1
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Miller C, Huntoon D, Kaley N, Ogutu I, Fiedler AT, Bennett B, Liu D, Holz R. Role of second-sphere arginine residues in metal binding and metallocentre assembly in nitrile hydratases. J Inorg Biochem 2024; 256:112565. [PMID: 38677005 DOI: 10.1016/j.jinorgbio.2024.112565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024]
Abstract
Two conserved second-sphere βArg (R) residues in nitrile hydratases (NHase), that form hydrogen bonds with the catalytically essential sulfenic and sulfinic acid ligands, were mutated to Lys and Ala residues in the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) and the Fe-type NHase from Rhodococcus equi TG328-2 (ReNHase). Only five of the eight mutants (PtNHase βR52A, βR52K, βR157A, βR157K and ReNHase βR61A) were successfully expressed and purified. Apart from the PtNHase βR52A mutant that exhibited no detectable activity, the kcat values obtained for the PtNHase and ReNHase βR mutant enzymes were between 1.8 and 12.4 s-1 amounting to <1% of the kcat values observed for WT enzymes. The metal content of each mutant was also significantly decreased with occupancies ranging from ∼10 to ∼40%. UV-Vis spectra coupled with EPR data obtained on the ReNHase mutant enzyme, suggest a decrease in the Lewis acidity of the active site metal ion. X-ray crystal structures of the four PtNHase βR mutant enzymes confirmed the mutation and the low active site metal content, while also providing insight into the active site hydrogen bonding network. Finally, DFT calculations suggest that the equatorial sulfenic acid ligand, which has been shown to be the catalytic nucleophile, is protonated in the mutant enzyme. Taken together, these data confirm the necessity of the conserved second-sphere βR residues in the proposed subunit swapping process and post-translational modification of the α-subunit in the α activator complex, along with stabilizing the catalytic sulfenic acid in its anionic form.
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Affiliation(s)
- Callie Miller
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Delanie Huntoon
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Nicholas Kaley
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Irene Ogutu
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Adam T Fiedler
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, WI 53233, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Richard Holz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
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2
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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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3
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Dey A, Albert T, Kong RY, Macmillan SN, Moënne-Loccoz P, Lancaster KM, Goldberg DP. Direct Reduction of NO to N 2O by a Mononuclear Nonheme Thiolate Ligated Iron(II) Complex via Formation of a Metastable {FeNO} 7 Complex. Inorg Chem 2022; 61:14909-14917. [PMID: 36107151 PMCID: PMC9555345 DOI: 10.1021/acs.inorgchem.2c02383] [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: 11/30/2022]
Abstract
Addition of NO to a nonheme dithiolate-ligated iron(II) complex, FeII(Me3TACN)(S2SiMe2) (1), results in the generation of N2O. Low-temperature spectroscopic studies reveal a metastable six-coordinate {FeNO}7 intermediate (S = 3/2) that was trapped at -135 °C and was characterized by low-temperature UV-vis, resonance Raman, EPR, Mössbauer, XAS, and DFT studies. Thermal decay of the {FeNO}7 species leads to the evolution of N2O, providing a rare example of a mononuclear thiolate-ligated {FeNO}7 that mediates NO reduction to N2O without the requirement of any exogenous electron or proton sources.
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Affiliation(s)
- Aniruddha Dey
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, United States
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, Unites States
| | - Richard Y. Kong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, Unites States
| | - Samantha N. Macmillan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, Unites States
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, Unites States
| | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, Unites States
| | - David P. Goldberg
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, United States
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4
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Pathiranage WLK, Gumataotao N, Fiedler AT, Holz RC, Bennett B. Identification of an Intermediate Species along the Nitrile Hydratase Reaction Pathway by EPR Spectroscopy. Biochemistry 2021; 60:3771-3782. [PMID: 34843221 PMCID: PMC8721871 DOI: 10.1021/acs.biochem.1c00574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A new method to trap catalytic intermediate species was employed with Fe-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase). ReNHase was incubated with substrates in a 23% (w/w) NaCl/H2O eutectic system that remained liquid at -20 °C, thereby permitting the observation of transient species that were present at electron paramagnetic resonance (EPR)-detectable levels in samples frozen while in the steady state. FeIII-EPR signals from the resting enzyme were unaffected by the presence of 23% NaCl, and the catalytic activity was ∼55% that in the absence of NaCl at the optimum pH of 7.5. The reaction of ReNHase in the eutectic system at -20 °C with the substrates acetonitrile or benzonitrile induced significant changes in the EPR spectra. A previously unobserved signal with highly rhombic g-values (g1 = 2.31) was observed during the steady state but did not persist beyond the exhaustion of the substrate, indicating that it arises from a catalytically competent intermediate. Distinct signals due to product complexes provide a detailed mechanism for product release, the rate-limiting step of the reaction. Assignment of the observed EPR signals was facilitated by density functional theory calculations, which provided candidate structures and g-values for various proposed ReNHase intermediates. Collectively, these results provide new insights into the catalytic mechanism of NHase and offer a new approach for isolating and characterizing EPR-active intermediates in metalloenzymes.
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Affiliation(s)
| | - Natalie Gumataotao
- Department of Chemistry and Biochemistry, Loyola University, Chicago, Illinois 60660, United States
| | - Adam T. Fiedler
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Richard C. Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin 53233, United States
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5
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Adams E, Maeda K, Kato T, Tokoro C. Mechanism of gold and palladium adsorption on thermoacidophilic red alga Galdieria sulphuraria. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Glueck DS. Intramolecular attack on coordinated nitriles: metallacycle intermediates in catalytic hydration and beyond. Dalton Trans 2021; 50:15953-15960. [PMID: 34643205 DOI: 10.1039/d1dt02795f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration of nitriles is catalyzed by the enzyme nitrile hydratase, with iron or cobalt active sites, and by a variety of synthetic metal complexes. This Perspective focuses on parallels between the reaction mechanism of the enzyme and a class of particularly active catalysts bearing secondary phosphine oxide (SPO) ligands. In both cases, the key catalytic step was proposed to be intramolecular attack on a coordinated nitrile, with either an S-OH or S-O- (enzyme) or a P-OH (synthetic) nucleophile. Attack of water on the heteroatom (S or P) in the resulting metallacycle and proton transfer yields the amide and regenerates the catalyst. Evidence for this mechanism, its relevance to the formation of related metallacycles, and its potential for design of more active catalysts for nitrile hydration is summarized.
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Affiliation(s)
- David S Glueck
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, New Hampshire, 03755, USA.
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7
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Ogutu IRAM, Holz RC, Bennett B. Insight into the Maturation Process of the Nitrile Hydratase Active Site. Inorg Chem 2021; 60:5432-5435. [PMID: 33779143 DOI: 10.1021/acs.inorgchem.0c02924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The metal binding motif of all nitrile hydratases (NHases, EC 4.2.1.84) is highly conserved (CXXCSCX) in the α-subunit. Accordingly, an eight amino acid peptide (VCTLCSCY), based on the metal binding motif of the Co-type NHase from Pseudonocardia thermophilia (PtNHase), was synthesized and shown to coordinate Fe(II) under anaerobic conditions. Parallel-mode EPR data on the mononuclear Fe(II)-peptide complex confirmed an integer-spin signal at g' ∼ 9, indicating an S = 2 system with unusually small axial ZFS, D = 0.29 cm-1 Exposure to air yielded a transient high-spin EPR signal most consistent with an intermediate/admixed S = 3/2 spin state, while the integer-spin signal was extinguished. Prolonged exposure to air resulted in the observation of EPR signals at g = 2.04, 2.16, and 2.20, consistent with the formation of a low-spin Fe(III)-peptide complex with electronic and structural similarity to the NHase from Rhodococcus equi TG328-2 (ReNHase). Coupled with MS data, these data support a progression for iron oxidation in NHases that proceeds from a reduced high spin to an oxidized high spin followed by formation of an oxidized low-spin iron center, something that heretofore has not been observed.
