1
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Samadi Khezri M, Housaindokht MR, Firouzi M. Designing and prototyping a novel biosensor based on a volumetric bar-chart chip for urea detection. LAB ON A CHIP 2024; 24:2298-2305. [PMID: 38517043 DOI: 10.1039/d3lc00730h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
A volumetric bar-chart chip (V-chip) is a microfluidic device based on distance-based quantitative measurement that visualizes analyte concentration without the need for apparatus or data processing. This typically utilizes special receptors and catalysis parts that generate oxygen, so ink can be moved inside the channels, and enables instant visual quantitation of the analyte. However, the low stability of some macromolecules, the use of expensive catalysts, and difficulty in controlling the process cause inaccurate readings, and therefore, limit further development and the use of these systems. In this article, we introduced a novel approach that eliminates the use of catalysts in V-chips and provides an efficient and simple path in the design of biosensors. The product of the enzymatic reaction of urease with urea is bicarbonate, which turns into CO2 gas in an acidic environment. Therefore, the amount of gas produced is proportional to the amount of urea in the sample, and it can be quantitatively measured by visual detection from the amount of ink movement caused by CO2 gas pressure. This biosensor has a linear response range of 0 to 1000 μg ml-1 and a detection limit of 3.6 μg ml-1 in raw milk. The recovery of urea in raw milk at 100 and 400 μg ml-1 concentrations was 96.5% and 98.9%, respectively. This volumetric chip shows potential for determining urea levels in real samples without requiring additional equipment. The combination of the sensitivity and specificity of enzymatic reactions, inherent gas-generating reactions, and the processability of microchips discussed in this paper can be the basis for the comprehensive development of volumetric chips, which can create a new path for the development of efficient and cheap biosensors.
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Affiliation(s)
- Mahdi Samadi Khezri
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mohammad Reza Housaindokht
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
- Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mojtaba Firouzi
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
- Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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2
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Shanmugavel D, Rusyn I, Solorza-Feria O, Kamaraj SK. Sustainable SMART fertilizers in agriculture systems: A review on fundamentals to in-field applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166729. [PMID: 37678530 DOI: 10.1016/j.scitotenv.2023.166729] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Agriculture will face the issue of ensuring food security for a growing global population without compromising environmental security as demand for the world's food systems increases in the next decades. To provide enough food and reduce the harmful effects of chemical fertilization and improper disposal or reusing of agricultural wastes on the environment, will be required to apply current technologies in agroecosystems. Combining biotechnology and nanotechnology has the potential to transform agricultural practices and offer answers to both immediate and long-term issues. This review study seeks to identify, categorize, and characterize the so-called smart fertilizers as the future frontier of sustainable agriculture. The conventional fertilizer and smart fertilizers in general are covered in the first section of this review. Another key barrier preventing the widespread use of smart fertilizers in agriculture is the high cost of materials. Nevertheless, smart fertilizers are widely represented on the world market and are actively used in farms that have already switched to sustainable technologies. The advantages and disadvantages of various raw materials used to create smart fertilizers, with a focus on inorganic and organic materials, synthetic and natural polymers, along with their physical and chemical preparation processes, are contrasted in the following sections. The rate and the mechanism of release are covered. The purpose of this study is to provide a deep understanding of the advancements in smart fertilizers during the last ten years. Trends are also recognized and studied to provide insight for upcoming agricultural research projects.
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Affiliation(s)
- Divya Shanmugavel
- Programa de Nanociencias y Nanotecnología, CINVESTAV - IPN, Hydrogen and Fuel Cells Group, A. Postal 14-760, 07360 CDMX, Mexico
| | - Iryna Rusyn
- Department of Ecology and Sustainable Environmental Management, Viacheslav Chornovil Institute of Sustainable Development, Lviv Polytechnic National University, Stepan Bandera St., 12, Lviv, 79013, Ukraine
| | - Omar Solorza-Feria
- Department of Chemistry, CINVESTAV - IPN, Hydrogen, and Fuel Cells Group, A. Postal 14-760, 07360 CDMX, Mexico.
| | - Sathish-Kumar Kamaraj
- Instituto Politécnico Nacional (IPN)-Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Altamira (CICATA-Altamira), Carretera Tampico-Puerto Industrial Altamira Km 14.5, C. Manzano, Industrial Altamira, 89600 Altamira, Tamps., Mexico.
