1
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Török P, Lakk-Bogáth D, Unjaroen D, Browne WR, Kaizer J. Effect of monodentate heterocycle co-ligands on the μ-1,2-peroxo-diiron(III) mediated aldehyde deformylation reactions. J Inorg Biochem 2024; 258:112620. [PMID: 38824901 DOI: 10.1016/j.jinorgbio.2024.112620] [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: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/04/2024]
Abstract
Peroxo-diiron(III) species are present in the active sites of many metalloenzymes that carry out challenging organic transformations. The reactivity of these species is influenced by various factors, such as the structure and topology of the supporting ligands, the identity of the axial and equatorial co-ligands, and the oxidation states of the metal ion(s). In this study, we aim to diversify the importance of equatorial ligands in controlling the reactivity of peroxo-diiron(III) species. As a model compound, we chose the previously published and fully characterized [(PBI)2(CH3CN)FeIII(μ-O2)FeIII(CH3CN)(PBI)2]4+ complex, where the steric effect of the four PBI ligands is minimal, so the labile CH3CN molecules easily can be replaced by different monodentate co-ligands (substituted pyridines and N-donor heterocyclic compounds). Thus, their effect on the electronic and spectral properties of peroxo-divas(III) intermediates could be easily investigated. The relationship between structure and reactivity was also investigated in the stoichiometric deformylation of PPA mediated by peroxo-diiron(III) complexes. It was found that the deformylation rates are influenced by the Lewis acidity and redox properties of the metal centers, and showed a linear correlation with the FeIII/FeII redox potentials (in the range of 197 to 415 mV).
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Affiliation(s)
- Patrik Török
- Research Group of Bioorganic and Biocoordination Chemistry, Universtiy of Pannonia, 8201 Veszprém, Hungary
| | - Dóra Lakk-Bogáth
- Research Group of Bioorganic and Biocoordination Chemistry, Universtiy of Pannonia, 8201 Veszprém, Hungary
| | - Duenpen Unjaroen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Wesley R Browne
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - József Kaizer
- Research Group of Bioorganic and Biocoordination Chemistry, Universtiy of Pannonia, 8201 Veszprém, Hungary.
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2
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Torić J, Karković Marković A, Mustać S, Pulitika A, Jakobušić Brala C, Pilepić V. Proton-Coupled Electron Transfer and Hydrogen Tunneling in Olive Oil Phenol Reactions. Int J Mol Sci 2024; 25:6341. [PMID: 38928048 PMCID: PMC11203655 DOI: 10.3390/ijms25126341] [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: 04/29/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Olive oil phenols are recognized as molecules with numerous positive health effects, many of which rely on their antioxidative activity, i.e., the ability to transfer hydrogen to radicals. Proton-coupled electron transfer reactions and hydrogen tunneling are ubiquitous in biological systems. Reactions of olive oil phenols, hydroxytyrosol, tyrosol, oleuropein, oleacein, oleocanthal, homovanillyl alcohol, vanillin, and a few phenolic acids with a DPPH• (2,2-diphenyl-1-picrylhydrazyl) radical in a 1,4-dioxane:water = 95:5 or 99:1 v/v solvent mixture were studied through an experimental kinetic analysis and computational chemistry calculations. The highest rate constants corresponding to the highest antioxidative activity are obtained for the ortho-diphenols hydroxytyrosol, oleuropein, and oleacein. The experimentally determined kinetic isotope effects (KIEs) for hydroxytyrosol, homovanillyl alcohol, and caffeic acid reactions are 16.0, 15.4, and 16.7, respectively. Based on these KIEs, thermodynamic activation parameters, and an intrinsic bond orbital (IBO) analysis along the IRC path calculations, we propose a proton-coupled electron transfer mechanism. The average local ionization energy and electron donor Fukui function obtained for the phenolic compounds show that the most reactive electron-donating sites are associated with π electrons above and below the aromatic ring, in support of the IBO analysis and proposed PCET reaction mechanism. Large KIEs and isotopic values of Arrhenius pre-exponential factor AH/AD determined for the hydroxytyrosol, homovanillyl alcohol, and caffeic acid reactions of 0.6, 1.3, and 0.3, respectively, reveal the involvement of hydrogen tunneling in the process.
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Affiliation(s)
- Jelena Torić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (J.T.); (A.K.M.); (S.M.)
| | - Ana Karković Marković
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (J.T.); (A.K.M.); (S.M.)
| | - Stipe Mustać
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (J.T.); (A.K.M.); (S.M.)
| | - Anamarija Pulitika
- Faculty of Chemical Engineering and Technology, University of Zagreb, 10000 Zagreb, Croatia;
| | - Cvijeta Jakobušić Brala
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (J.T.); (A.K.M.); (S.M.)
| | - Viktor Pilepić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (J.T.); (A.K.M.); (S.M.)
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3
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Deng WH, Liao RZ. Cysteine Radical and Glutamate Collaboratively Enable C-H Bond Activation and C-N Bond Cleavage in a Glycyl Radical Enzyme HplG. J Chem Inf Model 2024; 64:4168-4179. [PMID: 38745447 DOI: 10.1021/acs.jcim.4c00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Hydroxyprolines are abundant in nature and widely utilized by many living organisms. Isomerization of trans-4-hydroxy-d-proline (t4D-HP) to generate 2-amino-4-ketopentanoate has been found to need a glycyl radical enzyme HplG, which catalyzes the cleavage of the C-N bond, while dehydration of trans-4-hydroxy-l-proline involves a homologous enzyme of HplG. Herein, molecular dynamics simulations and quantum mechanics/molecular mechanics (QM/MM) calculations are employed to understand the reaction mechanism of HplG. Two possible reaction pathways of HplG have been explored to decipher the origin of its chemoselectivity. The QM/MM calculations reveal that the isomerization proceeds via an initial hydrogen shift from the Cγ site of t4D-HP to a catalytic cysteine radical, followed by cleavage of the Cδ-N bond in t4D-HP to form a radical intermediate that captures a hydrogen atom from the cysteine. Activation of the Cδ-H bond in t4D-HP to bring about dehydration of t4D-HP possesses an extremely high energy barrier, thus rendering the dehydration pathway implausible in HplG. On the basis of the current calculations, conserved residue Glu429 plays a pivotal role in the isomerization pathway: the hydrogen bonding between it and t4D-HP weakens the hydroxyalkyl Cγ-Hγ bond, and it acts as a proton acceptor to trigger the cleavage of the C-N bond in t4D-HP. Our current QM/MM calculations rationalize the origin of the experimentally observed chemoselectivity of HplG and propose an H-bond-assisted bond activation strategy in radical-containing enzymes. These findings have general implications on radical-mediated enzymatic catalysis and expand our understanding of how nature wisely and selectively activates the C-H bond to modulate catalytic selectivity.
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Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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4
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Moppel I, Elliott B, Chen S. Intermolecular hydrogen bonding behavior of amino acid radical cations. Org Biomol Chem 2024; 22:3966-3978. [PMID: 38690804 DOI: 10.1039/d4ob00301b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Amino acid and peptide radicals are of broad interest due to their roles in biochemical oxidative damage, pathogenesis and protein radical catalysis, among others. Using density functional theory (DFT) calculations at the ωB97X-D/def2-QZVPPD//ωB97X-D/def2-TZVPP level of theory, we systematically investigated the hydrogen bonding between water and fourteen α-amino acids (Ala, Asn, Cys, Gln, Gly, His, Met, Phe, Pro, Sel, Ser, Thr, Trp, and Tyr) in both neutral and radical cation forms. For all amino acids surveyed, stronger hydrogen-bonding interactions with water were observed upon single-electron oxidation, with the greatest increases in hydrogen-bonding strength occurring in Gly, Ala and His. We demonstrate that the side chain has a significant impact on the most favorable hydrogen-bonding modes experienced by amino acid radical cations. Our computations also explored the fragmentation of amino acid radical cations through the loss of a COOH radical facilitated by hydrogen bonding. The most favorable pathways provided stabilization of the resulting cationic fragments through hydrogen bonding, resulting in more favorable thermodynamics for the fragmentation process. These results indicate that non-covalent interactions with the environment have a profound impact on the structure and chemical fate of oxidized amino acids.
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Affiliation(s)
- Isabella Moppel
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA.
| | - BarbaraAnn Elliott
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA.
| | - Shuming Chen
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA.
