during aerobic assembly of the R2lox Mn/Fe cofactor. A MnIII(μ-O)(μ-OH)FeIII species is identified as the first EPR-active species and represents a common state between the two classes of redox-active Mn/Fe proteins. The species downstream from the MnIII(μ-O)(μ-OH)FeIII state exhibits unique EPR properties, including unprecedented spectral breadth and isotope-dependent g-tensors, which are attributed to a weakly coupled, hydrogen-bonded MnIII(μ-OH)FeIII species. This final intermediate precedes formation of the MnIII/FeIII resting state and is suggested to be relevant to understanding the endogenous reactivity of R2lox.
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Affiliation(s)
- Effie C Kisgeropoulos
- The Ohio State Biochemistry Program, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Yunqiao J Gan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Samuel M Greer
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Joseph M Hazel
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State Biochemistry Program, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
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12
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Carreon-Gonzalez M, Muñoz-Rugeles L, Vivier-Bunge A, Alvarez-Idaboy JR. Chemical repair of damaged leucine and tryptophane by thiophenols at close to diffusion-controlled rates: Mechanisms and kinetics. J Comput Chem 2022; 43:556-567. [PMID: 35106786 DOI: 10.1002/jcc.26813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/15/2022] [Indexed: 12/14/2022]
Abstract
Thiophenols are chemical species with multiple desirable biological properties, including their primary and secondary antioxidant capacity. In this work, the repairing antioxidant activity of eight different thiophenols has been investigated for damaged leucine and tryptophane. The investigation was carried out employing quantum mechanical and transition state methods to calculate the thermodynamic and kinetic data of the reactions involved, while simulating the biological conditions at physiological pH and aqueous and lipidic medium. The analysis of the atomic charges and the spin densities at each of the points on the potential energy surface was the tool that allowed the elucidation of the reaction mechanisms through which thiophenols repair the oxidative damage caused to the amino acids leucine and tryptophan. It was found that thiophenols can repair leucine via a hydrogen atom transfer mechanism in a manner which is similar to the one used by glutathione to repair the carbon-centered radicals of guanosine. In addition, thiophenols can also restore tryptophane, a nitrogen-centered radical, via proton-coupled electron transfer and single electron transfer mechanisms. Moreover, both processes occur at close to diffusion-controlled rates.
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Affiliation(s)
- Mirzam Carreon-Gonzalez
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Leonardo Muñoz-Rugeles
- Laboratorio de Espectroscopia Atómica y Molecular (LEAM), Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Annik Vivier-Bunge
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
| | - Juan Raul Alvarez-Idaboy
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México, Mexico City, Mexico
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13
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Püschmann J, Mahor D, de Geus DC, Strampraad MJF, Srour B, Hagen WR, Todorovic S, Hagedoorn PL. Unique Biradical Intermediate in the Mechanism of the Heme Enzyme Chlorite Dismutase. ACS Catal 2021; 11:14533-14544. [PMID: 34888122 PMCID: PMC8650003 DOI: 10.1021/acscatal.1c03432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/04/2021] [Indexed: 11/30/2022]
Abstract
![]()
The heme enzyme chlorite
dismutase (Cld) catalyzes O–O bond
formation as part of the conversion of the toxic chlorite (ClO2–) to chloride (Cl–) and
molecular oxygen (O2). Enzymatic O–O bond formation
is rare in nature, and therefore, the reaction mechanism of Cld is
of great interest. Microsecond timescale pre-steady-state kinetic
experiments employing Cld from Azospira oryzae (AoCld), the natural substrate chlorite, and the
model substrate peracetic acid (PAA) reveal the formation of distinct
intermediates. AoCld forms a complex with PAA rapidly,
which is cleaved heterolytically to yield Compound I, which is sequentially
converted to Compound II. In the presence of chlorite, AoCld forms an initial intermediate with spectroscopic characteristics
of a 6-coordinate high-spin ferric substrate adduct, which subsequently
transforms at kobs = 2–5 ×
104 s–1 to an intermediate 5-coordinated
high-spin ferric species. Microsecond-timescale freeze-hyperquench
experiments uncovered the presence of a transient low-spin ferric
species and a triplet species attributed to two weakly coupled amino
acid cation radicals. The intermediates of the chlorite reaction were
not observed with the model substrate PAA. These findings demonstrate
the nature of physiologically relevant catalytic intermediates and
show that the commonly used model substrate may not behave as expected,
which demands a revision of the currently proposed mechanism of Clds.
The transient triplet-state biradical species that we designate as
Compound T is, to the best of our knowledge, unique in heme enzymology.
The results highlight electron paramagnetic resonance spectroscopic
evidence for transient intermediate formation during the reaction
of AoCld with its natural substrate chlorite. In
the proposed mechanism, the heme iron remains ferric throughout the
catalytic cycle, which may minimize the heme moiety’s reorganization
and thereby maximize the enzyme’s catalytic efficiency.
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Affiliation(s)
- Julia Püschmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Durga Mahor
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniël C. de Geus
- Janssen Vaccines & Prevention, Archimedesweg 4-6, 2333 CN Leiden, The Netherlands
| | - Marc J. F. Strampraad
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Batoul Srour
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wilfred R. Hagen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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14
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Tian Z, Kale VS, Wang Y, Kandambeth S, Czaban-Jóźwiak J, Shekhah O, Eddaoudi M, Alshareef HN. High-Capacity NH 4+ Charge Storage in Covalent Organic Frameworks. J Am Chem Soc 2021; 143:19178-19186. [PMID: 34739750 DOI: 10.1021/jacs.1c09290] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ammonium ions (NH4+), as non-metallic charge carriers, have spurred great research interest in the realm of aqueous batteries. Unfortunately, most inorganic host materials used in these batteries are still limited by the sluggish diffusion kinetics. Here, we report a unique hydrogen bond chemistry to employ covalent organic frameworks (COFs) for NH4+ ion storage, which achieves a high capacity of 220.4 mAh g-1 at a current density of 0.5 A g-1. Combining the theoretical simulation and materials analysis, a universal mechanism for the reaction of nitrogen and oxygen bridged by hydrogen bonds is revealed. In addition, we explain the solvation behavior of NH4+, leading to a relationship between redox potential and desolvation energy barrier. This work provides a new insight into NH4+ ion storage in host materials based on hydrogen bond chemistry. This mechanism can be leveraged to design and develop COFs for electrochemical energy storage.