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3
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Huang M, Cui P, Zhou J, Liu C, Wang Y. Theoretical study on the inhibition mechanisms of heavy metal ions on urease activity. CHEMOSPHERE 2023; 345:140416. [PMID: 37827462 DOI: 10.1016/j.chemosphere.2023.140416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
Soil urease is highly sensitive to soil heavy metal pollution, and thus its activity can be used as bio-indicator of soil health. However, little is known about the inhibition mechanisms of heavy metals on urease. The effects of dimetallic substitution (i.e., Cd, Co, Cu, Hg, and Zn) on the binding of urea in the urease and its subsequent decomposition were studied using quantum chemical methodologies with a urease mimic (phthalazine-dinickel complex). The dimetallic substitution altered the structural features of the dimetal complexes and the M-O bond length between the dimetals and the carbonyl-O of coordinated urea molecules, weakening the binding energies of urea in dimetal complexes, which further affected the transformation of urea. In the urea decomposition via intra-molecular proton transfer, all dimetal complexes have a high activation barrier due to the weak binding of urea in complexes and hydrogen bonding within urea molecules, which are therefore difficult to occur spontaneously. In the urea decomposition via water-assisted inter-molecular proton transfer, the addition of water molecules decreased the energy barrier of urea decomposition. Regardless of the urea decomposition pathway, the dimetallic substitution altered the M-O bond length and hydrogen bond pattern of intermediates and transition states, and also affected the leave of the resulting NH3 from the dimetal complexes by regulating the C-N bond length within the decomposed urea molecule. Overall, the theoretical study provided insight into the molecular mechanisms of the inhibitory effects of heavy metals on urease activity.
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Affiliation(s)
- Meiying Huang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peixin Cui
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jing Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cun Liu
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Yujun Wang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Suenaga S, Takano Y, Saito T. Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study. Molecules 2023; 28:molecules28062697. [PMID: 36985670 PMCID: PMC10051795 DOI: 10.3390/molecules28062697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Soil bacteria can produce urease, which catalyzes the hydrolysis of urea to ammonia (NH3) and carbamate. A variety of urease inhibitors have been proposed to reduce NH3 volatilization by interfering with the urease activity. We report a quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) study on the mechanism employed for the inhibition of urease by three representative competitive inhibitors; namely, acetohydroxamic acid (AHA), hydroxyurea (HU), and N-(n-butyl)phosphorictriamide (NBPTO). The possible connections between the structural and thermodynamical properties and the experimentally observed inhibition efficiency were evaluated and characterized. We demonstrate that the binding affinity decreases in the order NBPTO >> AHA > HU in terms of the computed activation and reaction free energies. This trend also indicates that NBPTO shows the highest inhibitory activity and the lowest IC50 value of 2.1 nM, followed by AHA (42 μM) and HU (100 μM). It was also found that the X=O moiety (X = carbon or phosphorous) plays a crucial role in the inhibitor binding process. These findings not only elucidate why the potent urease inhibitors are effective but also have implications for the design of new inhibitors.
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Affiliation(s)
- Shunya Suenaga
- Faculty of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Toru Saito
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
- Correspondence: ; Tel.: +81-82-830-1617
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5
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Abstract
![]()
Urease
catalyzes the hydrolysis of urea to form ammonia and carbamate,
inducing an overall pH increase that affects both human health and
agriculture. Inhibition, mutagenesis, and kinetic studies have provided
insights into its enzymatic role, but there have been debates on the
substrate binding mode as well as the reaction mechanism. In the present
study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular
mechanics molecular dynamics (QM/MM MD) calculations on urease that
mainly investigate the binding mode of urea and the mechanism of the
urease-catalyzed hydrolysis reaction. Comparison between the experimental
data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that
urea hydrolysis via a complex with bidentate-bound urea is much more
favorable than via that with monodentate-bound urea for both nucleophilic
attack and the subsequent proton transfer steps. We also indicate
that the bidentate coordination of urea fits the active site with
a closed conformation of the mobile flap and can facilitate the stabilization
of transition states and intermediates by forming multiple hydrogen
bonds with certain active site residues.