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5
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Kass D, Larson VA, Corona T, Kuhlmann U, Hildebrandt P, Lohmiller T, Bill E, Lehnert N, Ray K. Trapping of a phenoxyl radical at a non-haem high-spin iron(II) centre. Nat Chem 2024; 16:658-665. [PMID: 38216752 DOI: 10.1038/s41557-023-01405-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 11/17/2023] [Indexed: 01/14/2024]
Abstract
The activation of dioxygen at haem and non-haem metal centres, and subsequent functionalization of unactivated C‒H bonds, has been a focal point of much research. In iron-mediated oxidation reactions, O2 binding at an iron(II) centre is often accompanied by an oxidation of the iron centre. Here we demonstrate dioxygen activation by sodium tetraphenylborate and protons in the presence of an iron(II) complex to form a reactive radical species, whereby the iron oxidation state remains unaltered in the presence of a highly oxidizing phenoxyl radical and O2. This complex, containing an unusual iron(II)-phenoxyl radical motif, represents an elusive example of a spectroscopically characterized oxygen-derived iron(II)-reactive intermediate during chemical and biological dioxygen activation at haem and non-haem iron active centres. The present report opens up strategies for the stabilization of a phenoxyl radical cofactor, with its full oxidizing capabilities, to act as an independent redox centre next to an iron(II) site during substrate oxidation reactions.
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Affiliation(s)
- Dustin Kass
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Virginia A Larson
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Teresa Corona
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Uwe Kuhlmann
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Thomas Lohmiller
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
- EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, Germany
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
| | - Kallol Ray
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany.
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6
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Takeyama T, Shimazaki Y. Diversity of oxidation state in copper complexes with phenolate ligands. Dalton Trans 2024; 53:3911-3929. [PMID: 38319292 DOI: 10.1039/d3dt04230h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The phenoxyl radical binding copper complexes have been widely developed and their detailed geometric and electronic structures have been clarified. While many one-electron oxidized CuII-phenolate complexes have been reported previously, recent studies of the Cu-phenolate complexes proceed toward elucidation of the complexes with other oxidation states, such as the phenoxyl radical binding CuI complexes and CuIV-phenolate complexes in the formal oxidation state. This Perspective focuses on new aspects of the properties and reactivities of various Cu-phenolate and Cu-phenoxyl radical complexes with emphasis on the relationship between geometric and electronic structures.
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Affiliation(s)
- Tomoyuki Takeyama
- Department of Applied Chemistry, Sanyo-Onoda City University, 1-1-1, Daigakudori, Sanyo-Onoda, 756-0884 Yamaguchi, Japan.
| | - Yuichi Shimazaki
- College of Science, Ibaraki University, Bunkyo, Mito 310-8512, Japan.
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7
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Zhong J, Soudackov AV, Hammes-Schiffer S. Probing Nonadiabaticity of Proton-Coupled Electron Transfer in Ribonucleotide Reductase. J Phys Chem Lett 2024; 15:1686-1693. [PMID: 38315651 DOI: 10.1021/acs.jpclett.3c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The enzyme ribonucleotide reductase, which is essential for DNA synthesis, initiates the conversion of ribonucleotides to deoxyribonucleotides via radical transfer over a 32 Å pathway composed of proton-coupled electron transfer (PCET) reactions. Previously, the first three PCET reactions in the α subunit were investigated with hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations. Herein, the fourth PCET reaction in this subunit between C439 and guanosine diphosphate (GDP) is simulated and found to be slightly exoergic with a relatively high free energy barrier. To further elucidate the mechanisms of all four PCET reactions, we analyzed the vibronic and electron-proton nonadiabaticities. This analysis suggests that interfacial PCET between Y356 and Y731 is vibronically and electronically nonadiabatic, whereas PCET between Y731 and Y730 and between C439 and GDP is fully adiabatic and PCET between Y730 and C439 is in the intermediate regime. These insights provide guidance for selecting suitable rate constant expressions for these PCET reactions.
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Affiliation(s)
- Jiayun Zhong
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alexander V Soudackov
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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8
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Epping RF, de Zwart FJ, van Leest NP, van der Vlugt JI, Siegler MA, Mathew S, Reek JNH, de Bruin B. PhenTAA: A Redox-Active N 4-Macrocyclic Ligand Featuring Donor and Acceptor Moieties. Inorg Chem 2024; 63:1974-1987. [PMID: 38215498 PMCID: PMC10828995 DOI: 10.1021/acs.inorgchem.3c03708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
Here, we present the development and characterization of the novel PhenTAA macrocycle as well as a series of [Ni(R2PhenTAA)]n complexes featuring two sites for ligand-centered redox-activity. These differ in the substituent R (R = H, Me, or Ph) and overall charge of the complex n (n = -2, -1, 0, +1, or +2). Electrochemical and spectroscopic techniques (CV, UV/vis-SEC, X-band EPR) reveal that all redox events of the [Ni(R2PhenTAA)] complexes are ligand-based, with accessible ligand charges of -2, -1, 0, +1, and +2. The o-phenylenediamide (OPD) group functions as the electron donor, while the imine moieties act as electron acceptors. The flanking o-aminobenzaldimine groups delocalize spin density in both the oxidized and reduced ligand states. The reduced complexes have different stabilities depending on the substituent R. For R = H, dimerization occurs upon reduction, whereas for R = Me/Ph, the reduced imine groups are stabilized. This also gives electrochemical access to a [Ni(R2PhenTAA)]2- species. DFT and TD-DFT calculations corroborate these findings and further illustrate the unique donor-acceptor properties of the respective OPD and imine moieties. The novel [Ni(R2PhenTAA)] complexes exhibit up to five different ligand-based oxidation states and are electrochemically stable in a range from -2.4 to +1.8 V for the Me/Ph complexes (vs Fc/Fc+).
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Affiliation(s)
- Roel F.
J. Epping
- Homogeneous,
Supramolecular Catalysis and Bio-Inspired Catalysis Group, van ’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Felix J. de Zwart
- Homogeneous,
Supramolecular Catalysis and Bio-Inspired Catalysis Group, van ’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Nicolaas P. van Leest
- Homogeneous,
Supramolecular Catalysis and Bio-Inspired Catalysis Group, van ’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jarl Ivar van der Vlugt
- Homogeneous,
Supramolecular Catalysis and Bio-Inspired Catalysis Group, van ’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Maxime A. Siegler
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Simon Mathew
- Homogeneous,
Supramolecular Catalysis and Bio-Inspired Catalysis Group, van ’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Joost N. H. Reek
- Homogeneous,
Supramolecular Catalysis and Bio-Inspired Catalysis Group, van ’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bas de Bruin
- Homogeneous,
Supramolecular Catalysis and Bio-Inspired Catalysis Group, van ’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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9
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Zou W, Zhou H, Wang M. Photoinduced Biomimetic Room-Temperature C-O Bond Cleavage over Mn Doped CdS. CHEMSUSCHEM 2023; 16:e202300727. [PMID: 37486587 DOI: 10.1002/cssc.202300727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 07/25/2023]
Abstract
Selective C-O bond cleavage is an efficient way for the biomass valorization to value-added chemicals, but is challenged to be operated at room temperature via conventional thermal catalysis. Herein, inspired from the DNA biosynthesis which involves a radical-mediated spin-center shift (SCS) C-O bond cleavage process, we report a biomimetic room-temperature C-O bond cleavage of vicinal diol (HOCHCH-OH). We construct a Mn doped CdS (Mn/CdS) as a photocatalyst to mimic the biologic SCS process. The Mn site plays pivotal role: (1) accelerates the photo-induced carrier separation, promoting the hole-mediated C-H bond cleavage to generate carbon-centered radicals, and (2) serves as the binding site for -OH groups, making it to be an easier leaving group. Mn/CdS achieves 0.28 mmol gcat -1 h-1 of hydroxyacetone (HA) from glycerol dehydration at room temperature under visible light irradiation, which is 3.5-fold that over pristine CdS and 40-fold that over bulk MnS/CdS. This study provides a new biomimetic room-temperature C-O bond cleavage process, which is promising for the biomass valorization.
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Affiliation(s)
- Wenjing Zou
- School of Chemistry, Dalian University of Technology, Dalian, 116024, Liaoning, P. R. China
| | - Hongru Zhou
- School of Chemistry, Dalian University of Technology, Dalian, 116024, Liaoning, P. R. China
| | - Min Wang
- School of Chemistry, Dalian University of Technology, Dalian, 116024, Liaoning, P. R. China
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10
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Cáceres JC, Dolmatch A, Greene BL. The Mechanism of Inhibition of Pyruvate Formate Lyase by Methacrylate. J Am Chem Soc 2023; 145:22504-22515. [PMID: 37797332 PMCID: PMC10591478 DOI: 10.1021/jacs.3c07256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Indexed: 10/07/2023]
Abstract
Pyruvate Formate Lyase (PFL) catalyzes acetyl transfer from pyruvate to coenzyme a by a mechanism involving multiple amino acid radicals. A post-translationally installed glycyl radical (G734· in Escherichia coli) is essential for enzyme activity and two cysteines (C418 and C419) are proposed to form thiyl radicals during turnover, yet their unique roles in catalysis have not been directly demonstrated with both structural and electronic resolution. Methacrylate is an isostructural analog of pyruvate and an informative irreversible inhibitor of pfl. Here we demonstrate the mechanism of inhibition of pfl by methacrylate. Treatment of activated pfl with methacrylate results in the conversion of the G734· to a new radical species, concomitant with enzyme inhibition, centered at g = 2.0033. Spectral simulations, reactions with methacrylate isotopologues, and Density Functional Theory (DFT) calculations support our assignment of the radical to a C2 tertiary methacryl radical. The reaction is specific for C418, as evidenced by mass spectrometry. The methacryl radical decays over time, reforming G734·, and the decay exhibits a H/D solvent isotope effect of 3.4, consistent with H-atom transfer from an ionizable donor, presumably the C419 sulfhydryl group. Acrylate also inhibits PFL irreversibly, and alkylates C418, but we did not observe an acryl secondary radical in H2O or in D2O within 10 s, consistent with our DFT calculations and the expected reactivity of a secondary versus tertiary carbon-centered radical. Together, the results support unique roles of the two active site cysteines of PFL and a C419 S-H bond dissociation energy between that of a secondary and tertiary C-H bond.