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Affiliation(s)
- Irene R A M Ogutu
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States.,Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Richard C Holz
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States.,Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Brian Bennett
- Department of Physics, Marquette University, 1420 W. Clybourn Street, Milwaukee, Wisconsin 53233, United States
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8
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The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases. Catalysts 2020. [DOI: 10.3390/catal10091038] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site.
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9
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Lankathilaka KPW, Bennett B, Holz RC. The Fe-type nitrile hydratase from Rhodococcus equi TG328-2 forms an alpha-activator protein complex. J Biol Inorg Chem 2020; 25:903-911. [DOI: 10.1007/s00775-020-01806-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
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10
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Yang X, Bennett B, Holz RC. Insights into the catalytic mechanism of a bacterial hydrolytic dehalogenase that degrades the fungicide chlorothalonil. J Biol Chem 2019; 294:13411-13420. [PMID: 31331935 DOI: 10.1074/jbc.ra119.009094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Indexed: 11/06/2022] Open
Abstract
Chlorothalonil (2,4,5,6-tetrachloroisophtalonitrile; TPN) is one of the most commonly used fungicides in the United States. Given TPN's widespread use, general toxicity, and potential carcinogenicity, its biodegradation has garnered significant attention. Here, we developed a direct spectrophotometric assay for the Zn(II)-dependent, chlorothalonil-hydrolyzing dehalogenase from Pseudomonas sp. CTN-3 (Chd), enabling determination of its metal-binding properties; pH dependence of the kinetic parameters k cat, Km , and k cat/Km ; and solvent isotope effects. We found that a single Zn(II) ion binds a Chd monomer with a Kd of 0.17 μm, consistent with inductively coupled plasma MS data for the as-isolated Chd dimer. We observed that Chd was maximally active toward chlorothalonil in the pH range 7.0-9.0, and fits of these data yielded a pK ES1 of 5.4 ± 0.2, a pK ES2 of 9.9 ± 0.1 (k'cat = 24 ± 2 s-1), a pK E1 of 5.4 ± 0.3, and a pK E2 of 9.5 ± 0.1 (k'cat/k' m = 220 ± 10 s-1 mm-1). Proton inventory studies indicated that one proton is transferred in the rate-limiting step of the reaction at pD 7.0. Fits of UV-visible stopped-flow data suggested a three-step model and provided apparent rate constants for intermediate formation (i.e. a k'2 of 35.2 ± 0.1 s-1) and product release (i.e. a k'3 of 1.1 ± 0.2 s-1), indicating that product release is the slow step in catalysis. On the basis of these results, along with those previously reported, we propose a mechanism for Chd catalysis.
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Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin 53233
| | - Richard C Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881; Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401.
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11
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Yu P, Long X, Zhang N, Feng X, Fu J, Zheng S, Ren G, Liu Z, Wang C, Liu X. Charge Distribution on S and Intercluster Bond Evolution in Mo 6S 8 during the Electrochemical Insertion of Small Cations Studied by X-ray Absorption Spectroscopy. J Phys Chem Lett 2019; 10:1159-1166. [PMID: 30789737 DOI: 10.1021/acs.jpclett.8b03622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mo6S8 is regarded as a promising cathode material in rechargeable Mg batteries. Despite extensive studies, some fundamental questions are still unclarified, including the origination of the chemical stability, key factors inducing the structural evolution, and the factors determining the electrochemical reversibility. Herein Mo L2,3 and S K-edge X-ray absorption spectroscopy are utilized to uncover the underlying mechanism. Two kinds of S with different effective charge are found, indicating the nonuniform charge distribution. With one cation inserted, the charge distribution becomes homogeneous, relevant to the chemical stability and electrochemical reversibility. The structural evolution is attributed to the change of bond length induced by the delocalization of inserted cations. Moreover, the evolution of intercluster Mo-Mo bond length can be revealed by the drastic change of the S K pre-edge and is closely related to the electrochemical reversibility. This study can shed light on the aforementioned questions and guide the development of Mg cathode material.
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Affiliation(s)
- Pengfei Yu
- State Key Laboratory of Functional Materials for Informatics , Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050 , China
- Tianmu Lake Institute of Advanced Energy Storage Technologies , Liyang City , Jiangsu 213300 , China
| | - Xinghui Long
- State Key Laboratory of Functional Materials for Informatics , Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050 , China
| | - Nian Zhang
- State Key Laboratory of Functional Materials for Informatics , Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050 , China
| | - Xuefei Feng
- Advanced Light Source , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Jiamin Fu
- State Key Laboratory of Functional Materials for Informatics , Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050 , China
- School of Physical Science and Technology , Shanghai Tech University , Shanghai 200031 , China
| | - Shun Zheng
- State Key Laboratory of Functional Materials for Informatics , Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050 , China
| | - Guoxi Ren
- State Key Laboratory of Functional Materials for Informatics , Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050 , China
| | - Zhi Liu
- State Key Laboratory of Functional Materials for Informatics , Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050 , China
- School of Physical Science and Technology , Shanghai Tech University , Shanghai 200031 , China
| | - Cheng Wang
- Advanced Light Source , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Xiaosong Liu
- State Key Laboratory of Functional Materials for Informatics , Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050 , China
- Tianmu Lake Institute of Advanced Energy Storage Technologies , Liyang City , Jiangsu 213300 , China
- School of Physical Science and Technology , Shanghai Tech University , Shanghai 200031 , China
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12
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Yang X, Bennett B, Holz RC. Analyzing the function of the insert region found between the α and β-subunits in the eukaryotic nitrile hydratase from Monosiga brevicollis. Arch Biochem Biophys 2018; 657:1-7. [PMID: 30205086 PMCID: PMC6201762 DOI: 10.1016/j.abb.2018.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
The functional roles of the (His)17 region and an insert region in the eukaryotic nitrile hydratase (NHase, EC 4.2.1.84) from Monosiga brevicollis (MbNHase), were examined. Two deletion mutants, MbNHaseΔ238-257 and MbNHaseΔ219-272, were prepared in which the (His)17 sequence and the entire insert region were removed. Each of these MbNHase enzymes provided an α2β2 heterotetramer, identical to that observed for prokaryotic NHases and contains their full complement of cobalt ions. Deletion of the (His)17 motif provides an MbNHase enzyme that is ∼55% as active as the WT enzyme when expressed in the absence of the Co-type activator (ε) protein from Pseudonocardia thermophila JCM 3095 (PtNHaseact) but ∼28% more active when expressed in the presence of PtNHaseact. MbNHaseΔ219-272 exhibits ∼55% and ∼89% of WT activity, respectively, when expressed in the absence or presence of PtNHaseact. Proteolytic cleavage of MbNHase provides an α2β2 heterotetramer that is modestly more active compared to WT MbNHase (kcat = 163 ± 4 vs 131 ± 3 s-1). Combination of these data establish that neither the (His)17 nor the insert region are required for metallocentre assembly and maturation, suggesting that Co-type eukaryotic NHases utilize a different mechanism for metal ion incorporation and post-translational activation compared to prokaryotic NHases.
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Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI, 53201, USA
| | - Brian Bennett
- Department of Physics, Marquette University, PO Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Richard C Holz
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI, 53201, USA.
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13
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Dey A, Confer AM, Vilbert AC, Moënne-Loccoz P, Lancaster KM, Goldberg DP. A Nonheme Sulfur-Ligated {FeNO} 6 Complex and Comparison with Redox-Interconvertible {FeNO} 7 and {FeNO} 8 Analogues. Angew Chem Int Ed Engl 2018; 57:13465-13469. [PMID: 30125450 DOI: 10.1002/anie.201806146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 01/23/2023]
Abstract
A nonheme {FeNO}6 complex, [Fe(NO)(N3PyS)]2+ , was synthesized by reversible, one-electron oxidation of an {FeNO}7 analogue. This complex completes the first known series of sulfur-ligated {FeNO}6-8 complexes. All three {FeNO}6-8 complexes are readily interconverted by one-electron oxidation/reduction. A comparison of spectroscopic data (UV/Vis, NMR, IR, Mössbauer, X-ray absorption) provides a complete picture of the electronic and structural changes that occur upon {FeNO}6 -{FeNO}8 interconversion. Dissociation of NO from the new {FeNO}6 complex is shown to be controlled by solvent, temperature, and photolysis, which is rare for a sulfur-ligated {FeNO}6 species.
