1
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Yang J, Mintmier B, Kc K, Metzger MC, Radhakrishnan M, McGarry J, Wilcoxen J, Basu P, Kirk ML. Active Site Characterization of a Campylobacter jejuni Nitrate Reductase Variant Provides Insight into the Enzyme Mechanism. Inorg Chem 2024; 63:13191-13196. [PMID: 38984973 DOI: 10.1021/acs.inorgchem.4c01991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Mo K-edge X-ray absorption spectroscopy (XAS) is used to probe the structure of wild-type Campylobacter jejuni nitrate reductase NapA and the C176A variant. The results of extended X-ray absorption fine structure (EXAFS) experiments on wt NapA support an oxidized Mo(VI) hexacoordinate active site coordinated by a single terminal oxo donor, four sulfur atoms from two separate pyranopterin dithiolene ligands, and an additional S atom from a conserved cysteine amino acid residue. We found no evidence of a terminal sulfido ligand in wt NapA. EXAFS analysis shows the C176A active site to be a 6-coordinate structure, and this is supported by EPR studies on C176A and small molecule analogs of Mo(V) enzyme forms. The SCys is replaced by a hydroxide or water ligand in C176A, and we find no evidence of a coordinated sulfhydryl (SH) ligand. Kinetic studies show that this variant has completely lost its catalytic activity toward nitrate. Taken together, the results support a critical role for the conserved C176 in catalysis and an oxygen atom transfer mechanism for the catalytic reduction of nitrate to nitrite that does not employ a terminal sulfido ligand in the catalytic cycle.
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Affiliation(s)
- Jing Yang
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University, 402 Blackford St., Indianapolis, Indiana 46202, United States
| | - Khadanand Kc
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Mikayla C Metzger
- Department of Chemistry and Chemical Biology, Indiana University, 402 Blackford St., Indianapolis, Indiana 46202, United States
| | - Manohar Radhakrishnan
- Department of Chemistry and Chemical Biology, Indiana University, 402 Blackford St., Indianapolis, Indiana 46202, United States
| | - Jennifer McGarry
- Department of Chemistry and Chemical Biology, Indiana University, 402 Blackford St., Indianapolis, Indiana 46202, United States
- Department of Chemistry and Biochemistry, University of Wisconsin, 3210 N. Cramer St., Milwaukee, Wisconsin 53211, United States
| | - Jarett Wilcoxen
- Department of Chemistry and Biochemistry, University of Wisconsin, 3210 N. Cramer St., Milwaukee, Wisconsin 53211, United States
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University, 402 Blackford St., Indianapolis, Indiana 46202, United States
| | - Martin L Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
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2
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Burgmayer SJN, Kirk ML. Advancing Our Understanding of Pyranopterin-Dithiolene Contributions to Moco Enzyme Catalysis. Molecules 2023; 28:7456. [PMID: 38005178 PMCID: PMC10673323 DOI: 10.3390/molecules28227456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The pyranopterin dithiolene ligand is remarkable in terms of its geometric and electronic structure and is uniquely found in mononuclear molybdenum and tungsten enzymes. The pyranopterin dithiolene is found coordinated to the metal ion, deeply buried within the protein, and non-covalently attached to the protein via an extensive hydrogen bonding network that is enzyme-specific. However, the function of pyranopterin dithiolene in enzymatic catalysis has been difficult to determine. This focused account aims to provide an overview of what has been learned from the study of pyranopterin dithiolene model complexes of molybdenum and how these results relate to the enzyme systems. This work begins with a summary of what is known about the pyranopterin dithiolene ligand in the enzymes. We then introduce the development of inorganic small molecule complexes that model aspects of a coordinated pyranopterin dithiolene and discuss the results of detailed physical studies of the models by electronic absorption, resonance Raman, X-ray absorption and NMR spectroscopies, cyclic voltammetry, X-ray crystallography, and chemical reactivity.
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Affiliation(s)
| | - Martin L. Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM 87131, USA
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3
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Winiarska A, Ramírez-Amador F, Hege D, Gemmecker Y, Prinz S, Hochberg G, Heider J, Szaleniec M, Schuller JM. A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire. SCIENCE ADVANCES 2023; 9:eadg6689. [PMID: 37267359 PMCID: PMC10413684 DOI: 10.1126/sciadv.adg6689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/28/2023] [Indexed: 06/04/2023]
Abstract
Aldehyde oxidoreductases (AORs) are tungsten enzymes catalyzing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the denitrifying betaproteobacterium Aromatoleum aromaticum (AORAa) consists of three different subunits (AorABC) and uses nicotinamide adenine dinucleotide (NAD) as an electron acceptor. Here, we reveal that the enzyme forms filaments of repeating AorAB protomers that are capped by a single NAD-binding AorC subunit, based on solving its structure via cryo-electron microscopy. The polyferredoxin-like subunit AorA oligomerizes to an electron-conducting nanowire that is decorated with enzymatically active and W-cofactor (W-co) containing AorB subunits. Our structure further reveals the binding mode of the native substrate benzoate in the AorB active site. This, together with quantum mechanics:molecular mechanics (QM:MM)-based modeling for the coordination of the W-co, enables formulation of a hypothetical catalytic mechanism that paves the way to further engineering for applications in synthetic biology and biotechnology.
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Affiliation(s)
- Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków, Poland
| | - Fidel Ramírez-Amador
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Dominik Hege
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Yvonne Gemmecker
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Simone Prinz
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Georg Hochberg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Johann Heider
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków, Poland
| | - Jan Michael Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
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4
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Comprehensive catalytic and biological studies on new designed oxo- and dioxo-metal (IV/VI) organic arylhydrazone frameworks. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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5
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Tian X, Xie H, Li J, Cui L, Yu YL, Li B, Li YF. Nano-WSe 2 Is Absorbable and Transformable by Rice Plants. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227826. [PMID: 36431926 PMCID: PMC9694913 DOI: 10.3390/molecules27227826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
As typical transition metal dichalcogenides (TMDC), tungsten selenide (WSe2) nanosheets (nano-WSe2) are widely used in various fields due to their layered structures and highly tunable electronic and magnetic properties, which results in the unwanted release of tungsten (W) and selenium (Se) into the environment. However, the environmental effects of nano-WSe2 in plants are still unclear. Herein, we evaluated the impacts and fate of nano-WSe2 and micro-WSe2 in rice plants (Oryza sativa L.). It was found that both nano-WSe2 and micro-WSe2 did not affect the germination of rice seeds up to 5000 mg/L but nano-WSe2 affected the growth of rice seedlings with shortened root lengths. The uptake and transportation of WSe2 was found to be size-dependent. Moreover, W in WSe2 was oxidized to tungstate while Se was transformed to selenocysteine, selenomethionine, SeIV and SeVI in the roots of rice when exposed to nano-WSe2, suggesting the transformation of nano-WSe2 in rice plants. The exposure to nano-WSe2 brought lipid peroxidative damage to rice seedlings. However, Se in nano-WSe2 did not contribute to the synthesis of glutathione peroxidase (GSH-Px) since the latter did not change when exposed to nano-WSe2. This is the first report on the impacts and fate of nano-WSe2 in rice plants, which has raised environmental safety concerns about the wide application of TMDCs, such as WSe2 nanosheets.