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Affiliation(s)
- Juan Carlos Cáceres
- Biomolecular
Science and Engineering Program, University
of California, Santa
Barbara, California 93106, United States
| | - August Dolmatch
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Brandon L. Greene
- Biomolecular
Science and Engineering Program, University
of California, Santa
Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
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11
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Zhang L, Liu X, Wang X, Zhu G, Song H, Cheng R, Naowarojna N, Costello CE, Liu P. Correspondence on "Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1". Angew Chem Int Ed Engl 2023; 62:e202218643. [PMID: 37541669 PMCID: PMC10528348 DOI: 10.1002/anie.202218643] [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: 01/03/2023] [Indexed: 08/06/2023]
Abstract
In their recent Angewandte Chemie publication (doi: 10.1002/anie.202112063), Cen, Wang, Zhou et al. reported the crystal structure of a ternary complex of the non-heme iron endoperoxidase FtmOx1 (PDB entry 7ETK). The biochemical data assessed in this study were from a retracted study (doi: 10.1038/nature15519) by Zhang, Liu, Zhang et al.; no additional biochemical data were included, yet there was no discussion on the source of the biochemical data in the report by Cen, Wang, Zhou et al. Based on this new crystal structure and subsequent QM/MM-MD calculations, Cen, Wang, Zhou et al. concluded that their work provided evidence supporting the CarC-like mechanistic model for FtmOx1 catalysis. However, the authors did not accurately describe either the CarC-like model or the COX-like model, and they did not address the differences between them. Further, and contrary to their interpretations in the manuscript, the authors' data are consistent with the COX-like model once the details of the CarC-like and COX-like models have been carefully analyzed.
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Affiliation(s)
- Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China,
University of Science and Technology, Shanghai 200237 (China)
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China,
University of Science and Technology, Shanghai 200237 (China)
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China,
University of Science and Technology, Shanghai 200237 (China)
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China,
University of Science and Technology, Shanghai 200237 (China)
| | - Heng Song
- College of Chemistry and Molecular Sciences, Wuhan University,
Wuhan 430072 (China)
| | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, 02215 MA
(USA)
| | | | | | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, 02215 MA
(USA)
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12
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Zhu Q, Costentin C, Stubbe J, Nocera DG. Disulfide radical anion as a super-reductant in biology and photoredox chemistry. Chem Sci 2023; 14:6876-6881. [PMID: 37389245 PMCID: PMC10306091 DOI: 10.1039/d3sc01867a] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 07/01/2023] Open
Abstract
Disulfides are involved in a broad range of radical-based synthetic organic and biochemical transformations. In particular, the reduction of a disulfide to the corresponding radical anion, followed by S-S bond cleavage to yield a thiyl radical and a thiolate anion plays critical roles in radical-based photoredox transformations and the disulfide radical anion in conjunction with a proton donor, mediates the enzymatic synthesis of deoxynucleotides from nucleotides within the active site of the enzyme, ribonucleotide reductase (RNR). To gain fundamental thermodynamic insight into these reactions, we have performed experimental measurements to furnish the transfer coefficient from which the standard E0(RSSR/RSSR˙-) reduction potential has been determined for a homologous series of disulfides. The electrochemical potentials are found to be strongly dependent on the structures and electronic properties of the substituents of the disulfides. In the case of cysteine, a standard potential of E0(RSSR/RSSR˙-) = -1.38 V vs. NHE is determined, making the disulfide radical anion of cysteine one of the most reducing cofactors in biology.
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Affiliation(s)
- Qilei Zhu
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street Cambridge Massachusetts 02138 USA
- Department of Chemistry, University of Utah Salt Lake City Utah 84112 USA
| | | | - JoAnne Stubbe
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street Cambridge Massachusetts 02138 USA
- Departments of Chemistry and Department of Biology, Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street Cambridge Massachusetts 02138 USA
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13
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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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14
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Battistella B, Lohmiller T, Cula B, Hildebrandt P, Kuhlmann U, Dau H, Mebs S, Ray K. A New Thiolate-Bound Dimanganese Cluster as a Structural and Functional Model for Class Ib Ribonucleotide Reductases. Angew Chem Int Ed Engl 2023; 62:e202217076. [PMID: 36583430 DOI: 10.1002/anie.202217076] [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: 11/20/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
In class Ib ribonucleotide reductases (RNRs) a dimanganese(II) cluster activates superoxide (O2 ⋅- ) rather than dioxygen (O2 ), to access a high valent MnIII -O2 -MnIV species, responsible for the oxidation of tyrosine to tyrosyl radical. In a biomimetic approach, we report the synthesis of a thiolate-bound dimanganese complex [MnII 2 (BPMT)(OAc)2 ](ClO)4 (BPMT=(2,6-bis{[bis(2-pyridylmethyl)amino]methyl}-4-methylthiophenolate) (1) and its reaction with O2 ⋅- to form a [(BPMT)MnO2 Mn]2+ complex 2. Resonance Raman investigation revealed the presence of an O-O bond in 2, while EPR analysis displayed a 16-line St =1/2 signal at g=2 typically associated with a MnIII MnIV core, as detected in class Ib RNRs. Unlike all other previously reported Mn-O2 -Mn complexes, generated by O2 ⋅- activation at Mn2 centers, 2 proved to be a capable electrophilic oxidant in aldehyde deformylation and phenol oxidation reactions, rendering it one of the best structural and functional models for class Ib RNRs.
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Affiliation(s)
- Beatrice Battistella
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Thomas Lohmiller
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany.,EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 16, 12489, Berlin, Germany
| | - Beatrice Cula
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Peter Hildebrandt
- Institut für Chemie, Fakultät II, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Uwe Kuhlmann
- Institut für Chemie, Fakultät II, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Holger Dau
- Institut für Physik, Freie Universität zu Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Stefan Mebs
- Institut für Physik, Freie Universität zu Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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15
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Kass D, Yao S, Krause KB, Corona T, Richter L, Braun T, Mebs S, Haumann M, Dau H, Lohmiller T, Limberg C, Drieß M, Ray K. Spectroscopic Properties of a Biologically Relevant [Fe 2 (μ-O) 2 ] Diamond Core Motif with a Short Iron-Iron Distance. Angew Chem Int Ed Engl 2023; 62:e202209437. [PMID: 36541062 DOI: 10.1002/anie.202209437] [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: 06/29/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Diiron cofactors in enzymes perform diverse challenging transformations. The structures of high valent intermediates (Q in methane monooxygenase and X in ribonucleotide reductase) are debated since Fe-Fe distances of 2.5-3.4 Å were attributed to "open" or "closed" cores with bridging or terminal oxido groups. We report the crystallographic and spectroscopic characterization of a FeIII 2 (μ-O)2 complex (2) with tetrahedral (4C) centres and short Fe-Fe distance (2.52 Å), persisting in organic solutions. 2 shows a large Fe K-pre-edge intensity, which is caused by the pronounced asymmetry at the TD FeIII centres due to the short Fe-μ-O bonds. A ≈2.5 Å Fe-Fe distance is unlikely for six-coordinate sites in Q or X, but for a Fe2 (μ-O)2 core containing four-coordinate (or by possible extension five-coordinate) iron centres there may be enough flexibility to accommodate a particularly short Fe-Fe separation with intense pre-edge transition. This finding may broaden the scope of models considered for the structure of high-valent diiron intermediates formed upon O2 activation in biology.