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Affiliation(s)
- Zhengnan Tian
- Materials Science and Engineering, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Vinayak S Kale
- Advanced Membranes and Porous Materials Center, Physical Science and Engineering Division, Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yizhou Wang
- Materials Science and Engineering, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sharath Kandambeth
- Advanced Membranes and Porous Materials Center, Physical Science and Engineering Division, Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Justyna Czaban-Jóźwiak
- Advanced Membranes and Porous Materials Center, Physical Science and Engineering Division, Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Osama Shekhah
- Advanced Membranes and Porous Materials Center, Physical Science and Engineering Division, Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohamed Eddaoudi
- Advanced Membranes and Porous Materials Center, Physical Science and Engineering Division, Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Husam N Alshareef
- Materials Science and Engineering, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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15
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Witwicki M, Lewińska A, Ozarowski A. o-Semiquinone radical anion isolated as an amorphous porous solid. Phys Chem Chem Phys 2021; 23:17408-17419. [PMID: 34351330 DOI: 10.1039/d1cp01596f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of metal cations is a commonly applied strategy to create S > 1/2 stable molecular systems containing semiquinone radicals. Persistent mono-semiquinonato complexes of diamagnetic metal ions (S = 1/2) have been hitherto less common and mostly limited to the complexes of heavy metal ions. In this work, a mono-semiquinonato complex of aluminum, derived from 1,2-dihydroxybenzene, is obtained using a surprisingly short and uncomplicated procedure. The isolated product is an amorphous and porous solid that exhibits very good stability under ambient conditions. To characterise its molecular and electronic structure, 9.7, 34 and 406 GHz EPR spectroscopy was used in concert with computational techniques (DFT and DLPNO-CCSD). It was revealed that the radical complex is composed of two chemically equivalent aluminum cations and two catechol-like ligands with the unpaired electron uniformly distributed between the two organic molecules. The good stability and porous structure make this complex applicable in heterogeneous aerobic reactions.
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Affiliation(s)
- Maciej Witwicki
- Faculty of Chemistry, Wroclaw University, Joliot-Curie 14, 50-383 Wroclaw, Poland.
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16
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Trapping a cross-linked lysine-tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB. Proc Natl Acad Sci U S A 2021; 118:2101571118. [PMID: 34001621 DOI: 10.1073/pnas.2101571118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The radical S-adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon-carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys-Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]2+ state, which is active in catalysis. We further report the trapping and characterization of an unprecedented cross-linked Lys-Trp radical (Lys-Trp•) in addition to the organometallic Ω intermediate, providing compelling support for the proposed rEAS mechanism. Finally, we observe oxidation of the Lys-Trp• intermediate by the redox-tuned [4Fe-4S]2+ AuxI cluster by EPR spectroscopy. Our findings provide direct evidence for a role of a SPASM domain auxiliary cluster and consolidate rEAS as a mechanistic paradigm for rSAM enzyme-catalyzed carbon-carbon bond-forming reactions.
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17
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Ohler A, Long H, Ohgo K, Tyson K, Murray D, Davis A, Whittington C, Hvastkovs EG, Duffy L, Haddy A, Sargent AL, Allen WE, Offenbacher AR. Synthesis of redox-active fluorinated 5-hydroxytryptophans as molecular reporters for biological electron transfer. Chem Commun (Camb) 2021; 57:3107-3110. [PMID: 33626126 DOI: 10.1039/d1cc00187f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorinated 5-hydroxytryptophans (Fn-5HOWs) were synthesized in gram scale quantities and incorporated into a β-hairpin peptide and the protein azurin. The redox-active Fn-5HOWs exhibit unique radical spectroscopic signatures that expand the function of as probes for biological electron transfer.
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Affiliation(s)
- Amanda Ohler
- Department of Chemistry, East Carolina University, Greenville, NC, USA.
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18
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Tyson KJ, Davis AN, Norris JL, Bartolotti LJ, Hvastkovs EG, Offenbacher AR. Impact of Local Electrostatics on the Redox Properties of Tryptophan Radicals in Azurin: Implications for Redox-Active Tryptophans in Proton-Coupled Electron Transfer. J Phys Chem Lett 2020; 11:2408-2413. [PMID: 32134666 DOI: 10.1021/acs.jpclett.0c00614] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tyrosine and tryptophan play critical roles in facilitating proton-coupled electron transfer (PCET) processes essential to life. The local protein environment is anticipated to modulate the thermodynamics of amino acid radicals to achieve controlled, unidirectional PCET. Herein, square-wave voltammetry was employed to investigate the electrostatic effects on the redox properties of tryptophan in two variants of the protein azurin. Each variant contains a single redox-active tryptophan, W48 or W108, in a unique and buried protein environment. These tryptophan residues exhibit reversible square-wave voltammograms. A Pourbaix plot, representing the reduction potentials versus pH, is presented for the non-H-bonded W48, which has potentials comparable to those of tryptophan in solution. The reduction potentials of W108 are seen to be increased by more than 100 mV across the same pH range. Molecular dynamics shows that, despite its buried indole ring, the N-H of W108 hydrogen bonds with a water cluster, while W48 is completely excluded from interactions with water or polar groups. These redox properties provide insight into the role of the protein in tuning the reactivity of tryptophan radicals, a requirement for controlled biological PCET.
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Affiliation(s)
- Kristin J Tyson
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Amanda N Davis
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Jessica L Norris
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Libero J Bartolotti
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Eli G Hvastkovs
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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19
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Muñoz-Rugeles L, Galano A, Alvarez-Idaboy JR. Chemical repair mechanisms of damaged tyrosyl and tryptophanyl residues in proteins by the superoxide radical anion. NEW J CHEM 2020. [DOI: 10.1039/c9nj04998c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Even though reaction of the superoxide anion radical/hydroperoxide radical could lead to oxidation of biomolecules, it can repair oxidized tyrosyl and tryptophanyl residues in proteins at diffusion-controlled rates.
