1
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Riegerová P, Horváth M, Šebesta F, Sýkora J, Šulc M, Vlček A. Single-step Purification and Characterization of Pseudomonas aeruginosa Azurin. Protein Expr Purif 2024:106566. [PMID: 39128594 DOI: 10.1016/j.pep.2024.106566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Azurin is a small periplasmic blue copper protein found in bacterial strains such as Pseudomonas and Alcaligenes where it facilitates denitrification. Azurin is extensively studied for its ability to mediate electron-transfer processes, but it has also sparked interest of the pharmaceutical community as a potential antimicrobial or anticancer agent. Here we offer a novel approach for expression and single-step purification of azurin in Escherichia coli with high yields and optimal metalation. A fusion tag strategy using an N-terminal GST tag was employed to obtain pure protein without requiring any additional purification steps. After the on-column cleavage by HRV 3C Protease, azurin is collected and additionally incubated with copper sulphate to ensure sufficient metalation. UV-VIS absorption, mass spectroscopy, and circular dichroism analysis all validated the effective production of azurin, appropriate protein folding and the development of an active site with an associated cofactor. MD simulations verified that incorporation of the N-terminal GPLGS segment does not affect azurin structure. In addition, the biological activity of azurin was tested in HeLa cells.
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Affiliation(s)
- Petra Riegerová
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic.
| | - Matej Horváth
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Department of Cell Biology, Charles University, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Filip Šebesta
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Jan Sýkora
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic
| | - Miroslav Šulc
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, CZ-12843 Prague 2, Czech Republic
| | - Antonín Vlček
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 2155/3, 182 23, Prague, Czech Republic; Queen Mary University of London, Department of Chemistry, Mile End Road, London E1 4NS, United Kingdom.
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2
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Sharma KK, Singh D, Mohite SV, Williamson PR, Kennedy JF. Metal manipulators and regulators in human pathogens: A comprehensive review on microbial redox copper metalloenzymes "multicopper oxidases and superoxide dismutases". Int J Biol Macromol 2023; 233:123534. [PMID: 36740121 DOI: 10.1016/j.ijbiomac.2023.123534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
The chemistry of metal ions with human pathogens is essential for their survival, energy generation, redox signaling, and niche dominance. To regulate and manipulate the metal ions, various enzymes and metal chelators are present in pathogenic bacteria. Metalloenzymes incorporate transition metal such as iron, zinc, cobalt, and copper in their reaction centers to perform essential metabolic functions; however, iron and copper have gained more importance. Multicopper oxidases have the ability to perform redox reaction on phenolic substrates with the help of copper ions. They have been reported from Enterobacteriaceae, namely Salmonella enterica, Escherichia coli, and Yersinia enterocolitica, but their role in virulence is still poorly understood. Similarly, superoxide dismutases participate in reducing oxidative stress and allow the survival of pathogens. Their role in virulence and survival is well established in Salmonella typhimurium and Mycobacterium tuberculosis. Further, to ensure survival against stress, like metal starvation or metal toxicity, redox metalloenzymes and metal transportation systems of pathogens actively participate in metal homeostasis. Recently, the omics and protein structure biology studies have helped to predict new targets for regulation the colonization potential of the pathogenic strains. The current review is focused on the major roles of redox metalloenzymes, especially MCOs and SODs of human pathogenic bacteria.
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Affiliation(s)
- Krishna Kant Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| | - Deepti Singh
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Shreya Vishwas Mohite
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Peter R Williamson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John F Kennedy
- Chembiotech Laboratories, Advanced Science and Technology Institute, 5 the Croft, Buntsford Drive, Stoke Heath, Bromsgrove, Worcs B60 4JE, UK
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3
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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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4
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Hedison T, Iorgu AI, Calabrese D, Heyes DJ, Shanmugam M, Scrutton NS. Solution-State Inter-Copper Distribution of Redox Partner-Linked Copper Nitrite Reductases: A Pulsed Electron-Electron Double Resonance Spectroscopy Study. J Phys Chem Lett 2022; 13:6927-6934. [PMID: 35867774 PMCID: PMC9358711 DOI: 10.1021/acs.jpclett.2c01584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Copper nitrite reductases (CuNiRs) catalyze the reduction of nitrite to form nitric oxide. In recent years, new classes of redox partner linked CuNiRs have been isolated and characterized by crystallographic techniques. Solution-state biophysical studies have shed light on the complex catalytic mechanisms of these enzymes and implied that protein dynamics may play a role in CuNiR catalysis. To investigate the structural, dynamical, and functional relationship of these CuNiRs, we have used protein reverse engineering and pulsed electron-electron double resonance (PELDOR) spectroscopy to determine their solution-state inter-copper distributions. Data show the multidimensional conformational landscape of this family of enzymes and the role of tethering in catalysis. The importance of combining high-resolution crystallographic techniques and low-resolution solution-state approaches in determining the structures and mechanisms of metalloenzymes is emphasized by our approach.
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Affiliation(s)
- Tobias
M. Hedison
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- EPSRC/BBSRC
funded Future Biomanufacturing Research Hub, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Andreea I. Iorgu
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Donato Calabrese
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Muralidharan Shanmugam
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- EPSRC/BBSRC
funded Future Biomanufacturing Research Hub, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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5
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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6
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Yu Y, Marshall NM, Garner DK, Nilges MJ, Lu Y. Tuning reduction potentials of type 1 copper center in azurin by replacing a histidine ligand with its isostructural analogues. J Inorg Biochem 2022; 234:111863. [DOI: 10.1016/j.jinorgbio.2022.111863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 05/02/2022] [Accepted: 05/08/2022] [Indexed: 11/16/2022]
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7
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Electrochemical Characterization of an Engineered Red Copper Protein Featuring an Unprecedented Entropic Control of the Reduction Potential. Bioelectrochemistry 2022; 146:108095. [DOI: 10.1016/j.bioelechem.2022.108095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/12/2022]
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8
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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:molecules27031077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
| | | | - Andrea Amadei
- Department of Chemical and Technological Sciences, Tor Vergata University, 00133 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
- Correspondence:
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9
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Di Rocco G, Battistuzzi G, Borsari M, Bortolotti CA, Ranieri A, Sola M. The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Stanojević IM, Glišić BĐ, Radanović DD, Djuran MI. Copper(II) complexes of aminopolycarboxylate ligands with N2O2, N2O3 and N2O4 donor sets. The relationship between the ligand structure and molecular geometry of the complex. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Zegarra FC, Homouz D, Wittung-Stafshede P, Cheung MS. The Zero-Order Loop in Apoazurin Modulates Folding Mechanism In Silico. J Phys Chem B 2021; 125:3501-3509. [PMID: 33818090 DOI: 10.1021/acs.jpcb.1c00219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pseudomonas aeruginosa apoazurin (apo, without the copper cofactor) has a single disulfide bond between residues 3 and 26 and unfolds in a two-state reaction in vitro. The disulfide bond covalently connects the N-termini of β-strands 1 and 3; thereby, it creates a zero-order loop or a "cinch" that restricts conformational space. Covalent loops and threaded topologies are emerging as important structural elements in folded proteins and may be important for function. In order to understand the role of a zero-order loop in the folding process of a protein, here we used coarse-grained molecular dynamics (CGMD) simulations in silico to compare two variants of apoazurin: one named "loop" which contained the disulfide, and another named "open" in which the disulfide bond between residues 3 and 26 was removed. CGMD simulations were performed to probe the stability and unfolding pathway of the two apoazurin variants at different urea concentrations and temperatures. Our results show that the covalent loop plays a prominent role in the unfolding mechanism of apoazurin; its removal alters both the folding-transition state and the unfolded-state ensemble of conformations. We propose that modulation of azurin's folding landscape by the disulfide bridge may be related to both copper capturing and redox sensing.