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Affiliation(s)
- Dustin Kass
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Shenglai Yao
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Konstantin B Krause
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Teresa Corona
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Liza Richter
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Thomas Braun
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Stefan Mebs
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Michael Haumann
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Holger Dau
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Thomas Lohmiller
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany.,EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 16, 12489, Berlin, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Matthias Drieß
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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16
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Sarkar S, Shah Tuglak Khan F, Guchhait T, Rath SP. Binuclear complexes with single M-F-M bridge (M: Fe, Mn, and Cu): A critical analysis of the impact of fluoride for isoelectronic hydroxide substitution. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.215003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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17
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Ziółkowska A, Witwicki M. Understanding the Exchange Interaction between Paramagnetic Metal Ions and Radical Ligands: DFT and Ab Initio Study on Semiquinonato Cu(II) Complexes. Int J Mol Sci 2023; 24:ijms24044001. [PMID: 36835412 PMCID: PMC9959031 DOI: 10.3390/ijms24044001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The exchange coupling, represented by the J parameter, is of tremendous importance in understanding the reactivity and magnetic behavior of open-shell molecular systems. In the past, it was the subject of theoretical investigations, but these studies are mostly limited to the interaction between metallic centers. The exchange coupling between paramagnetic metal ions and radical ligands has hitherto received scant attention in theoretical studies, and thus the understanding of the factors governing this interaction is lacking. In this paper, we use DFT, CASSCF, CASSCF/NEVPT2, and DDCI3 methods to provide insight into exchange interaction in semiquinonato copper(II) complexes. Our primary objective is to identify structural features that affect this magnetic interaction. We demonstrate that the magnetic character of Cu(II)-semiquinone complexes are mainly determined by the relative position of the semiquinone ligand to the Cu(II) ion. The results can support the experimental interpretation of magnetic data for similar systems and can be used for the in-silico design of magnetic complexes with radical ligands.
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Affiliation(s)
- Aleksandra Ziółkowska
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Maciej Witwicki
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-283 Wroclaw, Poland
- Correspondence:
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18
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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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19
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Peltier JL, Serrato MR, Thery V, Pecaut J, Tomás-Mendivil E, Bertrand G, Jazzar R, Martin D. An air-stable radical with a redox-chameleonic amide. Chem Commun (Camb) 2023; 59:595-598. [PMID: 36524847 DOI: 10.1039/d2cc05404c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An air-stable (amino)(amido)radical was synthesized by reacting a cyclic (alkyl)(amino)carbene with carbazoyl chloride, followed by one-electron reduction. We show that an adjacent radical center weakens the amide bond. It enables the amino group to act as a strong acceptor under steric contraint, thus enhancing the stabilizing capto-dative effect.
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Affiliation(s)
- Jesse L Peltier
- UCSD-CNRS Joint Research Chemistry Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, USA
| | - Melinda R Serrato
- UCSD-CNRS Joint Research Chemistry Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, USA
| | - Valentin Thery
- University Grenoble Alpes, CNRS, DCM, Grenoble 38000, France.
| | - Jacques Pecaut
- University Grenoble Alpes, CEA, CNRS, INAC-SyMMES, UMR 5819, Grenoble 38000, France
| | | | - Guy Bertrand
- UCSD-CNRS Joint Research Chemistry Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, USA
| | - Rodolphe Jazzar
- UCSD-CNRS Joint Research Chemistry Laboratory (IRL 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, USA
| | - David Martin
- University Grenoble Alpes, CNRS, DCM, Grenoble 38000, France.
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20
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Tyson K, Tangtartharakul CB, Zeug M, Findling N, Haddy A, Hvastkovs E, Choe JY, Kim JE, Offenbacher AR. Electrochemical and Structural Study of the Buried Tryptophan in Azurin: Effects of Hydration and Polarity on the Redox Potential of W48. J Phys Chem B 2023; 127:133-143. [PMID: 36542812 PMCID: PMC9841983 DOI: 10.1021/acs.jpcb.2c06677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/16/2022] [Indexed: 12/24/2022]
Abstract
Tryptophan serves as an important redox-active amino acid in mediating electron transfer and mitigating oxidative damage in proteins. We previously showed a difference in electrochemical potentials for two tryptophan residues in azurin with distinct hydrogen-bonding environments. Here, we test whether reducing the side chain bulk at position Phe110 to Leu, Ser, or Ala impacts the electrochemical potentials (E°) for tryptophan at position 48. X-ray diffraction confirmed the influx of crystallographically resolved water molecules for both the F110A and F110L tyrosine free azurin mutants. The local environments of W48 in all azurin mutants were further evaluated by UV resonance Raman (UVRR) spectroscopy to probe the impact of mutations on hydrogen bonding and polarity. A correlation between the frequency of the ω17 mode─considered a vibrational marker for hydrogen bonding─and E° is proposed. However, the trend is opposite to the expectation from a previous study on small molecules. Density functional theory calculations suggest that the ω17 mode reflects hydrogen bonding as well as local polarity. Further, the UVRR data reveal different intensity/frequency shifts of the ω9/ω10 vibrational modes that characterize the local H-bonding environments of tryptophan. The cumulative data support that the presence of water increases E° and reveal properties of the protein microenvironment surrounding tryptophan.
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Affiliation(s)
- Kristin Tyson
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Chanin B. Tangtartharakul
- Department
of Chemistry and Biochemistry, University
of California at San Diego, La Jolla, California 92093, United States
| | - Matthias Zeug
- Department
of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville North Carolina, 27858, United States
| | - Nathan Findling
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Alice Haddy
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Eli Hvastkovs
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Jun-yong Choe
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
- Department
of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville North Carolina, 27858, United States
| | - Judy E. Kim
- Department
of Chemistry and Biochemistry, University
of California at San Diego, La Jolla, California 92093, United States
| | - Adam R. Offenbacher
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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21
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Sil D, Khan FST, Rath SP. Effect of intermacrocyclic interactions: Modulation of metal spin-state in oxo/hydroxo/fluoro-bridged diiron(III)/dimanganese(III) porphyrin dimers. ADVANCES IN INORGANIC CHEMISTRY 2023. [DOI: 10.1016/bs.adioch.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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22
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Broderick JB, Broderick WE, Hoffman BM. Radical SAM enzymes: Nature's choice for radical reactions. FEBS Lett 2023; 597:92-101. [PMID: 36251330 PMCID: PMC9894703 DOI: 10.1002/1873-3468.14519] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/05/2022] [Indexed: 02/04/2023]
Abstract
Enzymes that use a [4Fe-4S]1+ cluster plus S-adenosyl-l-methionine (SAM) to initiate radical reactions (radical SAM) form the largest enzyme superfamily, with over half a million members across the tree of life. This review summarizes recent work revealing the radical SAM reaction pathway, which ultimately liberates the 5'-deoxyadenosyl (5'-dAdo•) radical to perform extremely diverse, highly regio- and stereo-specific, transformations. Most surprising was the discovery of an organometallic intermediate Ω exhibiting an Fe-C5'-adenosyl bond. Ω liberates 5'-dAdo• through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12 , previously viewed as biology's paradigmatic radical generator. The 5'-dAdo• has been trapped and characterized in radical SAM enzymes via a recently discovered photoreactivity of the [4Fe-4S]+ /SAM complex, and has been confirmed as a catalytically active intermediate in enzyme catalysis. The regioselective SAM S-C bond cleavage to produce 5'-dAdo• originates in the Jahn-Teller effect. The simplicity of SAM as a radical precursor, and the exquisite control of 5'-dAdo• reactivity in radical SAM enzymes, may be why radical SAM enzymes pervade the tree of life, while B12 enzymes are only a few.
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Affiliation(s)
- Joan B. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - William E. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - Brian M. Hoffman
- Department of Chemistry, 2145 Sheridan Rd, Northwestern University, Evanston, IL. 60208
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23
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Khan FF, Bera SK, Dey S, Lahiri GK. Redox activity as a tool for bond activations and functionalizations. INORGANIC CHEMISTRY IN INDIA 2023. [DOI: 10.1016/bs.adioch.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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24
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Corinti D, Paciotti R, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Elusive intermediates in cisplatin reaction with target amino acids: Platinum(II)-cysteine complexes assayed by IR ion spectroscopy and DFT calculations. J Inorg Biochem 2022; 237:112017. [PMID: 36209532 DOI: 10.1016/j.jinorgbio.2022.112017] [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: 06/22/2022] [Revised: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 01/18/2023]
Abstract
The reactivity of a widely used metal based antineoplastic drug, cisplatin, cis-PtCl2(NH3)2, with L-cysteine (Cys) has been investigated using a combination of electrospray ionization mass spectrometry (ESI-MS), IRMPD gas phase ion spectroscopy and DFT calculations. The cysteine lateral chain represents one of the main platination sites in proteins, which is believed to be related to the resistance mechanisms to cisplatin. The vibrational features of the mass-selected substitution product cis-[PtCl(NH3)2(Cys)]+ and the intercepted cis-[PtCl(NH3)2(H2O)(Cys)]+ intermediate complex were compared to calculated IR spectra, enabling the assessment of the sampled ions structures. In cis-[PtCl(NH3)2(Cys)]+, cysteine was found to bind platinum through the sulfur atom as a thiolate zwitterion, highlighting the enhanced acidity of the cysteine thiol group upon metal coordination. The cis-[PtCl(NH3)2(H2O)(Cys)]+ structure complies with the non-covalent encounter complex, formed by cis-[PtCl(NH3)2(H2O)]+ and neutral cysteine. This species is able to undergo the substitution process to produce cis-[PtCl(NH3)2(Cys)]+ when activated as a mass-isolated ion suggesting its participation in the reaction mechanism of cisplatin with cysteine in solution. Finally, the DFT-calculated energy profile for the substitution reaction was correlated with the peculiar gas-phase reactivity of this non-covalent complex, resulting to be 10-fold less reactive toward substitution than the corresponding methionine complex.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy.
| | - Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy.
