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Maranata GJ, Megantara S, Hasanah AN. An Update in Computational Methods for Environmental Monitoring: Theoretical Evaluation of the Molecular and Electronic Structures of Natural Pigment-Metal Complexes. Molecules 2024; 29:1680. [PMID: 38611959 PMCID: PMC11013237 DOI: 10.3390/molecules29071680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Metals are beneficial to life, but the presence of these elements in excessive amounts can harm both organisms and the environment; therefore, detecting the presence of metals is essential. Currently, metal detection methods employ powerful instrumental techniques that require a lot of time and money. Hence, the development of efficient and effective metal indicators is essential. Several synthetic metal detectors have been made, but due to their risk of harm, the use of natural pigments is considered a potential alternative. Experiments are needed for their development, but they are expensive and time-consuming. This review explores various computational methods and approaches that can be used to investigate metal-pigment interactions because choosing the right methods and approaches will affect the reliability of the results. The results show that quantum mechanical methods (ab initio, density functional theory, and semiempirical approaches) and molecular dynamics simulations have been used. Among the available methods, the density functional theory approach with the B3LYP functional and the LANL2DZ ECP and basis set is the most promising combination due to its good accuracy and cost-effectiveness. Various experimental studies were also in good agreement with the results of computational methods. However, deeper analysis still needs to be carried out to find the best combination of functions and basis sets.
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Affiliation(s)
- Gabriella Josephine Maranata
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM 21, 5, Jatinangor, Sumedang 45363, Indonesia (S.M.)
| | - Sandra Megantara
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM 21, 5, Jatinangor, Sumedang 45363, Indonesia (S.M.)
- Drug Development Study Centre, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Aliya Nur Hasanah
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM 21, 5, Jatinangor, Sumedang 45363, Indonesia (S.M.)
- Drug Development Study Centre, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
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2
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Yang D, Xu Y, Mo L, Shi M, Wu N, Lu L, Xue F, Xu Q, Zhang C. Enhancing l-Malic Acid Production in Aspergillus niger via Natural Activation of sthA Gene Expression. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4869-4879. [PMID: 38407053 DOI: 10.1021/acs.jafc.3c09321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The efficient production of l-malic acid using Aspergillus niger requires overcoming challenges in synthesis efficiency and excessive byproduct buildup. This study addresses these hurdles, improving the activity of NADH-dependent malate dehydrogenase (Mdh) in the early stages of the fermentation process. By employing a constitutive promoter to express the Escherichia coli sthA responsible for the transfer of reducing equivalents between NAD(H) and NADP(H) in A. niger, the l-malic acid production was significantly elevated. However, this resulted in conidiation defects of A. niger, limiting industrial viability. To mitigate this, we discovered and utilized the PmfsA promoter, enabling the specific expression of sthA during the fermentation stage. This conditional expression strain showed similar phenotypes to its parent strain while exhibiting exceptional performance in a 5 L fermenter. Notably, it achieved a 65.5% increase in productivity, reduced fermentation cycle by 1.5 days, and lowered succinic acid by 76.2%. This work marks a promising advancement in industrial l-malic acid synthesis via biological fermentation, showcasing the potential of synthetic biology in A. niger for broader applications.
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Affiliation(s)
- Dongdong Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Yingyan Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Li Mo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Man Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Na Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Ling Lu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Feng Xue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Qing Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Chi Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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3
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Li H, Jiang H, Huang Z, Chen Z, Chen N. Construction and validation of cuproptosis-related lncRNA prediction signature for bladder cancer and immune infiltration analysis. Aging (Albany NY) 2023; 15:8325-8344. [PMID: 37616061 PMCID: PMC10496989 DOI: 10.18632/aging.204972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023]
Abstract
Bladder cancer (BC) is a common urologic tumor with a high recurrence rate. Cuproptosis and long noncoding RNAs (lncRNAs) have demonstrated essential roles in the tumorigenesis of many malignancies. Nevertheless, the prognostic value of cuproptosis-related lncRNA (CRLs) in BC is still unclear. The public data used for this study were acquired from the Cancer Genome Atlas database. A comprehensive exploration of the expression profile, mutation, co-expression, and enrichment analyses of cuproptosis-related genes was performed. A total of 466 CRLs were identified using Pearson's correlation analysis. 16 prognostic CRLs were then retained by univariate Cox regression. Unsupervised clustering divided the patients into two clusters with diverse survival outcomes. The signature consists of 7 CRLs was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression analyses. Survival curves and receiver operating characteristics showed the prognostic signature possessed good predictive value, which was validated in the testing and entire sets. The reliability and stability of our signature were further confirmed by stratified analysis. Additionally, the signature-based risk score was confirmed as an independent prognostic factor. Gene set enrichment analysis showed molecular alteration in the high-risk group was closely associated with cancer. We then developed the clinical nomogram using independent prognostic indicators. Notably, the infiltration of immune cells and expression of immune checkpoints were higher in the high-risk group, suggesting that they may benefit more from immunotherapy. In summary, the prognostic signature might effectively predict the prognosis and provide new insight into the clinical treatment of BC patients.