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Affiliation(s)
- Fabio C Zegarra
- Laboratorio de Sistemas Inteligentes, EPIME, Universidad Nacional Tecnológica de Lima Sur (UNTELS), Lima 15834, Peru.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Dirar Homouz
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, 127788 United Arab Emirates.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Margaret S Cheung
- Pacific Northwest National Laboratory, Research Science Center, Seattle, Washington 98109, United States.,Department of Physics, University of Washington, Seattle, Washington 98195, United States.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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12
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Synthesis and Differential Antibacterial Activity of Bioconjugated Bimetallic Nanoparticles. Pharm Chem J 2020. [DOI: 10.1007/s11094-020-02289-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Uddin I, Ullah H, Bibi A, Taha M, Khan F, Rahim F, Wadood A, Ahmad N, Khan AA, Ahmad F, Rehman ZU, Khan KM. Synthesis, in vitro alpha glucosidase, urease activities and molecular docking study of bis-indole bearing Schiff base analogs. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cdc.2020.100396] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Yusseppone MS, Bianchi VA, Castro JM, Noya Abad T, Minaberry YS, Sabatini SE, Luquet CM, Rios de Molina MC, Rocchetta I. In situ experiment to evaluate biochemical responses in the freshwater mussel Diplodon chilensis under anthropogenic eutrophication conditions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 193:110341. [PMID: 32092582 DOI: 10.1016/j.ecoenv.2020.110341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
An in-situ experiment was performed to study metabolic responses of the freshwater mussel Diplodon chilensis to water contaminated by leachates from an open dump and cattle activity, in order to analyze both the effects of those contaminants on aquatic environments and the potential use of a native bivalve to evaluate the effects of anthropic influence and eutrophication. Bivalves from a reference site were cage-transplanted to a control site (site A) and to a temporal water pond (site B) over 30 and 60 periods. Water quality analyses revealed that the site B was affected by anthropogenic influence. Mussel's hemocytes from site B showed 50% lower reactive oxygen species production and 130% higher lysosomal membrane stability in the site B mussels. In addition, no oxidative stress was evident in gills, despite the elevated copper and iron concentrations recorded in the site B water samples (CuB = 0.3350 ± 0.0636 mg. L-1vs. CuA = 0.0045 ± 0.0007 mg. L-1; FeB = 3.8650 ± 0.4031 mg. L-1vs. FeA = 0.0365 ± 0.0049 mg. L-1). In contrast, the adductor muscle accumulated more Fe (~10-20-fold) than the gills and showed signs of oxidative stress, e.g. superoxide dismutase activity and TBARS levels were increased by 10% were 34%, respectively, in the site B compared with the site A after 60 days of exposure. Additionally, the adductor muscle showed signs of anaerobic metabolism activation. Cu is accumulated in gills from both sites' individuals, at 60 days, in concordance with the increase in the activity of the cu-containing enzyme cytochrome-c-oxidase. There was a reduction in the overall condition and digestive gland index in bivalves exposed at site B, associated with diminished levels of lipid and protein contents. Metal-pollution and eutrophication affects D. chilensis metabolism and is associated to tissue-specific exposure, anaerobic metabolism and general energetic condition depletion.
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Affiliation(s)
- M S Yusseppone
- Departamento de Química Biológica, IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - V A Bianchi
- Laboratorio de Ecotoxicología Acuática, INIBIOMA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-UNCo), CEAN, Junín de los Andes, Neuquén, Argentina
| | - J M Castro
- Laboratorio de Ecotoxicología Acuática, INIBIOMA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-UNCo), CEAN, Junín de los Andes, Neuquén, Argentina
| | - T Noya Abad
- Departamento de Química Biológica, IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Y S Minaberry
- Departamento de Química Inorgánica, Analítica y Química Física, INIQUIMAE, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - S E Sabatini
- Departamento de Química Biológica, IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - C M Luquet
- Laboratorio de Ecotoxicología Acuática, INIBIOMA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-UNCo), CEAN, Junín de los Andes, Neuquén, Argentina
| | - M C Rios de Molina
- Departamento de Química Biológica, IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - I Rocchetta
- Laboratorio de Ecotoxicología Acuática, INIBIOMA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-UNCo), CEAN, Junín de los Andes, Neuquén, Argentina.
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15
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Cahyono RN, Yamanaka M, Nagao S, Shibata N, Higuchi Y, Hirota S. 3D domain swapping of azurin from Alcaligenes xylosoxidans. Metallomics 2020; 12:337-345. [PMID: 31956880 DOI: 10.1039/c9mt00255c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein oligomers have gained interest, owing to their increased knowledge in cells and promising utilization for future materials. Various proteins have been shown to 3D domain swap, but there has been no domain swapping report on a blue copper protein. Here, we found that azurin from Alcaligenes xylosoxidans oligomerizes by the procedure of 2,2,2-trifluoroethanol addition to Cu(i)-azurin at pH 5.0, lyophilization, and dissolution at pH 7.0, whereas it slightly oligomerizes when using Cu(ii)-azurin. The amount of high order oligomers increased with the addition of Cu(ii) ions to the dissolution process of a similar procedure for apoazurin, indicating that Cu(ii) ions enhance azurin oligomerization. The ratio of the absorbance at 460 nm to that at ∼620 nm of the azurin dimer (Abs460/Abs618 = 0.113) was higher than that of the monomer (Abs460/Abs622 = 0.067) and the EPR A‖ value of the dimer (5.85 mT) was slightly smaller than that of the monomer (5.95 mT), indicating a slightly more rhombic copper coordination for the dimer. The redox potential of the azurin dimer was 342 ± 5 mV vs. NHE, which was 50 mV higher than that of the monomer. According to X-ray crystal analysis, the azurin dimer exhibited a domain-swapped structure, where the N-terminal region containing three β-strands was exchanged between protomers. The copper coordination structure was tetrahedrally distorted in the azurin dimer, similar to that in the monomer; however, the Cu-O(Gly45) bond length was longer for the dimer (monomer, 2.46-2.59 Å; dimer, 2.98-3.25 Å). These results open the door for designing oligomers of blue copper proteins by domain swapping.
