151
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Magacz M, Kędziora K, Sapa J, Krzyściak W. The Significance of Lactoperoxidase System in Oral Health: Application and Efficacy in Oral Hygiene Products. Int J Mol Sci 2019; 20:ijms20061443. [PMID: 30901933 PMCID: PMC6472183 DOI: 10.3390/ijms20061443] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/13/2019] [Accepted: 03/18/2019] [Indexed: 12/13/2022] Open
Abstract
Lactoperoxidase (LPO) present in saliva are an important element of the nonspecific immune response involved in maintaining oral health. The main role of this enzyme is to oxidize salivary thiocyanate ions (SCN-) in the presence of hydrogen peroxide (H₂O₂) to products that exhibit antimicrobial activity. LPO derived from bovine milk has found an application in food, cosmetics, and medical industries due to its structural and functional similarity to the human enzyme. Oral hygiene products enriched with the LPO system constitute an alternative to the classic fluoride caries prophylaxis. This review describes the physiological role of human salivary lactoperoxidase and compares the results of clinical trials and in vitro studies of LPO alone and complex dentifrices enriched with bovine LPO. The role of reactivators and inhibitors of LPO is discussed together with the possibility of using nanoparticles to increase the stabilization and activity of this enzyme.
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Affiliation(s)
- Marcin Magacz
- Department of Medical Diagnostics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland.
| | - Karolina Kędziora
- Department of Medical Diagnostics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland.
| | - Jacek Sapa
- Department of Pharmacodynamics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland.
| | - Wirginia Krzyściak
- Department of Medical Diagnostics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland.
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152
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Ehudin MA, Schaefer AW, Adam SM, Quist DA, Diaz DE, Tang JA, Solomon EI, Karlin KD. Influence of intramolecular secondary sphere hydrogen-bonding interactions on cytochrome c oxidase inspired low-spin heme-peroxo-copper complexes. Chem Sci 2019; 10:2893-2905. [PMID: 30996867 PMCID: PMC6431958 DOI: 10.1039/c8sc05165h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 11/21/2022] Open
Abstract
Dioxygen reduction by heme-copper oxidases is a critical biochemical process, wherein hydrogen bonding is hypothesized to participate in the critical step involving the active-site reductive cleavage of the O-O bond. Sixteen novel synthetic heme-(μ-O2 2-)-Cu(XTMPA) complexes, whose design is inspired by the cytochrome c oxidase active site structure, were generated in an attempt to form the first intramolecular H-bonded complexes. Derivatives of the "parent" ligand (XTMPA, TMPA = (tris((2-pyridyl)methyl)amine)) possessing one or two amine pendants preferentially form an H-bond with the copper-bound O-atom of the peroxide bridge. This is evidenced by a characteristic blue shift in the ligand-to-metal charge transfer (LMCT) bands observed in UV-vis spectroscopy (consistent with lowering of the peroxo π* relative to the iron orbitals) and a weakening of the O-O bond determined by resonance Raman spectroscopy (rR), with support from Density Functional Theory (DFT) calculations. Remarkably, with the TMPA-based infrastructure (versus similar heme-peroxo-copper complexes with different copper ligands), the typically undetected Cu-O stretch for these complexes was observed via rR, affording critical insights into the nature of the O-O peroxo core for the complexes studied. While amido functionalities have been shown to have greater H-bonding capabilities than their amino counterparts, in these heme-peroxo-copper complexes amido substituents distort the local geometry such that H-bonding with the peroxo core only imparts a weak electronic effect; optimal H-bonding interactions are observed by employing two amino groups on the copper ligand. The amino-substituted systems presented in this work reveal a key orientational anisotropy in H-bonding to the peroxo core for activating the O-O bond, offering critical insights into effective O-O cleavage chemistry. These findings indirectly support computational and protein structural studies suggesting the presence of an interstitial H-bonding water molecule in the CcO active site, which is critical for the desired reactivity. The results are evaluated with appropriate controls and discussed with respect to potential O2-reduction capabilities.
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Affiliation(s)
- Melanie A Ehudin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Andrew W Schaefer
- Department of Chemistry , Stanford University , Stanford , California 94305 , USA .
| | - Suzanne M Adam
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - David A Quist
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Daniel E Diaz
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Joel A Tang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , USA .
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , USA .
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153
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Vogiatzis KD, Polynski MV, Kirkland JK, Townsend J, Hashemi A, Liu C, Pidko EA. Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities. Chem Rev 2019; 119:2453-2523. [PMID: 30376310 PMCID: PMC6396130 DOI: 10.1021/acs.chemrev.8b00361] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 12/28/2022]
Abstract
Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.
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Affiliation(s)
| | | | - Justin K. Kirkland
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jacob Townsend
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ali Hashemi
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chong Liu
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Evgeny A. Pidko
- TheoMAT
group, ITMO University, Lomonosova 9, St. Petersburg 191002, Russia
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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154
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Increased susceptibility of airway epithelial cells from ataxia-telangiectasia to S. pneumoniae infection due to oxidative damage and impaired innate immunity. Sci Rep 2019; 9:2627. [PMID: 30796268 PMCID: PMC6385340 DOI: 10.1038/s41598-019-38901-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/19/2018] [Indexed: 12/25/2022] Open
Abstract
Respiratory disease is a major cause of morbidity and mortality in patients with ataxia-telangiectasia (A-T) who are prone to recurrent sinopulmonary infections, bronchiectasis, pulmonary fibrosis, and pulmonary failure. Upper airway infections are common in patients and S. pneumoniae is associated with these infections. We demonstrate here that the upper airway microbiome in patients with A-T is different from that to healthy controls, with S. pneumoniae detected largely in patients only. Patient-specific airway epithelial cells and differentiated air-liquid interface cultures derived from these were hypersensitive to infection which was at least in part due to oxidative damage since it was partially reversed by catalase. We also observed increased levels of the pro-inflammatory cytokines IL-8 and TNF-α (inflammasome-independent) and a decreased level of the inflammasome-dependent cytokine IL-β in patient cells. Further investigation revealed that the ASC-Caspase 1 signalling pathway was defective in A-T airway epithelial cells. These data suggest that the heightened susceptibility of these cells to S. pneumoniae infection is due to both increased oxidative damage and a defect in inflammasome activation, and has implications for lung disease in these patients.
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155
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Yadav N, Patel V, Singh S. Cerium Oxide-Based Nanozymes in Biology and Medicine. SPRINGER PROCEEDINGS IN PHYSICS 2019. [DOI: 10.1007/978-981-15-0202-6_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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156
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Abstract
In this Review, we focus on catalytic antioxidant study based on transition metal complexes, organoselenium compounds, supramolecules and protein scaffolds.