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Affiliation(s)
- Toru Saito
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
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6
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Zhu J, Shen D, Xie J, Tang C, Jin B, Wu S. Mechanism of urea decomposition catalyzed by Sporosarcina pasteurii urease based on quantum chemical calculations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1970156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jie Zhu
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
| | - Dejian Shen
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
| | - Jingjing Xie
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, People’s Republic of China
| | - Chunmei Tang
- College of Science, Hohai University, Nanjing, People’s Republic of China
| | - Baosheng Jin
- School of Energy and Environment, Southeast University, Nanjing, People’s Republic of China
| | - Shengxing Wu
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
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7
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Wang X, Shan J, Liu W, Li J, Tan H, Li X, Chen G. Theoretical Studies on the Binding Mode and Reaction Mechanism of TLP Hydrolase kpHIUH. Molecules 2021; 26:molecules26133884. [PMID: 34202153 PMCID: PMC8272043 DOI: 10.3390/molecules26133884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022] Open
Abstract
In this work, we have investigated the binding conformations of the substrate in the active site of 5-HIU hydrolase kpHIUH and its catalytic hydrolysis mechanism. Docking calculations revealed that the substrate adopts a conformation in the active site with its molecular plane laying parallel to the binding interface of the protein dimer of kpHIUH, in which His7 and His92 are located adjacent to the hydrolysis site C6 and have hydrogen bond interactions with the lytic water. Based on this binding conformation, density functional theory calculations indicated that the optimal catalytic mechanism consists of two stages: (1) the lytic water molecule is deprotonated by His92 and carries out nucleophilic attack on C6=O of 5-HIU, resulting in an oxyanion intermediate; (2) by accepting a proton transferred from His92, C6–N5 bond is cleaved to completes the catalytic cycle. The roles of His7, His92, Ser108 and Arg49 in the catalytic reaction were revealed and discussed in detail.
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8
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Madhura TR, kumar GG, Ramaraj R. Reduced graphene oxide supported 2D-NiO nanosheets modified electrode for urea detection. J Solid State Electrochem 2020. [DOI: 10.1007/s10008-020-04763-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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Polino D, Parrinello M. Kinetics of Aqueous Media Reactions via Ab Initio Enhanced Molecular Dynamics: The Case of Urea Decomposition. J Phys Chem B 2019; 123:6851-6856. [PMID: 31286763 DOI: 10.1021/acs.jpcb.9b05271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aqueous solutions provide a medium for many important reactions in chemical synthesis, industrial processes, environmental chemistry, and biological functions. It is an accepted fact that aqueous solvents can be direct participants in the reaction process and not act only as simple passive dielectrics. Assisting water molecules and proton wires are thus essential for the efficiency of many reactions. Here, we study the decomposition of urea into ammonia and isocyanic acid by means of enhanced ab initio molecular dynamics simulations. We highlight the role of the solvent molecules and their interactions with the reactants providing a proper description of the reaction mechanism and how the water hydrogen-bond network affects the reaction dynamics. Reaction free energy and rates have been calculated taking into account this important effect.
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Affiliation(s)
- Daniela Polino
- Department of Chemistry and Applied Biosciences , ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Facoltà di Informatica, Istituto di Scienze Computazionali , Università della Svizzera Italiana , Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences , ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Facoltà di Informatica, Istituto di Scienze Computazionali , Università della Svizzera Italiana , Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
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10
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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11
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Arqué X, Romero-Rivera A, Feixas F, Patiño T, Osuna S, Sánchez S. Intrinsic enzymatic properties modulate the self-propulsion of micromotors. Nat Commun 2019; 10:2826. [PMID: 31249381 PMCID: PMC6597730 DOI: 10.1038/s41467-019-10726-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/24/2019] [Indexed: 11/17/2022] Open
Abstract
Bio-catalytic micro- and nanomotors self-propel by the enzymatic conversion of substrates into products. Despite the advances in the field, the fundamental aspects underlying enzyme-powered self-propulsion have rarely been studied. In this work, we select four enzymes (urease, acetylcholinesterase, glucose oxidase, and aldolase) to be attached on silica microcapsules and study how their turnover number and conformational dynamics affect the self-propulsion, combining both an experimental and molecular dynamics simulations approach. Urease and acetylcholinesterase, the enzymes with higher catalytic rates, are the only enzymes capable of producing active motion. Molecular dynamics simulations reveal that urease and acetylcholinesterase display the highest degree of flexibility near the active site, which could play a role on the catalytic process. We experimentally assess this hypothesis for urease micromotors through competitive inhibition (acetohydroxamic acid) and increasing enzyme rigidity (β-mercaptoethanol). We conclude that the conformational changes are a precondition of urease catalysis, which is essential to generate self-propulsion. Self-propulsion of biocatalytic micro- and nanomotors is facilitated by enzymes converting substrates into products. Here, the authors show that intrinsic enzymatic properties such as conformational changes are crucial for the self-propulsion of silica microcapsules modified with urease.