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Affiliation(s)
- Leonardo Muñoz-Rugeles
- Facultad de Química
- Departamento de Física y Química Teórica
- Universidad Nacional Autónoma de México
- México DF 04510
- Mexico
| | - Annia Galano
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- San Rafael Atlixco 186
- Col. Vicentina. Iztapalapa. C. P. 09340
- México DF
| | - Juan Raúl Alvarez-Idaboy
- Facultad de Química
- Departamento de Física y Química Teórica
- Universidad Nacional Autónoma de México
- México DF 04510
- Mexico
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20
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McCaslin TG, Pagba CV, Chi SH, Hwang HJ, Gumbart JC, Perry JW, Olivieri C, Porcelli F, Veglia G, Guo Z, McDaniel M, Barry BA. Structure and Function of Tryptophan-Tyrosine Dyads in Biomimetic β Hairpins. J Phys Chem B 2019; 123:2780-2791. [PMID: 30888824 PMCID: PMC6463897 DOI: 10.1021/acs.jpcb.8b12452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Tyrosine–tryptophan (YW) dyads
are ubiquitous
structural motifs in enzymes and play roles in proton-coupled electron
transfer (PCET) and, possibly, protection from oxidative stress. Here,
we describe the function of YW dyads in de novo designed 18-mer, β
hairpins. In Peptide M, a YW dyad is formed between W14 and Y5. A
UV hypochromic effect and an excitonic Cotton signal are observed,
in addition to singlet, excited state (W*) and fluorescence emission
spectral shifts. In a second Peptide, Peptide MW, a Y5–W13
dyad is formed diagonally across the strand and distorts the backbone.
On a picosecond timescale, the W* excited-state decay kinetics are
similar in all peptides but are accelerated relative to amino acids
in solution. In Peptide MW, the W* spectrum is consistent with increased
conformational flexibility. In Peptide M and MW, the electron paramagnetic
resonance spectra obtained after UV photolysis are characteristic
of tyrosine and tryptophan radicals at 160 K. Notably, at pH 9, the
radical photolysis yield is decreased in Peptide M and MW, compared
to that in a tyrosine and tryptophan mixture. This protective effect
is not observed at pH 11 and is not observed in peptides containing
a tryptophan–histidine dyad or tryptophan alone. The YW dyad
protective effect is attributed to an increase in the radical recombination
rate. This increase in rate can be facilitated by hydrogen-bonding
interactions, which lower the barrier for the PCET reaction at pH
9. These results suggest that the YW dyad structural motif promotes
radical quenching under conditions of reactive oxygen stress.
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Affiliation(s)
| | | | | | | | | | | | | | - Fernando Porcelli
- Department for Innovation in Biological, Agro-Food and Forest Systems , University of Tuscia , 01100 Viterbo , Italy
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21
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Milikisiyants S, Nevzorov AA, Smirnov AI. Photonic band-gap resonators for high-field/high-frequency EPR of microliter-volume liquid aqueous samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 296:152-164. [PMID: 30268940 PMCID: PMC6235713 DOI: 10.1016/j.jmr.2018.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 05/12/2023]
Abstract
High-field EPR provides significant advantages for studying structure and dynamics of molecular systems possessing an unpaired electronic spin. However, routine use of high-field EPR in biophysical research, especially for aqueous biological samples, is still facing substantial technical difficulties stemming from high dielectric millimeter wave (mmW) losses associated with non-resonant absorption by water and other polar molecules. The strong absorbance of mmW's by water also limits the penetration depth to just fractions of mm or even less, thus making fabrication of suitable sample containers rather challenging. Here we describe a radically new line of high Q-factor mmW resonators that are based on forming lattice defects in one-dimensional photonic band-gap (PBG) structures composed of low-loss ceramic discs of λ/4 in thickness and having alternating dielectric constants. A sample (either liquid or solid) is placed within the E = 0 node of the standing mm wave confined within the defect. A resonator prototype has been built and tested at 94.3 GHz. The resonator performance is enhanced by employing ceramic nanoporous membranes as flat sample holders of controllable thickness and tunable effective dielectric constant. The experimental Q-factor of an empty resonator was ≈ 420. The Q-factor decreased slightly to ≈ 370 when loaded with a water-containing nanoporous disc of 50 μm in thickness. The resonator has been tested with a number of liquid biological samples and demonstrated about tenfold gain in concentration sensitivity vs. a high-Q cylindrical TE012-type cavity. Detailed HFSS Ansys simulations have shown that the resonator structure could be further optimized by properly choosing the thickness of the aqueous sample and employing metallized surfaces. The PBG resonator design is readily scalable to higher mmW frequencies and is capable of accommodating significantly larger sample volumes than previously achieved with either Fabry-Perot or cylindrical resonators.
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Affiliation(s)
- Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
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22
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Roessler MM, Salvadori E. Principles and applications of EPR spectroscopy in the chemical sciences. Chem Soc Rev 2018; 47:2534-2553. [PMID: 29498718 DOI: 10.1039/c6cs00565a] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Electron spins permeate every aspect of science and influence numerous chemical processes: they underpin transition metal chemistry and biochemistry, mediate photosynthesis and photovoltaics and are paramount in the field of quantum information, to name but a few. Electron paramagnetic resonance (EPR) spectroscopy detects unpaired electrons and provides detailed information on structure and bonding of paramagnetic species. In this tutorial review, aimed at non-specialists, we provide a theoretical framework and examples to illustrate the vast scope of the technique in chemical research. Case studies were chosen to exemplify systematically the different interactions that characterize a paramagnetic centre and to illustrate how EPR spectroscopy may be used to derive chemical information.
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Affiliation(s)
- Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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23
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Davis I, Koto T, Terrell JR, Kozhanov A, Krzystek J, Liu A. High-Frequency/High-Field Electron Paramagnetic Resonance and Theoretical Studies of Tryptophan-Based Radicals. J Phys Chem A 2018; 122:3170-3176. [PMID: 29488750 DOI: 10.1021/acs.jpca.7b12434] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Tryptophan-based free radicals have been implicated in a myriad of catalytic and electron transfer reactions in biology. However, very few of them have been trapped so that biophysical characterizations can be performed in a high-precision context. In this work, tryptophan derivative-based radicals were studied by high-frequency/high-field electron paramagnetic resonance (HFEPR) and quantum chemical calculations. Radicals were generated at liquid nitrogen temperature with a photocatalyst, sacrificial oxidant, and violet laser. The precise g-anisotropies of l- and d-tryptophan, 5-hydroxytryptophan, 5-methoxytryptophan, 5-fluorotryptophan, and 7-hydroxytryptophan were measured directly by HFEPR. Quantum chemical calculations were conducted to predict both neutral and cationic radical spectra for comparison with the experimental data. The results indicate that under the experimental conditions, all radicals formed were cationic. Spin densities of the radicals were also calculated. The various line patterns and g-anisotropies observed by HFEPR can be understood in terms of spin-density populations and the positioning of oxygen atom substitution on the tryptophan ring. The results are considered in the light of the tryptophan and 7-hydroxytryptophan diradical found in the biosynthesis of the tryptophan tryptophylquinone cofactor of methylamine dehydrogenase.