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Affiliation(s)
- Riku Kubota
- Department of Applied Chemistry for Environment
- Tokyo Metropolitan University
- Hachioji
- Japan
| | - Shoichiro Asayama
- Department of Applied Chemistry for Environment
- Tokyo Metropolitan University
- Hachioji
- Japan
| | - Hiroyoshi Kawakami
- Department of Applied Chemistry for Environment
- Tokyo Metropolitan University
- Hachioji
- Japan
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157
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Thammavongsy Z, Mercer IP, Yang JY. Promoting proton coupled electron transfer in redox catalysts through molecular design. Chem Commun (Camb) 2019; 55:10342-10358. [DOI: 10.1039/c9cc05139b] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mini-review on using the secondary coordination sphere to facilitate multi-electron, multi-proton catalysis.
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Affiliation(s)
| | - Ian P. Mercer
- Department of Chemistry
- University of California
- Irvine
- USA
| | - Jenny Y. Yang
- Department of Chemistry
- University of California
- Irvine
- USA
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158
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Kumar A, Sil D, Usman M, Rath SP. A dimanganese(iii) porphyrin dication diradical and its transformation to a μ-hydroxo porphyrin–oxophlorin heterodimer. Chem Commun (Camb) 2019; 55:1588-1591. [DOI: 10.1039/c8cc09366k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spin coupling models are different between iron and manganese in their dication diradical complexes, which is reflected in their reactivity as shown.
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Affiliation(s)
- Amit Kumar
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur-208016
- India
| | - Debangsu Sil
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur-208016
- India
| | - Mohammad Usman
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur-208016
- India
| | - Sankar Prasad Rath
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur-208016
- India
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159
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Activation of catalase via co-administration of aspirin and pioglitazone: Experimental and MLSD simulation approaches. Biochimie 2019; 156:100-108. [DOI: 10.1016/j.biochi.2018.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/11/2018] [Indexed: 12/16/2022]
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160
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Shi Y, Zhang Y. Mechanisms of HNO Reactions with Ferric Heme Proteins. Angew Chem Int Ed Engl 2018; 57:16654-16658. [PMID: 30347123 PMCID: PMC6522253 DOI: 10.1002/anie.201807699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Indexed: 02/06/2023]
Abstract
Many HNO-scavenging pathways exist to regulate its biological and pharmacological activities. Such reactions often involve ferric heme proteins and form an important basis for HNO probe development. However, mechanisms of HNO reactions with ferric heme proteins are largely unknown. We performed a computational investigation using metmyoglobin and catalase as representative ferric heme proteins with neutral and negatively charged axial ligands to provide the first detailed pathways. The results reproduced experimental barriers well with an average error of 0.11 kcal mol-1 . The rate-limiting step was found to be dissociation of the resting ligand or HNO coordination when there is no resting ligand. For both heme proteins, in contrast to the non-heme case, the reductive nitrosylation step was found to be barrierless proton-coupled electron transfer, which provides the major thermodynamic driving force for the overall reaction. The origin of the difference in reactivity between metmyoglobin and catalase was also revealed.
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Affiliation(s)
- Yelu Shi
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken, NJ, 07030, USA
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken, NJ, 07030, USA
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161
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162
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Enzymatic analysis, structural study and molecular docking of laccase and catalase from B. subtilis SK1 after textile dye exposure. ECOL INFORM 2018. [DOI: 10.1016/j.ecoinf.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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163
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Shao L, Gao H, Liu Z, Feng J, Tang L, Lin H. Identification of Antioxidant Proteins With Deep Learning From Sequence Information. Front Pharmacol 2018; 9:1036. [PMID: 30294271 PMCID: PMC6158654 DOI: 10.3389/fphar.2018.01036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/27/2018] [Indexed: 01/26/2023] Open
Abstract
Antioxidant proteins have been found closely linked to disease control for its ability to eliminate excess free radicals. Because of its medicinal value, the study of identifying antioxidant proteins is on the upsurge. Many machine-learning classifiers have performed poorly owing to the nonlinear and unbalanced nature of biological data. Recently, deep learning techniques showed advantages over many state-of-the-art machine learning methods in various fields. In this study, a deep learning based classifier was proposed to identify antioxidant proteins based on mixed g-gap dipeptide composition feature vector. The classifier employed deep autoencoder to extract nonlinear representation from raw input. The t-Distributed Stochastic Neighbor Embedding (t-SNE) was used for dimensionality reduction. Support vector machine was finally performed for classification. The classifier achieved F 1 score of 0.8842 and MCC of 0.7409 in 10-fold cross validation. Experimental results show that our proposed method outperformed the traditional machine learning methods and could be a promising tool for antioxidant protein identification. For the convenience of others' scientific research, we have developed a user-friendly web server called IDAod for antioxidant protein identification, which can be accessed freely at http://bigroup.uestc.edu.cn/IDAod/.
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Affiliation(s)
- Lifen Shao
- Center for Informational Biology, School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Hui Gao
- Center for Informational Biology, School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhen Liu
- Center for Informational Biology, School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Juan Feng
- Key Laboratory for Neuro-Information of Ministry of Education, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lixia Tang
- Key Laboratory for Neuro-Information of Ministry of Education, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
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164
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Černý M, Habánová H, Berka M, Luklová M, Brzobohatý B. Hydrogen Peroxide: Its Role in Plant Biology and Crosstalk with Signalling Networks. Int J Mol Sci 2018; 19:E2812. [PMID: 30231521 PMCID: PMC6163176 DOI: 10.3390/ijms19092812] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/30/2022] Open
Abstract
Hydrogen peroxide (H₂O₂) is steadily gaining more attention in the field of molecular biology research. It is a major REDOX (reduction⁻oxidation reaction) metabolite and at high concentrations induces oxidative damage to biomolecules, which can culminate in cell death. However, at concentrations in the low nanomolar range, H₂O₂ acts as a signalling molecule and in many aspects, resembles phytohormones. Though its signalling network in plants is much less well characterized than are those of its counterparts in yeast or mammals, accumulating evidence indicates that the role of H₂O₂-mediated signalling in plant cells is possibly even more indispensable. In this review, we summarize hydrogen peroxide metabolism in plants, the sources and sinks of this compound and its transport via peroxiporins. We outline H₂O₂ perception, its direct and indirect effects and known targets in the transcriptional machinery. We focus on the role of H₂O₂ in plant growth and development and discuss the crosstalk between it and phytohormones. In addition to a literature review, we performed a meta-analysis of available transcriptomics data which provided further evidence for crosstalk between H₂O₂ and light, nutrient signalling, temperature stress, drought stress and hormonal pathways.