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Affiliation(s)
- Xavier Arqué
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain
| | - Adrian Romero-Rivera
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Ferran Feixas
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Tania Patiño
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain.
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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12
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019; 58:7415-7419. [DOI: 10.1002/anie.201903565] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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13
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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14
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Uprety B, Arderne C, Bernal I. Catalytic Cleavage of the Amide Bond in Urea Using a Cobalt(III) Amino-Based Complex. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bhawna Uprety
- Department of Chemistry; University of Johannesburg; PO Box 524, Auckland Park 2006 Johannesburg South Africa
| | - Charmaine Arderne
- Department of Chemistry; University of Johannesburg; PO Box 524, Auckland Park 2006 Johannesburg South Africa
| | - Ivan Bernal
- Molecular Sciences Institute; School of Chemistry; University of the Witwatersrand; 2050 Johannesburg South Africa
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15
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Kappaun K, Piovesan AR, Carlini CR, Ligabue-Braun R. Ureases: Historical aspects, catalytic, and non-catalytic properties - A review. J Adv Res 2018; 13:3-17. [PMID: 30094078 PMCID: PMC6077230 DOI: 10.1016/j.jare.2018.05.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 12/11/2022] Open
Abstract
Urease (urea amidohydrolase, EC 3.5.1.5) is a nickel-containing enzyme produced by plants, fungi, and bacteria that catalyzes the hydrolysis of urea into ammonia and carbamate. Urease is of historical importance in Biochemistry as it was the first enzyme ever to be crystallized (1926). Finding nickel in urease's active site (1975) was the first indication of a biological role for this metal. In this review, historical and structural features, kinetics aspects, activation of the metallocenter and inhibitors of the urea hydrolyzing activity of ureases are discussed. The review also deals with the non-enzymatic biological properties, whose discovery 40 years ago started a new chapter in the study of ureases. Well recognized as virulence factors due to the production of ammonia and alkalinization in diseases by urease-positive microorganisms, ureases have pro-inflammatory, endocytosis-inducing and neurotoxic activities that do not require ureolysis. Particularly relevant in plants, ureases exert insecticidal and fungitoxic effects. Data on the jack bean urease and on jaburetox, a recombinant urease-derived peptide, have indicated that interactions with cell membrane lipids may be the basis of the non-enzymatic biological properties of ureases. Altogether, with this review we wanted to invite the readers to take a second look at ureases, very versatile proteins that happen also to catalyze the breakdown of urea into ammonia and carbamate.
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Affiliation(s)
- Karine Kappaun
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Angela Regina Piovesan
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Celia Regina Carlini
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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16
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Wang WJ, Wei WJ, Liao RZ. Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase. Phys Chem Chem Phys 2018; 20:15784-15794. [DOI: 10.1039/c8cp02683a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.
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Affiliation(s)
- Wen-Juan Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
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Abdel Hameed R, Medany SS. Enhanced electrocatalytic activity of NiO nanoparticles supported on graphite planes towards urea electro-oxidation in NaOH solution. INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 2017; 42:24117-24130. [DOI: 10.1016/j.ijhydene.2017.07.236] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
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18
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The synthesis and characterization of new nickel complexes with unusual coordination modes. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Dalle KE, Meyer F. Modelling Binuclear Metallobiosites: Insights from Pyrazole-Supported Biomimetic and Bioinspired Complexes. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500185] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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Belzile MN, Neverov AA, Brown RS. Cu(II)-Ion-Catalyzed Solvolysis of N,N-Bis(2-picolyl)ureas in Alcohol Solvents: Evidence for Cleavage Involving Nucleophilic Addition and Strong Assistance of Bis(2-picolyl)amine Leaving Group Departure. Inorg Chem 2014; 53:7916-25. [DOI: 10.1021/ic500620k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mei-Ni Belzile
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei. A. Neverov
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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Sokołowska M, Kostański M, Lorenc-Koci E, Bilska A, Iciek M, Włodek L. The effect of lipoic acid on cyanate toxicity in the rat heart. Pharmacol Rep 2014; 66:87-92. [PMID: 24905312 DOI: 10.1016/j.pharep.2013.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/26/2013] [Accepted: 08/02/2013] [Indexed: 01/25/2023]