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Affiliation(s)
- Hanrong Li
- Department of Extracorporeal Shock Wave Lithotripsy, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
| | - Huiming Jiang
- Department of Urology, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
| | - Zhicheng Huang
- Department of Urology, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
| | - Zhilin Chen
- Department of Urology, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
| | - Nanhui Chen
- Department of Urology, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
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4
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Wang D, Peng Y, Li Y, Kpegah JKSK, Chen S. Multifunctional inorganic biomaterials: New weapons targeting osteosarcoma. Front Mol Biosci 2023; 9:1105540. [PMID: 36660426 PMCID: PMC9846365 DOI: 10.3389/fmolb.2022.1105540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Osteosarcoma is the malignant tumor with the highest incidence rate among primary bone tumors and with a high mortality rate. The anti-osteosarcoma materials are the cross field between material science and medicine, having a wide range of application prospects. Among them, biological materials, such as compounds from black phosphorous, magnesium, zinc, copper, silver, etc., becoming highly valued in the biological materials field as well as in orthopedics due to their good biocompatibility, similar mechanical properties with biological bones, good biodegradation effect, and active antibacterial and anti-tumor effects. This article gives a comprehensive review of the research progress of anti-osteosarcoma biomaterials.
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Affiliation(s)
- Dong Wang
- Department of Spine Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shijie Chen,
| | - Yi Peng
- Department of Spine Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shijie Chen,
| | - Yuezhan Li
- Department of Spine Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,College of Medicine, Nursing and Health Science, School of Medicine, Regenerative Medicine Institute (REMEDI), University of Galway, Galway, Ireland,*Correspondence: Shijie Chen,
| | | | - Shijie Chen
- Department of Spine Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China,*Correspondence: Shijie Chen,
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5
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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6
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Gong B, Bai E, Feng X, Yi L, Wang Y, Chen X, Zhu X, Duan Y, Huang Y. Characterization of Chalkophomycin, a Copper(II) Metallophore with an Unprecedented Molecular Architecture. J Am Chem Soc 2021; 143:20579-20584. [PMID: 34851100 DOI: 10.1021/jacs.1c09311] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Metals play essential roles in life by coordination with small molecules, proteins, and nucleic acids. Although the coordination of copper ions in many proteins and methanobactins is known, the coordination chemistry of Cu(II) in natural products and their biological functions remain underexplored. Herein, we report the discovery of a Cu(II)-binding natural product, chalkophomycin (CHM, 1), from Streptomyces sp. CB00271, featuring an asymmetric square-coordination system of a bidentate diazeniumdiolate and a conjugated 1H-pyrrole 1-oxide-oxazoline. The structure of 1 may inspire the synthesis of Cu(II) chelators against neurodegenerative diseases or Cu(II)-based antitumor therapeutics.