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Affiliation(s)
- Xue Tian
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, Beijing Metallomics Facility, National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxin Xie
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, Beijing Metallomics Facility, National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Jincheng Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, Beijing Metallomics Facility, National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Liwei Cui
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Liang Yu
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
- Correspondence: (Y.-L.Y.); (Y.-F.L.); Tel.: +86-24-83688944 (Y.-L.Y.); +86-10-88233908 (Y.-F.L.)
| | - Bai Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, Beijing Metallomics Facility, National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yu-Feng Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, Beijing Metallomics Facility, National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.-L.Y.); (Y.-F.L.); Tel.: +86-24-83688944 (Y.-L.Y.); +86-10-88233908 (Y.-F.L.)
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6
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Nehzati S, Summers AO, Dolgova NV, Zhu J, Sokaras D, Kroll T, Pickering IJ, George GN. Hg(II) Binding to Thymine Bases in DNA. Inorg Chem 2021; 60:7442-7452. [PMID: 33938732 DOI: 10.1021/acs.inorgchem.1c00735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The compounds of mercury can be highly toxic and can interfere with a range of biological processes, although many aspects of the mechanism of toxicity are still obscure or unknown. One especially intriguing property of Hg(II) is its ability to bind DNA directly, making interstrand cross-links between thymine nucleobases in AT-rich sequences. We have used a combination of small molecule X-ray diffraction, X-ray spectroscopies, and computational chemistry to study the interactions of Hg(II) with thymine. We find that the energetically preferred mode of thymine binding in DNA is to the N3 and predict only minor distortions of the DNA structure on binding one Hg(II) to two cross-adjacent thymine nucleotides. The preferred geometry is predicted to be twisted away from coplanar through a torsion angle of between 32 and 43°. Using 1-methylthymine as a model, the bis-thymine coordination of Hg(II) is found to give a highly characteristic X-ray spectroscopic signature that is quite distinct from other previously described biological modes of binding of Hg(II). This work enlarges and deepens our view of significant biological targets of Hg(II) and demonstrates tools that can provide a characteristic signature for the binding of Hg(II) to DNA in more complex matrices including intact cells and tissues, laying the foundation for future studies of mechanisms of mercury toxicity.
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Affiliation(s)
- Susan Nehzati
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Anne O Summers
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Natalia V Dolgova
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Jianfeng Zhu
- Saskatchewan Structural Sciences Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Ingrid J Pickering
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Graham N George
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
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7
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Abbenseth J, Oudsen JPH, Venderbosch B, Demeshko S, Finger M, Herwig C, Würtele C, Holthausen MC, Limberg C, Tromp M, Schneider S. Examination of Protonation-Induced Dinitrogen Splitting by in Situ EXAFS Spectroscopy. Inorg Chem 2020; 59:14367-14375. [PMID: 32960050 DOI: 10.1021/acs.inorgchem.0c02134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The splitting of dinitrogen into nitride complexes emerged as a key reaction for nitrogen fixation strategies at ambient conditions. However, the impact of auxiliary ligands or accessible spin states on the thermodynamics and kinetics of N-N cleavage is yet to be examined in detail. We recently reported N-N bond splitting of a {Mo(μ2:η1:η1-N2)Mo}-complex upon protonation of the diphosphinoamide auxiliary ligands. The reactivity was associated with a low-spin to high-spin transition that was induced by the protonation reaction in the coordination periphery, mainly based on computational results. Here, this proposal is evaluated by an XAS study of a series of linearly N2 bridged Mo pincer complexes. Structural characterization of the transient protonation product by EXAFS spectroscopy confirms the proposed spin transition prior to N-N bond cleavage.
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Affiliation(s)
- Josh Abbenseth
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Jean-Pierre H Oudsen
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Bas Venderbosch
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Serhiy Demeshko
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Markus Finger
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Christian Herwig
- Institut für Chemie, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Christian Würtele
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Max C Holthausen
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Moniek Tromp
- Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sven Schneider
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
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8
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Kudreeva L, Kurbatov A, Kamysbayev D, Kalyyeva A, Zhumasheva N, Abilev M, Serikbayev B, Dauletbay A. Electrochemical Separation of Molybdenum and Tungsten Using Aqueous-Organic Electrolytes. EURASIAN CHEMICO-TECHNOLOGICAL JOURNAL 2020. [DOI: 10.18321/ectj980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Molybdenum is one of the valuable metals for the industry; its special properties make it extremely urgent to study the process of separation of molybdenum from other impurities. The article considers the optimization of electrochemical separation of molybdenum from Mo-W system. The electrochemical dissolution of molybdenum and tungsten in solutions of LiCl and NH4NO3 in dimethylsulfoxide was studied using polarization curves and calculation of the efficiency of anodic dissolution of molybdenum in the presence of tungsten. The electrolyte with a composition of 0.5 M LiCl; 5.2 M dimethylsulfoxide; 32.2 M water was selected as an effective solution for the electrochemical separation of molybdenum in the potential range of 1.0‒2.2 V. Results obtained in this study can be used for the development of selective separation method in the molybdenum production.
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9
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George SJ, Carpenter MH, Friedrich S, Cantor R. Feasibility of Laboratory-Based EXAFS Spectroscopy with Cryogenic Detectors. JOURNAL OF LOW TEMPERATURE PHYSICS 2020; 200:479-484. [PMID: 33776141 PMCID: PMC7990010 DOI: 10.1007/s10909-020-02474-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/15/2020] [Indexed: 06/12/2023]
Abstract
Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy is a powerful technique that gives element-specific information about the structure of molecules. The development of a laboratory EXAFS spectrometer capable of measuring transmission spectra would be a significant advance as the technique is currently only available at synchrotron radiation lightsources. Here, we explore the potential of cryogenic detectors as the energy resolving component of a laboratory transmission EXAFS instrument. We examine the energy resolution, count-rate, and detector stability needed for good EXAFS spectra and compare these to the properties of cryogenic detectors and conventional X-ray optics. We find that superconducting tunnel junction (STJ) detectors are well-suited for this application.