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Affiliation(s)
- Ian Davis
- Department of Chemistry , University of Texas , San Antonio , Texas 78249 , United States.,Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Teruaki Koto
- Department of Chemistry , University of Texas , San Antonio , Texas 78249 , United States
| | - James R Terrell
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Alexander Kozhanov
- Department of Physics and Astronomy , Georgia State University , Atlanta , Georgia 30303 , United States
| | - J Krzystek
- National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Aimin Liu
- Department of Chemistry , University of Texas , San Antonio , Texas 78249 , United States
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24
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Wilcoxen J, Bruender NA, Bandarian V, Britt RD. A Radical Intermediate in Bacillus subtilis QueE during Turnover with the Substrate Analogue 6-Carboxypterin. J Am Chem Soc 2018; 140:1753-1759. [PMID: 29303575 DOI: 10.1021/jacs.7b10860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
7-Carboxy-7-deazaguanine (CDG) synthase (QueE), a member of the radical S-deoxyadenosyl-l-methionine (SAM) superfamily of enzymes, catalyzes a radical-mediated ring rearrangement required to convert 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) into CDG, forming the 7-dezapurine precursor to all pyrrolopyrimidine metabolites. Members of the radical SAM superfamily bind SAM to a [4Fe-4S] cluster, leveraging the reductive cleavage of SAM by the cluster to produce a highly reactive 5'-deoxyadenosyl radical which initiates chemistry by H atom abstraction from the substrate. QueE has recently been shown to use 6-carboxypterin (6-CP) as an alternative substrate, forming 6-deoxyadenosylpterin as the product. This reaction has been proposed to occur by radical addition between 5'-dAdo· and 6-CP, which upon oxidative decarboxylation yields the modified pterin. Here, we present spectroscopic evidence for a 6-CP-dAdo radical. The structure of this intermediate is determined by characterizing its electronic structure by continuous wave and pulse electron paramagnetic resonance spectroscopy.
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Affiliation(s)
- Jarett Wilcoxen
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Nathan A Bruender
- Department of Chemistry and Biochemistry, St. Cloud State University , St. Cloud, Minnesota 56301, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
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25
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Glover SD, Tyburski R, Liang L, Tommos C, Hammarström L. Pourbaix Diagram, Proton-Coupled Electron Transfer, and Decay Kinetics of a Protein Tryptophan Radical: Comparing the Redox Properties of W 32• and Y 32• Generated Inside the Structurally Characterized α 3W and α 3Y Proteins. J Am Chem Soc 2017; 140:185-192. [PMID: 29190082 DOI: 10.1021/jacs.7b08032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-based "hole" hopping typically involves spatially arranged redox-active tryptophan or tyrosine residues. Thermodynamic information is scarce for this type of process. The well-structured α3W model protein was studied by protein film square wave voltammetry and transient absorption spectroscopy to obtain a comprehensive thermodynamic and kinetic description of a buried tryptophan residue. A Pourbaix diagram, correlating thermodynamic potentials (E°') with pH, is reported for W32 in α3W and compared to equivalent data recently presented for Y32 in α3Y ( Ravichandran , K. R. ; Zong , A. B. ; Taguchi , A. T. ; Nocera , D. G. ; Stubbe , J. ; Tommos , C. J. Am. Chem. Soc. 2017 , 139 , 2994 - 3004 ). The α3W Pourbaix diagram displays a pKOX of 3.4, a E°'(W32(N•+/NH)) of 1293 mV, and a E°'(W32(N•/NH); pH 7.0) of 1095 ± 4 mV versus the normal hydrogen electrode. W32(N•/NH) is 109 ± 4 mV more oxidizing than Y32(O•/OH) at pH 5.4-10. In the voltammetry measurements, W32 oxidation-reduction occurs on a time scale of about 4 ms and is coupled to the release and subsequent uptake of one full proton to and from bulk. Kinetic analysis further shows that W32 oxidation likely involves pre-equilibrium electron transfer followed by proton transfer to a water or small water cluster as the primary acceptor. A well-resolved absorption spectrum of W32• is presented, and analysis of decay kinetics show that W32• persists ∼104 times longer than aqueous W• due to significant stabilization by the protein. The redox characteristics of W32 and Y32 are discussed relative to global and local protein properties.
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Affiliation(s)
- Starla D Glover
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States.,Department of Chemistry, Ångström Laboratory, Uppsala University , Box 523, SE-75120 Uppsala, Sweden
| | - Robin Tyburski
- Department of Chemistry, Ångström Laboratory, Uppsala University , Box 523, SE-75120 Uppsala, Sweden
| | - Li Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | - Cecilia Tommos
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | - Leif Hammarström
- Department of Chemistry, Ångström Laboratory, Uppsala University , Box 523, SE-75120 Uppsala, Sweden
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26
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Blaszczyk AJ, Wang B, Silakov A, Ho JV, Booker SJ. Efficient methylation of C2 in l-tryptophan by the cobalamin-dependent radical S-adenosylmethionine methylase TsrM requires an unmodified N1 amine. J Biol Chem 2017; 292:15456-15467. [PMID: 28747433 PMCID: PMC5602403 DOI: 10.1074/jbc.m117.778548] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/20/2017] [Indexed: 11/06/2022] Open
Abstract
TsrM catalyzes the methylation of C2 in l-tryptophan (Trp). This reaction is the first step in the biosynthesis of the quinaldic acid moiety of the thiopeptide antibiotic thiostrepton, which exhibits potent activity against Gram-positive pathogens. TsrM is a member of the radical S-adenosylmethionine (SAM) superfamily of enzymes, but it does not catalyze the formation of 5'-deoxyadenosin-5'-yl or any other SAM-derived radical. In addition to a [4Fe-4S] cluster, TsrM contains a cobalamin cofactor that serves as an intermediate methyl carrier in its reaction. However, how this cofactor donates a methyl moiety to the Trp substrate is unknown. Here, we showed that the unmodified N1 position of Trp is important for turnover and that 1-thia-Trp and 1-oxa-Trp serve as competitive inhibitors. We also showed that β-cyclopropyl-Trp undergoes C2 methylation in the absence of cyclopropyl ring opening, disfavoring mechanisms that involve unpaired electron density at C3 of the indole ring. Moreover, we showed that all other indole-substituted analogs of Trp undergo methylation at varying but measurable rates and that the analog 7-aza-Trp, which is expected to temper the nucleophilicity of C2 in Trp, is a very poor substrate. Last, no formation of cob(II)alamin or substrate radicals was observed during the reaction with Trp or any molecule within a tested panel of Trp analogs. In summary, our results are most consistent with a mechanism that involves two polar nucleophilic displacements, the second of which requires deprotonation of the indole nitrogen in Trp during its attack on methylcobalamin.