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Affiliation(s)
- Robby Noor Cahyono
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. and Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Masaru Yamanaka
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Satoshi Nagao
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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16
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Abstract
Copper is a redox-active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein-metal complexes. Because free copper ions are toxic, living systems have elaborate copper-transport systems that include particular proteins that facilitate efficient and specific delivery of copper ions to target proteins. Therefore, these pathways become an integral part of copper protein folding in vivo. This review summarizes biophysical-molecular in vitro work assessing the role of copper in folding and stability of copper-binding proteins as well as protein-protein copper exchange reactions between human copper transport proteins. We also describe some recent findings about the participation of copper ions and copper proteins in protein misfolding and aggregation reactions in vitro.
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17
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Hoarau M, Koebke KJ, Chen Z, Marsh ENG. Probing Metal Ion Discrimination in a Protein Designed to Bind Uranyl Cation With Femtomolar Affinity. Front Mol Biosci 2019; 6:73. [PMID: 31552264 PMCID: PMC6736553 DOI: 10.3389/fmolb.2019.00073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
The design of metal-binding sites in proteins that combine high affinity with high selectivity for the desired metal ion remains a challenging goal. Recently, a protein designed to display femtomolar affinity for UO22+, dubbed “Super Uranyl-binding Protein” (SUP), was described, with potential applications for removing UO22+ in water. Although it discriminated most metal ions present in seawater, the protein showed a surprisingly high affinity for Cu2+ ions. Here, we have investigated Cu2+ binding to SUP using a combination of electron paramagnetic resonance, fluorescence and circular dichroism spectroscopies. Our results provide evidence for two Cu2+ binding sites on SUP that are distinct from the UO22+ binding site, but one of which interferes with UO22+ binding. They further suggest that in solution the protein's secondary structure changes significantly in response to binding UO22+; in contrast, the crystal structures of the apo- and holo-protein are almost superimposable. These results provide insights for further improving the selectivity of SUP for UO22+, paving the way toward protein-based biomaterials for decontamination and/or recovery of uranium.
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Affiliation(s)
- Marie Hoarau
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
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18
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Zegarra FC, Homouz D, Gasic AG, Babel L, Kovermann M, Wittung-Stafshede P, Cheung MS. Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico. J Phys Chem B 2019; 123:3607-3617. [PMID: 30963769 DOI: 10.1021/acs.jpcb.9b00782] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect based on the argument of volume exclusion. To explore the complex interactions beyond volume exclusion, we employed coarse-grained molecular dynamics simulations to explore the conformational ensemble of apoazurin in a box of monodisperse crowders under strong chemically denaturing conditions. The elongated conformation of unfolded apoazurin appears to result from the interplay of the effective attraction between the protein and crowders and the shape of the crowders. With a volume-conserving crowder model, we show that the crowder shape provides an anisotropic direction of the depletion force, in which a bundle of surrounding rodlike crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.
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Affiliation(s)
- Fabio C Zegarra
- Department of Physics , University of Houston , Houston 77204 , United States
| | - Dirar Homouz
- Department of Physics , University of Houston , Houston 77204 , United States.,Department of Physics , Khalifa University of Science and Technology , Abu Dhabi , UAE.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Andrei G Gasic
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Lucas Babel
- Department of Physics , University of Houston , Houston 77204 , United States
| | | | | | - Margaret S Cheung
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
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19
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Dijkstra M, Bawono P, Abeln S, Feenstra KA, Fokkink W, Heringa J. Motif-Aware PRALINE: Improving the alignment of motif regions. PLoS Comput Biol 2018; 14:e1006547. [PMID: 30383764 PMCID: PMC6233922 DOI: 10.1371/journal.pcbi.1006547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 11/13/2018] [Accepted: 10/05/2018] [Indexed: 11/21/2022] Open
Abstract
Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence motifs is still difficult to achieve, due to the fact that the contribution of these typically short fragments is overshadowed by the rest of the sequence. Here we extended the PRALINE multiple sequence alignment program with a novel motif-aware MSA algorithm in order to address this shortcoming. This method can incorporate explicit information about the presence of externally provided sequence motifs, which is then used in the dynamic programming step by boosting the amino acid substitution matrix towards the motif. The strength of the boost is controlled by a parameter, α. Using a benchmark set of alignments we confirm that a good compromise can be found that improves the matching of motif regions while not significantly reducing the overall alignment quality. By estimating α on an unrelated set of reference alignments we find there is indeed a strong conservation signal for motifs. A number of typical but difficult MSA use cases are explored to exemplify the problems in correctly aligning functional sequence motifs and how the motif-aware alignment method can be employed to alleviate these problems. The most important functional parts of proteins are often small—but very specific—sequence motifs. Moreover, these motifs tend to be strongly conserved during evolution due to their functional role. Nevertheless, when trying to align protein sequences of the same family, it is often very difficult to align such motifs using standard multiple sequence alignment methods. Aligning functional residues correctly is essential to detect motif conservation, which can be used to filter out spuriously occurring motifs. Additionally, many downstream analyses, such as phylogenetics, are strongly reliant on alignment quality. We have developed a sequence alignment program named Motif-Aware PRALINE (MA-PRALINE) that incorporates information about motifs explicitly. Motifs are provided to MA-PRALINE in the PROSITE pattern syntax; it then scans the input sequences for instances of the pattern and provides a score bonus to matching sequence positions. Our method provides a reproducible alternative to editing alignments by hand in order to account for motif conservation, which is a tedious and error-prone process. We will show that MA-PRALINE allows the alignment of motif-rich regions to be fine-tuned while not degrading the rest of the alignment. MA-PRALINE is available on GitHub as open source software; this allows it to be easily tailored to similar problems. We apply MA-PRALINE on the HIV-1 envelope glycoprotein (gp120) to get an improved alignment of the N-terminal glycosylation motifs. The presence of these motifs is essential for the virus in evading the immune response of the host.