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10
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Vogt LI, Cotelesage JJH, Dolgova NV, Titus CJ, Sharifi S, George SJ, Pickering IJ, George GN. X-ray absorption spectroscopy of organic sulfoxides. RSC Adv 2020; 10:26229-26238. [PMID: 35519739 PMCID: PMC9055334 DOI: 10.1039/d0ra04653a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/02/2020] [Indexed: 01/21/2023] Open
Abstract
Organic sulfoxides, a group of compounds containing the sulfinyl S
Created by potrace 1.16, written by Peter Selinger 2001-2019
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O group, are widespread in nature, important in health and disease, and used in a variety of applications in the pharmaceutical industry. We have examined the sulfur K-edge X-ray absorption near-edge spectra of a range of different sulfoxides and find that their spectra are remarkably similar. Spectra show an intense absorption peak that is comprised of two transitions; a S 1s → (S–O)σ* and a S 1s → [(S–O)π* + (S–C)σ*] transition. In most cases these are sufficiently close in energy that they are not properly resolved; however for dimethylsulfoxide the separation between these transitions increases in aqueous solution due to hydrogen bonding to the sulfinyl oxygen. We also examined tetrahydrothiophene sulfoxide using both the sulfur and oxygen K-edge. This compound has a mild degree of ring strain at the sulfur atom, which changes the energies of the two transitions so that the S 1s → [(S–O)π* + (S–C)σ*] is below the S 1s → (S–O)σ*. A comparison of the oxygen K-edge X-ray absorption near-edge spectra of tetrahydrothiophene sulfoxide with that of an unhindered sulfoxide shows little change, indicating that the electronic environment of oxygen is very similar. This study develops an understanding of the X-ray absorption near-edge spectra of organic sulfoxides using the sulfur and oxygen K-edges.![]()
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Affiliation(s)
- Linda I. Vogt
- Molecular and Environmental Sciences Group
- Department of Geological Sciences
- University of Saskatchewan
- Saskatoon
- Canada
| | - Julien J. H. Cotelesage
- Molecular and Environmental Sciences Group
- Department of Geological Sciences
- University of Saskatchewan
- Saskatoon
- Canada
| | - Natalia V. Dolgova
- Molecular and Environmental Sciences Group
- Department of Geological Sciences
- University of Saskatchewan
- Saskatoon
- Canada
| | | | | | | | - Ingrid J. Pickering
- Molecular and Environmental Sciences Group
- Department of Geological Sciences
- University of Saskatchewan
- Saskatoon
- Canada
| | - Graham N. George
- Molecular and Environmental Sciences Group
- Department of Geological Sciences
- University of Saskatchewan
- Saskatoon
- Canada
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11
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Djeghader A, Rossotti M, Abdulkarim S, Biaso F, Gerbaud G, Nitschke W, Schoepp-Cothenet B, Soulimane T, Grimaldi S. Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase. Chem Commun (Camb) 2020; 56:9850-9853. [DOI: 10.1039/d0cc03634j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We provide structural and spectroscopic evidence for a molybdenum–phosphate adduct mimicking a proposed reaction intermediate in the active site of a prokaryotic sulfite oxidizing enzyme.
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Affiliation(s)
- Ahmed Djeghader
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
| | | | - Saleh Abdulkarim
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
| | | | | | | | | | - Tewfik Soulimane
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
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12
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Amato A, Terzo S, Mulè F. Natural Compounds as Beneficial Antioxidant Agents in Neurodegenerative Disorders: A Focus on Alzheimer's Disease. Antioxidants (Basel) 2019; 8:antiox8120608. [PMID: 31801234 PMCID: PMC6943487 DOI: 10.3390/antiox8120608] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/19/2019] [Accepted: 11/27/2019] [Indexed: 12/22/2022] Open
Abstract
The positive role of nutrition in chronic neurodegenerative diseases (NDs) suggests that dietary interventions represent helpful tools for preventing NDs. In particular, diets enriched with natural compounds have become an increasingly attractive, non-invasive, and inexpensive option to support a healthy brain and to potentially treat NDs. Bioactive compounds found in vegetables or microalgae possess special properties able to counteract oxidative stress, which is involved as a triggering factor in neurodegeneration. Here, we briefly review the relevant experimental data on curcuminoids, silymarin, chlorogenic acid, and compounds derived from the microalga Aphanizomenon flos aquae (AFA) which have been demonstrated to possess encouraging beneficial effects on neurodegeneration, in particular on Alzheimer's disease models.
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Affiliation(s)
- Antonella Amato
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90127 Palermo, Italy; (S.T.); (F.M.)
- Correspondence:
| | - Simona Terzo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90127 Palermo, Italy; (S.T.); (F.M.)
- Department of Neuroscience and Cell Biology, University of Palermo, 90127 Palermo, Italy
| | - Flavia Mulè
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90127 Palermo, Italy; (S.T.); (F.M.)
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13
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George GN, Pickering IJ, Cotelesage JJH, Vogt LI, Dolgova NV, Regnier N, Sokaras D, Kroll T, Sneeden EY, Hackett MJ, Goto K, Block E. Visualizing sulfur with X-rays: From molecules to tissues. PHOSPHORUS SULFUR 2019. [DOI: 10.1080/10426507.2019.1602618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Graham N. George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Canada
- Department of Chemistry, University of Saskatchewan, Saskatoon, Canada
| | - Ingrid J. Pickering
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Canada
- Department of Chemistry, University of Saskatchewan, Saskatoon, Canada
| | | | - Linda I. Vogt
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Natalia V. Dolgova
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Nathan Regnier
- Department of Chemistry, University of Saskatchewan, Saskatoon, Canada
| | | | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, Menlo Park, California, USA
| | - Eileen Y. Sneeden
- Stanford Synchrotron Radiation Lightsource, Menlo Park, California, USA
| | - Mark J. Hackett
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Kei Goto
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
| | - Eric Block
- Department of Chemistry, University at Albany – State University of New York, Albany, New York, USA
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14
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Gisewhite DR, Nagelski AL, Cummins DC, Yap GPA, Burgmayer SJN. Modeling Pyran Formation in the Molybdenum Cofactor: Protonation of Quinoxalyl-Dithiolene Promoting Pyran Cyclization. Inorg Chem 2019; 58:5134-5144. [PMID: 30942584 PMCID: PMC6572731 DOI: 10.1021/acs.inorgchem.9b00194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mononuclear Mo and W enzymes require a unique ligand known as molybdopterin (MPT). This ligand binds the metal through a dithiolene chelate, and the dithiolene bridges a reduced pyranopterin group. Pyran scission and formation have been proposed as a reaction of the MPT ligand that may occur within the enzymes to adjust reactivity at the Mo atom. We address this issue by investigating oxo-Mo(IV) model complexes containing dithiolenes substituted by pterin or quinoxaline and a hydroxyalkyl poised to form a pyran ring. While the pterin-dithiolene model complex exhibits a low energy, reversible pyran cyclization, here we report that pyran cyclization does not spontaneously occur in the quinoxalyl-dithiolene model. However, protonating the quinoxalyl-dithiolene model induces pyran cyclization forming an unstable, pyrano-quinoxalyl-dithiolene complex which subsequently dehydrates and rearranges to a pyrrolo-quinoxlyl-dithiolene complex that was previously characterized. The protonated pyrano-quinoxalyl-dithiolene complex was characterized by absorption spectroscopy and cyclic voltammetry, and these results suggest pyran cyclization leads to a significant change in the Mo electronic structure exhibited as a strong intraligand charge transfer (ILCT) transition and 370 mV positive shift of the Mo(V/IV) reduction potential. The influence of protonation on quinoxaline reactivity supports the hypothesis that the local protein environment in the second coordination sphere of molybdenum cofactor (Moco) could control pyran cyclization. The results also demonstrate that the remarkable chemical reactivity of the pterin-dithiolene ligand is subtly distinct and not reproduced by the simpler quinoxaline analog that is often used to replace pterin in synthetic Moco models.
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Affiliation(s)
- Douglas R. Gisewhite
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Alexandra L. Nagelski
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Daniel C. Cummins
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sharon J. N. Burgmayer
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
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15
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Effects of the Aphanizomenon flos-aquae Extract (Klamin®) on a Neurodegeneration Cellular Model. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:9089016. [PMID: 30310529 PMCID: PMC6166380 DOI: 10.1155/2018/9089016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/30/2018] [Indexed: 11/29/2022]
Abstract
Cyanobacteria have been recognized as a source of bioactive molecules to be employed in nutraceuticals, pharmaceuticals, and functional foods. An extract of Aphanizomenon flos-aquae (AFA), commercialized as Klamin®, was subjected to chemical analysis to determine its compounds. The AFA extract Klamin® resulted to be nontoxic, also at high doses, when administered onto LAN5 neuronal cells. Its scavenging properties against ROS generation were evaluated by using DCFH-DA assay, and its mitochondrial protective role was determined by JC-1 and MitoSOX assays. Klamin® exerts a protective role against beta amyloid- (Aβ-) induced toxicity and against oxidative stress. Anti-inflammatory properties were demonstrated by NFβB nuclear localization and activation of IL-6 and IL-1β inflammatory cytokines through ELISA. Finally, by using thioflavin T (ThT) and fluorimetric measures, we found that Klamin® interferes with Aβ aggregation kinetics, supporting the formation of smaller and nontoxic structures compared to toxic Aβ aggregates alone. Altogether, these data indicate that the AFA extract may play a protective role against mechanisms leading to neurodegeneration.