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Affiliation(s)
- Bang Gong
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Enhe Bai
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Xueqiong Feng
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Liwei Yi
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Yeji Wang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Xin Chen
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, 410011, Changsha, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, 410011, Changsha, Hunan, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, 410011, Changsha, Hunan, China
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7
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Fernandes HS, Teixeira CSS, Sousa SF, Cerqueira NMFSA. Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:E2462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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Affiliation(s)
- Henrique S Fernandes
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
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8
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Yang X, Bennett B, Holz RC. Analyzing the function of the insert region found between the α and β-subunits in the eukaryotic nitrile hydratase from Monosiga brevicollis. Arch Biochem Biophys 2018; 657:1-7. [PMID: 30205086 PMCID: PMC6201762 DOI: 10.1016/j.abb.2018.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
The functional roles of the (His)17 region and an insert region in the eukaryotic nitrile hydratase (NHase, EC 4.2.1.84) from Monosiga brevicollis (MbNHase), were examined. Two deletion mutants, MbNHaseΔ238-257 and MbNHaseΔ219-272, were prepared in which the (His)17 sequence and the entire insert region were removed. Each of these MbNHase enzymes provided an α2β2 heterotetramer, identical to that observed for prokaryotic NHases and contains their full complement of cobalt ions. Deletion of the (His)17 motif provides an MbNHase enzyme that is ∼55% as active as the WT enzyme when expressed in the absence of the Co-type activator (ε) protein from Pseudonocardia thermophila JCM 3095 (PtNHaseact) but ∼28% more active when expressed in the presence of PtNHaseact. MbNHaseΔ219-272 exhibits ∼55% and ∼89% of WT activity, respectively, when expressed in the absence or presence of PtNHaseact. Proteolytic cleavage of MbNHase provides an α2β2 heterotetramer that is modestly more active compared to WT MbNHase (kcat = 163 ± 4 vs 131 ± 3 s-1). Combination of these data establish that neither the (His)17 nor the insert region are required for metallocentre assembly and maturation, suggesting that Co-type eukaryotic NHases utilize a different mechanism for metal ion incorporation and post-translational activation compared to prokaryotic NHases.
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Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI, 53201, USA
| | - Brian Bennett
- Department of Physics, Marquette University, PO Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Richard C Holz
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI, 53201, USA.
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A cobalt-containing eukaryotic nitrile hydratase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:107-112. [DOI: 10.1016/j.bbapap.2016.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/17/2016] [Accepted: 09/22/2016] [Indexed: 11/18/2022]
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10
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Halbwachs H, Simmel J, Bässler C. Tales and mysteries of fungal fruiting: How morphological and physiological traits affect a pileate lifestyle. FUNGAL BIOL REV 2016. [DOI: 10.1016/j.fbr.2016.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wang J, Han J, He D, Peng H, Xue Z, Xie X. Active, effective, and “green” iron( iii)/polar solvent catalysts for AGET ATRP of methyl methacrylate with various morphologies of elemental silver as a reducing agent. RSC Adv 2016. [DOI: 10.1039/c6ra20712j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
This article reports the AGET ATRP of MMA, with various morphologies of elemental silver as a reducing agent and an iron(iii)/polar solvent catalyst.
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Affiliation(s)
- Jirong Wang
- Key Laboratory for Material Chemistry of Energy Conversion and Storage
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Jianyu Han
- Key Laboratory for Material Chemistry of Energy Conversion and Storage
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Dan He
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education
- School of Chemical and Environmental Engineering
- Jianghan University
- Wuhan 430056
- China
| | - Haiyan Peng
- Key Laboratory for Material Chemistry of Energy Conversion and Storage
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Zhigang Xue
- Key Laboratory for Material Chemistry of Energy Conversion and Storage
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Xiaolin Xie
- Key Laboratory for Material Chemistry of Energy Conversion and Storage
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
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12
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Lin S, Zhang G, Liao Y, Gong D. The inhibitory kinetics and mechanism of dietary vitamins D3and B2on xanthine oxidase. Food Funct 2016; 7:2849-61. [DOI: 10.1039/c6fo00491a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dietary guidelines to promote health are usually based on the patterns’ prediction on disease risk of foods and nutrients.