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Affiliation(s)
- Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Phytophthora Research Centre, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Hana Habánová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Brno Ph.D. Talent, South Moravian Centre for International Mobility, 602 00 Brno, Czech Republic.
| | - Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Markéta Luklová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Institute of Biophysics AS CR, 613 00 Brno, Czech Republic.
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165
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Neumann B, Götz R, Wrzolek P, Scheller FW, Weidinger IM, Schwalbe M, Wollenberger U. Enhancement of the Electrocatalytic Activity of Thienyl‐Substituted Iron Porphyrin Electropolymers by a Hangman Effect. ChemCatChem 2018. [DOI: 10.1002/cctc.201800934] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Bettina Neumann
- Institute for Biochemistry and BiologyUniversity Potsdam Karl-Liebknecht-Str. 24–25 Potsdam 14476 Germany
| | - Robert Götz
- Department of Chemistry and Food ChemistryTechnische Universität Dresden Zellescher Weg 19 Dresden 01069 Germany
| | - Pierre Wrzolek
- Institute for ChemistryHumboldt-Universität zu Berlin Brook-Taylor-Str. 2 Berlin 12489 Germany
| | - Frieder W. Scheller
- Institute for Biochemistry and BiologyUniversity Potsdam Karl-Liebknecht-Str. 24–25 Potsdam 14476 Germany
| | - Inez M. Weidinger
- Department of Chemistry and Food ChemistryTechnische Universität Dresden Zellescher Weg 19 Dresden 01069 Germany
| | - Matthias Schwalbe
- Institute for ChemistryHumboldt-Universität zu Berlin Brook-Taylor-Str. 2 Berlin 12489 Germany
| | - Ulla Wollenberger
- Institute for Biochemistry and BiologyUniversity Potsdam Karl-Liebknecht-Str. 24–25 Potsdam 14476 Germany
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166
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Pandit YA, Shah SJ, Rath SP. Unusual Stabilization of Dication Diradical Intermediate of Dizinc(II) Porphyrin Dimer. Z Anorg Allg Chem 2018. [DOI: 10.1002/zaac.201800247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Younis Ahmad Pandit
- Department of Chemistry; Indian Institute of Technology Kanpur; 208016 Kanpur India
| | - Syed Jehanger Shah
- Department of Chemistry; Indian Institute of Technology Kanpur; 208016 Kanpur India
| | - Sankar Prasad Rath
- Department of Chemistry; Indian Institute of Technology Kanpur; 208016 Kanpur India
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167
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Murali R, Gennis RB. Functional importance of Glutamate-445 and Glutamate-99 in proton-coupled electron transfer during oxygen reduction by cytochrome bd from Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:577-590. [PMID: 29719208 DOI: 10.1016/j.bbabio.2018.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/27/2022]
Abstract
The recent X-ray structure of the cytochrome bd respiratory oxygen reductase showed that two of the three heme components, heme d and heme b595, have glutamic acid as an axial ligand. No other native heme proteins are known to have glutamic acid axial ligands. In this work, site-directed mutagenesis is used to probe the roles of these glutamic acids, E445 and E99 in the E. coli enzyme. It is concluded that neither glutamate is a strong ligand to the heme Fe and they are not the major determinates of heme binding to the protein. Although very important, neither glutamate is absolutely essential for catalytic function. The close interactions between the three hemes in cyt bd result in highly cooperative properties. For example, mutation of E445, which is near heme d, has its greatest effects on the properties of heme b595 and heme b558. It is concluded that 1) O2 binds to the hydrophilic side of heme d and displaces E445; 2) E445 forms a salt bridge with R448 within the O2 binding pocket, and both residues play a role to stabilize oxygenated states of heme d during catalysis; 3) E445 and E99 are each protonated accompanying electron transfer to heme d and heme b595, respectively; 4) All protons used to generate water within the heme d active site come from the cytoplasm and are delivered through a channel that must include internal water molecules to assist proton transfer: [cytoplasm] → E107 → E99 (heme b595) → E445 (heme d) → oxygenated heme d.
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Affiliation(s)
- Ranjani Murali
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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168
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Li C, Liu Y, Fu Y, Huang T, Kang L, Li C. The antiproliferative activity of di-2-pyridylketone dithiocarbamate is partly attributed to catalase inhibition: detailing the interaction by spectroscopic methods. MOLECULAR BIOSYSTEMS 2018; 13:1817-1826. [PMID: 28714505 DOI: 10.1039/c7mb00032d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The bioactivity of drugs is attributed to their interaction with biological molecules, embodied in either their direct or indirect influence on enzyme activity and conformation. Di-2-pyridylketone hydrazine dithiocarbamate (DpdtC) exhibits significant antitumor activity in our preliminary study. We speculated that its activity may partly stem from enzyme inhibition due to strong metal chelating ability. To this end, we assessed its effect on catalase from erythrocytes and found evidence of inhibition, which was further confirmed by ROS determination in vivo. Thus, detailing the interaction between the agent and catalase via spectroscopic methods and molecular docking was required to obtain information on both the dynamics and thermodynamic parameters. The Lineweaver-Burk plot implied an uncompetitive pattern between DpdtC and catalase from beef liver, and IC50 = ∼7 μM. The thermodynamic parameters from fluorescence quenching measurements indicated that DpdtC could bind to catalase with moderate affinity (Ka = approximately 104 M-1). CD spectra revealed that DpdtC could significantly disrupt the secondary structure of catalase. Docking studies indicated that DpdtC bound to a flexible region of catalase, involving hydrogen bonds and salt bond; this was consistent with thermodynamic results from spectral investigations. Our data clearly showed that catalase inhibition of DpdtC was not due to direct chelation of iron from heme (killing), but through an allosteric effect. Thus, it can be concluded that the antiproliferative activity of DpdtC is partially attributed to its catalase inhibition.
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Affiliation(s)
- Cuiping Li
- Department of Molecular Biology & Biochemistry, Xinxiang Medical University, Xinxiang, Henan 453003, P. R. China.