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16
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Jimenez-Halla JOC, Nazemi A, Cundari TR. DFT study of substituent effects in the hydroxylation of methane and toluene mediated by an ethylbenzene dehydrogenase active site model. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Dolgova NV, Nehzati S, Choudhury S, MacDonald TC, Regnier NR, Crawford AM, Ponomarenko O, George GN, Pickering IJ. X-ray spectroscopy and imaging of selenium in living systems. Biochim Biophys Acta Gen Subj 2018; 1862:2383-2392. [PMID: 29729308 DOI: 10.1016/j.bbagen.2018.04.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Selenium is an essential element with a rich and varied chemistry in living organisms. It plays a variety of important roles ranging from being essential in enzymes that are critical for redox homeostasis to acting as a deterrent for herbivory in hyperaccumulating plants. Despite its importance there are many open questions, especially related to its chemistry in situ within living organisms. SCOPE OF REVIEW This review discusses X-ray spectroscopy and imaging of selenium in biological samples, with an emphasis on the methods, and in particular the techniques of X-ray absorption spectroscopy (XAS) and X-ray fluorescence imaging (XFI). We discuss the experimental methods and capabilities of XAS and XFI, and review their advantages and their limitations. A perspective on future possibilities and next-generation of experiments is also provided. MAJOR CONCLUSIONS XAS and XFI provide powerful probes of selenium chemistry, together with unique in situ capabilities. The opportunities and capabilities of the next generation of advanced X-ray spectroscopy experiments are particularly exciting. GENERAL SIGNIFICANCE XAS and XFI provide versatile tools that are generally applicable to any element with a convenient X-ray absorption edge, suitable for investigating complex systems essentially without pre-treatment.
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Affiliation(s)
- Natalia V Dolgova
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Susan Nehzati
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Sanjukta Choudhury
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Tracy C MacDonald
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Nathan R Regnier
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N0X2, Canada
| | - Andrew M Crawford
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Olena Ponomarenko
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Graham N George
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada; Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N0X2, Canada.
| | - Ingrid J Pickering
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada; Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N0X2, Canada.
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18
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Andresen E, Peiter E, Küpper H. Trace metal metabolism in plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:909-954. [PMID: 29447378 DOI: 10.1093/jxb/erx465] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/04/2017] [Indexed: 05/18/2023]
Abstract
Many trace metals are essential micronutrients, but also potent toxins. Due to natural and anthropogenic causes, vastly different trace metal concentrations occur in various habitats, ranging from deficient to toxic levels. Therefore, one focus of plant research is on the response to trace metals in terms of uptake, transport, sequestration, speciation, physiological use, deficiency, toxicity, and detoxification. In this review, we cover most of these aspects for the essential micronutrients copper, iron, manganese, molybdenum, nickel, and zinc to provide a broader overview than found in other recent reviews, to cross-link aspects of knowledge in this very active research field that are often seen in a separated way. For example, individual processes of metal usage, deficiency, or toxicity often were not mechanistically interconnected. Therefore, this review also aims to stimulate the communication of researchers following different approaches, such as gene expression analysis, biochemistry, or biophysics of metalloproteins. Furthermore, we highlight recent insights, emphasizing data obtained under physiologically and environmentally relevant conditions.
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Affiliation(s)
- Elisa Andresen
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Plant Biophysics and Biochemistry, Branišovská, Ceské Budejovice, Czech Republic
| | - Edgar Peiter
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Plant Nutrition Laboratory, Betty-Heimann-Strasse, Halle (Saale), Germany
| | - Hendrik Küpper
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Plant Biophysics and Biochemistry, Branišovská, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, Department of Experimental Plant Biology, Branišovská, České Budějovice, Czech Republic
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19
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Warelow TP, Pushie MJ, Cotelesage JJH, Santini JM, George GN. The active site structure and catalytic mechanism of arsenite oxidase. Sci Rep 2017; 7:1757. [PMID: 28496149 PMCID: PMC5432002 DOI: 10.1038/s41598-017-01840-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/04/2017] [Indexed: 11/09/2022] Open
Abstract
Arsenite oxidase is thought to be an ancient enzyme, originating before the divergence of the Archaea and the Bacteria. We have investigated the nature of the molybdenum active site of the arsenite oxidase from the Alphaproteobacterium Rhizobium sp. str. NT-26 using a combination of X-ray absorption spectroscopy and computational chemistry. Our analysis indicates an oxidized Mo(VI) active site with a structure that is far from equilibrium. We propose that this is an entatic state imposed by the protein on the active site through relative orientation of the two molybdopterin cofactors, in a variant of the Rây-Dutt twist of classical coordination chemistry, which we call the pterin twist hypothesis. We discuss the implications of this hypothesis for other putatively ancient molybdopterin-based enzymes.
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Affiliation(s)
- Thomas P Warelow
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - M Jake Pushie
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.,Molecular and Environmental Sciences Research Group, Department of Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
| | - Julien J H Cotelesage
- Molecular and Environmental Sciences Research Group, Department of Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Graham N George
- Molecular and Environmental Sciences Research Group, Department of Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada. .,Department of Chemistry, University of Saskatchewan, Saskatoon, SK, S7N 5C9, Canada.
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20
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Rendon J, Biaso F, Ceccaldi P, Toci R, Seduk F, Magalon A, Guigliarelli B, Grimaldi S. Elucidating the Structures of the Low- and High-pH Mo(V) Species in Respiratory Nitrate Reductase: A Combined EPR, 14,15N HYSCORE, and DFT Study. Inorg Chem 2017; 56:4423-4435. [DOI: 10.1021/acs.inorgchem.6b03129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julia Rendon
- Aix Marseille Univ, CNRS, BIP, Marseille, France
| | | | - Pierre Ceccaldi
- Aix Marseille Univ, CNRS, BIP, Marseille, France
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - René Toci
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Farida Seduk
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Axel Magalon
- Aix Marseille Univ, CNRS, LCB, Marseille, France
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21
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Ghosh AC, Samuel PP, Schulzke C. Synthesis, characterization and oxygen atom transfer reactivity of a pair of Mo(iv)O- and Mo(vi)O2-enedithiolate complexes – a look at both ends of the catalytic transformation. Dalton Trans 2017; 46:7523-7533. [DOI: 10.1039/c7dt01470h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel pair of mono-oxo and di-oxo bis-dithiolene molybdenum complexes were synthesized, characterized and catalytically investigated as models for a molybdenum dependent oxidoreductase.