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Affiliation(s)
- Maurits Dijkstra
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| | - Punto Bawono
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sanne Abeln
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - K. Anton Feenstra
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wan Fokkink
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jaap Heringa
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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20
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Sereikaitė V, Jensen TMT, Bartling CRO, Jemth P, Pless SA, Strømgaard K. Probing Backbone Hydrogen Bonds in Proteins by Amide-to-Ester Mutations. Chembiochem 2018; 19:2136-2145. [PMID: 30073762 DOI: 10.1002/cbic.201800350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 01/09/2023]
Abstract
All proteins contain characteristic backbones formed of consecutive amide bonds, which can engage in hydrogen bonds. However, the importance of these is not easily addressed by conventional technologies that only allow for side-chain substitutions. By contrast, technologies such as nonsense suppression mutagenesis and protein ligation allow for manipulation of the protein backbone. In particular, replacing the backbone amide groups with ester groups, that is, amide-to-ester mutations, is a powerful tool to examine backbone-mediated hydrogen bonds. In this minireview, we showcase examples of how amide-to-ester mutations can be used to uncover pivotal roles of backbone-mediated hydrogen bonds in protein recognition, folding, function, and structure.
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Affiliation(s)
- Vita Sereikaitė
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Thomas M T Jensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Christian R O Bartling
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, 75123, Uppsala, Sweden
| | - Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
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21
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Taha M, Wadood A. Synthesis and molecular docking study of piperazine derivatives as potent urease inhibitors. Bioorg Chem 2018; 78:411-417. [DOI: 10.1016/j.bioorg.2018.04.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/03/2018] [Accepted: 04/13/2018] [Indexed: 01/08/2023]
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22
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Chatterjee SD, Ubbink M, van Ingen H. Removal of slow-pulsing artifacts in in-phase 15N relaxation dispersion experiments using broadband 1H decoupling. JOURNAL OF BIOMOLECULAR NMR 2018; 71:69-77. [PMID: 29860650 PMCID: PMC6061081 DOI: 10.1007/s10858-018-0193-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such dynamic changes in protein conformations. In particular, Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments are a powerful tool to investigate protein dynamics on a millisecond time scale. CPMG experiments that probe the chemical shift modulation of 15N in-phase magnetization are particularly attractive, due to their high sensitivity. These experiments require high power 1H decoupling during the CPMG period to keep the 15N magnetization in-phase. Recently, an improved version of the in-phase 15N-CPMG experiment was introduced, offering greater ease of use by employing a single 1H decoupling power for all CPMG pulsing rates. In these experiments however, incomplete decoupling of off-resonance amide 1H spins introduces an artefactual dispersion of relaxation rates, the so-called slow-pulsing artifact. Here, we analyze the slow-pulsing artifact in detail and demonstrate that it can be suppressed through the use of composite pulse decoupling (CPD). We report the performances of various CPD schemes and show that CPD decoupling based on the 90x-240y-90x element results in high-quality dispersion curves free of artifacts, even for amides with high 1H offset.
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Affiliation(s)
- Soumya Deep Chatterjee
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands
| | - Marcellus Ubbink
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands.
- NMR Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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23
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Hussain A, AlAjmi MF, Rehman MT, Khan AA, Shaikh PA, Khan RA. Evaluation of Transition Metal Complexes of Benzimidazole-Derived Scaffold as Promising Anticancer Chemotherapeutics. Molecules 2018; 23:E1232. [PMID: 29883398 PMCID: PMC6100524 DOI: 10.3390/molecules23051232] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/08/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023] Open
Abstract
Three new transition metal complexes, Cu(II) 1, Co(II) 2, and Zn(II) 3 with ligand “bimnap” derived from 1-methyl-2-aminobenzimidazole and 2-hydroxynapthaldehyde were synthesized and characterized. The structure of the ligand was determined by single X-ray crystallography. All the three complexes, 1⁻3, were examined for the mode of interaction with biomolecule viz., calf thymus-DNA (CT-DNA) using various spectroscopic methods. The nuclease activity was performed against pBR322 DNA that exhibited concentration-dependent degradation of the nucleic acid. The mechanism of DNA cleavage was studied by the electrophoretic pattern in the presence of the radical scavengers. Also, the complexes 1⁻3 were analyzed for groove binding affinity. Moreover, in vitro cytotoxicities of the complexes 1⁻3 were tested against the five human cancer cell lines, i.e., HeLa, SK-MEL-1, HepG2, HT108, and MDA-MB 231. Also, the cell adhesion and migration properties upon treatment of cell lines with complexes 1⁻3, and consequently, their cell death pathway via apoptosis and necrosis were analyzed. Further, complexes 1⁻3 were studied in vivo for their toxicities and tolerabilities in mice. In sum, the complexes 1⁻3 showed merits of an effective anticancer agent in cell lines⁻based study while minor side effects were observed in vivo.A green solvent extraction technology involving a microwave processing method was used to increase the content of minor ginsenosides from Panax notoginseng. This article aims to investigate the optimization of preparation of the minor ginsenosides by this microwave processing method using single-factor experiments and response surface methodology (RSM), and discuss the blood-enriching activity and hemostatic activity of the extract of microwave processed P. notoginseng (EMPN) The RSM for production of the minor ginsenosides was based on a three-factor and three-level Box-Behnken design. When the optimum conditions of microwave power, temperature and time were 495.03 W, 150.68 °C and 20.32 min, respectively, results predicted that the yield of total minor ginsenosides (Y₉) would be 93.13%. The actual value of Y₉ was very similar to the predicted value. In addition, the pharmacological results of EMPN in vivo showed that EMPN had the effect of enriching blood in N-acetylphenylhydrazine (APH) and cyclophosphamide (CTX)-induced blood deficient mice because of the increasing content of white blood cells (WBCs) and hemoglobin (HGB) in blood. Hemostatic activity in vitro of EMPN showed that it had significantly shortened the clotting time in PT testing (p < 0.05). The hemostatic effect of EMPN was mainly caused by its components of Rh₄, 20(S)-Rg₃ and 20(R)-Rg₃. This microwave processing method is simple and suitable to mass-produce the minor ginsenosides from P. notoginseng.
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Affiliation(s)
- Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, 11451 Riyadh, Saudi Arabia.
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, 11451 Riyadh, Saudi Arabia.