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Affiliation(s)
- Aniruddha Dey
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alex M Confer
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Avery C Vilbert
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Pierre Moënne-Loccoz
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD, 21218, USA
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14
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Dey A, Confer AM, Vilbert AC, Moënne‐Loccoz P, Lancaster KM, Goldberg DP. A Nonheme Sulfur‐Ligated {FeNO}
6
Complex and Comparison with Redox‐Interconvertible {FeNO}
7
and {FeNO}
8
Analogues. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Aniruddha Dey
- Department of Chemistry The Johns Hopkins University Baltimore MD 21218 USA
| | - Alex M. Confer
- Department of Chemistry The Johns Hopkins University Baltimore MD 21218 USA
| | - Avery C. Vilbert
- Department of Chemistry and Chemical Biology Cornell University Ithaca NY 14853 USA
| | - Pierre Moënne‐Loccoz
- Division of Environmental and Biomolecular Systems Oregon Health and Science University Portland OR 97239 USA
| | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology Cornell University Ithaca NY 14853 USA
| | - David P. Goldberg
- Department of Chemistry The Johns Hopkins University Baltimore MD 21218 USA
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15
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Hong S, Yan JJ, Karmalkar DG, Sutherlin KD, Kim J, Lee YM, Goo Y, Mascharak PK, Hedman B, Hodgson KO, Karlin KD, Solomon EI, Nam W. A mononuclear nonheme {FeNO} 6 complex: synthesis and structural and spectroscopic characterization. Chem Sci 2018; 9:6952-6960. [PMID: 30210769 PMCID: PMC6124912 DOI: 10.1039/c8sc01962b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/18/2018] [Indexed: 01/19/2023] Open
Abstract
While the synthesis and characterization of {FeNO}7,8,9 complexes have been well documented in heme and nonheme iron models, {FeNO}6 complexes have been less clearly understood. Herein, we report the synthesis and structural and spectroscopic characterization of mononuclear nonheme {FeNO}6 and iron(iii)-nitrito complexes bearing a tetraamido macrocyclic ligand (TAML), such as [(TAML)FeIII(NO)]- and [(TAML)FeIII(NO2)]2-, respectively. First, direct addition of NO(g) to [FeIII(TAML)]- results in the formation of [(TAML)FeIII(NO)]-, which is sensitive to moisture and air. The spectroscopic data of [(TAML)FeIII(NO)]-, such as 1H nuclear magnetic resonance and X-ray absorption spectroscopies, combined with computational study suggest the neutral nature of nitric oxide with a diamagnetic Fe center (S = 0). We also provide alternative pathways for the generation of [(TAML)FeIII(NO)]-, such as the iron-nitrite reduction triggered by protonation in the presence of ferrocene, which acts as an electron donor, and the photochemical iron-nitrite reduction. To the best of our knowledge, the present study reports the first photochemical nitrite reduction in nonheme iron models.
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Affiliation(s)
- Seungwoo Hong
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea . .,Department of Chemistry , Sookmyung Women's University , Seoul 04310 , Korea
| | - James J Yan
- Department of Chemistry , Stanford University , Stanford , California 94305 , USA .
| | - Deepika G Karmalkar
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea .
| | - Kyle D Sutherlin
- Department of Chemistry , Stanford University , Stanford , California 94305 , USA .
| | - Jin Kim
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea .
| | - Yong-Min Lee
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea .
| | - Yire Goo
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea .
| | - Pradip K Mascharak
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource , SLAC National Accelerator Laboratory , Stanford University , California 94025 , USA . ;
| | - Keith O Hodgson
- Department of Chemistry , Stanford University , Stanford , California 94305 , USA . .,Stanford Synchrotron Radiation Lightsource , SLAC National Accelerator Laboratory , Stanford University , California 94025 , USA . ;
| | - Kenneth D Karlin
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , USA . .,Stanford Synchrotron Radiation Lightsource , SLAC National Accelerator Laboratory , Stanford University , California 94025 , USA . ;
| | - Wonwoo Nam
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea . .,School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , P. R. China
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16
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Leipzig BK, Rees JA, Kowalska JK, Theisen RM, Kavčič M, Poon PCY, Kaminsky W, DeBeer S, Bill E, Kovacs JA. How Do Ring Size and π-Donating Thiolate Ligands Affect Redox-Active, α-Imino-N-heterocycle Ligand Activation? Inorg Chem 2018; 57:1935-1949. [PMID: 29411979 PMCID: PMC8312276 DOI: 10.1021/acs.inorgchem.7b02748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable effort has been devoted to the development of first-row transition-metal catalysts containing redox-active imino-pyridine ligands that are capable of storing multiple reducing equivalents. This property allows abundant and inexpensive first-row transition metals, which favor sequential one-electron redox processes, to function as competent catalysts in the concerted two-electron reduction of substrates. Herein we report the syntheses and characterization of a series of iron complexes that contain both π-donating thiolate and π-accepting (α-imino)-N-heterocycle redox-active ligands, with progressively larger N-heterocycle rings (imidazole, pyridine, and quinoline). A cooperative interaction between these complementary redox-active ligands is shown to dictate the properties of these complexes. Unusually intense charge-transfer (CT) bands, and intraligand metrical parameters, reminiscent of a reduced (α-imino)-N-heterocycle ligand (L•-), initially suggested that the electron-donating thiolate had reduced the N-heterocycle. Sulfur K-edge X-ray absorption spectroscopic (XAS) data, however, provides evidence for direct communication, via backbonding, between the thiolate sulfur and the formally orthogonal (α-imino)-N-heterocycle ligand π*-orbitals. DFT calculations provide evidence for extensive delocalization of bonds over the sulfur, iron, and (α-imino)-N-heterocycle, and TD-DFT shows that the intense optical CT bands involve transitions between a mixed Fe/S donor, and (α-imino)-N-heterocycle π*-acceptor orbital. The energies and intensities of the optical and S K-edge pre-edge XAS transitions are shown to correlate with N-heterocycle ring size, as do the redox potentials. When the thiolate is replaced with a thioether, or when the low-spin S = 0 Fe(II) is replaced with a high-spin S = 3/2 Co(II), the N-heterocycle ligand metrical parameters and electronic structure do not change relative to the neutral L0 ligand. With respect to the development of future catalysts containing redox-active ligands, the energy cost of storing reducing equivalents is shown to be lowest when a quinoline, as opposed to imidazole or pyridine, is incorporated into the ligand backbone of the corresponding Fe complex.