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Affiliation(s)
- Ashta C. Ghosh
- Institute of Condensed Matter and Nanosciences
- Molecules
- Solids and Reactivity (IMCN/MOST)
- Université catholique de Louvain
- 1348 Louvain-la-Neuve
| | - Prinson P. Samuel
- Universität Göttingen
- Institut für Anorganische Chemie
- 37077 Göttingen
- Germany
| | - Carola Schulzke
- Institut für Biochemie
- Ernst-Moritz-Arndt-Universitat Greifswald
- 17487 Greifswald
- Germany
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22
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Maurya MR, Uprety B, Avecilla F. Dioxidomolybdenum(VI) Complexes of Tripodal Tetradentate Ligands for Catalytic Oxygen Atom Transfer between Benzoin and Dimethyl Sulfoxide and for Oxidation of Pyrogallol. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600694] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mannar R. Maurya
- Department of Chemistry; Indian Institute of Technology Roorkee; 247667 Roorkee India
| | - Bhawna Uprety
- Department of Chemistry; Indian Institute of Technology Roorkee; 247667 Roorkee India
| | - Fernando Avecilla
- Departamento de Química Fundamental; Universidade da Coruña; Campus de A Zapateira 15071 A Coruña Spain
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23
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Young CG. Chemical systems modeling the d1 Mo(V) states of molybdenum enzymes. J Inorg Biochem 2016; 162:238-252. [PMID: 27432259 DOI: 10.1016/j.jinorgbio.2016.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/14/2016] [Accepted: 06/03/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Charles G Young
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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24
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Okamura T, Yamada T, Hasenaka Y, Yamashita S, Onitsuka K. Unexpected Reaction Promoted by NH+···O=Mo Hydrogen Bonds in Nonpolar Solvents. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Taka‐aki Okamura
- Department of Macromolecular Science Graduate School of Science Osaka University 560‐0043 Toyonaka Osaka Japan
| | - Takayoshi Yamada
- Department of Macromolecular Science Graduate School of Science Osaka University 560‐0043 Toyonaka Osaka Japan
| | - Yuki Hasenaka
- Department of Macromolecular Science Graduate School of Science Osaka University 560‐0043 Toyonaka Osaka Japan
| | - Satoshi Yamashita
- Department of Macromolecular Science Graduate School of Science Osaka University 560‐0043 Toyonaka Osaka Japan
| | - Kiyotaka Onitsuka
- Department of Macromolecular Science Graduate School of Science Osaka University 560‐0043 Toyonaka Osaka Japan
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25
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Wu SY, Rothery RA, Weiner JH. Pyranopterin Coordination Controls Molybdenum Electrochemistry in Escherichia coli Nitrate Reductase. J Biol Chem 2015; 290:25164-73. [PMID: 26297003 DOI: 10.1074/jbc.m115.665422] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Indexed: 11/06/2022] Open
Abstract
We test the hypothesis that pyranopterin (PPT) coordination plays a critical role in defining molybdenum active site redox chemistry and reactivity in the mononuclear molybdoenzymes. The molybdenum atom of Escherichia coli nitrate reductase A (NarGHI) is coordinated by two PPT-dithiolene chelates that are defined as proximal and distal based on their proximity to a [4Fe-4S] cluster known as FS0. We examined variants of two sets of residues involved in PPT coordination: (i) those interacting directly or indirectly with the pyran oxygen of the bicyclic distal PPT (NarG-Ser(719), NarG-His(1163), and NarG-His(1184)); and (ii) those involved in bridging the two PPTs and stabilizing the oxidation state of the proximal PPT (NarG-His(1092) and NarG-His(1098)). A S719A variant has essentially no effect on the overall Mo(VI/IV) reduction potential, whereas the H1163A and H1184A variants elicit large effects (ΔEm values of -88 and -36 mV, respectively). Ala variants of His(1092) and His(1098) also elicit large ΔEm values of -143 and -101 mV, respectively. An Arg variant of His(1092) elicits a small ΔEm of +18 mV on the Mo(VI/IV) reduction potential. There is a linear correlation between the molybdenum Em value and both enzyme activity and the ability to support anaerobic respiratory growth on nitrate. These data support a non-innocent role for the PPT moieties in controlling active site metal redox chemistry and catalysis.
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Affiliation(s)
- Sheng-Yi Wu
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rothery
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joel H Weiner
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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26
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Ceccaldi P, Rendon J, Léger C, Toci R, Guigliarelli B, Magalon A, Grimaldi S, Fourmond V. Reductive activation of E. coli respiratory nitrate reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1055-63. [PMID: 26073890 DOI: 10.1016/j.bbabio.2015.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/01/2015] [Accepted: 06/07/2015] [Indexed: 11/25/2022]
Abstract
Over the past decades, a number of authors have reported the presence of inactive species in as-prepared samples of members of the Mo/W-bisPGD enzyme family. This greatly complicated the spectroscopic studies of these enzymes, since it is impossible to discriminate between active and inactive species on the basis of the spectroscopic signatures alone. Escherichia coli nitrate reductase A (NarGHI) is a member of the Mo/W-bisPGD family that allows anaerobic respiration using nitrate as terminal electron acceptor. Here, using protein film voltammetry on NarGH films, we show that the enzyme is purified in a functionally heterogeneous form that contains between 20 and 40% of inactive species that activate the first time they are reduced. This activation proceeds in two steps: a non-redox reversible reaction followed by an irreversible reduction. By carefully correlating electrochemical and EPR spectroscopic data, we show that neither the two major Mo(V) signals nor those of the two FeS clusters that are the closest to the Mo center are associated with the two inactive species. We also conclusively exclude the possibility that the major "low-pH" and "high-pH" Mo(V) EPR signatures correspond to species in acid-base equilibrium.
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Affiliation(s)
- Pierre Ceccaldi
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille cedex 20, France
| | - Julia Rendon
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille cedex 20, France
| | - Christophe Léger
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille cedex 20, France
| | - René Toci
- Aix-Marseille Université, CNRS, LCB UMR 7283, 31 chemin J. Aiguier, F-13402 Marseille cedex 20, France
| | - Bruno Guigliarelli
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille cedex 20, France
| | - Axel Magalon
- Aix-Marseille Université, CNRS, LCB UMR 7283, 31 chemin J. Aiguier, F-13402 Marseille cedex 20, France
| | - Stéphane Grimaldi
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille cedex 20, France
| | - Vincent Fourmond
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, F-13402 Marseille cedex 20, France.
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27
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Hasenaka Y, Okamura TA, Tatsumi M, Inazumi N, Onitsuka K. Behavior of anionic molybdenum(IV, VI) and tungsten(IV, VI) complexes containing bulky hydrophobic dithiolate ligands and intramolecular NH···S hydrogen bonds in nonpolar solvents. Dalton Trans 2015; 43:15491-502. [PMID: 25190301 DOI: 10.1039/c4dt01646g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molybdenum(IV, VI) and tungsten(IV, VI) complexes, (Et4N)2[M(IV)O{1,2-S2-3,6-(RCONH)2C6H2}2] and (Et4N)2[M(VI)O2{1,2-S2-3,6-(RCONH)2C6H2}2] (M = Mo, W; R = (4-(t)BuC6H4)3C), with bulky hydrophobic dithiolate ligands containing NH···S hydrogen bonds were synthesized. These complexes are soluble in nonpolar solvents like toluene, which allows the detection of unsymmetrical coordination structures and elusive intermolecular interactions in solution. The (1)H NMR spectra of the complexes in toluene-d8 revealed an unsymmetrical coordination structure, and proximity of the counterions to the anion moiety was suggested at low temperatures. The oxygen-atom-transfer reaction between the molybdenum(IV) complex and Me3NO in toluene was considerably accelerated in nonpolar solvents, and this increase was attributed to the favorable access of the substrate to the active center in the hydrophobic environment.