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, 11451 Riyadh, Saudi Arabia.
| | - Azmat Ali Khan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, 11451 Riyadh, Saudi Arabia.
| | - Perwez Alam Shaikh
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, 11451 Riyadh, Saudi Arabia.
| | - Rais Ahmad Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, 11451 Riyadh, Saudi Arabia.
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24
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Atrián-Blasco E, del Barrio M, Faller P, Hureau C. Ascorbate Oxidation by Cu(Amyloid-β) Complexes: Determination of the Intrinsic Rate as a Function of Alterations in the Peptide Sequence Revealing Key Residues for Reactive Oxygen Species Production. Anal Chem 2018; 90:5909-5915. [PMID: 29611698 PMCID: PMC6120677 DOI: 10.1021/acs.analchem.8b00740] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Along with aggregation of the amyloid-β (Aβ) peptide and subsequent deposit of amyloid plaques, oxidative stress is an important feature in Alzheimer's disease. Cu bound to Aβ is able to produce reactive oxygen species (ROS) by the successive reductions of molecular dioxygen, and the ROS produced contribute to oxidative stress. In vitro, ascorbate consumption parallels ROS production, where ascorbate is the reductant that fuels the reactions. Because the affinity of Cu for Aβ is moderate compared to other biomolecules, the rate of ascorbate consumption is a combination of two contributions. The first one is due to peptide-unbound Cu and the second one to peptide-bound Cu complexes. In the present Article, we aim to determine the amounts of the second contribution in the global ascorbate consumption process. It is defined as the intrinsic rate of ascorbate oxidation, which mathematically corresponds to the rate at an infinite peptide to Cu ratio, i.e., without any contribution from peptide-unbound Cu. We show that, for the wild-type Cu(Aβ) complex, this value equals 10% of the value obtained for peptide-unbound Cu and that this value is strongly dependent on peptide alterations. By examination of the dependence of the intrinsic rate of ascorbate oxidation, followed by UV-vis spectroscopy, for several altered peptides, we determine some of the key residues that influence ROS production.
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Affiliation(s)
- Elena Atrián-Blasco
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France
- Université de Toulouse, UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Melisa del Barrio
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France
- Université de Toulouse, UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Peter Faller
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France
- Université de Toulouse, UPS, INPT, F-31077 Toulouse Cedex 4, France
- Biometals and Biological Chemistry, Institut de Chimie UMR 7177. Université de Strasbourg. Le Bel, rue B. Pascal 67081 Strasbourg, France. +33 68856949
| | - Christelle Hureau
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France
- Université de Toulouse, UPS, INPT, F-31077 Toulouse Cedex 4, France
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25
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El-Refaey A, Shaban SY, El-Kemary M, El-Khouly ME. A light harvesting perylene derivative - zinc phthalocyanine complex in water: spectroscopic and thermodynamic studies. Photochem Photobiol Sci 2018; 16:861-869. [PMID: 28379265 DOI: 10.1039/c7pp00055c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A perylene derivative, namely N,N'-bis(2(trimethylammonium iodide)ethylene)perylene-3,4,9,10-tetracarboxyldiimide (TAIPDI) forms nanoscale columnar stacks in water that have been characterized by using optical absorption and emission measurements, dynamic light scattering (DLS), and transmission electron microscopy (TEM). This behaviour was compared with that of unstacked TAIPDI in methanol. Assembly formation between the one-dimensional TAIPDI stacks and zinc phthalocyanine tetrasulphonic groups (ZnPcS4) via strong π-π and ionic interactions has been described in an aqueous medium. The formation constant of the supramolecular dyad has been determined as 2.94 × 104 M-1 from both the absorption and fluorescence measurements. Upon addition of ZnPcS4, the fluorescence quenching of the singlet-excited state of TAIPDI was observed because of the electron transfer process from ZnPcS4 to TAIPDI via the singlet-excited states of ZnPcS4 and TAIPDI entities. The electrochemical studies supported the electron transfer pathways via the singlet states of ZnPcS4 and TAIPDI. The thermodynamic parameters of the supramolecular complex have been determined from stopped-flow measurements. The interaction between ZnPcS4 and TAIPDI occurs in two steps, where the rate constant of the second step with TAIPDI (207 ± 8 M-1 s-1) is much slower than the first one (3515 ± 101 M-1 s-1). Activation parameters for the complex formation (ΔH# = 76 ± 11 kJ mol-1 and ΔS# = 83 ± 37 J K-1 mol-1, and ΔH# = 221 ± 15 kJ mol-1 and ΔS# = 540 ± 50 J K-1 mol-1) were determined from variable temperature studies for the first and second steps, respectively. The significantly positive ΔS# values found for both steps of the interaction reactions are consistent with a dissociative mechanism.
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Affiliation(s)
- Ahmed El-Refaey
- Department of Chemistry, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt.
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26
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Banerjee S, Ghorai P, Brandão P, Ghosh D, Bhuiya S, Chattopadhyay D, Das S, Saha A. Syntheses, crystal structures, DNA binding, DNA cleavage, molecular docking and DFT study of Cu(ii) complexes involving N2O4 donor azo Schiff base ligands. NEW J CHEM 2018. [DOI: 10.1039/c7nj03293e] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA binding and cleavage properties of three novel copper(ii) complexes involving azo Schiff base ligands have been studied.