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Affiliation(s)
- Suyun Lin
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Yijing Liao
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Deming Gong
- School of Biological Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
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13
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Abstract
This review describes the two main systems, namely the Isc (iron-sulfur cluster) and Suf (sulfur assimilation) systems, utilized by Escherichia coli and Salmonella for the biosynthesis of iron-sulfur (Fe-S) clusters, as well as other proteins presumably participating in this process. In the case of Fe-S cluster biosynthesis, it is assumed that the sulfur atoms from the cysteine desulfurase end up at cysteine residues of the scaffold protein, presumably waiting for iron atoms for cluster assembly. The review discusses the various potential iron donor proteins. For in vitro experiments, in general, ferrous salts are used during the assembly of Fe-S clusters, even though this approach is unlikely to reflect the physiological conditions. The fact that sulfur atoms can be directly transferred from cysteine desulfurases to scaffold proteins supports a mechanism in which the latter bind sulfur atoms first and iron atoms afterwards. In E. coli, fdx gene inactivation results in a reduced growth rate and reduced Fe-S enzyme activities. Interestingly, the SufE structure resembles that of IscU, strengthening the notion that the two proteins share the property of acting as acceptors of sulfur atoms provided by cysteine desulfurases. Several other factors have been suggested to participate in cluster assembly and repair in E. coli and Salmonella. Most of them were identified by their abilities to act as extragenic and/or multicopy suppressors of mutations in Fe-S cluster metabolism, while others possess biochemical properties that are consistent with a role in Fe-S cluster biogenesis.
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Abstract
This article reviews the preparation of polymers using iron-catalyzed atom transfer radical polymerization.
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Affiliation(s)
- Zhigang Xue
- Key Laboratory for Large-Format Battery Materials and Systems
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Dan He
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education
- School of Chemical and Environmental Engineering
- Jianghan University
- Wuhan 430056
- China
| | - Xiaolin Xie
- Key Laboratory for Large-Format Battery Materials and Systems
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
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15
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Furnholm TR, Tisa LS. The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. BMC Genomics 2014; 15:1092. [PMID: 25495525 PMCID: PMC4531530 DOI: 10.1186/1471-2164-15-1092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison. RESULTS Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia. CONCLUSIONS Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.
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Affiliation(s)
- Teal R Furnholm
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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16
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Kamei A, Watanabe Y, Kondo K, Okada S, Shinozaki F, Ishijima T, Nakai Y, Kondo T, Arai S, Abe K. Influence of a short-term iron-deficient diet on hepatic gene expression profiles in rats. PLoS One 2013; 8:e65732. [PMID: 23755274 PMCID: PMC3674005 DOI: 10.1371/journal.pone.0065732] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 04/27/2013] [Indexed: 11/19/2022] Open
Abstract
Iron is an essential mineral for the body, and iron deficiency generally leads to anemia. However, because non-anemic iron deficiency can exist, we performed a comprehensive transcriptome analysis of the liver to define the effects of this condition on the body. Four-week-old male rats were fed a low-iron diet (approximately 3 ppm iron) for 3 days and compared with those fed a normal diet (48 ppm iron) by pair feeding as a control. The rats in the iron-deficient diet group developed a non-anemic iron-deficient state. DNA microarray analysis revealed that during this short time, this state conferred a variety of effects on nutrient metabolism in the liver. In comparison with long-term (17 days) iron-deficiency data from a previous study, some of the changed genes were found to be common to both short- and long-term iron deficiency models, some were specific to the short-term iron deficiency model, and the others were oppositely regulated between the two feeding terms. Taken together, these data suggest that although the blood hemoglobin level itself remains unchanged during non-anemic iron deficiency, a variety of metabolic processes involved in the maintenance of the energy balance are altered.