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Affiliation(s)
- Yuki Hasenaka
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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28
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Majumdar A. Structural and functional models in molybdenum and tungsten bioinorganic chemistry: description of selected model complexes, present scenario and possible future scopes. Dalton Trans 2015; 43:8990-9003. [PMID: 24798698 DOI: 10.1039/c4dt00631c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A brief description about some selected model complexes in molybdenum and tungsten bioinorganic chemistry is provided. The synthetic strategies involved and their limitations are discussed. Current status of molybdenum and tungsten bioinorganic modeling chemistry is presented briefly and synthetic problems associated therein are analyzed. Possible future directions which may expand the scope of modeling chemistry are suggested.
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Affiliation(s)
- Amit Majumdar
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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29
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Maiti BK, Maia LB, Silveira CM, Todorovic S, Carreira C, Carepo MSP, Grazina R, Moura I, Pauleta SR, Moura JJG. Incorporation of molybdenum in rubredoxin: models for mononuclear molybdenum enzymes. J Biol Inorg Chem 2015; 20:821-9. [PMID: 25948393 DOI: 10.1007/s00775-015-1268-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/29/2015] [Indexed: 12/21/2022]
Abstract
Molybdenum is found in the active site of enzymes usually coordinated by one or two pyranopterin molecules. Here, we mimic an enzyme with a mononuclear molybdenum-bis pyranopterin center by incorporating molybdenum in rubredoxin. In the molybdenum-substituted rubredoxin, the metal ion is coordinated by four sulfurs from conserved cysteine residues of the apo-rubredoxin and two other exogenous ligands, oxygen and thiol, forming a Mo((VI))-(S-Cys)4(O)(X) complex, where X represents -OH or -SR. The rubredoxin molybdenum center is stabilized in a Mo(VI) oxidation state, but can be reduced to Mo(IV) via Mo(V) by dithionite, being a suitable model for the spectroscopic properties of resting and reduced forms of molybdenum-bis pyranopterin-containing enzymes. Preliminary experiments indicate that the molybdenum site built in rubredoxin can promote oxo transfer reactions, as exemplified with the oxidation of arsenite to arsenate.
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Affiliation(s)
- Biplab K Maiti
- UCIBIO, REQUIMTE, Departamento Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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30
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Nitrite reduction by molybdoenzymes: a new class of nitric oxide-forming nitrite reductases. J Biol Inorg Chem 2015; 20:403-33. [DOI: 10.1007/s00775-014-1234-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/14/2014] [Indexed: 02/07/2023]
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Rothery RA, Weiner JH. Shifting the metallocentric molybdoenzyme paradigm: the importance of pyranopterin coordination. J Biol Inorg Chem 2014; 20:349-72. [PMID: 25267303 DOI: 10.1007/s00775-014-1194-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/15/2014] [Indexed: 01/10/2023]
Abstract
In this review, we test the hypothesis that pyranopterin coordination plays a critical role in defining substrate reactivities in the four families of mononuclear molybdenum and tungsten enzymes (Mo/W-enzymes). Enzyme families containing a single pyranopterin dithiolene chelate have been demonstrated to have reactivity towards two (sulfite oxidase, SUOX-fold) and five (xanthine dehydrogenase, XDH-fold) types of substrate, whereas the major family of enzymes containing a bis-pyranopterin dithiolene chelate (dimethylsulfoxide reductase, DMSOR-fold) is reactive towards eight types of substrate. A second bis-pyranopterin enzyme (aldehyde oxidoreductase, AOR-fold) family catalyzes a single type of reaction. The diversity of reactions catalyzed by each family correlates with active site variability, and also with the number of pyranopterins and their coordination by the protein. In the case of the AOR-fold enzymes, inflexibility of pyranopterin coordination correlates with their limited substrate specificity (oxidation of aldehydes). In examples of the SUOX-fold and DMSOR-fold enzymes, we observe three types of histidine-containing charge-transfer relays that can: (1) connect the piperazine ring of the pyranopterin to the substrate-binding site (SUOX-fold enzymes); (2) provide inter-pyranopterin communication (DMSOR-fold enzymes); and (3) connect a pyran ring oxygen to deeply buried water molecules (the DMSOR-fold NarGHI-type nitrate reductases). Finally, sequence data mining reveals a number of bacterial species whose predicted proteomes contain large numbers (up to 64) of Mo/W-enzymes, with the DMSOR-fold enzymes being dominant. These analyses also reveal an inverse correlation between Mo/W-enzyme content and pathogenicity.
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Affiliation(s)
- Richard A Rothery
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
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32
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Giles LJ, Ruppelt C, Yang J, Mendel RR, Bittner F, Kirk ML. Molybdenum site structure of MOSC family proteins. Inorg Chem 2014; 53:9460-2. [PMID: 25166909 PMCID: PMC4164224 DOI: 10.1021/ic5015863] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mo K-edge X-ray absorption spectroscopy has been used to probe as-isolated structures of the MOSC family proteins pmARC-1 and HMCS-CT. The Mo K-edge near-edge spectrum of HMCS-CT is shifted ~2.5 eV to lower energy compared to the pmARC-1 spectrum, which indicates that as-isolated HMCS-CT is in a more reduced state than pmARC-1. Extended X-ray absorption fine structure analysis indicates significant structural differences between pmARC-1 and HMCS-CT, with the former being a dioxo site and the latter possessing only a single terminal oxo ligand. The number of terminal oxo donors is consistent with pmARC-1 being in the Mo(VI) oxidation state and HMCS-CT in the Mo(IV) state. These structures are in accord with oxygen-atom-transfer reactivity for pmARC-1 and persulfide bond cleavage chemistry for HMCS-CT.
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Affiliation(s)
- Logan J Giles
- Department of Chemistry and Chemical Biology, The University of New Mexico , MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
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Sparacino-Watkins C, Stolz JF, Basu P. Nitrate and periplasmic nitrate reductases. Chem Soc Rev 2014; 43:676-706. [PMID: 24141308 DOI: 10.1039/c3cs60249d] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.
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van Stipdonk MJ, Basu P, Dille SA, Gibson JK, Berden G, Oomens J. Infrared multiple photon dissociation spectroscopy of a gas-phase oxo-molybdenum complex with 1,2-dithiolene ligands. J Phys Chem A 2014; 118:5407-18. [PMID: 24988369 PMCID: PMC4338922 DOI: 10.1021/jp503222v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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Electrospray
ionization (ESI) in the negative ion mode was used
to create anionic, gas-phase oxo-molybdenum complexes with dithiolene
ligands. By varying ESI and ion transfer conditions, both doubly and
singly charged forms of the complex, with identical formulas, could
be observed. Collision-induced dissociation (CID) of the dianion generated
exclusively the monoanion, while fragmentation of the monoanion involved
decomposition of the dithiolene ligands. The intrinsic structure of
the monoanion and the dianion were determined by using wavelength-selective
infrared multiple-photon dissociation (IRMPD) spectroscopy and density
functional theory calculations. The IRMPD spectrum for the dianion
exhibits absorptions that can be assigned to (ligand) C=C,
C–S, C—C≡N, and Mo=O stretches. Comparison
of the IRMPD spectrum to spectra predicted for various possible conformations
allows assignment of a pseudo square pyramidal structure with C2v symmetry, equatorial coordination
of MoO2+ by the S atoms of the dithiolene ligands, and
a singlet spin state. A single absorption was observed for the oxidized
complex. When the same scaling factor employed for the dianion is
used for the oxidized version, theoretical spectra suggest that the
absorption is the Mo=O stretch for a distorted square pyramidal
structure and doublet spin state. A predicted change in conformation
upon oxidation of the dianion is consistent with a proposed bonding
scheme for the bent-metallocene dithiolene compounds [Lauher, J. W.; Hoffmann, R. J. Am.