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Affiliation(s)
- Saikat Banerjee
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | - Pravat Ghorai
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | - Paula Brandão
- Departamento de Química
- CICECO
- Universidade de Aveiro
- 3810-193 Aveiro
- Portugal
| | | | - Sutanwi Bhuiya
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | | | - Suman Das
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | - Amrita Saha
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
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27
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Kroneck PMH. Walking the seven lines: binuclear copper A in cytochrome c oxidase and nitrous oxide reductase. J Biol Inorg Chem 2017; 23:27-39. [PMID: 29218634 DOI: 10.1007/s00775-017-1510-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/20/2017] [Indexed: 01/19/2023]
Abstract
The enzymes nitrous oxide reductase (N2OR) and cytochrome c oxidase (COX) are constituents of important biological processes. N2OR is the terminal reductase in a respiratory chain converting N2O to N2 in denitrifying bacteria; COX is the terminal oxidase of the aerobic respiratory chain of certain bacteria and eukaryotic organisms transforming O2 to H2O accompanied by proton pumping. Different spectroscopies including magnetic resonance techniques, were applied to show that N2OR has a mixed-valent Cys-bridged [Cu1.5+(CyS)2Cu1.5+] copper site, and that such a binuclear center, called CuA, does also exist in COX. A sequence motif shared between the CuA center of N2OR and the subunit II of COX raises the issue of a putative evolutionary relationship of the two enzymes. The suggestion of a binuclear CuA in COX, with one unpaired electron delocalized between two equivalent Cu nuclei, was difficult to accept originally, even though regarded as a clever solution to many experimental observations. This minireview in honor of Helmut Sigel traces several of the critical steps forward in understanding the nature of CuA in N2OR and COX, and discusses its unique electronic features to some extent including the contributions made by the development of methodology and the discovery of a novel multi-copper enzyme. Left: X-band (9.130 GHz) and C-band (4.530 GHz, 1st harmonic display of experimental spectrum) EPR spectra of bovine heart cytochrome c oxidase, recorded at 20K. Right: Ribbon presentation of the CuA domain in cytochrome c oxidase and nitrous oxide reductase.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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28
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Gnanasekaran R. Computational study to understand the energy transfer pathways within amicyanin. J Mol Graph Model 2017; 78:88-95. [PMID: 29054098 DOI: 10.1016/j.jmgm.2017.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/28/2017] [Accepted: 09/30/2017] [Indexed: 11/27/2022]
Abstract
Vibrational energy diffusivities between the residues present in Amicyanin copper protein are calculated and presented in form of communication map. From those results energy flow pathways from the copper metal ion to the inter protein residue Glu31 are identified. Our finding suggests many different pathways are possible and copper metal ion in oxidized and reduced state switches the pathways. Our finding also suggests the cooperative nature of surrounding residues and water molecules towards selecting the pathways. The major transport channels in the oxidised state are, Cu2+---> MET28---> LYS29---> TYR30---> GLU31 and Cu2+---> MET98---> TYR30--- > GLU31. And in the reduced state Cu+---> CYS9---> TYR30---> GLU31 and Cu+---> MET28---> LYS2---> TYR30---> GLU31. We studied further the interaction energies between the copper ion and neighbouring residues using B3LYP/QZVP method. Both the methods complement each other in predicting the energy flow pathways and the cooperative nature of residues.
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29
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Periplasmic Nicotine Dehydrogenase NdhAB Utilizes Pseudoazurin as Its Physiological Electron Acceptor in Agrobacterium tumefaciens S33. Appl Environ Microbiol 2017. [PMID: 28625985 DOI: 10.1128/aem.01050-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium tumefaciens S33 can grow with nicotine as the sole source of carbon, nitrogen, and energy via a novel hybrid of the pyridine pathway and the pyrrolidine pathway. Characterization of the enzymes involved in the hybrid pathway is important for understanding its biochemical mechanism. Here, we report that the molybdenum-containing nicotine dehydrogenase (NdhAB), which catalyzes the initial step of nicotine degradation, is located in the periplasm of strain S33, while the 6-hydroxynicotine oxidase and 6-hydroxypseudooxynicoine oxidase are in the cytoplasm. This is consistent with the fact that NdhA has a Tat signal peptide. Interestingly, an open reading frame (ORF) adjacent to the ndhAB gene was verified to encode a copper-containing electron carrier, pseudoazurin (Paz), which has a signal peptide typical of bacterial Paz proteins. Both were transported into the periplasm after being produced in the cytoplasm. We purified NdhAB from the periplasmic fraction of strain S33 and found that with Paz as the physiological electron acceptor, NdhAB catalyzed the hydroxylation of nicotine at a specific rate of 110.52 ± 8.09 μmol · min-1 · mg of protein-1, where the oxygen atom in the hydroxyl group of the product 6-hydroxynicotine was derived from H2O. The apparent Km values for nicotine and Paz were 1.64 ± 0.07 μM and 3.61 ± 0.23 μM, respectively. NAD(P)+, O2, and ferredoxin could not serve as electron acceptors. Disruption of the paz gene disabled the strain for nicotine degradation, indicating that Paz is required for nicotine catabolism in the strain. These findings help our understanding of electron transfer during nicotine degradation in bacteria.IMPORTANCE Nicotine is a toxic and addictive N-heterocyclic aromatic alkaloid produced in tobacco. Its catabolism in organisms and degradation in tobacco wastes have become major concerns for human health and the environment. Bacteria usually decompose nicotine using the classical strategy of hydroxylating the pyridine ring with the help of activated oxygen by nicotine dehydrogenase, which binds one molybdopterin, two [2Fe2S] clusters, and usually one flavin adenine dinucleotide (FAD) as well. However, the physiological electron acceptor for the reaction is still unknown. In this study, we found that the two-component nicotine dehydrogenase from Agrobacterium tumefaciens S33, naturally lacking an FAD-binding domain, is located in the periplasmic space and uses a copper-containing electron carrier, pseudoazurin, as its physiological electron acceptor. We report here the role of pseudoazurin in a reaction catalyzed by a molybdopterin-containing hydroxylase occurring in the periplasmic space. These results provide new biochemical knowledge on microbial degradation of N-heterocyclic aromatic compounds.
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Roger M, Sciara G, Biaso F, Lojou E, Wang X, Bauzan M, Giudici-Orticoni MT, Vila AJ, Ilbert M. Impact of copper ligand mutations on a cupredoxin with a green copper center. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:351-359. [DOI: 10.1016/j.bbabio.2017.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 11/26/2022]
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Yu Y, Petrik ID, Chacón KN, Hosseinzadeh P, Chen H, Blackburn NJ, Lu Y. Effect of circular permutation on the structure and function of type 1 blue copper center in azurin. Protein Sci 2017; 26:218-226. [PMID: 27759897 PMCID: PMC5275729 DOI: 10.1002/pro.3071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022]
Abstract
Type 1 copper (T1Cu) proteins are electron transfer (ET) proteins involved in many important biological processes. While the effects of changing primary and secondary coordination spheres in the T1Cu ET function have been extensively studied, few report has explored the effect of the overall protein structural perturbation on active site configuration or reduction potential of the protein, even though the protein scaffold has been proposed to play a critical role in enforcing the entatic or "rack-induced" state for ET functions. We herein report circular permutation of azurin by linking the N- and C-termini and creating new termini in the loops between 1st and 2nd β strands or between 3rd and 4th β strands. Characterization by electronic absorption, electron paramagnetic spectroscopies, as well as crystallography and cyclic voltammetry revealed that, while the overall structure and the primary coordination sphere of the circular permutated azurins remain the same as those of native azurin, their reduction potentials increased by 18 and 124 mV over that of WTAz. Such increases in reduction potentials can be attributed to subtle differences in the hydrogen-bonding network in secondary coordination sphere around the T1Cu center.