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169
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Wang B, Fita I, Rovira C. Theory Uncovers the Role of the Methionine-Tyrosine-Tryptophan Radical Adduct in the Catalase Reaction of KatGs: O2
Release Mediated by Proton-Coupled Electron Transfer. Chemistry 2018; 24:5388-5395. [DOI: 10.1002/chem.201706076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Binju Wang
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB); Universitat de Barcelona; Martí i Franquès 1 08028 Barcelona Spain
| | - Ignacio Fita
- Instituto de Biología Molecular (IBMB-CSIC) and; Maria de Maeztu Unit of Excellence. Barcelona Science Park; Baldiri i Reixac 10. 08028 Barcelona Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB); Universitat de Barcelona; Martí i Franquès 1 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Passeig Lluís Companys 23 08010 Barcelona Spain
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170
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Wang L, Song X, Song L. The oyster immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 80:99-118. [PMID: 28587860 DOI: 10.1016/j.dci.2017.05.025] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/21/2017] [Accepted: 05/21/2017] [Indexed: 06/07/2023]
Abstract
Oysters, the common name for a number of different bivalve molluscs, are the worldwide aquaculture species and also play vital roles in the function of ecosystem. As invertebrate, oysters have evolved an integrated, highly complex innate immune system to recognize and eliminate various invaders via an array of orchestrated immune reactions, such as immune recognition, signal transduction, synthesis of antimicrobial peptides, as well as encapsulation and phagocytosis of the circulating haemocytes. The hematopoietic tissue, hematopoiesis, and the circulating haemocytes have been preliminary characterized, and the detailed annotation of the Pacific oyster Crassostrea gigas genome has revealed massive expansion and functional divergence of innate immune genes in this animal. Moreover, immune priming and maternal immune transfer are reported in oysters, suggesting the adaptability of invertebrate immunity. Apoptosis and autophagy are proved to be important immune mechanisms in oysters. This review will summarize the research progresses of immune system and the immunomodulation mechanisms of the primitive catecholaminergic, cholinergic, neuropeptides, GABAergic and nitric oxidase system, which possibly make oysters ideal model for studying the origin and evolution of immune system and the neuroendocrine-immune regulatory network in lower invertebrates.
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Affiliation(s)
- Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, DalianOcean University, Dalian 116023, China
| | - Xiaorui Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, DalianOcean University, Dalian 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, DalianOcean University, Dalian 116023, China.
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171
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Amperometric glucose sensing with polyaniline/poly(acrylic acid) composite film bearing glucose oxidase and catalase based on competitive oxygen consumption reactions. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.01.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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172
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Carocho M, Morales P, Ferreira IC. Antioxidants: Reviewing the chemistry, food applications, legislation and role as preservatives. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2017.11.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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173
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Kubota R, Takabe T, Arima K, Taniguchi H, Asayama S, Kawakami H. New class of artificial enzyme composed of Mn-porphyrin, imidazole, and cucurbit[10]uril toward use as a therapeutic antioxidant. J Mater Chem B 2018; 6:7050-7059. [DOI: 10.1039/c8tb01204k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this study, we investigated a new class of artificial enzymes composed of Mn-porphyrin, imidazole, and cucurbit[10]uril (CB[10]) toward therapeutic antioxidants.
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Affiliation(s)
- Riku Kubota
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Taiga Takabe
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Kohe Arima
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Hideaki Taniguchi
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Shoichiro Asayama
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
| | - Hiroyoshi Kawakami
- Department of Applied Chemistry
- Tokyo Metropolitan University
- Hachioji Tokyo
- Japan
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174
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Peciulyte A, Samuelsson L, Olsson L, McFarland KC, Frickmann J, Østergård L, Halvorsen R, Scott BR, Johansen KS. Redox processes acidify and decarboxylate steam-pretreated lignocellulosic biomass and are modulated by LPMO and catalase. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:165. [PMID: 29946356 PMCID: PMC6004669 DOI: 10.1186/s13068-018-1159-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/31/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND The bioconversion of lignocellulosic feedstocks to ethanol is being commercialised, but further process development is required to improve their economic feasibility. Efficient saccharification of lignocellulose to fermentable sugars requires oxidative cleavage of glycosidic linkages by lytic polysaccharide monooxygenases (LPMOs). However, a proper understanding of the catalytic mechanism of this enzyme class and the interaction with other redox processes associated with the saccharification of lignocellulose is still lacking. The in-use stability of LPMO-containing enzyme cocktails is increased by the addition of catalase implying that hydrogen peroxide (H2O2) is generated in the slurry during incubation. Therefore, we sought to characterize the effects of enzymatic and abiotic sources of H2O2 on lignocellulose hydrolysis to identify parameters that could improve this process. Moreover, we studied the abiotic redox reactions of steam-pretreated wheat straw as a function of temperature and dry-matter (DM) content. RESULTS Abiotic reactions in pretreated wheat straw consume oxygen, release carbon dioxide (CO2) to the slurry, and decrease the pH. The magnitude of these reactions increased with temperature and with DM content. The presence of LPMO during saccharification reduced the amount of CO2 liberated, while the effect on pH was insignificant. Catalase led to increased decarboxylation through an unknown mechanism. Both in situ-generated and added H2O2 caused a decrease in pH. CONCLUSIONS Abiotic redox processes similar to those that occur in natural water-logged environments also affect the saccharification of pretreated lignocellulose. Heating of the lignocellulosic material and adjustment of pH trigger rapid oxygen consumption and acidification of the slurry. In industrial settings, it will be of utmost importance to control these processes. LPMOs interact with the surrounding redox compounds and redirect abiotic electron flow from decarboxylating reactions to fuel the oxidative cleavage of glycosidic bonds in cellulose.
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Affiliation(s)
- Ausra Peciulyte
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Louise Samuelsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | | | - Jesper Frickmann
- Novozymes North America, 77 Perry’s Chapel Church Road, Franklinton, NC 27525 USA
| | | | | | | | - Katja S. Johansen
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
- Novozymes A/S, Krogshøjvej 36, 2880 Bagsværd, Denmark
- Department of Geosciences and Natural Resource Management, Copenhagen University, Rolighedsvej 23, 1958 Frederiksberg, Denmark
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175
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Mokhtari R, Rezaeifard A, Jafarpour M, Farrokhi A. Visible-light driven catalase-like activity of blackberry-shaped {Mo72Fe30} nanovesicles: combined kinetic and mechanistic studies. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00603b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Catalase-like activity of blackberry-shaped {Mo72Fe30} nanovesicles was exploited in aqueous solution under visible-light irradiation.