Abstract
BACKGROUND Cyanate is a uremic toxin formed principally via spontaneous urea biodegradation. Its active isoform, isocyanate, is capable of reaction with proteins by N and S carbamoylation, which influences their structure and function. Sulfurtransferases implicated in anaerobic cysteine transformation and cyanide detoxification belong to the enzymes possessing SH groups in their active centers. The present studies aimed to demonstrate the effect of cyanate and lipoic acid on the activity of these enzymes as well as on the level of antioxidants and prooxidants in the rat heart. METHODS Wistar rats, which received intraperitoneal injections of cyanate and lipoic acid alone and in combination were sacrificed 2.5 h after the first injection. The hearts were isolated and homogenized in phosphate buffer and next biochemical assays were performed comprising determination of the level of glutathione, malondialdehyde and sulfane sulfur and the activity of antioxidant enzymes as well as glutathione S-transferase and gamma glutamyl transferase. RESULTS Sulfurtransferases and glutathione S-transferase were deactivated by cyanate treatment. It was accompanied by the decreased level of glutathione and sulfane sulfur and the increased level of reactive oxygen species and malondialdehyde. In parallel, antioxidant enzymes: catalase, glutathione peroxidase and gamma glutamyl transferase were activated under such circumstances. Lipoic acid, administered in combination with cyanate prevented the decrease in the level of glutathione and reduction of a pool of sulfane sulfur-containing compounds, concomitantly preserving the activity of antioxidant enzymes. CONCLUSIONS Since uremia, characterized by the elevated cyanate/isocyanate level, is accompanied by frequent cases of cardiovascular diseases, the addition of lipoic acid to the therapy seems promising in prophylaxis of heart diseases in uremic patients.
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Affiliation(s)
- Maria Sokołowska
- The Chair of Medical Biochemistry, Jagiellonian University, Collegium Medicum, Kraków, Poland.
| | - Maciej Kostański
- The Chair of Medical Biochemistry, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Elżbieta Lorenc-Koci
- Department of Neuropsychopharmacology, Institute of Pharmacology, Polish Academy of Science, Kraków, Poland
| | - Anna Bilska
- The Chair of Medical Biochemistry, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Małgorzata Iciek
- The Chair of Medical Biochemistry, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Lidia Włodek
- The Chair of Medical Biochemistry, Jagiellonian University, Collegium Medicum, Kraków, Poland
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22
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Estiu G, Chacón Villalba M, Camí G, Echeverria G, Soria D. Synthesis, crystal structure, spectroscopic, thermogravimetric and theoretical characterization of Ni(II) and Zn(II) complexes with 4-chloro-2-nitrobenzenesulfonamide. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.11.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Boer JL, Mulrooney SB, Hausinger RP. Nickel-dependent metalloenzymes. Arch Biochem Biophys 2014; 544:142-52. [PMID: 24036122 PMCID: PMC3946514 DOI: 10.1016/j.abb.2013.09.002] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
Abstract
This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.
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Affiliation(s)
- Jodi L Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Scott B Mulrooney
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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Perreault NN, Halasz A, Thiboutot S, Ampleman G, Hawari J. Joint photomicrobial process for the degradation of the insensitive munition N-guanylurea-dinitramide (FOX-12). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:5193-5198. [PMID: 23594309 DOI: 10.1021/es4006652] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
N-Guanylurea-dinitramide (FOX-12) is a very insensitive energetic material intended to be used in the composition of next-generation insensitive munitions. To help predict the environmental behavior and fate of FOX-12, we conducted a study to determine its photodegradability and biodegradability. When dissolved in water, FOX-12, a guanylurea-dinitramide salt, also named GUDN, dissociated instantly to produce the dinitramide moiety and guanylurea, as demonstrated by high-performance liquid chromatography (HPLC) analysis. When an aqueous solution of FOX-12 was subjected to photolysis using a solar-simulated photoreactor, we found a rapid removal of the dinitramide with concurrent formation of N₂O, NO₂(-), and NO₃(-). The second component, guanylurea, was photostable. However, when FOX-12 was incubated aerobically with the soil isolate Variovorax strain VC1 and protected from light, the dinitramide component of FOX-12 was recalcitrant but guanylurea degraded effectively to ammonia, guanidine, and presumably CO₂. When FOX-12 was incubated with strain VC1 in the presence of light, both components of FOX-12 degraded, giving similar products to those described above. We concluded that the new insensitive explosive FOX-12 can be effectively degraded by a joint photomicrobial process and, therefore, should not cause persistent contamination of surface waters.