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Affiliation(s)
- Benjamin K. Leipzig
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Julian A. Rees
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Joanna K. Kowalska
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D–45470 Mülheim an der Ruhr, Germany
| | - Roslyn M. Theisen
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | | | | | - Werner Kaminsky
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D–45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D–45470 Mülheim an der Ruhr, Germany
| | - Julie A. Kovacs
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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17
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Prejanò M, Marino T, Rizzuto C, Madrid Madrid JC, Russo N, Toscano M. Reaction Mechanism of Low-Spin Iron(III)- and Cobalt(III)-Containing Nitrile Hydratases: A Quantum Mechanics Investigation. Inorg Chem 2017; 56:13390-13400. [DOI: 10.1021/acs.inorgchem.7b02121] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mario Prejanò
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Tiziana Marino
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Carmen Rizzuto
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Josè Carlos Madrid Madrid
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Nino Russo
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Marirosa Toscano
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
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18
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Stein N, Gumataotao N, Hajnas N, Wu R, Wasantha Lankathilaka KP, Bornscheuer UT, Liu D, Fiedler AT, Holz RC, Bennett B. Multiple States of Nitrile Hydratase from Rhodococcus equi TG328-2: Structural and Mechanistic Insights from Electron Paramagnetic Resonance and Density Functional Theory Studies. Biochemistry 2017; 56:3068-3077. [PMID: 28520398 PMCID: PMC5821057 DOI: 10.1021/acs.biochem.6b00876] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-type nitrile hydratases (NHases) contain an Fe(III) ion coordinated in a characteristic "claw setting" by an axial cysteine thiolate, two equatorial peptide nitrogens, the sulfur atoms of equatorial cysteine-sulfenic and cysteine-sulfinic acids, and an axial water/hydroxyl moiety. The cysteine-sulfenic acid is susceptible to oxidation, and the enzyme is traditionally prepared using butyric acid as an oxidative protectant. The as-prepared enzyme exhibits a complex electron paramagnetic resonance (EPR) spectrum due to multiple low-spin (S = 1/2) Fe(III) species. Four distinct signals can be assigned to the resting active state, the active state bound to butyric acid, an oxidized Fe(III)-bis(sulfinic acid) form, and an oxidized complex with butyric acid. A combination of comparison with earlier work, development of methods to elicit individual signals, and design and application of a novel density functional theory method for reproducing g tensors to unprecedentedly high precision was used to assign the signals. These species account for the previously reported EPR spectra from Fe-NHases, including spectra observed upon addition of substrates. Completely new EPR signals were observed upon addition of inhibitory boronic acids, and the distinctive g1 features of these signals were replicated in the steady state with the slow substrate acetonitrile. This latter signal constitutes the first EPR signal from a catalytic intermediate of NHase and is assigned to a key intermediate in the proposed catalytic cycle. Earlier, apparently contradictory, electron nuclear double resonance reports are reconsidered in the context of this work.
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Affiliation(s)
- Natalia Stein
- Department of Physics, Marquette University, 540 North 15th Street, Milwaukee, Wisconsin 53233, United States
| | - Natalie Gumataotao
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Natalia Hajnas
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Rui Wu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - K. P. Wasantha Lankathilaka
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Adam T. Fiedler
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Richard C. Holz
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Brian Bennett
- Department of Physics, Marquette University, 540 North 15th Street, Milwaukee, Wisconsin 53233, United States
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19
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Juncal LC, Avila J, Asensio MC, Della Védova CO, Romano RM. Electronic structure determination using an assembly of conventional and synchrotron techniques: The case of a xanthate complex. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 180:183-192. [PMID: 28285243 DOI: 10.1016/j.saa.2017.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 02/26/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
The electronic properties of the coordination complex nickel (II) bis-n-propylxanthate, Ni(CH3(CH2)2OC(S)S)2, were studied by a combination of complementary experimental (both laboratory and synchrotron based techniques) and theoretical methods. Energy differences between HOMOs and LUMOs were determined from UV-visible spectroscopy. The assignment of the transitions were performed with the aid of TD-DFT calculations and based in symmetry considerations. The analysis of the Raman excitation profiles of selected vibrational modes of the complex, taken in resonance with a particular electronic transition, was found to reinforce the electronic assignment. Experimental binding energies of inner and core electrons were determined by PES measurements. Ni K-edge, S K-edge, Ni L-edge, O K-edge and C K-edge XANES spectra were interpreted in terms of the promotion of core electrons to unoccupied electronic levels. An experimental quantitative molecular orbital diagram was constructed using the information extracted from the different techniques.
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Affiliation(s)
- Luciana C Juncal
- CEQUINOR (UNLP, CCT-CONICET La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Blvd. 120 N° 1465, CC 962, La Plata CP 1900, Argentina
| | - José Avila
- Synchrotron SOLEIL, Orme des Merisiers - Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
| | - Maria Carmen Asensio
- Synchrotron SOLEIL, Orme des Merisiers - Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
| | - Carlos O Della Védova
- CEQUINOR (UNLP, CCT-CONICET La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Blvd. 120 N° 1465, CC 962, La Plata CP 1900, Argentina
| | - Rosana M Romano
- CEQUINOR (UNLP, CCT-CONICET La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Blvd. 120 N° 1465, CC 962, La Plata CP 1900, Argentina.
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20
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Ochmann M, von Ahnen I, Cordones AA, Hussain A, Lee JH, Hong K, Adamczyk K, Vendrell O, Kim TK, Schoenlein RW, Huse N. Light-Induced Radical Formation and Isomerization of an Aromatic Thiol in Solution Followed by Time-Resolved X-ray Absorption Spectroscopy at the Sulfur K-Edge. J Am Chem Soc 2017; 139:4797-4804. [PMID: 28219243 DOI: 10.1021/jacs.6b12992] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We applied time-resolved sulfur-1s absorption spectroscopy to a model aromatic thiol system as a promising method for tracking chemical reactions in solution. Sulfur-1s absorption spectroscopy allows tracking multiple sulfur species with a time resolution of ∼70 ps at synchrotron radiation facilities. Experimental transient spectra combined with high-level electronic structure theory allow identification of a radical and two thione isomers, which are generated upon illumination with 267 nm radiation. Moreover, the regioselectivity of the thione isomerization is explained by the resulting radical frontier orbitals. This work demonstrates the usefulness and potential of time-resolved sulfur-1s absorption spectroscopy for tracking multiple chemical reaction pathways and transient products of sulfur-containing molecules in solution.
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Affiliation(s)
- Miguel Ochmann
- Department of Physics, University of Hamburg and Center for Free Electron Laser Science , 22761 Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter , 22761 Hamburg, Germany
| | - Inga von Ahnen
- Department of Physics, University of Hamburg and Center for Free Electron Laser Science , 22761 Hamburg, Germany
| | - Amy A Cordones
- Ultrafast X-ray Science Lab, Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Abid Hussain
- Department of Physics, University of Hamburg and Center for Free Electron Laser Science , 22761 Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter , 22761 Hamburg, Germany
| | - Jae Hyuk Lee
- Ultrafast X-ray Science Lab, Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Kiryong Hong
- Ultrafast X-ray Science Lab, Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University , Busan 46241, South Korea
| | - Katrin Adamczyk
- Department of Physics, University of Hamburg and Center for Free Electron Laser Science , 22761 Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter , 22761 Hamburg, Germany
| | - Oriol Vendrell
- Center for Free-Electron Laser Science, DESY and The Hamburg Centre for Ultrafast Imaging , 22607 Hamburg, Germany
| | - Tae Kyu Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University , Busan 46241, South Korea
| | - Robert W Schoenlein
- Ultrafast X-ray Science Lab, Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Nils Huse
- Department of Physics, University of Hamburg and Center for Free Electron Laser Science , 22761 Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter , 22761 Hamburg, Germany
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21
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Yan JJ, Gonzales MA, Mascharak PK, Hedman B, Hodgson KO, Solomon EI. L-Edge X-ray Absorption Spectroscopic Investigation of {FeNO} 6: Delocalization vs Antiferromagnetic Coupling. J Am Chem Soc 2017; 139:1215-1225. [PMID: 28006897 PMCID: PMC5322818 DOI: 10.1021/jacs.6b11260] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
NO is a classic non-innocent ligand, and iron nitrosyls can have different electronic structure descriptions depending on their spin state and coordination environment. These highly covalent ligands are found in metalloproteins and are also used as models for Fe-O2 systems. This study utilizes iron L-edge X-ray absorption spectroscopy (XAS), interpreted using a valence bond configuration interaction multiplet model, to directly experimentally probe the electronic structure of the S = 0 {FeNO}6 compound [Fe(PaPy3)NO]2+ (PaPy3 = N,N-bis(2-pyridylmethyl)amine-N-ethyl-2-pyridine-2-carboxamide) and the S = 0 [Fe(PaPy3)CO]+ reference compound. This method allows separation of the σ-donation and π-acceptor interactions of the ligand through ligand-to-metal and metal-to-ligand charge-transfer mixing pathways. The analysis shows that the {FeNO}6 electronic structure is best described as FeIII-NO(neutral), with no localized electron in an NO π* orbital or electron hole in an Fe dπ orbital. This delocalization comes from the large energy gap between the Fe-NO π-bonding and antibonding molecular orbitals relative to the exchange interactions between electrons in these orbitals. This study demonstrates the utility of L-edge XAS in experimentally defining highly delocalized electronic structures.