Chem. Soc.1976, 98, 1729−1742], where a large
folding of the dithiolene moiety along the S···S vector
is dependent on the occupancy of the in-plane metal d-orbital.
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Affiliation(s)
- Michael J van Stipdonk
- Department of Chemistry and Biochemistry, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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35
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Lima FA, Bjornsson R, Weyhermüller T, Chandrasekaran P, Glatzel P, Neese F, DeBeer S. High-resolution molybdenum K-edge X-ray absorption spectroscopy analyzed with time-dependent density functional theory. Phys Chem Chem Phys 2014; 15:20911-20. [PMID: 24197060 DOI: 10.1039/c3cp53133c] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
X-ray absorption spectroscopy (XAS) is a widely used experimental technique capable of selectively probing the local structure around an absorbing atomic species in molecules and materials. When applied to heavy elements, however, the quantitative interpretation can be challenging due to the intrinsic spectral broadening arising from the decrease in the core-hole lifetime. In this work we have used high-energy resolution fluorescence detected XAS (HERFD-XAS) to investigate a series of molybdenum complexes. The sharper spectral features obtained by HERFD-XAS measurements enable a clear assignment of the features present in the pre-edge region. Time-dependent density functional theory (TDDFT) has been previously shown to predict K-pre-edge XAS spectra of first row transition metal compounds with a reasonable degree of accuracy. Here we extend this approach to molybdenum K-edge HERFD-XAS and present the necessary calibration. Modern pure and hybrid functionals are utilized and relativistic effects are accounted for using either the Zeroth Order Regular Approximation (ZORA) or the second order Douglas-Kroll-Hess (DKH2) scalar relativistic approximations. We have found that both the predicted energies and intensities are in excellent agreement with experiment, independent of the functional used. The model chosen to account for relativistic effects also has little impact on the calculated spectra. This study provides an important calibration set for future applications of molybdenum HERFD-XAS to complex catalytic systems.
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Affiliation(s)
- Frederico A Lima
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D- 45470, Mülheim an der Ruhr, Germany.
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36
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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37
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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38
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Bjornsson R, Lima FA, Spatzal T, Weyhermüller T, Glatzel P, Bill E, Einsle O, Neese F, DeBeer S. Identification of a spin-coupled Mo(iii) in the nitrogenase iron–molybdenum cofactor. Chem Sci 2014. [DOI: 10.1039/c4sc00337c] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The molybdenum atom in FeMoco is imperative to the high activity of the enzyme and has been proposed to be Mo(iv). We demonstrate that only Mo(iii) fits Mo HERFD XAS data, the first example of Mo(iii) in biology. Theoretical calculations further reveal an unusual spin-coupled Mo(iii).
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Affiliation(s)
- Ragnar Bjornsson
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Frederico A. Lima
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Thomas Spatzal
- Institute for Biochemistry
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg, Germany
| | - Thomas Weyhermüller
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Pieter Glatzel
- European Synchrotron Radiation Facility
- 38043 Grenoble Cedex, France
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Oliver Einsle
- Institute for Biochemistry
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg, Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca, USA
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39
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Pushie MJ, Cotelesage JJ, George GN. Molybdenum and tungsten oxygen transferases – structural and functional diversity within a common active site motif. Metallomics 2014; 6:15-24. [DOI: 10.1039/c3mt00177f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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40
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McDonald A, Pushie MJ, Millhauser GL, George GN. New insights into metal interactions with the prion protein: EXAFS analysis and structure calculations of copper binding to a single octarepeat from the prion protein. J Phys Chem B 2013; 117:13822-41. [PMID: 24102071 PMCID: PMC3890359 DOI: 10.1021/jp408239h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Copper coordination to the prion protein (PrP) has garnered considerable interest for almost 20 years, due in part to the possibility that this interaction may be part of the normal function of PrP. The most characterized form of copper binding to PrP has been Cu(2+) interaction with the conserved tandem repeats in the N-terminal domain of PrP, termed the octarepeats, with many studies focusing on single and multiple repeats of PHGGGWGQ. Extended X-ray absorption fine structure (EXAFS) spectroscopy has been used in several previous instances to characterize the solution structure of Cu(2+) binding into the peptide backbone in the HGGG portion of the octarepeats. All previous EXAFS studies, however, have benefitted from crystallographic structure information for [Cu(II) (Ac-HGGGW-NH2)(-2H)] but have not conclusively demonstrated that the complex EXAFS spectrum represents the same coordination environment for Cu(2+) bound to the peptide backbone. Density functional structure calculations as well as full multiple scattering EXAFS curve fitting analysis are brought to bear on the predominant coordination mode for Cu(2+) with the Ac-PHGGGWGQ-NH2 peptide at physiological pH, under high Cu(2+) occupancy conditions. In addition to the structure calculations, which provide a thermodynamic link to structural information, methods are also presented for extensive deconvolution of the EXAFS spectrum. We demonstrate how the EXAFS data can be analyzed to extract the maximum structural information and arrive at a structural model that is significantly improved over previous EXAFS characterizations. The EXAFS spectrum for the chemically reduced form of copper binding to the Ac-PHGGGWGQ-NH2 peptide is presented, which is best modeled as a linear two-coordinate species with a single His imidazole ligand and a water molecule. The extent of in situ photoreduction of the copper center during standard data collection is also presented, and EXAFS curve fitting of the photoreduced species reveals an intermediate structure that is similar to the Cu(2+) form with reduced coordination number.
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Affiliation(s)
- Alex McDonald
- Department of Geological Sciences, University of Saskatchewan , Saskatoon, Saskatchewan S7N 5E2, Canada
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41
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Detrimental effect of the 6 His C-terminal tag on YedY enzymatic activity and influence of the TAT signal sequence on YedY synthesis. BMC BIOCHEMISTRY 2013; 14:28. [PMID: 24180491 PMCID: PMC4228395 DOI: 10.1186/1471-2091-14-28] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 10/25/2013] [Indexed: 11/21/2022]
Abstract
Background YedY, a molybdoenzyme belonging to the sulfite oxidase family, is found in most Gram-negative bacteria. It contains a twin-arginine signal sequence that is cleaved after its translocation into the periplasm. Despite a weak reductase activity with substrates such as dimethyl sulfoxide or trimethylamine N-oxide, its natural substrate and its role in the cell remain unknown. Although sequence conservation of the YedY family displays a strictly conserved hydrophobic C-terminal residue, all known studies on Escherichia coli YedY have been performed with an enzyme containing a 6 histidine-tag at the C-terminus which could hamper enzyme activity. Results In this study, we demonstrate that the tag fused to the C-terminus of Rhodobacter sphaeroides YedY is detrimental to the enzyme’s reductase activity and results in an eight-fold decrease in catalytic efficiency. Nonetheless this C-terminal tag does not influence the properties of the molybdenum active site, as assayed by EPR spectroscopy. When a cleavable His-tag was fused to the N-terminus of the mature enzyme in the absence of the signal sequence, YedY was expressed and folded with its cofactor. However, when the signal sequence was added upstream of the N-ter tag, the amount of enzyme produced was approximately ten-fold higher. Conclusion Our study thus underscores the risk of using a C-terminus tagged enzyme while studying YedY, and presents an alternative strategy to express signal sequence-containing enzymes with an N-terminal tag. It brings new insights into molybdoenzyme maturation in R. sphaeroides showing that for some enzymes, maturation can occur in the absence of the signal sequence but that its presence is required for high expression of active enzyme.