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Affiliation(s)
- Nancy N Perreault
- National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
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25
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The effect of lipoic acid on cyanate toxicity in different structures of the rat brain. Neurotox Res 2013; 24:345-57. [PMID: 23625581 PMCID: PMC3753499 DOI: 10.1007/s12640-013-9395-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 03/27/2013] [Accepted: 04/19/2013] [Indexed: 01/17/2023]
Abstract
Cyanate is formed mostly during nonenzymatic urea biodegradation. Its active form isocyanate reacts with protein -NH2 and -SH groups, which changes their structure and function. The present studies aimed to investigate the effect of cyanate on activity of the enzymes, which possess -SH groups in the active centers and are implicated in anaerobic cysteine transformation and cyanide detoxification, as well as on glutathione level and peroxidative processes in different brain structures of the rat: cortex, striatum, hippocampus, and substantia nigra. In addition, we examined whether a concomitant treatment with lipoate, a dithiol that may act as a target of S-carbamoylation, can prevent these changes. Cyanate-inhibited sulfurtransferase activities and lowered sulfide level, which was accompanied by a decrease in glutathione concentration and elevation of reactive oxygen species level in almost all rat brain structures. Lipoate administered in combination with cyanate was able to prevent the above-mentioned negative cyanate-induced changes in a majority of the examined brain structures. These observations can be promising for chronic renal failure patients since lipoate can play a double role in these patients contributing to efficient antioxidant defense and protection against cyanate and cyanide toxicity.
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Ligabue-Braun R, Andreis FC, Verli H, Carlini CR. 3-to-1: unraveling structural transitions in ureases. Naturwissenschaften 2013; 100:459-67. [PMID: 23619940 DOI: 10.1007/s00114-013-1045-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/05/2013] [Accepted: 04/05/2013] [Indexed: 01/08/2023]
Abstract
Ureases are nickel-dependent enzymes which catalyze the hydrolysis of urea to ammonia and carbamate. Despite the apparent wealth of data on ureases, many crucial aspects regarding these enzymes are still unknown, or constitute matter for ongoing debates. One of these is most certainly their structural organization: ureases from plants and fungi have a single unit, while bacterial and archaean ones have three-chained structures. However, the primitive state of these proteins--single- or three-chained--is yet unknown, despite many efforts in the field. Through phylogenetic inference using three different datasets and two different algorithms, we were able to observe chain number transitions displayed in a 3-to-1 fashion. Our results imply that the ancestral state for ureases is the three-chained organization, with single-chained ureases deriving from them. The two-chained variants are not evolutionary intermediates. A fusion process, different from those already studied, may explain this structural transition.
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Affiliation(s)
- Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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Abstract
Metalloenzymes often require elaborate metallocenter assembly systems to create functional active sites. The medically important dinuclear nickel enzyme urease provides an excellent model for studying metallocenter assembly. Nickel is inserted into the urease active site in a GTP-dependent process with the assistance of UreD/UreH, UreE, UreF, and UreG. These accessory proteins orchestrate apoprotein activation by delivering the appropriate metal, facilitating protein conformational changes, and possibly providing a requisite post-translational modification. The activation mechanism and roles of each accessory protein in urease maturation are the subject of ongoing studies, with the latest findings presented in this minireview.
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Affiliation(s)
- Mark A Farrugia
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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28
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Crystal structure, spectroscopy and theoretical studies of p-cyanobenzenosulfonamide and a Cu(II) complex. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Substrate ingress and product egress from the active site of urease is tightly controlled by an active-site flap. Molecular dynamics simulations of urease have revealed a previously unobserved wide-open flap state that, unlike the well-characterized closed and open states, allows ready access to the metal cluster in the active site. This state is easily reached from the open state via low free energy barriers. Additionally, we have found that even when the flap is closed, a region of the binding pocket is solvent-exposed, leading to the hypothesis that it may act as a substrate/product reservoir. The newly identified wide-open state offers further opportunities for small-molecule drug discovery by defining a more extensive active-site pocket than has been previously described.