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Affiliation(s)
- Asuka Kamei
- Project on Health and Anti-aging, Kanagawa Academy of Science and Technology Life Science & Environment Research Center 4F C-4, Kawasaki, Kanagawa, Japan
| | - Yuki Watanabe
- Project on Health and Anti-aging, Kanagawa Academy of Science and Technology Life Science & Environment Research Center 4F C-4, Kawasaki, Kanagawa, Japan
| | - Kaori Kondo
- Research Center for Allergy and Immunology, Institute of Physical and Chemical Research (RIKEN), Yokohama, Kanagawa, Japan
| | - Shinji Okada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Fumika Shinozaki
- Project on Health and Anti-aging, Kanagawa Academy of Science and Technology Life Science & Environment Research Center 4F C-4, Kawasaki, Kanagawa, Japan
| | - Tomoko Ishijima
- Project on Health and Anti-aging, Kanagawa Academy of Science and Technology Life Science & Environment Research Center 4F C-4, Kawasaki, Kanagawa, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuji Nakai
- Project on Health and Anti-aging, Kanagawa Academy of Science and Technology Life Science & Environment Research Center 4F C-4, Kawasaki, Kanagawa, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Kondo
- Research Center for Allergy and Immunology, Institute of Physical and Chemical Research (RIKEN), Yokohama, Kanagawa, Japan
| | - Soichi Arai
- Project on Health and Anti-aging, Kanagawa Academy of Science and Technology Life Science & Environment Research Center 4F C-4, Kawasaki, Kanagawa, Japan
- General Research Institute, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Keiko Abe
- Project on Health and Anti-aging, Kanagawa Academy of Science and Technology Life Science & Environment Research Center 4F C-4, Kawasaki, Kanagawa, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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17
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Heme incorporation into the cytochrome bo3 occurs at a late stage of assembly. FEBS Lett 2012; 586:4197-202. [PMID: 23089180 DOI: 10.1016/j.febslet.2012.10.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 10/10/2012] [Indexed: 11/22/2022]
Abstract
Respiratory complexes in both prokaryotes and eukaryotes contain multiple co-factors, which are coordinated in defined positions so that they can function as electron wires. Intriguingly, co-factors are usually buried deep within hetero-oligomeric protein complexes and it is not clear when or how they are incorporated. In this study we show that heme is incorporated into the cytochrome bo(3) complex of Escherichia coli at a late stage of assembly. Specifically the apo-form of subunit I (the catalytic subunit) interacts with subunits III and IV before accepting heme. Assembly of subunit II is stalled until heme is incorporated.
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18
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Coneyworth LJ, Jackson KA, Tyson J, Bosomworth HJ, van der Hagen E, Hann GM, Ogo OA, Swann DC, Mathers JC, Valentine RA, Ford D. Identification of the human zinc transcriptional regulatory element (ZTRE): a palindromic protein-binding DNA sequence responsible for zinc-induced transcriptional repression. J Biol Chem 2012; 287:36567-81. [PMID: 22902622 DOI: 10.1074/jbc.m112.397000] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Many genes with crucial roles in zinc homeostasis in mammals respond to fluctuating zinc supply through unknown mechanisms, and uncovering these mechanisms is essential to understanding the process at cellular and systemic levels. We detected zinc-dependent binding of a zinc-induced protein to a specific sequence, the zinc transcriptional regulatory element (ZTRE), in the SLC30A5 (zinc transporter ZnT5) promoter and showed that substitution of the ZTRE abrogated the repression of a reporter gene in response to zinc. We identified the ZTRE in other genes, including (through an unbiased search) the CBWD genes and (through targeted analysis) in multiple members of the SLC30 family, including SLC30A10, which is repressed by zinc. The function of the CBWD genes is currently unknown, but roles for homologs in metal homeostasis are being uncovered in bacteria. We demonstrated that CBWD genes are repressed by zinc and that substitution of the ZTRE in SLC30A10 and CBWD promoter-reporter constructs abrogates this response. Other metals did not affect expression of the transcriptional regulator, binding to the ZTRE or promoter-driven reporter gene expression. These findings provide the basis for elucidating how regulation of a network of genes through this novel mechanism contributes to zinc homeostasis and how the cell orchestrates this response.
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Affiliation(s)
- Lisa J Coneyworth
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4NN, United Kingdom
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19
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Remarkably fast and selective aromatization of Hantzsch esters with MoOCl4 and MoCl5: A chemical model for possible biologically relevant properties of molybdenum-containing enzymes. Bioorg Med Chem Lett 2012; 22:3676-81. [DOI: 10.1016/j.bmcl.2012.04.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 04/06/2012] [Accepted: 04/07/2012] [Indexed: 11/15/2022]
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20
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Zhang Y, Gladyshev VN. Comparative genomics of trace element dependence in biology. J Biol Chem 2011; 286:23623-9. [PMID: 21566146 DOI: 10.1074/jbc.r110.172833] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biological trace elements are needed in small quantities but are used by all living organisms. A growing list of trace element-dependent proteins and trace element utilization pathways highlights the importance of these elements for life. In this minireview, we focus on recent advances in comparative genomics of trace elements and explore the evolutionary dynamics of the dependence of user proteins on these elements. Many zinc protein families evolved representatives that lack this metal, whereas selenocysteine in proteins is dynamically exchanged with cysteine. Several other elements, such as molybdenum and nickel, have a limited number of user protein families, but they are strictly dependent on these metals. Comparative genomics of trace elements provides a foundation for investigating the fundamental properties, functions, and evolutionary dynamics of trace element dependence in biology.