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42
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Smeltz JL, Lilly CP, Boyle PD, Ison EA. The electronic nature of terminal oxo ligands in transition-metal complexes: ambiphilic reactivity of oxorhenium species. J Am Chem Soc 2013; 135:9433-41. [PMID: 23725588 DOI: 10.1021/ja401390v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The synthesis of the Lewis acid-base adducts of B(C6F5)3 and BF3 with [DAAmRe(O)(X)] DAAm = N,N-bis(2-arylaminoethyl)methylamine; aryl = C6F5 (X = Me, 1, COCH3, 2, Cl, 3) as well as their diamidopyridine (DAP) (DAP=(2,6-bis((mesitylamino)methyl)pyridine) analogues, [DAPRe(O)(X)] (X = Me, 4, Cl, 5, I, 6, and COCH3,7), are described. In these complexes the terminal oxo ligands act as nucleophiles. In addition we also show that stoichiometric reactions between 3 and triarylphosphine (PAr3) result in the formation of triarylphosphine oxide (OPAr3). The electronic dependence of this reaction was studied by comparing the rates of oxygen atom transfer for various para-substituted triaryl phosphines in the presence of CO. From these experiments a reaction constant ρ = -0.29 was obtained from the Hammett plot. This suggests that the oxygen atom transfer reaction is consistent with nucleophilic attack of phosphorus on an electrophilic metal oxo. To the best of our knowledge, these are the first examples of mono-oxo d(2) metal complexes in which the oxo ligand exhibits ambiphilic reactivity.
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Affiliation(s)
- Jessica L Smeltz
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8204, United States
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43
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Ng VWL, White JM, Young CG. Structural Characterization and Unusual Reactivity of Oxosulfido-Mo(V) Compounds: Implications for the Structure and Electronic Description of the Very Rapid Form of Xanthine Oxidase. J Am Chem Soc 2013; 135:7106-9. [DOI: 10.1021/ja4022057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Victor W. L. Ng
- School
of Chemistry and ‡Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010,
Australia
| | - Jonathan M. White
- School
of Chemistry and ‡Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010,
Australia
| | - Charles G. Young
- School
of Chemistry and ‡Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010,
Australia
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44
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Mitra J, Sarkar S. Oxo-Mo(IV)(dithiolene)thiolato complexes: analogue of reduced sulfite oxidase. Inorg Chem 2013; 52:3032-42. [PMID: 23461669 DOI: 10.1021/ic302485c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A series of [Mo(IV)O(mnt)(SR)(N-N)](-) (mnt = maleonitriledithiolate; R = Ph, nap, p-Cl-Ph, p-CO2H-Ph, and p-NO2-Ph; N-N = 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen)) complexes analogous to the reduced active site of enzymes of the sulfite oxidase family has been synthesized and their participation in electron transfer reactions studied. Equatorial thiolate and dithiolene ligations have been used to closely simulate the three sulfur coordinations present in the native molybdenum active site. These synthetic analogues have been shown to participate in electron transfer via a pentavalent EPR-active Mo(V) intermediate with minimal structural change as observed electrochemically by reversible oxidative responses. The role of the redox-active dithiolene ligand as an electron transfer gate between external oxidants and the molybdenum center could be envisaged in one of the analogue systems where the initial transient EPR signal with <g> = 2.008 is replaced by the appearance of a typical Mo(V)-centered EPR (<g> = 1.976) signal. The appearance of such a ligand-based transient radical at the initial stage has been supported by the ligand-centered frontier orbital from DFT calculation. A stepwise rationale has been provided by computational study to show that the coupled effects of the diimine bite angle and the thiolato dihedral angle determine the metal- or ligand-based frontier orbital occupancy. DFT calculation has further supported the similarity between the reduced, semireduced, and oxidized resting state of the molybdenum center in Moco of SO with the synthesized complexes and their corresponding one-electron and fully oxidized species.
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Affiliation(s)
- Joyee Mitra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
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45
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Pushie MJ, Cotelesage JJH, Lyashenko G, Hille R, George GN. X-ray Absorption Spectroscopy of a Quantitatively Mo(V) Dimethyl Sulfoxide Reductase Species. Inorg Chem 2013; 52:2830-7. [DOI: 10.1021/ic301660e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- M. Jake Pushie
- Molecular and Environmental Sciences Research Group, Department of
Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
| | - Julien J. H. Cotelesage
- Molecular and Environmental Sciences Research Group, Department of
Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
- Canadian Light Source, 101 Perimeter Road,
Saskatoon, SK, S7N 0X4, Canada
| | - Ganna Lyashenko
- Department of Biochemistry, University of California-Riverside, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California-Riverside, Riverside, California 92521, United States
| | - Graham N. George
- Molecular and Environmental Sciences Research Group, Department of
Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
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46
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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47
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Sugimoto H, Tatemoto S, Toyota K, Ashikari K, Kubo M, Ogura T, Itoh S. Oxo-sulfido- and oxo-selenido-molybdenum(vi) complexes possessing a dithioleneligand related to the active sites of hydroxylases of molybdoenzymes: low temperature preparation and characterisation. Chem Commun (Camb) 2013; 49:4358-60. [PMID: 23091820 DOI: 10.1039/c2cc35345h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Hideki Sugimoto
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 56500871, Japan.
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48
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Okamura TA, Kunisue K, Omi Y, Onitsuka K. Strong NH⋯S hydrogen bonds in molybdoenzyme models containing anilide moieties. Dalton Trans 2013; 42:7569-78. [DOI: 10.1039/c3dt50139f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Okamura TA, Ushijima Y, Omi Y, Onitsuka K. Systematic Investigation of Relationship between Strength of NH···S Hydrogen Bond and Reactivity of Molybdoenzyme Models. Inorg Chem 2012; 52:381-94. [DOI: 10.1021/ic302149p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Taka-aki Okamura
- Department
of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhito Ushijima
- Department
of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yui Omi
- Department
of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Kiyotaka Onitsuka
- Department
of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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50
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George GN, Pickering IJ, Pushie MJ, Nienaber K, Hackett MJ, Ascone I, Hedman B, Hodgson KO, Aitken JB, Levina A, Glover C, Lay PA. X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:875-86. [PMID: 23093745 PMCID: PMC3480274 DOI: 10.1107/s090904951203943x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 09/16/2012] [Indexed: 05/03/2023]
Abstract
As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts.
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Affiliation(s)
- Graham N. George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Ingrid J. Pickering
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - M. Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Kurt Nienaber
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Mark J. Hackett
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Isabella Ascone
- ENSCP Chimie ParisTech, LCF, CNRS, UMR 7223, 75005 Paris, France
| | - Britt Hedman
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jade B. Aitken
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Synchrotron, Clayton, VIC 3168, Australia
- Institute of Materials Structure Science, KEK, Tsukuba, Ibaraki 305-0801, Japan
| | - Aviva Levina
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Peter A. Lay
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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