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Affiliation(s)
- Yang Yu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin300308China
| | - Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| | | | - Parisa Hosseinzadeh
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| | - Honghui Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin300308China
- Tianjin University of Science and TechnologyTianjin300457China
| | - Ninian J. Blackburn
- Institute of Environmental Health, Oregon Health and Science UniversityPortlandOregon97239
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana‐ChampaignUrbanaIllinois61801
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois61801
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Hu C, Yu Y, Wang J. Improving artificial metalloenzymes' activity by optimizing electron transfer. Chem Commun (Camb) 2017; 53:4173-4186. [DOI: 10.1039/c6cc09921a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This feature article discusses the strategies to optimize electron transfer efficiency, towards enhancing the activity of artificial metalloenzymes.
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Affiliation(s)
- Cheng Hu
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Chaoyang District
- China
| | - Yang Yu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Jiangyun Wang
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Chaoyang District
- China
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Vilhena FS, Felcman J, Szpoganicz B, Miranda FS. Potentiometric and DFT studies of Cu(II) complexes with glycylglycine and methionine of interest for the brain chemistry. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.07.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Theoretical study on the degree of delocalization of unpaired spin in two mixed valence copper(II/I) complexes with isomeric chelating diamines and iodide. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.05.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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36
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Affiliation(s)
- Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering; Chalmers University of Technology; 41296 Gothenburg Sweden
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Jana S, Santra RC, Frontera A, Drew MGB, Ortega-Castro J, Fernández D, Das S, Chattopadhyay S. Copper(II) pseudohalide complexes with isomeric N2O donor Schiff base ligands: Synthesis, characterization and molecular dynamics simulations of interactions with DNA. ChemistrySelect 2016. [DOI: 10.1002/slct.201500018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Subrata Jana
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Ramesh Chandra Santra
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Antonio Frontera
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - Michael G. B. Drew
- School of Chemistry; The University of Reading; P.O. Box 224 Whiteknights Reading RG6 6AD UK
| | - Joaquín Ortega-Castro
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - David Fernández
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - Saurabh Das
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Shouvik Chattopadhyay
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
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Dai J, Nanayakkara S, Lamb TC, Clark AJ, Guo SX, Zhang J, Patti AF, Saito K. Effect of the N-based ligands in copper complexes for depolymerisation of lignin. NEW J CHEM 2016. [DOI: 10.1039/c5nj03152d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several organic soluble N-based ligands and their copper complexes were firstly investigated as catalysts to depolymerise organosolv lignin in the organic solvent, dimethylformamide (DMF) and an ionic liquid (1-ethyl-3-methylimidazolium xylenesulfonate, [emim][ABS]).
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Affiliation(s)
- Jinhuo Dai
- School of Chemistry
- Monash University
- Clayton
- Australia
| | | | | | | | - Si-Xuan Guo
- School of Chemistry
- Monash University
- Clayton
- Australia
| | - Jie Zhang
- School of Chemistry
- Monash University
- Clayton
- Australia
| | | | - Kei Saito
- School of Chemistry
- Monash University
- Clayton
- Australia
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Chatterjee D, Jaiswal N, Bose K JC, Mahato RB, Bhattacharyya D. Interaction of Ru III(EDTA) with cellular thiols and O 2: biological implications thereof. J COORD CHEM 2015. [DOI: 10.1080/00958972.2015.1056172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Debabrata Chatterjee
- Chemistry & Biomimetics Group, CSIR-Central Mechanical Engineering Research Institute, Durgapur, India
| | - Namita Jaiswal
- Chemistry & Biomimetics Group, CSIR-Central Mechanical Engineering Research Institute, Durgapur, India
| | - Jagadeesh C. Bose K
- Department of Biotechnology, National Institute of Technology, Durgapur, India
| | - Ram Balak Mahato
- Department of Biotechnology, National Institute of Technology, Durgapur, India
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Komori H, Higuchi Y. Structure and molecular evolution of multicopper blue proteins. Biomol Concepts 2015; 1:31-40. [PMID: 25961983 DOI: 10.1515/bmc.2010.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The multicopper blue protein family, which contains cupredoxin-like domains as a structural unit, is one of the most diverse groups of proteins. This protein family is divided into two functionally different types of enzymes: multicopper oxidase and nitrite reductase. Multicopper oxidase catalyzes the oxidation of the substrate and then reduces dioxygen. The structures of many multicopper oxidases are already known, and until recently they were classified into two main groups: the three- and six-domain types. Both function as monomers and have three spectroscopically different copper sites: Types I (blue), II, and III (tri-nuclear). Nitrite reductase is a closely related protein that contains Types I and II (mono-nuclear) coppers but reduces nitrite instead of dioxygen. Nitrite reductase, which consists of two domains, forms a homotrimer. Multicopper oxidase and nitrite reductase share similar structural architectures and also contain Type I copper. Therefore, it is proposed that they have a common ancestor protein. Recently, some two-domain type multicopper oxidases have been found and their crystal structures have been determined. They have a trimeric quaternary structure and contain an active site at the molecular interface such as nitrite reductase. These results support previous hypotheses and provide an insight into the molecular evolution of multicopper blue proteins.
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Deeudom M, Huston W, Moir JWB. Lipid-modified azurin of Neisseria meningitidis is a copper protein localized on the outer membrane surface and not regulated by FNR. Antonie van Leeuwenhoek 2015; 107:1107-16. [PMID: 25666376 DOI: 10.1007/s10482-015-0400-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/29/2015] [Indexed: 11/24/2022]
Abstract
The laz gene of Neisseria meningitidis is predicted to encode a lipid-modified azurin (Laz). Laz is very similar to azurin, a periplasmic protein, which belongs to the copper-containing proteins in the cupredoxin superfamily. In other bacteria, azurin is an electron donor to nitrite reductase, an important enzyme in the denitrifying process. It is not known whether Laz could function as an electron transfer protein in this important pathogen. Laz protein was heterologously expressed in Escherichia coli and purified. Electrospray mass spectrometry indicated that the Laz protein contains one copper ion. Laz was shown to be redox-active in the presence of its redox center copper ion. When oxidized, Laz exhibits an intense blue colour and absorbs visible light around 626 nm. The absorption is lost when exposed to diethyldithiocarbamate, a copper chelating agent. Polyclonal antibodies were raised against purified Laz for detecting expression of Laz under different growth conditions and to determine the orientation of Laz on the outer membrane. The expression of Laz under microaerobic and microaerobic denitrifying conditions was slightly higher than that under aerobic conditions. However, the expression of Laz was similar between the wild type strain and an fnr mutant, suggesting that Fumarate/Nitrate reduction regulator (FNR) does not regulate the expression of Laz despite the presence of a partial FNR box upstream of the laz gene. We propose that some Laz protein is exposed on the outer membrane surface of N. meningitidis as the αLaz antibodies can increase killing by complement in a capsule deficient N. meningitidis strain, in a dose-dependent fashion.