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Affiliation(s)
| | - Bo Wang
- the Department of Chemistry, and
| | | | | | - Squire J Booker
- From the Department of Biochemistry and Molecular Biology,
- the Department of Chemistry, and
- the Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802
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27
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Juszczak LJ, Eisenberg AS. The Color of Cation-π Interactions: Subtleties of Amine-Tryptophan Interaction Energetics Allow for Radical-like Visible Absorbance and Fluorescence. J Am Chem Soc 2017; 139:8302-8311. [PMID: 28537725 DOI: 10.1021/jacs.7b03442] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Several peptides and a protein with an inter- or intramolecular cation-π interaction between tryptophan (Trp) and an amine cation are shown to absorb and fluoresce in the visible region of the spectrum. Titration of indole with sodium hydroxide or ammonium hydroxide yields an increasing visible fluorescence as well. Visible absorption and multipeaked fluorescence excitation spectra correlate with experimental absorption spectra and the vibrational modes of calculated absorption spectra for the neutral Trp radical. The radical character of the cation-indole interaction is predicted to stem from the electrostatic dislocation of indole highest occupied molecular orbital (HOMO) charge density toward the cation with a subsequent electronic transition from the HOMO-2 to the HOMO. Because this is a vertical transition, fluorescence is possible. Hydrogen bonding at the indole amine most likely stabilizes the radical-like state. These results provide new spectroscopic tools for the investigation of cation-π interactions in numerous biological systems, among them, proteins and their myriad ligands, and show that one, or at most, two, point mutations with natural amino acids are all that is required to impart visible fluorescence to proteins.
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Affiliation(s)
- Laura J Juszczak
- Chemistry Department, Brooklyn College, The City University of New York , New York, New York 11210, United States.,PhD programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York , New York, New York 10016, United States
| | - Azaria S Eisenberg
- Chemistry Department, Brooklyn College, The City University of New York , New York, New York 11210, United States
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28
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Muñoz-Rugeles L, Galano A, Alvarez-Idaboy JR. The role of acid–base equilibria in formal hydrogen transfer reactions: tryptophan radical repair by uric acid as a paradigmatic case. Phys Chem Chem Phys 2017; 19:15296-15309. [DOI: 10.1039/c7cp01557g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The sequential proton gain electron transfer and proton electron sequential transfer mechanisms play the most important roles in tryptophan repair by uric acid.
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Affiliation(s)
- Leonardo Muñoz-Rugeles
- Facultad de Química
- Departamento de Física y Química Teórica
- Universidad Nacional Autónoma de México
- México
- Mexico
| | - Annia Galano
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- México
- Mexico
| | - Juan Raúl Alvarez-Idaboy
- Facultad de Química
- Departamento de Física y Química Teórica
- Universidad Nacional Autónoma de México
- México
- Mexico
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29
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Miller DC, Tarantino KT, Knowles RR. Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities. Top Curr Chem (Cham) 2016; 374:30. [PMID: 27573270 PMCID: PMC5107260 DOI: 10.1007/s41061-016-0030-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/21/2016] [Indexed: 10/21/2022]
Abstract
Proton-coupled electron transfers (PCETs) are unconventional redox processes in which both protons and electrons are exchanged, often in a concerted elementary step. While PCET is now recognized to play a central a role in biological redox catalysis and inorganic energy conversion technologies, its applications in organic synthesis are only beginning to be explored. In this chapter, we aim to highlight the origins, development, and evolution of the PCET processes most relevant to applications in organic synthesis. Particular emphasis is given to the ability of PCET to serve as a non-classical mechanism for homolytic bond activation that is complimentary to more traditional hydrogen atom transfer processes, enabling the direct generation of valuable organic radical intermediates directly from their native functional group precursors under comparatively mild catalytic conditions. The synthetically advantageous features of PCET reactivity are described in detail, along with examples from the literature describing the PCET activation of common organic functional groups.
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Affiliation(s)
- David C Miller
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Kyle T Tarantino
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Robert R Knowles
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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30
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Dongare P, Maji S, Hammarström L. Direct Evidence of a Tryptophan Analogue Radical Formed in a Concerted Electron−Proton Transfer Reaction in Water. J Am Chem Soc 2016; 138:2194-9. [DOI: 10.1021/jacs.5b08294] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prateek Dongare
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
| | - Somnath Maji
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
| | - Leif Hammarström
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
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31
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Hirst J, Roessler MM. Energy conversion, redox catalysis and generation of reactive oxygen species by respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:872-83. [PMID: 26721206 PMCID: PMC4893023 DOI: 10.1016/j.bbabio.2015.12.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 12/30/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is critical for respiration in mammalian mitochondria. It oxidizes NADH produced by the Krebs' tricarboxylic acid cycle and β-oxidation of fatty acids, reduces ubiquinone, and transports protons to contribute to the proton-motive force across the inner membrane. Complex I is also a significant contributor to cellular oxidative stress. In complex I, NADH oxidation by a flavin mononucleotide, followed by intramolecular electron transfer along a chain of iron–sulfur clusters, delivers electrons and energy to bound ubiquinone. Either at cluster N2 (the terminal cluster in the chain) or upon the binding/reduction/dissociation of ubiquinone/ubiquinol, energy from the redox process is captured to initiate long-range energy transfer through the complex and drive proton translocation. This review focuses on current knowledge of how the redox reaction and proton transfer are coupled, with particular emphasis on the formation and role of semiquinone intermediates in both energy transduction and reactive oxygen species production. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. Current knowledge of the redox reactions catalyzed by complex I is reviewed. Possible quinone reduction pathways are presented. The presence and number of semiquinone intermediates are deliberated. The involvement of cluster N2/semiquinones in coupled proton transfer is discussed. Evidence for reactive oxygen species production by semiquinones is examined.