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Carter EL, Flugga N, Boer JL, Mulrooney SB, Hausinger RP. Interplay of metal ions and urease. Metallomics 2011; 1:207-21. [PMID: 20046957 DOI: 10.1039/b903311d] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Urease, the first enzyme to be crystallized, contains a dinuclear nickel metallocenter that catalyzes the decomposition of urea to produce ammonia, a reaction of great agricultural and medical importance. Several mechanisms of urease catalysis have been proposed on the basis of enzyme crystal structures, model complexes, and computational efforts, but the precise steps in catalysis and the requirement of nickel versus other metals remain unclear. Purified bacterial urease is partially activated via incubation with carbon dioxide plus nickel ions; however, in vitro activation also has been achieved with manganese and cobalt. In vivo activation of most ureases requires accessory proteins that function as nickel metallochaperones and GTP-dependent molecular chaperones or play other roles in the maturation process. In addition, some microorganisms control their levels of urease by metal ion-dependent regulatory mechanisms.
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Affiliation(s)
- Eric L Carter
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
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31
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Camí G, Chacón Villalba E, Di Santi Y, Colinas P, Estiu G, Soria D. Synthesis, thermogravimetric, spectroscopic and theoretical characterization of copper(II) complex with 4-chloro-2-nitrobenzenosulfonamide. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.03.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Sokołowska M, Niedzielska E, Iciek M, Bilska A, Lorenc-Koci E, Włodek L. The effect of the uremic toxin cyanate (CNO⁻) on anaerobic cysteine metabolism and oxidative processes in the rat liver: a protective effect of lipoate. Toxicol Mech Methods 2011; 21:473-8. [PMID: 21417628 DOI: 10.3109/15376516.2011.556155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic renal failure (CRF) patients have an increased plasma level of urea, which can be a source of cyanate. This compound can cause protein carbamoylation thereby changing biological activity of proteins. Therefore, in renal failure patients, cyanate can disturb metabolism and functioning of the liver. This work presents studies demonstrating that the treatment of rats with cyanate alone causes the following changes in the liver: (1) inhibition of rhodanese (TST), cystathionase (CST) and 3-mercaptopyruvate sulfotransferase (MPST) activities, (2) decrease in sulfane sulfur level (S*), (3) lowering of nonprotein sulfhydryl groups (NPSH) group level, and (4) enhancement of prooxidant processes (rise in reactive oxygen species (ROS) and malondialdehyde (MDA) level). This indicates that cyanate inhibits anaerobic cysteine metabolism and shows prooxidant action in the liver. Out of the above-mentioned changes, lipoate administered with cyanate jointly was able to correct MDA, ROS and NPSH levels, and TST activity. It had no significant effect on MPST and CST activities. It indicates that lipoate can prevent prooxidant cyanate action and cyanate-induced TST inhibition. These observations can be promising for CRF patients since lipoate can play a dual role in these patients as an efficient antioxidant defense and a protection against cyanate and cyanide toxicity.
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Affiliation(s)
- Maria Sokołowska
- Department of Medical Biochemistry, Jagiellonian University, Kraków, Poland.
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33
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Iciek M, Bilska A, Lorenc-Koci E, Wlodek LB, Sokołowska MM. The effect of uremic toxin cyanate (OCN–) on anaerobic sulfur metabolism and prooxidative processes in the rat kidney: a protective role of lipoate. Hum Exp Toxicol 2010; 30:1601-8. [PMID: 21177730 DOI: 10.1177/0960327110394225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cyanate and its active form isocyanate are formed mainly in the process of nonenzymatic urea biodegradation. Cyanate is capable of protein S- and N-carbamoylation, which can affect their activity. The present studies aimed to demonstrate the effect of cyanate on activity of the enzymes implicated in anaerobic cysteine metabolism and cyanide detoxification and on glutathione (GSH) level and peroxidative processes in the kidney. In addition, we examined whether a concomitant treatment with lipoate, a dithiol that may act as a target of S-carbamoylation, can prevent these changes. The studies were conducted in Wistar rats. The animals were assigned to four groups, which received injections of physiological saline, cyanate (200 mg/kg), cyanate (200 mg/kg) + lipoate (100 mg/kg) and lipoate alone (100 mg/kg). The animals were killed 2 h after the first injection, the kidneys were isolated and kept at -80°C until biochemical assays were performed. Cyanate inhibited rhodanese (TST) and mercaptopyruvate sulfotransferase (MPST) activity, decreased GSH level and enhanced peroxidative processes in the kidney. All these changes were abolished by cyanate treatment in combination with lipoate.