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Affiliation(s)
- James J Yan
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Margarita A Gonzales
- Department of Chemistry, Foothill College , Los Altos Hills, California 94022, United States
| | - Pradip K Mascharak
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University , Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University , Menlo Park, California 94025, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University , Menlo Park, California 94025, United States
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22
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Villar-Acevedo G, Lugo-Mas P, Blakely MN, Rees JA, Ganas AS, Hanada EM, Kaminsky W, Kovacs JA. Metal-Assisted Oxo Atom Addition to an Fe(III) Thiolate. J Am Chem Soc 2016; 139:119-129. [PMID: 28033001 DOI: 10.1021/jacs.6b03512] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cysteinate oxygenation is intimately tied to the function of both cysteine dioxygenases (CDOs) and nitrile hydratases (NHases), and yet the mechanisms by which sulfurs are oxidized by these enzymes are unknown, in part because intermediates have yet to be observed. Herein, we report a five-coordinate bis-thiolate ligated Fe(III) complex, [FeIII(S2Me2N3(Pr,Pr))]+ (2), that reacts with oxo atom donors (PhIO, IBX-ester, and H2O2) to afford a rare example of a singly oxygenated sulfenate, [FeIII(η2-SMe2O)(SMe2)N3(Pr,Pr)]+ (5), resembling both a proposed intermediate in the CDO catalytic cycle and the essential NHase Fe-S(O)Cys114 proposed to be intimately involved in nitrile hydrolysis. Comparison of the reactivity of 2 with that of a more electron-rich, crystallographically characterized derivative, [FeIIIS2Me2NMeN2amide(Pr,Pr)]- (8), shows that oxo atom donor reactivity correlates with the metal ion's ability to bind exogenous ligands. Density functional theory calculations suggest that the mechanism of S-oxygenation does not proceed via direct attack at the thiolate sulfurs; the average spin-density on the thiolate sulfurs is approximately the same for 2 and 8, and Mulliken charges on the sulfurs of 8 are roughly twice those of 2, implying that 8 should be more susceptible to sulfur oxidation. Carboxamide-ligated 8 is shown to be unreactive towards oxo atom donors, in contrast to imine-ligated 2. Azide (N3-) is shown to inhibit sulfur oxidation with 2, and a green intermediate is observed, which then slowly converts to sulfenate-ligated 5. This suggests that the mechanism of sulfur oxidation involves initial coordination of the oxo atom donor to the metal ion. Whether the green intermediate is an oxo atom donor adduct, Fe-O═I-Ph, or an Fe(V)═O remains to be determined.
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Affiliation(s)
- Gloria Villar-Acevedo
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Priscilla Lugo-Mas
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Maike N Blakely
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Julian A Rees
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Abbie S Ganas
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Erin M Hanada
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Werner Kaminsky
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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23
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The iron-type nitrile hydratase activator protein is a GTPase. Biochem J 2016; 474:247-258. [PMID: 27807009 DOI: 10.1042/bcj20160884] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/27/2016] [Accepted: 11/02/2016] [Indexed: 01/01/2023]
Abstract
The Fe-type nitrile hydratase activator protein from Rhodococcus equi TG328-2 (ReNHase TG328-2) was successfully expressed and purified. Sequence analysis and homology modeling suggest that it is a G3E P-loop guanosine triphosphatase (GTPase) within the COG0523 subfamily. Kinetic studies revealed that the Fe-type activator protein is capable of hydrolyzing GTP to GDP with a kcat value of 1.2 × 10-3 s-1 and a Km value of 40 μM in the presence of 5 mM MgCl2 in 50 mM 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid at a pH of 8.0. The addition of divalent metal ions, such as Co(II), which binds to the ReNHase TG328-2 activator protein with a Kd of 2.9 μM, accelerated the rate of GTP hydrolysis, suggesting that GTP hydrolysis is potentially connected to the proposed metal chaperone function of the ReNHase TG328-2 activator protein. Circular dichroism data reveal a significant conformational change upon the addition of GTP, which may be linked to the interconnectivity of the cofactor binding sites, resulting in an activator protein that can be recognized and can bind to the NHase α-subunit. A combination of these data establishes, for the first time, that the ReNHase TG328-2 activator protein falls into the COG0523 subfamily of G3E P-loop GTPases, many of which play a role in metal homeostasis processes.
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24
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25
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Abstract
CytP450s have a cysteine-bound heme cofactor that, in its as-isolated resting (oxidized) form, can be conclusively described as a ferric thiolate species. Unlike the native enzyme, most synthetic thiolate-bound ferric porphyrins are unstable in air unless the axial thiolate ligand is sterically protected. Spectroscopic investigations on a series of synthetic mimics of cytP450 indicate that a thiolate-bound ferric porphyrin coexists in organic solutions at room temperature (RT) with a thiyl-radical bound ferrous porphyrin, i.e., its valence tautomer. The ferric thiolate state is favored by greater enthalpy and is air stable. The ferrous thiyl state is favored by entropy, populates at RT, and degrades in air. These ground states can be reversibly interchanged at RT by the addition or removal of water to the apolar medium. It is concluded that hydrogen bonding and local electrostatics protect the resting oxidized cytP450 active site from degradation in air by stabilizing the ferric thiolate ground state in contrast to its synthetic analogs.
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26
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Kayanuma M, Shoji M, Yohda M, Odaka M, Shigeta Y. Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study. J Phys Chem B 2016; 120:3259-66. [DOI: 10.1021/acs.jpcb.5b11363] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Megumi Kayanuma
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Mitsuo Shoji
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Masafumi Yohda
- Graduate
School of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masafumi Odaka
- Graduate
School of Engineering and Resource Science, Akita University, 1-1
Tegata Gakuen-machi, Akita, Akita 010-8502, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
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27
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Pierce BS, Subedi BP, Sardar S, Crowell JK. The "Gln-Type" Thiol Dioxygenase from Azotobacter vinelandii is a 3-Mercaptopropionic Acid Dioxygenase. Biochemistry 2015; 54:7477-90. [PMID: 26624219 DOI: 10.1021/acs.biochem.5b00636] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cysteine dioxygenase (CDO) is a non-heme iron enzyme that catalyzes the O2-dependent oxidation of l-cysteine to produce cysteinesulfinic acid. Bacterial CDOs have been subdivided as either "Arg-type" or "Gln-type" on the basis of the identity of conserved active site residues. To date, "Gln-type" enzymes remain largely uncharacterized. It was recently noted that the "Gln-type" enzymes are more homologous with another thiol dioxygenase [3-mercaptopropionate dioxygenase (MDO)] identified in Variovorax paradoxus, suggesting that enzymes of the "Gln-type" subclass are in fact MDOs. In this work, a putative "Gln-type" thiol dioxygenase from Azotobacter vinelandii (Av) was purified to homogeneity and characterized. Steady-state assays were performed using three substrates [3-mercaptopropionic acid (3mpa), l-cysteine (cys), and cysteamine (ca)]. Despite comparable maximal velocities, the "Gln-type" Av enzyme exhibited a specificity for 3mpa (kcat/KM = 72000 M(-1) s(-1)) nearly 2 orders of magnitude greater than those for cys (110 M(-1) s(-1)) and ca (11 M(-1) s(-1)). Supporting X-band electron paramagnetic resonance (EPR) studies were performed using nitric oxide (NO) as a surrogate for O2 binding to confirm obligate-ordered addition of substrate prior to NO. Stoichimetric addition of NO to solutions of 3mpa-bound enzyme quantitatively yields an iron-nitrosyl species (Av ES-NO) with EPR features consistent with a mononuclear (S = (3)/2) {FeNO}(7) site. Conversely, two distinct substrate-bound conformations were observed in Av ES-NO samples prepared with cys and ca, suggesting heterogeneous binding within the enzymatic active site. Analytical EPR simulations are provided to establish the relative binding affinity for each substrate (3map > cys > ca). Both kinetic and spectroscopic results presented here are consistent with 3mpa being the preferred substrate for this enzyme.