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Affiliation(s)
- Rezvan Mokhtari
- Catalysis Research Laboratory
- Department of Chemistry
- Faculty of Science
- University of Birjand
- Birjand
| | - Abdolreza Rezaeifard
- Catalysis Research Laboratory
- Department of Chemistry
- Faculty of Science
- University of Birjand
- Birjand
| | - Maasoumeh Jafarpour
- Catalysis Research Laboratory
- Department of Chemistry
- Faculty of Science
- University of Birjand
- Birjand
| | - Alireza Farrokhi
- Catalysis Research Laboratory
- Department of Chemistry
- Faculty of Science
- University of Birjand
- Birjand
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176
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Muzika F, Jurašek R, Schreiberová L, Radojković V, Schreiber I. Identifying the Oscillatory Mechanism of the Glucose Oxidase–Catalase Coupled Enzyme System. J Phys Chem A 2017; 121:7518-7523. [DOI: 10.1021/acs.jpca.7b08564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- František Muzika
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha 6, Czech Republic
| | - Radovan Jurašek
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha 6, Czech Republic
| | - Lenka Schreiberová
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha 6, Czech Republic
| | - Vuk Radojković
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha 6, Czech Republic
| | - Igor Schreiber
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha 6, Czech Republic
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177
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Rashtbari S, Dehghan G, Yekta R, Jouyban A. Investigation of the binding mechanism and inhibition of bovine liver catalase by quercetin: Multi-spectroscopic and computational study. ACTA ACUST UNITED AC 2017; 7:147-153. [PMID: 29159142 PMCID: PMC5684506 DOI: 10.15171/bi.2017.18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/01/2017] [Accepted: 07/08/2017] [Indexed: 11/09/2022]
Abstract
Introduction: The study on the side effects of various drugs and compounds on enzymes is a main issue for monitoring the conformational and functional changes of them. Quercetin (3,5,7,3',4'-pentahydroxyflavone, QUE), a polyphenolic flavonoid, widely found in fruits, vegetables and it is used as an ingredient in foods and beverages. The interaction of bovine liver catalase (BLC) with QUE has been studied in this research by using different spectroscopic methods. Methods: In this work, the interaction of QUE with BLC was investigated using different spectroscopic methods including ultraviolet-visible (UV-vis) absorption, circular dichroism (CD) and fluorescence spectroscopy and molecular docking studies. Results: Fluorescence data at different temperatures, synchronous fluorescence and CD studies revealed conformational changes in the BLC structure in the presence of different concentration of QUE. Also, the fluorescence quenching data showed that QUE can form a non-fluorescent complex with BLC and quench its intrinsic emission by a static process. The binding constant (Ka) for the interaction was 104, and the number of binding site was obtained ~1. The ∆H, ∆S and ∆G changes were obtained, indicating that hydrophobic interactions play a main role in the complex formation. In vitro kinetic studies revealed that QUE can inhibit BLC activity through non-competitive manner. Molecular docking study results were in good agreement with experimental data, confirming only one binding site on BLC for QUE at a cavity among the wrapping domain, threating arm and β-barrel. Conclusion: Inhibition of BLC activity upon interaction with QUE demonstrated that in addition to their beneficial effects, they should not be overlooked for their side effects.
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Affiliation(s)
- Samaneh Rashtbari
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Yekta
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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178
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Loco D, Lagardère L, Caprasecca S, Lipparini F, Mennucci B, Piquemal JP. Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding. J Chem Theory Comput 2017; 13:4025-4033. [DOI: 10.1021/acs.jctc.7b00572] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniele Loco
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Louis Lagardère
- UPMC Univ. Paris
06, Institut des Sciences du Calcul et des Données, F-75005, Paris, France
| | - Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Jean-Philip Piquemal
- UPMC Univ. Paris
06, UMR7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Institut Universitaire de France, Paris
Cedex 05, 75231, France
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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179
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Stress Responses, Adaptation, and Virulence of Bacterial Pathogens During Host Gastrointestinal Colonization. Microbiol Spectr 2017; 4. [PMID: 27227312 DOI: 10.1128/microbiolspec.vmbf-0007-2015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Invading pathogens are exposed to a multitude of harmful conditions imposed by the host gastrointestinal tract and immune system. Bacterial defenses against these physical and chemical stresses are pivotal for successful host colonization and pathogenesis. Enteric pathogens, which are encountered due to the ingestion of or contact with contaminated foods or materials, are highly successful at surviving harsh conditions to colonize and cause the onset of host illness and disease. Pathogens such as Campylobacter, Helicobacter, Salmonella, Listeria, and virulent strains of Escherichia have evolved elaborate defense mechanisms to adapt to the diverse range of stresses present along the gastrointestinal tract. Furthermore, these pathogens contain a multitude of defenses to help survive and escape from immune cells such as neutrophils and macrophages. This chapter focuses on characterized bacterial defenses against pH, osmotic, oxidative, and nitrosative stresses with emphasis on both the direct and indirect mechanisms that contribute to the survival of each respective stress response.
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180
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Majumder D, Das A, Saha C. Catalase inhibition an anti cancer property of flavonoids: A kinetic and structural evaluation. Int J Biol Macromol 2017; 104:929-935. [PMID: 28663152 DOI: 10.1016/j.ijbiomac.2017.06.100] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/23/2017] [Accepted: 06/24/2017] [Indexed: 11/15/2022]
Abstract
Flavonoids are dietary polyphenols that present abundantly in fruits and vegetables. Flavonoids have inhibitory effects on enzymes and catalase is one among them. Catalase is a common enzyme ubiquitously found in all living organisms exposed to oxygen. It catalyzes the decomposition of hydrogen peroxide to water and oxygen (2H2O2→2H2O+O2). Inhibition of pure and cellular catalase from K562 cells by flavonoids was similar and exhibited the following efficacy; Myrecetin>Quercetin>Kaempferol and Quercetin>Luteolin>Apigenin demonstrating structure activity relationship. Circular Dichroism (CD) spectra have shown distinct loss in α-helical structure of the catalase on interaction with the flavonoids. All flavonoids inhibited the catalase activity by uncompetitive mechanism. The Km and Vmax values of pure catalase were observed to be 294mM-1 and 0.222mM-1s-1 respectively and on inhibition with myrecetin the values decreased to a minimum of 23mM-1 and 0.014mM-1s-1 respectively. Inhibition of catalase will directly results in increased production of Reactive Oxygen Species (ROS) and pro-oxidant property of flavonoids. This inhibition was reversed in presence of Cu2+ ions because of the chelating affect of flavonoids.
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Affiliation(s)
- Debashis Majumder
- School of Biotechnology, Maulana Abul Kalam Institute of Technology, BF142, Salt lake, Kolkata 700064, India
| | - Asmita Das
- School of Biotechnology, Maulana Abul Kalam Institute of Technology, BF142, Salt lake, Kolkata 700064, India
| | - Chabita Saha
- School of Biotechnology, Maulana Abul Kalam Institute of Technology, BF142, Salt lake, Kolkata 700064, India.