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
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25
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Rivera JJ, Trinh C, Kim JE. Photoinduced Electron Transfer from the Tryptophan Triplet State in Zn-Azurin. ACS PHYSICAL CHEMISTRY AU 2022; 3:63-73. [PMID: 36718260 PMCID: PMC9881450 DOI: 10.1021/acsphyschemau.2c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022]
Abstract
Tryptophan is one of few residues that participates in biological electron transfer reactions. Upon substitution of the native Cu2+ center with Zn2+ in the blue-copper protein azurin, a long-lived tryptophan neutral radical can be photogenerated. We report the following quantum yield values for Zn-substituted azurin in the presence of the electron acceptor Cu(II)-azurin: formation of the tryptophan neutral radical (Φrad), electron transfer (ΦET), fluorescence (Φfluo), and phosphorescence (Φphos), as well as the efficiency of proton transfer of the cation radical (ΦPT). Increasing the concentration of the electron acceptor increased Φrad and ΦET values and decreased Φphos without affecting Φfluo. At all concentrations of the acceptor, the value of ΦPT was nearly unity. These observations indicate that the phosphorescent triplet state is the parent state of electron transfer and that nearly all electron transfer events lead to proton loss. Similar results regarding the parent state were obtained with a different electron acceptor, [Co(NH3)5Cl]2+; however, Stern-Volmer graphs revealed that [Co(NH3)5Cl]2+ was a more effective phosphorescence quencher (K SV = 230 000 M-1) compared to Cu(II)-azurin (K SV = 88 000 M-1). Competition experiments in the presence of both [Co(NH3)5Cl]2+ and Cu(II)-azurin suggested that [Co(NH3)5Cl]2+ is the preferred electron acceptor. Implications of these results in terms of quenching mechanisms are discussed.
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26
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Kielb PJ, Teutloff C, Bittl R, Gray HB, Winkler JR. Does Tyrosine Protect S. coelicolor Laccase from Oxidative Degradation or Act as an Extended Catalytic Site? J Phys Chem B 2022; 126:7943-7949. [PMID: 36191240 PMCID: PMC10231039 DOI: 10.1021/acs.jpcb.2c04835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the roles of tyrosine (Tyr) and tryptophan (Trp) residues in the four-electron reduction of oxygen catalyzed by Streptomyces coelicolor laccase (SLAC). During normal enzymatic turnover in laccases, reducing equivalents are delivered to a type 1 Cu center (CuT1) and then are transferred over 13 Å to a trinuclear Cu site (TNC: (CuT3)2CuT2) where O2 reduction occurs. The TNC in SLAC is surrounded by a large cluster of Tyr and Trp residues that can provide reducing equivalents when the normal flow of electrons is disrupted. Prior studies by Canters and co-workers [J. Am. Chem. Soc. 2009, 131 (33), 11680-11682] have shown that when O2 reacts with a reduced SLAC variant lacking the CuT1 center, a Tyr108• radical near the TNC forms rapidly. We have found that the Tyr108• radical is reduced 10 times faster than CuT12+ by excess ascorbate, possibly because of radical transfer along Tyr/Trp chains.
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Affiliation(s)
- Patrycja J. Kielb
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | | | - Robert Bittl
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
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27
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Tomasini M, Caporaso L, Trouvé J, Poater J, Gramage‐Doria R, Poater A. Unravelling Enzymatic Features in a Supramolecular Iridium Catalyst by Computational Calculations. Chemistry 2022; 28:e202201970. [PMID: 35788999 PMCID: PMC9804516 DOI: 10.1002/chem.202201970] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Indexed: 01/05/2023]
Abstract
Non-biological catalysts following the governing principles of enzymes are attractive systems to disclose unprecedented reactivities. Most of those existing catalysts feature an adaptable molecular recognition site for substrate binding that are prone to undergo conformational selection pathways. Herein, we present a non-biological catalyst that is able to bind substrates via the induced fit model according to in-depth computational calculations. The system, which is constituted by an inflexible substrate-recognition site derived from a zinc-porphyrin in the second coordination sphere, features destabilization of ground states as well as stabilization of transition states for the relevant iridium-catalyzed C-H bond borylation of pyridine. In addition, this catalyst appears to be most suited to tightly bind the transition state rather than the substrate. Besides these features, which are reminiscent of the action modes of enzymes, new elementary catalytic steps (i. e. C-B bond formation and catalyst regeneration) have been disclosed owing to the unique distortions encountered in the different intermediates and transition states.
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Affiliation(s)
- Michele Tomasini
- Institut de Química Computacional i CatàlisiDepartament de QuímicaUniversitat de Gironac/Mª Aurèlia Capmany 6917003GironaCataloniaSpain,Department of ChemistryUniversity of SalernoVia Ponte Don Melillo84084FiscianoItaly
| | - Lucia Caporaso
- Department of ChemistryUniversity of SalernoVia Ponte Don Melillo84084FiscianoItaly
| | | | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & IQTCUBUniversitat de Barcelona08028BarcelonaSpain,ICREA08010BarcelonaSpain
| | | | - Albert Poater
- Institut de Química Computacional i CatàlisiDepartament de QuímicaUniversitat de Gironac/Mª Aurèlia Capmany 6917003GironaCataloniaSpain
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28
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Radical Mediated Rapid In Vitro Formation of c-Type Cytochrome. Biomolecules 2022; 12:biom12101329. [PMID: 36291538 PMCID: PMC9599503 DOI: 10.3390/biom12101329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
A cytochrome c552 mutant from Thermus thermophilus HB8 (rC552 C14A) was reported, where the polypeptide with replaced Cys14 by alanine, overexpressed in the cytosol of E. coli. The apo-form of the C14A mutant (apo-C14A) without the original prosthetic group was obtained by simple chemical treatments that retained compact conformation amenable to reconstitution with heme b and zinc(II)-protoporphyrin(IX), gradually followed by spontaneous formation of a covalent bond between the polypeptide and porphyrin ring in the reconstituted apo-C14A. Further analysis suggested that the residual Cys11 and vinyl group of the porphyrin ring linked through the thiol-ene reaction promoted by light under ambient conditions. In this study, we describe the kinetic improvement of the covalent bond formation in accordance with the mechanism of the photoinduced thiol-ene reaction, which involves a thiyl radical as a reaction intermediate. Adding a radical generator to the reconstituted C14A mutant with either heme-b or zinc(II) porphyrin accelerated the bond-forming reaction, which supported the involvement of a radical species in the reaction. Partial observation of the reconstituted C14A in a dimer form and detection of sulfuryl radical by EPR spectroscopy indicated a thiyl radical on Cys11, a unique cysteinyl residue in rC552 C14A. The covalent bond forming mediated by the radical generator was also adaptable to the reconstituted apo-C14A with manganese(II)-protoporphyrin(IX), which also exhibits light-mediated covalent linkage formation. Therefore, the radical generator extends the versatility of producing c-type-like cytochrome starting from a metallo-protoporphyrin(IX) and the apo-C14A instantaneously.
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29
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Gruber K, Csitkovits V, Łyskowski A, Kratky C, Kräutler B. Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues. Angew Chem Int Ed Engl 2022; 61:e202208295. [PMID: 35793207 PMCID: PMC9545868 DOI: 10.1002/anie.202208295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 12/04/2022]
Abstract
Catalysis by radical enzymes dependent on coenzyme B12 (AdoCbl) relies on the reactive primary 5'-deoxy-5'adenosyl radical, which originates from reversible Co-C bond homolysis of AdoCbl. This bond homolysis is accelerated roughly 1012 -fold upon binding the enzyme substrate. The structural basis for this activation is still strikingly enigmatic. As revealed here, a displaced firm adenosine binding cavity in substrate-loaded glutamate mutase (GM) causes a structural misfit for intact AdoCbl that is relieved by the homolytic Co-C bond cleavage. Strategically interacting adjacent adenosine- and substrate-binding protein cavities provide a tight caged radical reaction space, controlling the entire radical path. The GM active site is perfectly structured for promoting radical catalysis, including "negative catalysis", a paradigm for AdoCbl-dependent mutases.