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Affiliation(s)
- Brad S Pierce
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Bishnu P Subedi
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Sinjinee Sardar
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Joshua K Crowell
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
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28
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Sriskandakumar T, Behyan S, Habtemariam A, Sadler PJ, Kennepohl P. Electrophilic Activation of Oxidized Sulfur Ligands and Implications for the Biological Activity of Ruthenium(II) Arene Anticancer Complexes. Inorg Chem 2015; 54:11574-80. [DOI: 10.1021/acs.inorgchem.5b02493] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Shirin Behyan
- The University of British Columbia, Department of Chemistry, Vancouver, BC V6T 1Z1, Canada
| | - Abraha Habtemariam
- University of Warwick, Department
of Chemistry, Coventry CV4 7AL, United Kingdom
| | - Peter J. Sadler
- University of Warwick, Department
of Chemistry, Coventry CV4 7AL, United Kingdom
| | - Pierre Kennepohl
- The University of British Columbia, Department of Chemistry, Vancouver, BC V6T 1Z1, Canada
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29
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Light KM, Yamanaka Y, Odaka M, Solomon EI. Spectroscopic and Computational Studies of Nitrile Hydratase: Insights into Geometric and Electronic Structure and the Mechanism of Amide Synthesis. Chem Sci 2015; 6:6280-6294. [PMID: 26508996 PMCID: PMC4618400 DOI: 10.1039/c5sc02012c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nitrile hydratases (NHases) are mononuclear nonheme enzymes that catalyze the hydration of nitriles to amides. NHase is unusual in that it utilizes a low-spin (LS) FeIII center and a unique ligand set comprised of two deprotonated backbone amides, cysteine-based sulfenic acid (RSO(H)) and sulfinic acid (RSO2-), and an unmodified cysteine trans to an exogenous ligand site. Electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD) and low-temperature absorption (LT-Abs) spectroscopies are used to determine the geometric and electronic structures of butyrate-bound (NHaseBA) and active (NHaseAq) NHase. These data calibrate DFT models, which are then extended to explore the mechanism of nitrile hydration by NHase. In particular, the nitrile is activated by coordination to the LS FeIII and the sulfenate group is found to be deprotonated and a significantly better nucleophile than water that can attack the coordinated nitrile to form a cyclic species. Attack at the sulfenate S atom of the cyclic species is favorable and leads to a lower kinetic barrier than attack by water on coordinated, uncyclized nitrile, while attack at the C of the cyclic species is unfavorable. The roles of the unique ligand set and low-spin nature of the NHase active site in function are also explored. It is found that the oxidized thiolate ligands are crucial to maintaining the LS state, which is important in the binding and activation of nitrile susbtrates. The dominant role of the backbone amidate ligands appears to be as a chelate in keeping the sulfenate properly oriented for nucleophilic attack on the coordinated substrate.
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Affiliation(s)
- Kenneth M Light
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Yasuaki Yamanaka
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, Japan
| | - Masafumi Odaka
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, Japan
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
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Analyzing the catalytic role of active site residues in the Fe-type nitrile hydratase from Comamonas testosteroni Ni1. J Biol Inorg Chem 2015; 20:885-94. [DOI: 10.1007/s00775-015-1273-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 05/24/2015] [Indexed: 10/23/2022]
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31
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Kayanuma M, Hanaoka K, Shoji M, Shigeta Y. A QM/MM study of the initial steps of catalytic mechanism of nitrile hydratase. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Zhang R, Yan W, Jing C. Mechanistic study of PFOS adsorption on kaolinite and montmorillonite. Colloids Surf A Physicochem Eng Asp 2014. [DOI: 10.1016/j.colsurfa.2014.09.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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33
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Lo FC, Li YW, Hsu IJ, Chen CH, Liaw WF. Insight into the Reactivity and Electronic Structure of Dinuclear Dinitrosyl Iron Complexes. Inorg Chem 2014; 53:10881-92. [DOI: 10.1021/ic501055w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Feng-Chun Lo
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ya-Wen Li
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei 10608, Taiwan
| | - I-Jui Hsu
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei 10608, Taiwan
| | - Chien-Hong Chen
- School of Medical Applied Chemistry, Chung Shan Medical University, Taichung 40201, Taiwan
- Department of Medical Education, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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34
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Nguyen VH, Chew HQ, Su B, Yip JHK. Synthesis and Spectroscopy of Anionic Cyclometalated Iridium(III)-Dithiolate and -Sulfinates—Effect of Sulfur Dioxygenation on Electronic Structure and Luminescence. Inorg Chem 2014; 53:9739-50. [DOI: 10.1021/ic501278n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Van Ha Nguyen
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Hui Qi Chew
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Bochao Su
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - John H. K. Yip
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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35
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Hopmann KH. Full Reaction Mechanism of Nitrile Hydratase: A Cyclic Intermediate and an Unexpected Disulfide Switch. Inorg Chem 2014; 53:2760-2. [DOI: 10.1021/ic500091k] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Kathrin H. Hopmann
- Centre for Theoretical and
Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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36
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Martinez S, Wu R, Sanishvili R, Liu D, Holz R. The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile. J Am Chem Soc 2014; 136:1186-9. [PMID: 24383915 PMCID: PMC3968781 DOI: 10.1021/ja410462j] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Indexed: 01/10/2023]
Abstract
Nitrile hydratase (NHase) catalyzes the hydration of nitriles to their corresponding commercially valuable amides at ambient temperatures and physiological pH. Several reaction mechanisms have been proposed for NHase enzymes; however, the source of the nucleophile remains a mystery. Boronic acids have been shown to be potent inhibitors of numerous hydrolytic enzymes due to the open shell of boron, which allows it to expand from a trigonal planar (sp(2)) form to a tetrahedral form (sp(3)). Therefore, we examined the inhibition of the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) by boronic acids via kinetics and X-ray crystallography. Both 1-butaneboronic acid (BuBA) and phenylboronic acid (PBA) function as potent competitive inhibitors of PtNHase. X-ray crystal structures for BuBA and PBA complexed to PtNHase were solved and refined at 1.5, 1.6, and 1.2 Å resolution. The resulting PtNHase-boronic acid complexes represent a "snapshot" of reaction intermediates and implicate the cysteine-sulfenic acid ligand as the catalytic nucleophile, a heretofore unknown role for the αCys(113)-OH sulfenic acid ligand. Based on these data, a new mechanism of action for the hydration of nitriles by NHase is presented.
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Affiliation(s)
- Salette Martinez
- Department
of Chemistry, Marquette
University, Milwaukee, Wisconsin 53201, United States
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Rui Wu
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Ruslan Sanishvili
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Dali Liu
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Richard Holz
- Department
of Chemistry, Marquette
University, Milwaukee, Wisconsin 53201, United States
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37
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Feng X, Song MK, Stolte WC, Gardenghi D, Zhang D, Sun X, Zhu J, Cairns EJ, Guo J. Understanding the degradation mechanism of rechargeable lithium/sulfur cells: a comprehensive study of the sulfur–graphene oxide cathode after discharge–charge cycling. Phys Chem Chem Phys 2014; 16:16931-40. [DOI: 10.1039/c4cp01341g] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Degradation mechanism of rechargeable lithium/sulfur-graphene oxide cell was studied using scanning electron microscopy and X-ray spectroscopy.