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181
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David R, Jamet H, Nivière V, Moreau Y, Milet A. Iron Hydroperoxide Intermediate in Superoxide Reductase: Protonation or Dissociation First? MM Dynamics and QM/MM Metadynamics Study. J Chem Theory Comput 2017; 13:2987-3004. [DOI: 10.1021/acs.jctc.7b00126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rolf David
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/MCT, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Hélène Jamet
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
| | - Vincent Nivière
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/BioCat, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Yohann Moreau
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/MCT, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Anne Milet
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
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182
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183
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Wible RS, Sutter TR. Soft Cysteine Signaling Network: The Functional Significance of Cysteine in Protein Function and the Soft Acids/Bases Thiol Chemistry That Facilitates Cysteine Modification. Chem Res Toxicol 2017; 30:729-762. [DOI: 10.1021/acs.chemrestox.6b00428] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ryan S. Wible
- Department
of Chemistry, ‡Department of Biological Sciences, and §W. Harry Feinstone Center for Genomic
Research, University of Memphis, 3700 Walker Avenue, Memphis, Tennessee 38152-3370, United States
| | - Thomas R. Sutter
- Department
of Chemistry, ‡Department of Biological Sciences, and §W. Harry Feinstone Center for Genomic
Research, University of Memphis, 3700 Walker Avenue, Memphis, Tennessee 38152-3370, United States
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184
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Exploring the catalase activity of unspecific peroxygenases and the mechanism of peroxide-dependent heme destruction. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.10.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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185
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Mori G, Doniselli N, Faroldi F, Percudani R. Heme binding and peroxidase activity of a secreted minicatalase. FEBS Lett 2016; 590:4495-4506. [PMID: 27859138 DOI: 10.1002/1873-3468.12493] [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: 09/29/2016] [Revised: 10/29/2016] [Accepted: 11/07/2016] [Indexed: 11/10/2022]
Abstract
Microbial pathogens often require efficient and robust H2 O2 scavenger activities to survive in the presence of reactive oxygen species generated by inflammatory responses. In addition to catalases and peroxidases, enzymes known to scavenge H2 O2 , a novel class of secreted minicatalases is found in diderm bacteria. Here, we characterize the Helicobacter pylori (Hp) minicatalase: a monomeric hemoprotein with catalase core homology. Overexpression of Hp minicatalase rescued a catalase/peroxidase-deficient Escherichia coli phenotype under aerobic conditions and limited H2 O2 stress. The purified enzyme lacks catalase activity, but has strong (kcat > 100 s-1 ) H2 O2 -dependent peroxidase activity toward a variety of organic substrates. Our investigations into heme binding revealed that the heme cofactor is assembled in the periplasm to form the functional holoprotein. Furthermore, we observed the presence of a disulfide bond near the heme cavity of Hp minicatalase, which is conserved in secreted minicatalases and, therefore, may play a role in heme binding.
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Affiliation(s)
- Giulia Mori
- Department of Life Sciences, University of Parma, Italy
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186
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Kätelhön E, Sepunaru L, Karyakin AA, Compton RG. Can Nanoimpacts Detect Single-Enzyme Activity? Theoretical Considerations and an Experimental Study of Catalase Impacts. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02633] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Enno Kätelhön
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Lior Sepunaru
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Arkady A. Karyakin
- Chemistry
Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Richard G. Compton
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, United Kingdom
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187
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Flint A, Stintzi A, Saraiva LM. Oxidative and nitrosative stress defences of Helicobacter and Campylobacter species that counteract mammalian immunity. FEMS Microbiol Rev 2016; 40:938-960. [PMID: 28201757 PMCID: PMC5091033 DOI: 10.1093/femsre/fuw025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/29/2016] [Accepted: 07/02/2016] [Indexed: 12/18/2022] Open
Abstract
Helicobacter and Campylobacter species are Gram-negative microaerophilic host-associated heterotrophic bacteria that invade the digestive tract of humans and animals. Campylobacter jejuni is the major worldwide cause of foodborne gastroenteritis in humans, while Helicobacter pylori is ubiquitous in over half of the world's population causing gastric and duodenal ulcers. The colonisation of the gastrointestinal system by Helicobacter and Campylobacter relies on numerous cellular defences to sense the host environment and respond to adverse conditions, including those imposed by the host immunity. An important antimicrobial tool of the mammalian innate immune system is the generation of harmful oxidative and nitrosative stresses to which pathogens are exposed during phagocytosis. This review summarises the regulators, detoxifying enzymes and subversion mechanisms of Helicobacter and Campylobacter that ultimately promote the successful infection of humans.
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Affiliation(s)
- Annika Flint
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica, NOVA, Av. da República, 2780-157 Oeiras, Portugal
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188
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Barman P, Faponle AS, Vardhaman AK, Angelone D, Löhr AM, Browne WR, Comba P, Sastri CV, de Visser SP. Influence of Ligand Architecture in Tuning Reaction Bifurcation Pathways for Chlorite Oxidation by Non-Heme Iron Complexes. Inorg Chem 2016; 55:10170-10181. [PMID: 27704794 DOI: 10.1021/acs.inorgchem.6b01384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction bifurcation processes are often encountered in the oxidation of substrates by enzymes and generally lead to a mixture of products. One particular bifurcation process that is common in biology relates to electron transfer versus oxygen atom transfer by high-valent iron(IV)-oxo complexes, which nature uses for the oxidation of metabolites and drugs. In biomimicry and bioremediation, an important reaction relates to the detoxification of ClOx- in water, which can lead to a mixture of products through bifurcated reactions. Herein we report the first three water-soluble non-heme iron(II) complexes that can generate chlorine dioxide from chlorite at ambient temperature and physiological pH. These complexes are highly active oxygenation oxidants and convert ClO2- into either ClO2 or ClO3¯ via high-valent iron(IV)-oxo intermediates. We characterize the short-lived iron(IV)-oxo species and establish rate constants for the bifurcation mechanism leading to ClO2 and ClO3- products. We show that the ligand architecture of the metal center plays a dominant role by lowering the reduction potential of the metal center. Our experiments are supported by computational modeling, and a predictive valence bond model highlights the various factors relating to the substrate and oxidant that determine the bifurcation pathway and explains the origins of the product distributions. Our combined kinetic, spectroscopic, and computational studies reveal the key components necessary for the future development of efficient chlorite oxidation catalysts.