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Affiliation(s)
- Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
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32
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Pagba CV, McCaslin TG, Veglia G, Porcelli F, Yohannan J, Guo Z, McDaniel M, Barry BA. A tyrosine-tryptophan dyad and radical-based charge transfer in a ribonucleotide reductase-inspired maquette. Nat Commun 2015; 6:10010. [PMID: 26627888 PMCID: PMC4686667 DOI: 10.1038/ncomms10010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/23/2015] [Indexed: 01/29/2023] Open
Abstract
In class 1a ribonucleotide reductase (RNR), a substrate-based radical is generated in the α2 subunit by long-distance electron transfer involving an essential tyrosyl radical (Y122O·) in the β2 subunit. The conserved W48 β2 is ∼10 Å from Y122OH; mutations at W48 inactivate RNR. Here, we design a beta hairpin peptide, which contains such an interacting tyrosine–tryptophan dyad. The NMR structure of the peptide establishes that there is no direct hydrogen bond between the phenol and the indole rings. However, electronic coupling between the tyrosine and tryptophan occurs in the peptide. In addition, downshifted ultraviolet resonance Raman (UVRR) frequencies are observed for the radical state, reproducing spectral downshifts observed for β2. The frequency downshifts of the ring and CO bands are consistent with charge transfer from YO· to W or another residue. Such a charge transfer mechanism implies a role for the β2 Y-W dyad in electron transfer. Tyrosine-tryptophan dyads are known to mediate electron transfer reactions in a range of different proteins. Here, the authors study a beta hairpin peptide, probing the tyrosine-tryptophan interaction and showing no hydrogen bonding but rather charge transfer between the tyrosyl radical and tryptophan'.
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Affiliation(s)
- Cynthia V Pagba
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Tyler G McCaslin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Fernando Porcelli
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo 01100, Italy
| | - Jiby Yohannan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zhanjun Guo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Miranda McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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33
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Benjdia A, Pierre S, Gherasim C, Guillot A, Carmona M, Amara P, Banerjee R, Berteau O. The thiostrepton A tryptophan methyltransferase TsrM catalyses a cob(II)alamin-dependent methyl transfer reaction. Nat Commun 2015; 6:8377. [PMID: 26456915 PMCID: PMC4632189 DOI: 10.1038/ncomms9377] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 08/17/2015] [Indexed: 11/09/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a novel class of natural products including several antibiotics and bacterial toxins. In countless RiPP biosynthetic pathways, cobalamin-dependent radical SAM (B12/rSAM) enzymes play a pivotal role. In the biosynthetic pathway of the antibiotic and anti-cancer agent thiostrepton A, TsrM, a B12/rSAM enzyme, catalyses the transfer of a methyl group to an electrophilic carbon atom of tryptophan. Here we show that methylcob(III)alamin is the probable physiological enzyme cofactor, and cob(II)alamin rather than cob(I)alamin is a key reaction intermediate. Furthermore, we establish that TsrM and a triple-alanine mutant alkylate cob(II)alamin efficiently leading to the synthesis of MeCbl. Exploiting TsrM substrate ambiguity, we demonstrate that TsrM does not catalyse substrate H-atom abstraction like most radical SAM enzymes. Based on these data, we propose an unprecedented radical-based C-methylation mechanism, which further expands the chemical versatility of rSAM enzymes.
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Affiliation(s)
- Alhosna Benjdia
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Stéphane Pierre
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Carmen Gherasim
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, USA
| | - Alain Guillot
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Manon Carmona
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Patricia Amara
- Metalloproteins Unit, Institut de Biologie Structurale, UMR5075, CEA, CNRS, Univ. Grenoble-Alpes. 71, Avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, USA
| | - Olivier Berteau
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
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34
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Larson BC, Pomponio JR, Shafaat HS, Kim RH, Leigh BS, Tauber MJ, Kim JE. Photogeneration and Quenching of Tryptophan Radical in Azurin. J Phys Chem B 2015; 119:9438-49. [PMID: 25625660 PMCID: PMC5092234 DOI: 10.1021/jp511523z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan and tyrosine can form radical intermediates that enable long-range, multistep electron transfer (ET) reactions in proteins. This report describes the mechanisms of formation and quenching of a neutral tryptophan radical in azurin, a blue-copper protein that contains native tyrosine (Y108 and Y72) and tryptophan (W48) residues. A long-lived neutral tryptophan radical W48• is formed upon UV-photoexcitation of a zinc(II)-substituted azurin mutant in the presence of an external electron acceptor. The quantum yield of W48• formation (Φ) depends upon the tyrosine residues in the protein. A tyrosine-deficient mutant, Zn(II)Az48W, exhibited a value of Φ = 0.080 with a Co(III) electron acceptor. A nearly identical quantum yield was observed when the electron acceptor was the analogous tyrosine-free, copper(II) mutant; this result for the Zn(II)Az48W:Cu(II)Az48W mixture suggests there is an interprotein ET path. A single tyrosine residue at one of the native positions reduced the quantum yield to 0.062 (Y108) or 0.067 (Y72). Wild-type azurin with two tyrosine residues exhibited a quantum yield of Φ = 0.045. These data indicate that tyrosine is able to quench the tryptophan radical in azurin.