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Affiliation(s)
- Xuefei Feng
- National Synchrotron Radiation Laboratory & Collaborative Innovation Center of Suzhou Nano Science and Technology
- University of Science and Technology of China
- Hefei 230029, China
- Advanced Light Source
- Lawrence Berkeley National Laboratory
| | - Min-Kyu Song
- The Molecular Foundry
- Lawrence Berkeley National Laboratory
- Berkeley, USA
- Department of Chemical and Biomolecular Engineering
- University of California
| | - Wayne C. Stolte
- Advanced Light Source
- Lawrence Berkeley National Laboratory
- Berkeley, USA
- Department of Chemistry
- University of Nevada
| | - David Gardenghi
- Advanced Light Source
- Lawrence Berkeley National Laboratory
- Berkeley, USA
- Department of Chemistry
- University of Nevada
| | - Duo Zhang
- Advanced Light Source
- Lawrence Berkeley National Laboratory
- Berkeley, USA
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
| | - Xuhui Sun
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou 215123, China
| | - Junfa Zhu
- National Synchrotron Radiation Laboratory & Collaborative Innovation Center of Suzhou Nano Science and Technology
- University of Science and Technology of China
- Hefei 230029, China
| | - Elton J. Cairns
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley, USA
- Environmental Energy Technologies Division
- Lawrence Berkeley National Laboratory
| | - Jinghua Guo
- Advanced Light Source
- Lawrence Berkeley National Laboratory
- Berkeley, USA
- Department of Chemical and Biochemistry
- University of California
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38
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Reinvestigation of the first structurally characterized metal-coordinated sulfenic acid complex. INORG CHEM COMMUN 2013. [DOI: 10.1016/j.inoche.2013.09.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Yamanaka Y, Arakawa T, Watanabe T, Namima S, Sato M, Hori S, Ohtaki A, Noguchi K, Katayama Y, Yohda M, Odaka M. Two arginine residues in the substrate pocket predominantly control the substrate selectivity of thiocyanate hydrolase. J Biosci Bioeng 2013; 116:22-7. [DOI: 10.1016/j.jbiosc.2013.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/20/2013] [Accepted: 01/22/2013] [Indexed: 10/27/2022]
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40
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Dutta A, Flores M, Roy S, Schmitt JC, Hamilton GA, Hartnett HE, Shearer J, Jones AK. Sequential oxidations of thiolates and the cobalt metallocenter in a synthetic metallopeptide: implications for the biosynthesis of nitrile hydratase. Inorg Chem 2013; 52:5236-45. [PMID: 23587023 PMCID: PMC4046696 DOI: 10.1021/ic400171z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cobalt nitrile hydratases (Co-NHase) contain a catalytic cobalt(III) ion coordinated in an N2S3 first coordination sphere composed of two amidate nitrogens and three cysteine-derived sulfur donors: a thiolate (-SR), a sulfenate (-S(R)O(-)), and a sulfinate (-S(R)O2(-)). The sequence of biosynthetic reactions that leads to the post-translational oxidations of the metal and the sulfur ligands is unknown, but the process is believed to be initiated directly by oxygen. Herein we utilize cobalt bound in an N2S2 first coordination sphere by a seven amino acid peptide known as SODA (ACDLPCG) to model this oxidation process. Upon exposure to oxygen, Co-SODA is oxidized in two steps. In the first fast step (seconds), magnetic susceptibility measurements demonstrated that the metallocenter remains paramagnetic, that is, Co(2+), and sulfur K-edge X-ray absorption spectroscopy (XAS) is used to show that one of the thiolates is oxidized to sulfinate. In a second process on a longer time scale (hours), magnetic susceptibility measurements and Co K-edge XAS show that the metal is oxidized to Co(3+). Unlike other model complexes, additional slow oxidation of the second thiolate in Co-SODA is not observed, and a catalytically active complex is never formed. The likely reason is the absence of the axial thiolate ligand. In essence, the reactivity of Co-SODA can be described as between previously described models which either quickly convert to final product or are stable in air, and it offers a first glimpse into a possible oxidation pathway for nitrile hydratase biosynthesis.
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Affiliation(s)
- Arnab Dutta
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
| | - Marco Flores
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
| | - Souvik Roy
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
| | | | | | - Hilairy E. Hartnett
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration; Arizona State University, Tempe, AZ 85287
| | - Jason Shearer
- Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Anne K. Jones
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
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41
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Gumataotao N, Kuhn ML, Hajnas N, Holz RC. Identification of an active site-bound nitrile hydratase intermediate through single turnover stopped-flow spectroscopy. J Biol Chem 2013; 288:15532-6. [PMID: 23589282 DOI: 10.1074/jbc.m112.398909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stopped-flow kinetic data were obtained for the iron-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase) using methacrylonitrile as the substrate. Multiple turnover experiments suggest a three-step kinetic model that allows for the reversible binding of substrate, the presence of an intermediate, and the formation of product. Microscopic rate constants determined from these data are in good agreement with steady state data confirming that the stopped-flow method used was appropriate for the reaction. Single turnover stopped-flow experiments were used to identify catalytic intermediates. These data were globally fit confirming a three-step kinetic model. Independent absorption spectra acquired between 0.005 and 0.5 s of the reaction reveal a significant increase in absorbance at 375, 460, and 550 nm along with the hypsochromic shift of an Fe(3+)←S ligand-to-metal charge transfer band from 700 to 650 nm. The observed UV-visible absorption bands for the Fe(3+)-nitrile intermediate species are similar to low spin Fe(3+)-enzyme and model complexes bound by NO or N3((-)). These data provide spectroscopic evidence for the direct coordination of the nitrile substrate to the nitrile hydratase active site low spin Fe(3+) center.
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Affiliation(s)
- Natalie Gumataotao
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, USA
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42
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The Active Site of Nitrile Hydratase: An Assembly of Unusual Coordination Features by Nature. MOLECULAR DESIGN IN INORGANIC BIOCHEMISTRY 2013. [DOI: 10.1007/430_2012_85] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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43
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44
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Kumar D, Masitas CA, Nguyen TN, Grapperhaus CA. Bioinspired catalytic nitrile hydration by dithiolato, sulfinato/thiolato, and sulfenato/sulfinato ruthenium complexes. Chem Commun (Camb) 2013. [DOI: 10.1039/c2cc35256g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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45
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Daly SR, Keith JM, Batista ER, Boland KS, Clark DL, Kozimor SA, Martin RL. Sulfur K-edge X-ray Absorption Spectroscopy and Time-Dependent Density Functional Theory of Dithiophosphinate Extractants: Minor Actinide Selectivity and Electronic Structure Correlations. J Am Chem Soc 2012; 134:14408-22. [DOI: 10.1021/ja303999q] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Scott R. Daly
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Jason M. Keith
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Enrique R. Batista
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Kevin S. Boland
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - David L. Clark
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Stosh A. Kozimor
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Richard L. Martin
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
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46
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Shearer J, Callan PE, Masitas CA, Grapperhaus CA. Influence of sequential thiolate oxidation on a nitrile hydratase mimic probed by multiedge X-ray absorption spectroscopy. Inorg Chem 2012; 51:6032-45. [PMID: 22591049 DOI: 10.1021/ic202453c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nitrile hydratases (NHases) are Fe(III)- and Co(III)-containing hydrolytic enzymes that convert nitriles into amides. The metal-center is contained within an N(2)S(3) coordination motif with two post-translationally modified cysteinates contained in a cis arrangement, which have been converted into a sulfinate (R-SO(2)(-)) and a sulfenate (R-SO(-)) group. Herein, we utilize Ru L-edge and ligand (N-, S-, and P-) K-edge X-ray absorption spectroscopies to probe the influence that these modifications have on the electronic structure of a series of sequentially oxidized thiolate-coordinated Ru(II) complexes ((bmmp-TASN)RuPPh(3), (bmmp-O(2)-TASN)RuPPh(3), and (bmmp-O(3)-TASN)RuPPh(3)). Included is the use of N K-edge spectroscopy, which was used for the first time to extract N-metal covalency parameters. We find that upon oxygenation of the bis-thiolate compound (bmmp-TASN)RuPPh(3) to the sulfenato species (bmmp-O(2)-TASN)RuPPh(3) and then to the mixed sulfenato/sulfinato speices (bmmp-O(3)-TASN)RuPPh(3) the complexes become progressively more ionic, and hence the Ru(II) center becomes a harder Lewis acid. These findings are reinforced by hybrid DFT calculations (B(38HF)P86) using a large quadruple-ζ basis set. The biological implications of these findings in relation to the NHase catalytic cycle are discussed in terms of the creation of a harder Lewis acid, which aids in nitrile hydrolysis.