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Affiliation(s)
- Prasenjit Barman
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Anil Kumar Vardhaman
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Davide Angelone
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Anna-Maria Löhr
- Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Peter Comba
- Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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189
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Rindler PM, Cacciola A, Kinter M, Szweda LI. Catalase-dependent H2O2 consumption by cardiac mitochondria and redox-mediated loss in insulin signaling. Am J Physiol Heart Circ Physiol 2016; 311:H1091-H1096. [PMID: 27614223 DOI: 10.1152/ajpheart.00066.2016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 09/01/2016] [Indexed: 12/23/2022]
Abstract
We have recently demonstrated that catalase content in mouse cardiac mitochondria is selectively elevated in response to high dietary fat, a nutritional state associated with oxidative stress and loss in insulin signaling. Catalase and various isoforms of glutathione peroxidase and peroxiredoxin each catalyze the consumption of H2O2 Catalase, located primarily within peroxisomes and to a lesser extent mitochondria, has a low binding affinity for H2O2 relative to glutathione peroxidase and peroxiredoxin. As such, the contribution of catalase to mitochondrial H2O2 consumption is not well understood. In the current study, using highly purified cardiac mitochondria challenged with micromolar concentrations of H2O2, we found that catalase contributes significantly to mitochondrial H2O2 consumption. In addition, catalase is solely responsible for removal of H2O2 in nonrespiring or structurally disrupted mitochondria. Finally, in mice fed a high-fat diet, mitochondrial-derived H2O2 is responsible for diminished insulin signaling in the heart as evidenced by reduced insulin-stimulated Akt phosphorylation. While elevated mitochondrial catalase content (∼50%) enhanced the capacity of mitochondria to consume H2O2 in response to high dietary fat, the selective increase in catalase did not prevent H2O2-induced loss in cardiac insulin signaling. Taken together, our results indicate that mitochondrial catalase likely functions to preclude the formation of high levels of H2O2 without perturbing redox-dependent signaling.
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Affiliation(s)
- Paul M Rindler
- Affiliation: Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Angela Cacciola
- Affiliation: Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Michael Kinter
- Affiliation: Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Luke I Szweda
- Affiliation: Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
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190
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Dal S, Sigrist S. The Protective Effect of Antioxidants Consumption on Diabetes and Vascular Complications. Diseases 2016; 4:E24. [PMID: 28933404 PMCID: PMC5456287 DOI: 10.3390/diseases4030024] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/20/2016] [Accepted: 06/23/2016] [Indexed: 12/14/2022] Open
Abstract
Obesity and diabetes is generally accompanied by a chronic state of oxidative stress, disequilibrium in the redox balance, implicated in the development and progression of complications such as micro- and macro-angiopathies. Disorders in the inner layer of blood vessels, the endothelium, play an early and critical role in the development of these complications. Blunted endothelium-dependent relaxation and/or contractions are quietly associated to oxidative stress. Thus, preserving endothelial function and oxidative stress seems to be an optimization strategy in the prevention of vascular complications associated with diabetes. Diet is a major lifestyle factor that can greatly influence the incidence and the progression of type 2 diabetes and cardiovascular complications. The notion that foods not only provide basic nutrition but can also prevent diseases and ensure good health and longevity is now attained greater prominence. Some dietary and lifestyle modifications associated to antioxidative supply could be an effective prophylactic means to fight against oxidative stress in diabesity and complications. A significant benefit of phytochemicals (polyphenols in wine, grape, teas), vitamins (ascorbate, tocopherol), minerals (selenium, magnesium), and fruits and vegetables in foods is thought to be capable of scavenging free radicals, lowering the incidence of chronic diseases. In this review, we discuss the role of oxidative stress in diabetes and complications, highlight the endothelial dysfunction, and examine the impact of antioxidant foods, plants, fruits, and vegetables, currently used medication with antioxidant properties, in relation to the development and progression of diabetes and cardiovascular complications.
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Affiliation(s)
- Stéphanie Dal
- DIATHEC EA 7294 UMR Centre Européen d'Etude du Diabète (CeeD), Université de Strasbourg (UdS), boulevard René Leriche, Strasbourg 67200, France.
| | - Séverine Sigrist
- DIATHEC EA 7294 UMR Centre Européen d'Etude du Diabète (CeeD), Université de Strasbourg (UdS), boulevard René Leriche, Strasbourg 67200, France.
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191
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Sahoo D, Guchhait T, Rath SP. Spin Modulation in Highly Distorted FeIIIPorphyrinates by Using Axial Coordination and Their π-Cation Radicals. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600255] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dipankar Sahoo
- Department of Chemistry; Indian Institute of Technology Kanpur; 208016 Kanpur India
| | - Tapas Guchhait
- Department of Chemistry; Indian Institute of Technology Kanpur; 208016 Kanpur India
| | - Sankar Prasad Rath
- Department of Chemistry; Indian Institute of Technology Kanpur; 208016 Kanpur India
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192
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Duan Y, Qin L, Liu H. Different evolutionary pathways from B4 to B1 phase in AlN and InN: metadynamics investigations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:205403. [PMID: 27120439 DOI: 10.1088/0953-8984/28/20/205403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Pressure-induced B4-B1 phase transitions of AlN and InN at ambient temperature are systematically investigated using density functional-based metadynamics simulations. A homogeneous deformation path, which is energetically favorable, is through a hexagonal structure for AlN, and through a tetragonal structure for InN. Furthermore, the dynamical stability, instead of the mechanical stability, is crucial to determining the phase-transition paths: the intermediate hexagonal structure can remain stable, whereas the tetragonal structure is always unstable. The B4 phase always shows the direct band gap before the occurrence of structure transition, while the band gap of stable intermediate hexagonal phase is indirect for AlN. Finally, the band gap of the ultimate cubic phase is direct for AlN and indirect for InN, due to the strong p-d repulsion at the R point.
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Affiliation(s)
- Yifeng Duan
- Department of Physics, China University of Mining and Technology, Xuzhou 221116, People's Republic of China
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193
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Zhao Y, Nickels LM, Wang H, Ling J, Zhong Z, Zhu J. OxyR-regulated catalase activity is critical for oxidative stress resistance, nodulation and nitrogen fixation in Azorhizobium caulinodans. FEMS Microbiol Lett 2016; 363:fnw130. [PMID: 27190162 DOI: 10.1093/femsle/fnw130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2016] [Indexed: 11/13/2022] Open
Abstract
The legume-rhizobial interaction results in the formation of symbiotic nodules in which rhizobia fix nitrogen. During the process of symbiosis, reactive oxygen species (ROS) are generated. Thus, the response of rhizobia to ROS is important for successful nodulation and nitrogen fixation. In this study, we investigated how Azorhizobium caulinodans, a rhizobium that forms both root and stem nodules on its host plant, regulates ROS resistance. We found that in-frame deletions of a gene encoding the putative catalase-peroxidase katG or a gene encoding a LysR-family regulatory protein, oxyR, exhibited increased sensitivity to H2O2 We then showed that OxyR positively regulated katG expression in an H2O2-independent fashion. Furthermore, we found that deletion of katG or oxyR led to significant reduction in the number of stem nodules and decrease of nitrogen fixation capacities in symbiosis. Our results revealed that KatG and OxyR are not only critical for antioxidant defense in vitro, but also important for nodule formation and nitrogen fixation during interaction with plant hosts.