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Affiliation(s)
- Karl Gruber
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- BioTechMed-Graz8010GrazAustria
- Field of Excellence “BioHealth”University of Graz8010GrazAustria
| | - Vanessa Csitkovits
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Andrzej Łyskowski
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- Present address: Department of Biotechnology and BioinformaticsRzeszów University of Technologyal. Powstańców Warszawy 1235-959RzeszówPoland
| | - Christoph Kratky
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Bernhard Kräutler
- Institute of Organic ChemistryUniversity of InnsbruckInnrain 80/826020InnsbruckAustria
- Center of Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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30
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Gruber K, Csitkovits V, Łyskowski A, Kratky C, Kräutler B. Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202208295. [PMID: 38505740 PMCID: PMC10947579 DOI: 10.1002/ange.202208295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 03/21/2024]
Abstract
Catalysis by radical enzymes dependent on coenzyme B12 (AdoCbl) relies on the reactive primary 5'-deoxy-5'adenosyl radical, which originates from reversible Co-C bond homolysis of AdoCbl. This bond homolysis is accelerated roughly 1012-fold upon binding the enzyme substrate. The structural basis for this activation is still strikingly enigmatic. As revealed here, a displaced firm adenosine binding cavity in substrate-loaded glutamate mutase (GM) causes a structural misfit for intact AdoCbl that is relieved by the homolytic Co-C bond cleavage. Strategically interacting adjacent adenosine- and substrate-binding protein cavities provide a tight caged radical reaction space, controlling the entire radical path. The GM active site is perfectly structured for promoting radical catalysis, including "negative catalysis", a paradigm for AdoCbl-dependent mutases.
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Affiliation(s)
- Karl Gruber
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- BioTechMed-Graz8010GrazAustria
- Field of Excellence “BioHealth”University of Graz8010GrazAustria
| | - Vanessa Csitkovits
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Andrzej Łyskowski
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- Present address: Department of Biotechnology and BioinformaticsRzeszów University of Technologyal. Powstańców Warszawy 1235-959RzeszówPoland
| | - Christoph Kratky
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Bernhard Kräutler
- Institute of Organic ChemistryUniversity of InnsbruckInnrain 80/826020InnsbruckAustria
- Center of Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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31
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López-Peña I, Lee CT, Rivera JJ, Kim JE. Role of the Triplet State and Protein Dynamics in the Formation and Stability of the Tryptophan Radical in an Apoazurin Mutant. J Phys Chem B 2022; 126:6751-6761. [PMID: 35977067 PMCID: PMC9483921 DOI: 10.1021/acs.jpcb.2c02441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The protein, azurin,
has enabled the study of the tryptophan radical.
Upon UV excitation of tyrosine-deficient apoazurin and in the presence
of a Co(III) electron acceptor, the neutral radical (W48•)
is formed. The lifetime of W48• in apoazurin is 41 s, which
is shorter than the lifetime of several hours in Zn-substituted azurin.
Molecular dynamics simulations revealed enhanced fluctuations of apoazurin
which likely destabilize W48•. The photophysics of W48 was
investigated to probe the precursor state for ET. The phosphorescence
intensity was eliminated in the presence of an electron acceptor while
the fluorescence was unchanged; this quenching of the phosphorescence
is attributed to ET. The kinetics associated with W48• were
examined with a model that incorporates intersystem crossing, ET,
deprotonation, and decay of the cation radical. The estimated rate
constants for ET (6 × 106 s–1) and
deprotonation (3 × 105 s–1) are
in agreement with a photoinduced mechanism where W48• is derived
from the triplet state. The triplet as the precursor state for ET
was supported by photolysis of apoazurin with 280 nm in the absence
and presence of triplet-absorbing 405 nm light. Absorption bands from
the neutral radical were observed only in the presence of blue light.
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Affiliation(s)
- Ignacio López-Peña
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Christopher T Lee
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Joel J Rivera
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
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32
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Zhu G, Yan W, Wang X, Cheng R, Naowarojna N, Wang K, Wang J, Song H, Wang Y, Liu H, Xia X, Costello CE, Liu X, Zhang L, Liu P. Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues. JACS AU 2022; 2:1686-1698. [PMID: 35911443 PMCID: PMC9326825 DOI: 10.1021/jacsau.2c00248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
FtmOx1 is a nonheme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol dehydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. In this study, we use two substrate analogues to simplify the FtmOx1-catalyzed reaction to either a dealkylation or an alcohol dehydrogenation reaction for structure-function relationship analysis to address two key FtmOx1 mechanistic questions: (1) Y224 flipping in the proposed COX-like model vs α-ketoglutarate (αKG) rotation proposed in the CarC-like mechanistic model and (2) the involvement of a Y224 radical (COX-like model) or a Y68 radical (CarC-like model) in FtmOx1-catalysis. When 13-oxo-fumitremorgin B (7) is used as the substrate, FtmOx1-catalysis changes from the endoperoxidation to a hydroxylation reaction and leads to dealkylation. In addition, consistent with the dealkylation side-reaction in the COX-like model prediction, the X-ray structure of the FtmOx1•CoII•αKG•7 ternary complex reveals a flip of Y224 to an alternative conformation relative to the FtmOx1•FeII•αKG binary complex. Verruculogen (2) was used as a second substrate analogue to study the alcohol dehydrogenation reaction to examine the involvement of the Y224 radical or Y68 radical in FtmOx1-catalysis, and again, the results from the verruculogen reaction are more consistent with the COX-like model.
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Affiliation(s)
- Guoliang Zhu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wupeng Yan
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Xinye Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronghai Cheng
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Kun Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jun Wang
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Heng Song
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei Province 430072, China
| | - Yuyang Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hairong Liu
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Xuekui Xia
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Catherine E. Costello
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Xueting Liu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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33
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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34
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Kinetic model for reversible radical transfer in ribonucleotide reductase. Proc Natl Acad Sci U S A 2022; 119:e2202022119. [PMID: 35714287 DOI: 10.1073/pnas.2202022119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.
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35
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Das A, Schleinitz J, Karmazin L, Vincent B, Le Breton N, Rogez G, Guenet A, Choua S, Grimaud L, Desage‐El Murr M. A Single Bioinspired Hexameric Nickel Catechol–Alloxazine Catalyst Combines Metal and Radical Mechanisms for Alkene Hydrosilylation. Chemistry 2022; 28:e202200596. [DOI: 10.1002/chem.202200596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Agnideep Das
- Université de Strasbourg Institut de Chimie, CNRS UMR7177 67000 Strasbourg France
| | - Jules Schleinitz
- Laboratoire des biomolécules LBM, Chemistry Department École normale supérieure PSL University Sorbonne Université, CNRS 75005 Paris France
| | - Lydia Karmazin
- Université de Strasbourg Institut de Chimie, CNRS UMR7177 67000 Strasbourg France
| | - Bruno Vincent
- Université de Strasbourg Institut de Chimie, CNRS UMR7177 67000 Strasbourg France
| | - Nolwenn Le Breton
- Université de Strasbourg Institut de Chimie, CNRS UMR7177 67000 Strasbourg France
| | - Guillaume Rogez
- Institut de Physique et Chimie des Matériaux de Strasbourg Université de Strasbourg, CNRS, UMR 7504 67000 Strasbourg France
| | - Aurélie Guenet
- Université de Strasbourg Institut de Chimie, CNRS UMR7177 67000 Strasbourg France
| | - Sylvie Choua
- Université de Strasbourg Institut de Chimie, CNRS UMR7177 67000 Strasbourg France
| | - Laurence Grimaud
- Laboratoire des biomolécules LBM, Chemistry Department École normale supérieure PSL University Sorbonne Université, CNRS 75005 Paris France
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36
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Mukhopadhyay N, Sengupta A, Vijay AK, Lloret F, Mukherjee R. Ni(II) complexes of a new tetradentate NN'N''O picolinoyl-1,2-phenylenediamide-phenolate redox-active ligand at different redox levels. Dalton Trans 2022; 51:9017-9029. [PMID: 35638812 DOI: 10.1039/d2dt01043g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Three square planar nickel(II) complexes of a new asymmetric tetradentate redox-active ligand H3L2 in its deprotonated form, at three redox levels, open-shell semiquinonate(1-) π radical, quinone(0) and closed-shell dianion of its 2-aminophenolate part, have been synthesized. The coordinated ligand provides N (pyridine) and N' and N'' (carboxamide and 1,2-phenylenediamide, respectively) and O (phenolate) donor sites. Cyclic voltammetry on the parent complex [Ni(L2)] 1 in CH2Cl2 established a three-membered electron-transfer series (oxidative response at E1/2 = 0.57 V and reductive response at -0.32 V vs. SCE) consisting of neutral, monocationic and monoanionic [Ni(L2)]z (z = 0, 1+ and 1-). Oxidation of 1 with AgSbF6 affords [Ni(L2)](SbF6) (2) and reduction of 1 with cobaltocene yields [Co(η5-C5H5)2][Ni(L2)] (3). The molecular structures of 1·CH3CN, 2·0.5CH2Cl2 and 3·C6H6 have been determined by X-ray crystallography at 100 K. Characterization by 1H NMR, X-band EPR (gav = 2.006 (solid); 2.008 (CH2Cl2-C6H5CH3 glass); 80 K) and UV-VIS-NIR spectral properties established that 1, 2 and 3 have [NiII{(L2)˙2-}], [NiII{(L2)-}]+/1+ and [NiII{(L2)3-}]-/1- electronic states, respectively. Thus, the redox processes are ligand-centred. While 1 possesses paramagnetic St (total spin) = 1/2, 2 and 3 possess diamagnetic ground-state St = 0. Interestingly, the variable-temperature (2-300 K) magnetic measurement reveals that 1 with the St = 1/2 ground state attains the antiferromagnetic St = 0 state at a very low temperature, due to weak noncovalent interactions via π-π stacking. Density functional theory (DFT) electronic structural calculations at the B3LYP level of theory rationalized the experimental results. In the UV-VIS-NIR spectra, broad absorptions are recorded for 1 and 2 in the range of 800-1600 nm; however, such an absorption is absent for 3. Time-dependent (TD)-DFT calculations provide a very good fit with the experimental spectra and allow us to identify the observed electronic transitions.