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Affiliation(s)
- Jason Shearer
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA.
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47
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Crawford JA, Li W, Pierce BS. Single turnover of substrate-bound ferric cysteine dioxygenase with superoxide anion: enzymatic reactivation, product formation, and a transient intermediate. Biochemistry 2011; 50:10241-53. [PMID: 21992268 DOI: 10.1021/bi2011724] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine dioxygenase (CDO) is a non-heme mononuclear iron enzyme that catalyzes the O(2)-dependent oxidation of L-cysteine (Cys) to produce cysteine sulfinic acid (CSA). In this study we demonstrate that the catalytic cycle of CDO can be "primed" by one electron through chemical oxidation to produce CDO with ferric iron in the active site (Fe(III)-CDO, termed 2). While catalytically inactive, the substrate-bound form of Fe(III)-CDO (2a) is more amenable to interrogation by UV-vis and EPR spectroscopy than the 'as-isolated' Fe(II)-CDO enzyme (1). Chemical-rescue experiments were performed in which superoxide (O(2)(•-)) anions were introduced to 2a to explore the possibility that a Fe(III)-superoxide species represents the first intermediate within the catalytic pathway of CDO. In principle, O(2)(•-) can serve as a suitable acceptor for the remaining 3-electrons necessary for CSA formation and regeneration of the active Fe(II)-CDO enzyme (1). Indeed, addition of O(2)(•-) to 2a resulted in the rapid formation of a transient species (termed 3a) observable at 565 nm by UV-vis spectroscopy. The subsequent decay of 3a is kinetically matched to CSA formation. Moreover, a signal attributed to 3a was also identified using parallel mode X-band EPR spectroscopy (g ~ 11). Spectroscopic simulations, observed temperature dependence, and the microwave power saturation behavior of 3a are consistent with a ground state S = 3 from a ferromagnetically coupled (J ~ -8 cm(-1)) high-spin ferric iron (S(A) = 5/2) with a bound radical (S(B) = 1/2), presumably O(2)(•-). Following treatment with O(2)(•-), the specific activity of recovered CDO increased to ~60% relative to untreated enzyme.
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Affiliation(s)
- Joshua A Crawford
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington, Arlington, Texas 76019, United States
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48
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Lu TT, Lai SH, Li YW, Hsu IJ, Jang LY, Lee JF, Chen IC, Liaw WF. Discrimination of Mononuclear and Dinuclear Dinitrosyl Iron Complexes (DNICs) by S K-Edge X-ray Absorption Spectroscopy: Insight into the Electronic Structure and Reactivity of DNICs. Inorg Chem 2011; 50:5396-406. [DOI: 10.1021/ic102108b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Tsai-Te Lu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Szu-Hsueh Lai
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ya-Wen Li
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei 10608, Taiwan
| | - I-Jui Hsu
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei 10608, Taiwan
| | - Ling-Yun Jang
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Jyh-Fu Lee
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - I-Chia Chen
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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49
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Sun N, Liu LV, Dey A, Villar-Acevedo G, Kovacs JA, Darensbourg MY, Hodgson KO, Hedman B, Solomon EI. S K-edge X-ray absorption spectroscopy and density functional theory studies of high and low spin {FeNO}7 thiolate complexes: exchange stabilization of electron delocalization in {FeNO}7 and {FeO2}8. Inorg Chem 2011; 50:427-36. [PMID: 21158471 PMCID: PMC3130116 DOI: 10.1021/ic1006378] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
S K-edge X-ray absorption spectroscopy (XAS) is a direct experimental probe of metal ion electronic structure as the pre-edge energy reflects its oxidation state, and the energy splitting pattern of the pre-edge transitions reflects its spin state. The combination of sulfur K-edge XAS and density functional theory (DFT) calculations indicates that the electronic structures of {FeNO}(7) (S = 3/2) (S(Me2)N4(tren)Fe(NO), complex I) and {FeNO}(7) (S = 1/2) ((bme-daco)Fe(NO), complex II) are Fe(III)(S = 5/2)-NO(-)(S = 1) and Fe(III)(S = 3/2)-NO(-)(S = 1), respectively. When an axial ligand is computationally added to complex II, the electronic structure becomes Fe(II)(S = 0)-NO•(S = 1/2). These studies demonstrate how the ligand field of the Fe center defines its spin state and thus changes the electron exchange, an important factor in determining the electron distribution over {FeNO}(7) and {FeO2}(8) sites.
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Affiliation(s)
- Ning Sun
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Lei V. Liu
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Abhishek Dey
- Department of Chemistry, Stanford University, Stanford, California 94305
| | | | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | | | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025
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50
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Masitas CA, Kumar M, Mashuta MS, Kozlowski PM, Grapperhaus CA. Controlled sulfur oxygenation of the ruthenium dithiolate (4,7-bis-(2'-methyl-2'-mercaptopropyl)-1-thia-4,7-diazacyclononane)RuPPh(3) under limiting O(2) conditions yields thiolato/sulfinato, sulfenato/sulfinato, and bis-sulfinato derivatives. Inorg Chem 2010; 49:10875-81. [PMID: 20973591 DOI: 10.1021/ic101221z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ruthenium(II) dithiolate complex (bmmp-TASN)RuPPh(3) (1) reacts with O(2) under limiting conditions to yield isolable sulfur oxygenated derivatives as a function of reaction time. With this approach, a family of sulfur-oxygenates has been prepared and isolated without the need for O-atom transfer agents or column chromatography. Addition of 5 equiv of O(2) to 1 yields the thiolato/sulfinato complex (bmmp-O(2)-TASN)RuPPh(3) (2) in 70% yield within 5 min. Increasing the reaction time to 12 h yields the sulfenato/sulfinato derivative (bmmp-O(3)-TASN)RuPPh(3) (3) in 82% yield. Longer reaction times and/or additional O(2) exposure yield the bis-sulfinato complex (bmmp-O(4)-TASN)RuPPh(3) (4). All products remain in the Ru(II) oxidation state under the conditions employed. Stoichiometric hydrolysis of acetonitrile to acetamide by 2 and 3 is observed in mixed acetonitrile, methanol, PIPES buffer (pH = 7.0) mixtures. The Ru(III)/(II) reduction potential of -0.85 V (versus ferrocenium/ferrocene) for 1 shifts to -0.39 and -0.26 V for 2 and 3, respectively, because of the decreased donor ability of sulfur upon oxygenation. X-ray diffraction studies reveal a decrease in Ru-S bond distances upon oxygenation by 0.045(1) and 0.158(1) Å for the sulfenato and sulfinato donors, respectively. Conversely, sulfur-oxygenation increases the Ru-P bond distance by 0.061(1) Å from 1 to 2 and an additional 0.027(1) Å from 2 to 3. Density functional theory investigations using the BP86 and B3LYP functionals with a LANL2DZ basis set for Ru and the 6-31G(d) basis set for all other atoms reveal a direct correlation between the oxygenation level and the Ru-P distance with an increase of 0.031 Å per O-atom.
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Affiliation(s)
- César A Masitas
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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