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Affiliation(s)
- Yue Zhao
- Department of Microbiology, College of Biological Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China 210095
| | - Logan M Nickels
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hui Wang
- Department of Microbiology, College of Biological Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China 210095
| | - Jun Ling
- Department of Microbiology, College of Biological Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China 210095
| | - Zengtao Zhong
- Department of Microbiology, College of Biological Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China 210095
| | - Jun Zhu
- Department of Microbiology, College of Biological Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China 210095 Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
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194
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de Visser SP, Stillman MJ. Challenging Density Functional Theory Calculations with Hemes and Porphyrins. Int J Mol Sci 2016; 17:519. [PMID: 27070578 PMCID: PMC4848975 DOI: 10.3390/ijms17040519] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 01/09/2023] Open
Abstract
In this paper we review recent advances in computational chemistry and specifically focus on the chemical description of heme proteins and synthetic porphyrins that act as both mimics of natural processes and technological uses. These are challenging biochemical systems involved in electron transfer as well as biocatalysis processes. In recent years computational tools have improved considerably and now can reproduce experimental spectroscopic and reactivity studies within a reasonable error margin (several kcal·mol(-1)). This paper gives recent examples from our groups, where we investigated heme and synthetic metal-porphyrin systems. The four case studies highlight how computational modelling can correctly reproduce experimental product distributions, predicted reactivity trends and guide interpretation of electronic structures of complex systems. The case studies focus on the calculations of a variety of spectroscopic features of porphyrins and show how computational modelling gives important insight that explains the experimental spectra and can lead to the design of porphyrins with tuned properties.
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Affiliation(s)
- Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, the University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada.
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195
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Quesne MG, Senthilnathan D, Singh D, Kumar D, Maldivi P, Sorokin AB, de Visser SP. Origin of the Enhanced Reactivity of μ-Nitrido-Bridged Diiron(IV)-Oxo Porphyrinoid Complexes over Cytochrome P450 Compound I. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02720] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Matthew G. Quesne
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Dhurairajan Senthilnathan
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- Center for
Computational Chemistry, CRD, PRIST University, Vallam, Thanjavur, Tamilnadu 613403, India
| | - Devendra Singh
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Devesh Kumar
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Pascale Maldivi
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- CEA, INAC-SCIB, F-38000 Grenoble, France
| | - Alexander B. Sorokin
- Institut
de Recherches sur la Catalyse et l’Environnement de Lyon (IRCELYON),
UMR 5256, CNRS-Université Lyon 1, 2, av. A. Einstein, 69626 Villeurbanne, France
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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196
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Sengupta K, Chatterjee S, Dey A. Catalytic H2O2 Disproportionation and Electrocatalytic O2 Reduction by a Functional Mimic of Heme Catalase: Direct Observation of Compound 0 and Compound I in Situ. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02668] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kushal Sengupta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Sudipta Chatterjee
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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197
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Quesne MG, Borowski T, de Visser SP. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs. Chemistry 2015; 22:2562-81. [PMID: 26696271 DOI: 10.1002/chem.201503802] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/08/2022]
Abstract
Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
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Affiliation(s)
- Matthew G Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland. .,Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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198
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Dey S, Sil D, Rath SP. A Highly Oxidized Cobalt Porphyrin Dimer: Spin Coupling and Stabilization of the Four-Electron Oxidation Product. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509430] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Soumyajit Dey
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur- 208016 India
| | - Debangsu Sil
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur- 208016 India
| | - Sankar Prasad Rath
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur- 208016 India
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199
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Dey S, Sil D, Rath SP. A Highly Oxidized Cobalt Porphyrin Dimer: Spin Coupling and Stabilization of the Four-Electron Oxidation Product. Angew Chem Int Ed Engl 2015; 55:996-1000. [DOI: 10.1002/anie.201509430] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Soumyajit Dey
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur- 208016 India
| | - Debangsu Sil
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur- 208016 India
| | - Sankar Prasad Rath
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur- 208016 India
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200
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Sil D, Dey S, Kumar A, Bhowmik S, Rath SP. Oxidation triggers extensive conjugation and unusual stabilization of two di-heme dication diradical intermediates: role of bridging group for electronic communication. Chem Sci 2015; 7:1212-1223. [PMID: 29910877 PMCID: PMC5975787 DOI: 10.1039/c5sc03120f] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/26/2015] [Indexed: 11/21/2022] Open
Abstract
Synthetic analogs of diheme enzyme MauG have been reported. Unlike the bis-Fe(iv) state in MauG, the 2e-oxidation stabilizes two ferric hemes, each coupled with a porphyrin π-cation radical.
MauG is a diheme enzyme that utilizes two covalently bound c-type hemes to catalyse the biosynthesis of the protein-derived cofactor tryptophan tryptophylquinone. The two hemes are physically separated by 14.5 Å and a hole-hopping mechanism is proposed in which a tryptophan residue located between the hemes undergoes reversible oxidation and reduction to increase the effective electronic coupling element and enhance the rate of reversible electron transfer between the hemes in bis-Fe(iv) MauG. The present work describes the structure and spectroscopic investigation of 2e-oxidations of the synthetic diheme analogs in which two heme centers are covalently connected through a conjugated ethylene bridge that leads to the stabilization of two unusual trans conformations (U and P′ forms) with different and distinct spectroscopic and geometric features. Unlike in MauG, where the two oxidizing equivalents are distributed within the diheme system giving rise to the bis-Fe(iv) redox state, the synthetic analog stabilizes two ferric hemes, each coupled with a porphyrin cation radical, a scenario resembling the binuclear dication diradical complex. Interestingly, charge resonance-transition phenomena are observed here both in 1e and 2e-oxidised species from the same system, which are also clearly distinguishable by their relative position and intensity. Detailed UV-vis-NIR, X-ray, Mössbauer, EPR and 1H NMR spectroscopic investigations as well as variable temperature magnetic studies have unraveled strong electronic communications between two porphyrin π-cation radicals through the bridging ethylene group. The extensive π-conjugation also allows antiferromagnetic coupling between iron(iii) centers and porphyrin radical spins of both rings. DFT calculations revealed extended π-conjugation and H-bonding interaction as the major factors in controlling the stability of the conformers.
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Affiliation(s)
- Debangsu Sil
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur-208016 , India . ;
| | - Soumyajit Dey
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur-208016 , India . ;
| | - Amit Kumar
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur-208016 , India . ;
| | - Susovan Bhowmik
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur-208016 , India . ;
| | - Sankar Prasad Rath
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur-208016 , India . ;
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