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Daramola DA, Singh D, Botte GG. Dissociation Rates of Urea in the Presence of NiOOH Catalyst: A DFT Analysis. J Phys Chem A 2010; 114:11513-21. [DOI: 10.1021/jp105159t] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Damilola A. Daramola
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
| | - Deepika Singh
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
| | - Gerardine G. Botte
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
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35
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Computational modeling of the mechanism of urease. Bioinorg Chem Appl 2010. [PMID: 20886006 PMCID: PMC2945649 DOI: 10.1155/2010/364891] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 05/31/2010] [Indexed: 12/02/2022] Open
Abstract
In order to elucidate aspects of the mechanism of the hydrolytic enzyme urease, theoretical calculations were undertaken on a model of the active site, using density functional theory. The bridging oxygen donor that has been found in the crystal structures was determined to be a hydroxide ion. The initial coordination of urea at the active site occurs most likely through the urea oxygen to the nickel ion with the lowest coordination number. This coordination can be made without much gain in energy. The calculations also showed that weak coordination of one of the urea amine nitrogen atoms to the second nickel atom is energetically feasible. Furthermore, a proposed mechanism including a tetrahedral intermediate generated by hydrolytic attack on the urea carbon by the bridging hydroxide was modeled, and the tetrahedral intermediate was found to be energetically unfavorable relative to terminal coordination of the substrate (urea).
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Sim YL, Khan MN. Kinetics and mechanism of tertiary amine-catalyzed cleavage of N′-morpholino- N-(2′-methoxyphenyl)phthalamide: Kinetic evidence for the presence of a reactive intermediate on the reaction path. INT J CHEM KINET 2010. [DOI: 10.1002/kin.20477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Lemus L, Guerrero J, Costamagna J, Estiu G, Ferraudi G, Lappin AG, Oliver A, Noll BC. Unfolding of the [Cu2(1,3-bis(9-methyl-1,10-phenanthrolin-2-yl)propane)2]2+ Helicate. Coupling of the Chlorocarbon Dehalogenation to the Unfolding Process. Inorg Chem 2010; 49:4023-35. [DOI: 10.1021/ic9018986] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- L. Lemus
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo ÓHiggins 3363, Estación Central, Santiago, Chile
| | - J. Guerrero
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo ÓHiggins 3363, Estación Central, Santiago, Chile
| | - J. Costamagna
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo ÓHiggins 3363, Estación Central, Santiago, Chile
| | - G. Estiu
- Department of Chemistry and Biochemistry
| | | | | | - A. Oliver
- Department of Chemistry and Biochemistry
| | - B. C. Noll
- Department of Chemistry and Biochemistry
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Adamczyk K, Dreyer J, Pines D, Pines E, Nibbering ETJ. Ultrafast Protonation of Cyanate Anion in Aqueous Solution. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.217] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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40
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41
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Khan MN. Experimental versus theoretical evidence for the rate-limiting steps in uncatalyzed and H+
- and HO−
-catalyzed hydrolysis of the amide bond. INT J CHEM KINET 2009. [DOI: 10.1002/kin.20435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ferraudi G, Estiu G, Lappin A, Villagran M, Muena J, Costamagna J, Zagal J. The (Tetraazaannulene)copper-Catalyzed Reduction of Sulfur(IV) Species. A Pulse-Radiolysis and Theoretical Study of the Associated Reaction Mechanism. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200800319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Soria DB, Barquín M, Garmendia MJG, Estiu G. Magnetic properties, infrared spectroscopy, thermal and theoretical studies of oxomolybdenum(V) complexes with 2,2′-bipyrimidine. J COORD CHEM 2008. [DOI: 10.1080/00958970802136354] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Delia B. Soria
- a Cequinor, Facultad de Ciencias Exactas , Universidad Nacional de La Plata , CC 962, 1900-La Plata, Argentina
| | - Montserrat Barquín
- b Grupo de Química Inorgánica, Facultad de Ciencias Químicas , Universidad del País Vasco , UPV/EHU, Apartado 1072, 20080-San Sebastian, Spain
| | - Maria J. Gonzalez Garmendia
- b Grupo de Química Inorgánica, Facultad de Ciencias Químicas , Universidad del País Vasco , UPV/EHU, Apartado 1072, 20080-San Sebastian, Spain
| | - Guillermina Estiu
- c Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame, IN 46556, USA
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