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Affiliation(s)
- Bethany C. Larson
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jennifer R. Pomponio
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | | | - Rachel H. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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35
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Baratto MC, Sinicropi A, Linde D, Sáez-Jiménez V, Sorace L, Ruiz-Duenas FJ, Martinez AT, Basosi R, Pogni R. Redox-Active Sites in Auricularia auricula-judae Dye-Decolorizing Peroxidase and Several Directed Variants: A Multifrequency EPR Study. J Phys Chem B 2015; 119:13583-92. [PMID: 26120933 DOI: 10.1021/acs.jpcb.5b02961] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peroxide-activated Auricularia auricula-judae dye-decolorizing peroxidase (DyP) forms a mixed Trp377 and Tyr337 radical, the former being responsible for oxidation of the typical DyP substrates (Linde et al. Biochem. J., 2015, 466, 253-262); however, a pure tryptophanyl radical EPR signal is detected at pH 7 (where the enzyme is inactive), in contrast with the mixed signal observed at pH for optimum activity, pH 3. On the contrary, the presence of a second tyrosine radical (at Tyr147) is deduced by a multifrequency EPR study of a variety of simple and double-directed variants (including substitution of the above and other tryptophan and tyrosine residues) at different freezing times after their activation by H2O2 (at pH 3). This points out that subsidiary long-range electron-transfer pathways enter into operation when the main pathway(s) is removed by directed mutagenesis, with catalytic efficiencies progressively decreasing. Finally, self-reduction of the Trp377 neutral radical is observed when reaction time (before freezing) is increased in the absence of reducing substrates (from 10 to 60 s). Interestingly, the tryptophanyl radical is stable in the Y147S/Y337S variant, indicating that these two tyrosine residues are involved in the self-reduction reaction.
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Affiliation(s)
- Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy
| | - Dolores Linde
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Verónica Sáez-Jiménez
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Lorenzo Sorace
- Department of Chemistry, "Ugo Schiff" and INSTM RU, University of Florence , 50019 Sesto Fiorentino, Florence, Italy
| | | | - Angel T Martinez
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy
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36
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Manjunath S, Satish Rao BS, Satyamoorthy K, Mahato KK. Laser induced autofluorescence in the monitoring of β-mercaptoethanol mediated photo induced proton coupled electron transfer in proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 149:607-614. [PMID: 25985124 DOI: 10.1016/j.saa.2015.04.096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/18/2015] [Accepted: 04/22/2015] [Indexed: 06/04/2023]
Abstract
Photo induced proton coupled electron transfer (PCET) is an important process that many organisms use for progression of catalytic reactions leading to energy conversion. In the present study, the influence of SDS and BME on the redox properties of tyrosine and tryptophan for five different globular proteins, BSA, HSA, RNase-A, trypsin and lysozyme were studied using laser induced autofluorescence. The proteins were subjected to denaturation under SDS, SDS plus heat and SDS plus β-mercaptoethanol (BME) plus heat and the corresponding fluorescence were recorded. The influence of BME on the autofluorescence properties of the proteins were evaluated upon tris-2-corboxy-ethyl phosphine (TCEP) denaturation. The BSA and HSA when exposed to SDS alone, exhibited hydrophobic collapse around their tryptophan moieties. However, these proteins when treated with SDS plus BME plus heat, an unusual red shift in the emission was observed, may be due to proton transfer from hydroxyl group of the excited tyrosine residues to the local microenvironments. The observation was further confirmed with similar proton transfer in absence of tryptophan in RNase-A showing involvement of tyrosine in the process. A drastic quenching of fluorescence in all of the proteins under study were also observed, may be due to photo-induced electron transfer (PET) from BME to the intrinsic fluorophores resulting in radical ions formation, evaluated upon DCFDA measurements.
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Affiliation(s)
- S Manjunath
- Department of Biophysics, School of Life Sciences, Manipal University, Manipal, India
| | - B S Satish Rao
- Department of Radiation Biology and Toxicology, School of Life Sciences, Manipal University, Manipal, India
| | - K Satyamoorthy
- School of Life Sciences, Manipal University, Manipal 576104, Karnataka, India
| | - K K Mahato
- Department of Biophysics, School of Life Sciences, Manipal University, Manipal, India.
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37
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Witwicki M. Theoretical Characterisation of Phosphinyl Radicals and Their Magnetic Properties: g Matrix. Chemphyschem 2015; 16:1912-25. [PMID: 25873130 DOI: 10.1002/cphc.201500121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Indexed: 11/11/2022]
Abstract
The g matrices (g tensors) of various phosphinyl radicals (R2 P(.) ) were calculated using the DFT and multireference configuration interaction (MRCI) methods. The g matrices were distinctly dependent on the molecular structure of the radical. To thoroughly examine this dependence, the contributions from individual atoms and excited states were calculated. The former revealed the gain from the phosphorus atom to be preeminent unless PO or PS bonds are present in the radical molecule. The contributions owing to excited states arising from electronic transitions between doubly occupied molecular orbitals and the SOMO were clearly positive, as in the case of semiquinone and niroxide radicals. The transitions from the phosphorus lone pair were of paramount importance. Surprisingly, unlike for semiquinones and nitroxides, a significant negative contribution was observed from excitations from the SOMO to unoccupied molecular orbitals. For radicals with PO bonds, this contribution to the g2 component was dominant.
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Affiliation(s)
- Maciej Witwicki
- Faculty of Chemistry, Wroclaw University, 14 F. Joliot-Curie St., Wroclaw 50-283 (Poland).
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38
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Tan L, Tureček F, Francisco JS, Xia Y. Probing the radical and base dual properties of peptide sulfinyl radicals via mass spectrometry. J Phys Chem A 2014; 118:11828-35. [PMID: 25428214 DOI: 10.1021/jp510362p] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heteroatom-centered radicals are known to play critical roles in atmospheric chemistry, organic synthesis, and biology. While most studies have focused on the radical reactivity such as hydrogen abstraction, the base properties of heteroatom-centered radicals have long been overlooked, despite the profound consequences, such as their ability to participate in hydrogen-bonding networks. In this study, we use the sulfinyl radical (-SO(•)) as a model to show that the dual properties of heteroatom-centered radicals, that is, their ability to function as a radical and a base, can coexist in peptides and be differentiated by examining the loss of hydrosulfinyl radical (SOH) upon unimolecular dissociation of the peptide sulfinyl radical ions in the gas phase. The loss of SOH can result from two channels; one involves hydrogen atom abstraction, which reflects the radical property; the other is initiated by proton transfer to the sulfinyl radical, manifesting its base property. Tuning of the two properties of peptide sulfinyl radicals can be achieved by varying the chemical properties of the neighboring functional groups, which demonstrates the influence of the local chemical environment on the behavior of the radical species. The experimental approach established in this study to probe the dual chemical property of the peptide sulfinyl radical can be potentially applied to studying other types of heteroatom-centered radical species of biological significance.