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Affiliation(s)
- Narottam Mukhopadhyay
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741 246, India
| | - Arunava Sengupta
- Department of Chemistry, Techno India University, West Bengal, Kolkata 700091, India
| | - Aswin Kottapurath Vijay
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741 246, India
| | - Francesc Lloret
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMOL), Universitat de València, Polígono de la Coma, s/n, 46980 Paterna, València, Spain
| | - Rabindranath Mukherjee
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India.
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37
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Haslem L, Hays JM, Hays FA. p66Shc in Cardiovascular Pathology. Cells 2022; 11:cells11111855. [PMID: 35681549 PMCID: PMC9180016 DOI: 10.3390/cells11111855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 02/06/2023] Open
Abstract
p66Shc is a widely expressed protein that governs a variety of cardiovascular pathologies by generating, and exacerbating, pro-apoptotic ROS signals. Here, we review p66Shc’s connections to reactive oxygen species, expression, localization, and discuss p66Shc signaling and mitochondrial functions. Emphasis is placed on recent p66Shc mitochondrial function discoveries including structure/function relationships, ROS identity and regulation, mechanistic insights, and how p66Shc-cyt c interactions can influence p66Shc mitochondrial function. Based on recent findings, a new p66Shc mitochondrial function model is also put forth wherein p66Shc acts as a rheostat that can promote or antagonize apoptosis. A discussion of how the revised p66Shc model fits previous findings in p66Shc-mediated cardiovascular pathology follows.
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Affiliation(s)
- Landon Haslem
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
| | - Jennifer M. Hays
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
| | - Franklin A. Hays
- Biochemistry and Molecular Biology Department, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (L.H.); (J.M.H.)
- Stephenson Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
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38
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Oslund RC, Reyes-Robles T, White CH, Tomlinson JH, Crotty KA, Bowman EP, Chang D, Peterson VM, Li L, Frutos S, Vila-Perelló M, Vlerick D, Cromie K, Perlman DH, Ingale S, Hara SDO, Roberts LR, Piizzi G, Hett EC, Hazuda DJ, Fadeyi OO. Detection of cell-cell interactions via photocatalytic cell tagging. Nat Chem Biol 2022; 18:850-858. [PMID: 35654846 DOI: 10.1038/s41589-022-01044-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/22/2022] [Indexed: 02/07/2023]
Abstract
The growing appreciation of immune cell-cell interactions within disease environments has led to extensive efforts to develop immunotherapies. However, characterizing complex cell-cell interfaces in high resolution remains challenging. Thus, technologies leveraging therapeutic-based modalities to profile intercellular environments offer opportunities to study cell-cell interactions with molecular-level insight. We introduce photocatalytic cell tagging (PhoTag) for interrogating cell-cell interactions using single-domain antibodies (VHHs) conjugated to photoactivatable flavin-based cofactors. Following irradiation with visible light, the flavin photocatalyst generates phenoxy radical tags for targeted labeling. Using this technology, we demonstrate selective synaptic labeling across the PD-1/PD-L1 axis in antigen-presenting cell-T cell systems. In combination with multiomics single-cell sequencing, we monitored interactions between peripheral blood mononuclear cells and Raji PD-L1 B cells, revealing differences in transient interactions with specific T cell subtypes. The utility of PhoTag in capturing cell-cell interactions will enable detailed profiling of intercellular communication across different biological systems.
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Affiliation(s)
- Rob C Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
| | | | - Cory H White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Jake H Tomlinson
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Kelly A Crotty
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Edward P Bowman
- Discovery Research, Merck & Co., Inc., San Francisco, CA, USA
| | - Dan Chang
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | - Lixia Li
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | | | | | | | - David H Perlman
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Sampat Ingale
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | | | - Lee R Roberts
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Grazia Piizzi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Erik C Hett
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Daria J Hazuda
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.,Infectious Diseases and Vaccine Research, Merck & Co., Inc., West Point, PA, USA
| | - Olugbeminiyi O Fadeyi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
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39
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Shima Y, Suzuki T, Abe H, Yajima T, Mori S, Shimazaki Y. Non-innocent redox behavior of Cu II- p-dimethylaminophenolate complexes: formation and characterization of the Cu I-phenoxyl radical species. Chem Commun (Camb) 2022; 58:6401-6404. [PMID: 35543291 DOI: 10.1039/d2cc01409b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cu complexes with p-dimethylaminophenolate ligands were synthesized by the reaction of CuII ions with the ligands under inert gas atmosphere and characterized. The complexes showed a valence state change from CuII-phenolate to CuI-phenoxyl radical on loss of the coordinated solvent. The CuI-phenoxyl radical species showed the characteristic properties and reactivities.
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Affiliation(s)
- Yuto Shima
- Graduate School of Science and Engineering, Ibaraki University. Bunkyo, Mito 310-8512, Japan.
| | - Takashi Suzuki
- Graduate School of Science and Engineering, Ibaraki University. Bunkyo, Mito 310-8512, Japan.
| | - Hitoshi Abe
- Graduate School of Science and Engineering, Ibaraki University. Bunkyo, Mito 310-8512, Japan. .,Department of Materials Structure Science, School of High Energy Accelerator Science, SOKENDAI (the Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,Institute of Materials Structure Science (IMSS), High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tatsuo Yajima
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680, Japan
| | - Seiji Mori
- Graduate School of Science and Engineering, Ibaraki University. Bunkyo, Mito 310-8512, Japan. .,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan
| | - Yuichi Shimazaki
- Graduate School of Science and Engineering, Ibaraki University. Bunkyo, Mito 310-8512, Japan.
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40
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Zhang FL, Li B, Houk KN, Wang YF. Application of the Spin-Center Shift in Organic Synthesis. JACS AU 2022; 2:1032-1042. [PMID: 35647602 PMCID: PMC9131482 DOI: 10.1021/jacsau.2c00051] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 05/09/2023]
Abstract
Spin-center shift (SCS) is a radical process involving 1,2-radical translocation along with a two-electron ionic movement, such as elimination of an adjacent leaving group. Such a process was initially observed in some important biochemical transformations, and the unique property has also attracted considerable interest in synthetic chemistry. Experimental, kinetic, as well as computational studies have been performed, and a series of useful radical transformations have been developed and applied in organic synthesis based on SCS processes in the last 20 years. This Perspective is an overview of radical transformations involving the SCS mechanism.