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Affiliation(s)
- Yan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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GAPDH regulates cellular heme insertion into inducible nitric oxide synthase. Proc Natl Acad Sci U S A 2010; 107:18004-9. [PMID: 20921417 DOI: 10.1073/pnas.1008133107] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heme proteins play essential roles in biology, but little is known about heme transport inside mammalian cells or how heme is inserted into soluble proteins. We recently found that nitric oxide (NO) blocks cells from inserting heme into several proteins, including cytochrome P450s, hemoglobin, NO synthases, and catalase. This finding led us to explore the basis for NO inhibition and to identify cytosolic proteins that may be involved, using inducible NO synthase (iNOS) as a model target. Surprisingly, we found that GAPDH plays a key role. GAPDH was associated with iNOS in cells. Pure GAPDH bound tightly to heme or to iNOS in an NO-sensitive manner. GAPDH knockdown inhibited heme insertion into iNOS and a GAPDH mutant with defective heme binding acted as a dominant negative inhibitor of iNOS heme insertion. Exposing cells to NO either from a chemical donor or by iNOS induction caused GAPDH to become S-nitrosylated at Cys152. Expressing a GAPDH C152S mutant in cells or providing a drug to selectively block GAPDH S-nitrosylation both made heme insertion into iNOS resistant to the NO inhibition. We propose that GAPDH delivers heme to iNOS through a process that is regulated by its S-nitrosylation. Our findings may uncover a fundamental step in intracellular heme trafficking, and reveal a mechanism whereby NO can govern the process.
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22
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Cemek M, Büyükokuroğlu ME, Büyükben A, Aymelek F, Yilmaz F, Doğan M, Sanli F, Uner A, Yildirim D. Bio-element status in children with acute rheumatic fever: before treatment and after clinical improvement. Pediatr Cardiol 2010; 31:1002-7. [PMID: 20593282 DOI: 10.1007/s00246-010-9752-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 06/09/2010] [Indexed: 11/26/2022]
Abstract
Acute rheumatic fever (ARF) is an autoimmune multisystem disease. Bio-elements are required in different quantities by an organism to maintain its physiologic function. Monitoring the status of bio-elements is critical in human health. This study aimed to determine possible changes in levels of bio-elements in children with ARF before and after treatment. Levels of trace and major elements in children with ARF were investigated. The study included 33 children with ARF (17 boys and 16 girls) and 20 healthy control children (11 boys and 9 girls). The ages ranged from 5 to 16 years (mean 11.4 ± 3.82 years) in the study group and from 6 to 15 years (mean, 10.7 ± 3.22 years) in the control group. Trace and major element concentrations (total of 14 elements) in the serum were measured by inductively coupled plasma-optical emission spectroscopy. Before treatment, the levels of the major elements potassium (K) and magnesium (Mg) in children with ARF were higher than in the control group, whereas the calcium (Ca) level was lower. Before treatment, the levels of trace elements iron (Fe), selenium (Se), zinc (Zn), aluminum (Al), and barium (Ba) were lower, whereas the copper (Cu), beryllium (Be), cadmium (Cd), chromium (Cr), gallium (Ga), and strontium (Sr) levels were higher in the serum of the patients with ARF than in the control patients. The major findings show that the homeostasis of some trace and major elements were altered in the children with ARF and that these alterations may be a contributing factor in the pathogenesis of this disease.
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Affiliation(s)
- Mustafa Cemek
- Department of Chemistry, Biochemistry Division, Faculty of Sciences and Arts, Afyon Kocatepe University, Afyonkarahisar, Turkey.