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Affiliation(s)
- Lei Tan
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
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39
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Abstract
Electron transfer (ET) reactions within proteins are accomplished by a broad set of redox-active molecules, including natural amino acids. Tryptophan participates in ET chemistry as both a cation and a neutral radical. Identification and characterization of the biologically relevant species is essential to understand efficient ET mechanisms in proteins. We present resonance Raman spectra and excitation profiles of the tryptophan cation radical generated by combining a strong oxidant, Ce(IV), with tryptophan model compounds in a fast-flow mixing device. Isotopically modified derivatives, coupled with calculations, allowed the assignment of the normal modes of this radical. Raman bands that are sensitive to protonation state and hydrogen bonding environment of the cation radical were identified. The present findings, along with resonance Raman spectra of the closed-shell and neutral radical counterparts, form a foundation for probing tryptophan-mediated ET reactions in proteins.
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Affiliation(s)
- Hannah S Shafaat
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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40
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Bernini C, Arezzini E, Basosi R, Sinicropi A. In silico spectroscopy of tryptophan and tyrosine radicals involved in the long-range electron transfer of cytochrome c peroxidase. J Phys Chem B 2014; 118:9525-37. [PMID: 25084495 DOI: 10.1021/jp5025153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c peroxidase (CcP) is a heme-containing enzyme that catalyzes the oxidation of the ferrocytochrome c to ferricytochrome c with concomitant reduction of H2O2 to H2O. Its catalytic cycle involves the formation of a double oxidized species (compound I) consisting of an oxoferryl center (Fe(IV)═O) and an amino acid radical (R(•)). Here we use a quantum-mechanics/molecular-mechanics (QM/MM) computational protocol based on density functional theory (DFT) and multiconfigurational perturbation theory (CASPT2) methods to reproduce specific features of compound I EPR and UV-vis spectra. The results show that the employed QM/MM models can correctly predict the magnetic, electronic and vibrational properties of the observed amino acid radicals of compound I. Furthermore, we have been able to confirm that the principal radical species of compound I is a tryptophan cationic radical located on residue 191 (Trp191(•+)) and that three tyrosine residues (Tyr203, Tyr236, and Tyr251), located along two possible ET pathways involving Trp191(•+), are possible candidates to host the secondary radical species.
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Affiliation(s)
- Caterina Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , Via A. Moro 2, 53100 Siena, Italy
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41
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High-frequency and high-field electron paramagnetic resonance (HFEPR): a new spectroscopic tool for bioinorganic chemistry. J Biol Inorg Chem 2014; 19:297-318. [DOI: 10.1007/s00775-013-1084-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/27/2013] [Indexed: 12/27/2022]
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42
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Kao D, Chaintreau A, Lepoittevin JP, Giménez-Arnau E. Mechanistic studies on the reactivity of sensitizing allylic hydroperoxides: investigation of the covalent modification of amino acids by carbon-radical intermediates. Toxicol Res (Camb) 2014. [DOI: 10.1039/c3tx50109d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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43
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Günaydın-Şen Ö, Chen P, Fosso-Tande J, Allen TL, Cherian J, Tokumoto T, Lahti PM, McGill S, Harrison RJ, Musfeldt JL. Magnetoelectric coupling in 4,4'-stilbenedinitrene. J Chem Phys 2013; 138:204716. [PMID: 23742509 DOI: 10.1063/1.4807053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We investigated the optical properties of 4,4'-stilbenedinitrene at low temperature and in high magnetic fields and compared the results with complementary first principles calculations. Both physical tuning parameters allow us to manipulate the singlet-triplet equilibrium, and by doing so, control the optical contrast (which is on the order of -2.5 × 10(2) cm(-1) at 555 nm and 35 T). Moreover, analysis of the magneto-optical response using a combined population and Beer's law framework reveals the singlet-triplet spin gap and identifies particular features in the absorption difference spectrum as deriving from singlet or triplet state excitations. These findings deepen our understanding of coupling in open shell molecules and show how chemical structure modification can modulate charge-spin interactions in organic biradicals.
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Affiliation(s)
- Ö Günaydın-Şen
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
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44
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Bernini C, Andruniów T, Olivucci M, Pogni R, Basosi R, Sinicropi A. Effects of the Protein Environment on the Spectral Properties of Tryptophan Radicals in Pseudomonas aeruginosa Azurin. J Am Chem Soc 2013; 135:4822-33. [DOI: 10.1021/ja400464n] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Caterina Bernini
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Tadeusz Andruniów
- Quantum Chemistry and Molecular
Modelling Lab, Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego
27, 50-370 Wroclaw, Poland
| | - Massimo Olivucci
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio
43403, United States
| | - Rebecca Pogni
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Riccardo Basosi
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Adalgisa Sinicropi
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
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45
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Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis. Proc Natl Acad Sci U S A 2013; 110:4569-73. [PMID: 23487750 DOI: 10.1073/pnas.1215011110] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the importance of tryptophan (Trp) radicals in biology, very few radicals have been trapped and characterized in a physiologically meaningful context. Here we demonstrate that the diheme enzyme MauG uses Trp radical chemistry to catalyze formation of a Trp-derived tryptophan tryptophylquinone cofactor on its substrate protein, premethylamine dehydrogenase. The unusual six-electron oxidation that results in tryptophan tryptophylquinone formation occurs in three discrete two-electron catalytic steps. Here the exact order of these oxidation steps in the processive six-electron biosynthetic reaction is determined, and reaction intermediates are structurally characterized. The intermediates observed in crystal structures are also verified in solution using mass spectrometry. Furthermore, an unprecedented Trp-derived diradical species on premethylamine dehydrogenase, which is an intermediate in the first two-electron step, is characterized using high-frequency and -field electron paramagnetic resonance spectroscopy and UV-visible absorbance spectroscopy. This work defines a unique mechanism for radical-mediated catalysis of a protein substrate, and has broad implications in the areas of applied biocatalysis and understanding of oxidative protein modification during oxidative stress.
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46
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Tomter AB, Zoppellaro G, Andersen NH, Hersleth HP, Hammerstad M, Røhr ÅK, Sandvik GK, Strand KR, Nilsson GE, Bell CB, Barra AL, Blasco E, Le Pape L, Solomon EI, Andersson KK. Ribonucleotide reductase class I with different radical generating clusters. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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