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Affiliation(s)
- Feng-Lian Zhang
- Department
of Chemistry, University of Science and
Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Bin Li
- Department
of Chemistry, University of Science and
Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - Yi-Feng Wang
- Department
of Chemistry, University of Science and
Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- State
Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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41
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Probing the Role of Cysteine Thiyl Radicals in Biology: Eminently Dangerous, Difficult to Scavenge. Antioxidants (Basel) 2022; 11:antiox11050885. [PMID: 35624747 PMCID: PMC9137623 DOI: 10.3390/antiox11050885] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 11/17/2022] Open
Abstract
Thiyl radicals are exceptionally interesting reactive sulfur species (RSS), but rather rarely considered in a biological or medical context. We here review the reactivity of protein thiyl radicals in aqueous and lipid phases and provide an overview of their most relevant reaction partners in biological systems. We deduce that polyunsaturated fatty acids (PUFAs) are their preferred reaction substrates in lipid phases, whereas protein side chains arguably prevail in aqueous phases. In both cellular compartments, a single, dominating thiyl radical-specific antioxidant does not seem to exist. This conclusion is rationalized by the high reaction rate constants of thiyl radicals with several highly concentrated substrates in the cell, precluding effective interception by antioxidants, especially in lipid bilayers. The intractable reactivity of thiyl radicals may account for a series of long-standing, but still startling biochemical observations surrounding the amino acid cysteine: (i) its global underrepresentation on protein surfaces, (ii) its selective avoidance in aerobic lipid bilayers, especially the inner mitochondrial membrane, (iii) the inverse correlation between cysteine usage and longevity in animals, (iv) the mitochondrial synthesis and translational incorporation of cysteine persulfide, and potentially (v) the ex post introduction of selenocysteine into the genetic code.
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42
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Zhong J, Reinhardt CR, Hammes-Schiffer S. Role of Water in Proton-Coupled Electron Transfer between Tyrosine and Cysteine in Ribonucleotide Reductase. J Am Chem Soc 2022; 144:7208-7214. [PMID: 35426309 PMCID: PMC9197590 DOI: 10.1021/jacs.1c13455] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides and is critical for DNA synthesis and repair in all organisms. Its mechanism requires radical transfer along a ∼32 Å pathway through a series of proton-coupled electron transfer (PCET) steps. Previous simulations suggested that a glutamate residue (E623) mediates the PCET reaction between two stacked tyrosine residues (Y730 and Y731) through a proton relay mechanism. This work focuses on the adjacent PCET reaction between Y730 and a cysteine residue (C439). Quantum mechanical/molecular mechanical free energy simulations illustrate that when Y730 and Y731 are stacked, E623 stabilizes the radical on C439 through hydrogen bonding with the Y730 hydroxyl group. When Y731 is flipped away from Y730, a water molecule stabilizes the radical on C439 through hydrogen bonding with Y730 and lowers the free energy barrier for radical transfer from Y730 to C439 through electrostatic interactions with the transferring hydrogen but does not directly accept the proton. These simulations indicate that the conformational motions and electrostatic interactions of the tyrosines, cysteine, glutamate, and water strongly impact the thermodynamics and kinetics of these two coupled PCET reactions. Such insights are important for protein engineering efforts aimed at altering radical transfer in RNR.
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Affiliation(s)
- Jiayun Zhong
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Clorice R. Reinhardt
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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43
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The Intriguing Role of Iron-Sulfur Clusters in the CIAPIN1 Protein Family. INORGANICS 2022. [DOI: 10.3390/inorganics10040052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Iron-sulfur (Fe/S) clusters are protein cofactors that play a crucial role in essential cellular functions. Their ability to rapidly exchange electrons with several redox active acceptors makes them an efficient system for fulfilling diverse cellular needs. They include the formation of a relay for long-range electron transfer in enzymes, the biosynthesis of small molecules required for several metabolic pathways and the sensing of cellular levels of reactive oxygen or nitrogen species to activate appropriate cellular responses. An emerging family of iron-sulfur cluster binding proteins is CIAPIN1, which is characterized by a C-terminal domain of about 100 residues. This domain contains two highly conserved cysteine-rich motifs, which are both involved in Fe/S cluster binding. The CIAPIN1 proteins have been described so far to be involved in electron transfer pathways, providing electrons required for the biosynthesis of important protein cofactors, such as Fe/S clusters and the diferric-tyrosyl radical, as well as in the regulation of cell death. Here, we have first investigated the occurrence of CIAPIN1 proteins in different organisms spanning the entire tree of life. Then, we discussed the function of this family of proteins, focusing specifically on the role that the Fe/S clusters play. Finally, we describe the nature of the Fe/S clusters bound to CIAPIN1 proteins and which are the cellular pathways inserting the Fe/S clusters in the two cysteine-rich motifs.
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44
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π-π Stacking Interaction of Metal Phenoxyl Radical Complexes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031135. [PMID: 35164397 PMCID: PMC8840625 DOI: 10.3390/molecules27031135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022]
Abstract
π-π stacking interaction is well-known to be one of the weak interactions. Its importance in the stabilization of protein structures and functionalization has been reported for various systems. We have focused on a single copper oxidase, galactose oxidase, which has the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with the indole ring of the proximal tryptophan residue and catalyzes primary alcohol oxidation to give the corresponding aldehyde. This stacking interaction has been considered to stabilize the alkylthio-phenoxyl radical, but further details of the interaction are still unclear. In this review, we discuss the effect of the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with an indole ring.
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45
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Affiliation(s)
- Xin‐Xin Peng
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
- Spin-X Institute, School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510641 P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials Guangzhou 510641 P. R. China
| | - Jun‐Long Zhang
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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46
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Mondal R, Guin AK, Chakraborty G, Paul ND. Metal-ligand cooperative approaches in homogeneous catalysis using transition metal complex catalysts of redox noninnocent ligands. Org Biomol Chem 2022; 20:296-328. [PMID: 34904619 DOI: 10.1039/d1ob01153g] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Catalysis offers a straightforward route to prepare various value-added molecules starting from readily available raw materials. The catalytic reactions mostly involve multi-electron transformations. Hence, compared to the inexpensive and readily available 3d-metals, the 4d and 5d-transition metals get an extra advantage for performing multi-electron catalytic reactions as the heavier transition metals prefer two-electron redox events. However, for sustainable development, these expensive and scarce heavy metal-based catalysts need to be replaced by inexpensive, environmentally benign, and economically affordable 3d-metal catalysts. In this regard, a metal-ligand cooperative approach involving transition metal complexes of redox noninnocent ligands offers an attractive alternative. The synergistic participation of redox-active ligands during electron transfer events allows multi-electron transformations using 3d-metal catalysts and allows interesting chemical transformations using 4d and 5d-metals as well. Herein we summarize an up-to-date literature report on the metal-ligand cooperative approaches using transition metal complexes of redox noninnocent ligands as catalysts for a few selected types of catalytic reactions.
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Affiliation(s)
- Rakesh Mondal
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur Botanic Garden, Howrah 711103, India.
| | - Amit Kumar Guin
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur Botanic Garden, Howrah 711103, India.
| | - Gargi Chakraborty
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur Botanic Garden, Howrah 711103, India.
| | - Nanda D Paul
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur Botanic Garden, Howrah 711103, India.
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47
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Sarkar P, Sarmah A, Mukherjee C. Where is the unpaired electron density? A combined experimental and theoretical finding on the geometric and electronic structures of the Co( iii) and Mn( iv) complexes of the unsymmetrical non-innocent pincer ONS ligand. Dalton Trans 2022; 51:16723-16732. [DOI: 10.1039/d2dt01868c] [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
The geometry and electronic structures of the Co and Mn complexes of the pincer H3LONS ligand composed of both hard and soft donor atoms at the coordinating sites are reported.
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Affiliation(s)
- Prasenjit Sarkar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Amrit Sarmah
- Department of Molecular Modelling, Institute of Organic Chemistry and Biochemistry ASCR, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Chandan Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
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48
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Cáceres JC, Bailey CA, Yokoyama K, Greene BL. Selenocysteine substitutions in thiyl radical enzymes. Methods Enzymol 2022; 662:119-141. [DOI: 10.1016/bs.mie.2021.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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49
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Deng WH, Lu Y, Liao RZ. Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations. J Chem Inf Model 2021; 61:5871-5882. [PMID: 34806370 DOI: 10.1021/acs.jcim.1c00978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Isethionate sulfite-lyase (IseG) is a recently characterized glycyl radical enzyme (GRE) that catalyzes radical-mediated C-S bond cleavage of isethionate to produce acetaldehyde and sulfite. Herein, we use quantum mechanical/molecular mechanical (QM/MM) calculations to investigate the detailed catalytic reaction mechanism of IseG. Our calculations indicate that a previously proposed direct 1,2-elimination mechanism is disfavored. Instead, we suggest a new 1,2-migration mechanism for this enzymatic reaction: a key stepwise 1,2-SO3- radical migration occurs after the catalytically active cysteinyl radical grabs a hydrogen atom from isethionate, followed by hydrogen atom transfer from cysteine to a 1-hydroxylethane-1-sulfonate radical intermediate. Finally, the elimination of sulfite from 1-hydroxylethane-1-sulfonate to result in the final product is likely to occur outside the enzyme. Glu468 in the active site is found to help orient the substrate rather than grabbing a proton from the hydroxyl group of the substrate. Our findings help reveal the mechanisms of radical-mediated C-S bond cleavage of organosulfonates catalyzed by GREs and expand the understanding of radical-based enzymatic catalysis.
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Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - You Lu
- Scientific Computing Department, UKRI STFC Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
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50
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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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