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Affiliation(s)
- Manu Deeudom
- Department of Biology (Area 10), University of York, Heslington, York, YO10 5YW, UK,
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42
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Hadt RG, Gorelsky S, Solomon EI. Anisotropic covalency contributions to superexchange pathways in type one copper active sites. J Am Chem Soc 2014; 136:15034-45. [PMID: 25310460 PMCID: PMC4210080 DOI: 10.1021/ja508361h] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 01/29/2023]
Abstract
Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu-S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (H(DA)) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu-S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites.
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Affiliation(s)
- Ryan G. Hadt
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Serge
I. Gorelsky
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Centre
for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N6, Canada
| | - Edward I. Solomon
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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Thiebaut F, Rojas CA, Grativol C, Motta MR, Vieira T, Regulski M, Martienssen RA, Farinelli L, Hemerly AS, Ferreira PCG. Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize. BMC Genomics 2014; 15:766. [PMID: 25194793 PMCID: PMC4168055 DOI: 10.1186/1471-2164-15-766] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 08/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays – hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. Results Deep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription. Conclusion Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-766) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Paulo C G Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Avenida Carlos Chagas Filho, 373, CCS, Bl,L-29ss, Rio de Janeiro RJ 21941-599, Brazil.
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Colombo A, Dragonetti C, Magni M, Roberto D, Demartin F, Caramori S, Bignozzi CA. Efficient copper mediators based on bulky asymmetric phenanthrolines for DSSCs. ACS APPLIED MATERIALS & INTERFACES 2014; 6:13945-13955. [PMID: 25078128 DOI: 10.1021/am503306f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the context of the development of new electron mediators for dye-sensitized solar cells that could efficiently substitute the more common I3(-)/I(-) redox couple, we have prepared a series of Cu(I)- phenanthroline complexes through an easy synthetic route. The novel [Cu(2-mesityl-4,7-dimethyl-1,10-phenanthroline)2]PF6 (3) is of particular interest because the presence of the bulky mesityl groups protects as a kiss lock the Cu center, leading to superior dye regeneration kinetics with respect to simpler phenanthroline-based Cu(I) complexes and to a lower dark current with respect the I3(-)/I(-). The exploitation of a dual-component electrolyte constituted by (3) and a Fe(II) comediator, in combination with the [Ru(4,4'-dicarboxy-2,2'-bipyridine)2(4,4'-dinonyl-2,2'-bipyridine)](PF6)2 sensitizer, allowed us to increase the performance of the cell, reaching Jsc values of 4.0 mA cm(-2), comparable to that recorded with I3(-)/I(-) (3.8 mA cm(-2)).
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Affiliation(s)
- Alessia Colombo
- Dipartimento di Chimica, Università degli Studi di Milano , UdR dell'INSTM, Via Golgi 19, Milano 20133 Italy
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Moshkov KA, Zaitsev VN, Grishina TV, Stefanov VE. Multinuclear blue copper-proteins: the evolutionary design. J EVOL BIOCHEM PHYS+ 2014. [DOI: 10.1134/s0022093014030016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Roger M, Biaso F, Castelle CJ, Bauzan M, Chaspoul F, Lojou E, Sciara G, Caffarri S, Giudici-Orticoni MT, Ilbert M. Spectroscopic characterization of a green copper site in a single-domain cupredoxin. PLoS One 2014; 9:e98941. [PMID: 24932914 PMCID: PMC4059628 DOI: 10.1371/journal.pone.0098941] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/09/2014] [Indexed: 12/13/2022] Open
Abstract
Cupredoxins are widespread copper-binding proteins, mainly involved in electron transfer pathways. They display a typical rigid greek key motif consisting of an eight stranded β-sandwich. A fascinating feature of cupredoxins is the natural diversity of their copper center geometry. These geometry variations give rise to drastic changes in their color, such as blue, green, red or purple. Based on several spectroscopic and structural analyses, a connection between the geometry of their copper-binding site and their color has been proposed. However, little is known about the relationship between such diversity of copper center geometry in cupredoxins and possible implications for function. This has been difficult to assess, as only a few naturally occurring green and red copper sites have been described so far. We report herein the spectrocopic characterization of a novel kind of single domain cupredoxin of green color, involved in a respiratory pathway of the acidophilic organism Acidithiobacillus ferrooxidans. Biochemical and spectroscopic characterization coupled to bioinformatics analysis reveal the existence of some unusual features for this novel member of the green cupredoxin sub-family. This protein has the highest redox potential reported to date for a green-type cupredoxin. It has a constrained green copper site insensitive to pH or temperature variations. It is a green-type cupredoxin found for the first time in a respiratory pathway. These unique properties might be explained by a region of unknown function never found in other cupredoxins, and by an unusual length of the loop between the second and the fourth copper ligands. These discoveries will impact our knowledge on non-engineered green copper sites, whose involvement in respiratory chains seems more widespread than initially thought.
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Affiliation(s)
- Magali Roger
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Frédéric Biaso
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Cindy J. Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, California, United States of America
| | - Marielle Bauzan
- Unité de Fermentation, Institut de Microbiologie de la Méditerranée, CNRS-FR 3479, Aix Marseille Université, Marseille, France
| | - Florence Chaspoul
- Unité Chimie Physique, Prévention des Risques et Nuisances Technologiques, Faculté de Pharmacie, CNRS-UMR 7263, Aix-Marseille Université, Marseille, France
| | - Elisabeth Lojou
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Giuliano Sciara
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Stefano Caffarri
- Unité de Biologie Végétale et Microbiologie Environnementales, CNRS-UMR 7265, CEA, Aix Marseille Université, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Marianne Ilbert
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
- * E-mail:
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Wise O, Coskuner O. New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue. J Comput Chem 2014; 35:1278-89. [DOI: 10.1002/jcc.23622] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/06/2014] [Accepted: 03/23/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Olivia Wise
- Department of Chemistry; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
- Neurosciences Institute; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
| | - Orkid Coskuner
- Department of Chemistry; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
- Neurosciences Institute; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Affiliation(s)
- Jay R. Winkler
- Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125
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50
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