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23
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Yatsyshyn VY, Fedorovych DV, Sibirny AА. Medium optimization for production of flavin mononucleotide by the recombinant strain of the yeast Candida famata using statistical designs. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2009.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Abstract
UNLABELLED Biological trace elements are required for numerous biological processes and by all organisms. We describe a database, dbTEU (DataBase of Trace Element Utilization), that features known transporters and user proteins for five trace elements (copper, molybdenum, nickel, cobalt and selenium) and represents sequenced organisms from the three domains of life. The manually curated dbTEU currently includes approximately 16,500 proteins from >700 organisms, and offers interactive trace element, protein, organism and sequence search and browse tools. AVAILABILITY AND IMPLEMENTATION dbTEU is freely available at http://gladyshevlab.bwh.harvard.edu/trace_element/
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Affiliation(s)
- Yan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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25
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Abstract
Iron-sulfur (Fe/S) proteins play crucial roles in living cells by participating in enzyme catalysis, electron transfer and the regulation of gene expression. The biosynthesis of the inorganic Fe/S centers and their insertion into apoproteins require complex cellular machinery located in the mitochondria (Fe/S cluster (ISC) assembly machinery systems) and cytosol (cytosolic Fe/S protein assembly (CIA) systems). Functional defects in Fe/S proteins or their biogenesis components lead to human diseases underscoring the functional importance of these inorganic cofactors for life. In this protocol, we describe currently available methods to follow the activity and de novo biogenesis of Fe/S proteins in eukaryotic cells. The assay systems are useful to follow Fe/S protein maturation in different cellular compartments, identify novel Fe/S proteins and their biogenesis factors, investigate the molecular mechanisms underlying the maturation process in vivo and analyze the effects of genetic mutations in Fe/S protein-related genes. Comprehensive analysis of one biogenesis component or target Fe/S protein takes about 10 d.
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Affiliation(s)
- Antonio J Pierik
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
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26
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Zhang Y, Gladyshev VN. Comparative Genomics of Trace Elements: Emerging Dynamic View of Trace Element Utilization and Function. Chem Rev 2009; 109:4828-61. [DOI: 10.1021/cr800557s] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yan Zhang
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Vadim N. Gladyshev
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
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27
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Ba LA, Doering M, Burkholz T, Jacob C. Metal trafficking: from maintaining the metal homeostasis to future drug design. Metallomics 2009; 1:292-311. [DOI: 10.1039/b904533c] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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28
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Nishino T, Okamoto K, Eger BT, Pai EF, Nishino T. Mammalian xanthine oxidoreductase - mechanism of transition from xanthine dehydrogenase to xanthine oxidase. FEBS J 2008; 275:3278-89. [PMID: 18513323 DOI: 10.1111/j.1742-4658.2008.06489.x] [Citation(s) in RCA: 249] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Reactive oxygen species are generated by various biological systems, including NADPH oxidases, xanthine oxidoreductase, and mitochondrial respiratory enzymes, and contribute to many physiological and pathological phenomena. Mammalian xanthine dehydrogenase (XDH) can be converted to xanthine oxidase (XO), which produces both superoxide anion and hydrogen peroxide. Recent X-ray crystallographic and site-directed mutagenesis studies have revealed a highly sophisticated mechanism of conversion from XDH to XO, suggesting that the conversion is not a simple artefact, but rather has a function in mammalian organisms. Furthermore, this transition seems to involve a thermodynamic equilibrium between XDH and XO; disulfide bond formation or proteolysis can then lock the enzyme in the XO form. In this review, we focus on recent advances in our understanding of the mechanism of conversion from XDH to XO.
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Affiliation(s)
- Tomoko Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
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29
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Marquet A, Bui BTS, Smith AG, Warren MJ. Iron–sulfur proteins as initiators of radical chemistry. Nat Prod Rep 2007; 24:1027-40. [PMID: 17898896 DOI: 10.1039/b703109m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-sulfur proteins are very versatile biological entities for which many new functions are continuously being unravelled. This review focus on their role in the initiation of radical chemistry, with special emphasis on radical-SAM enzymes, since several members of the family catalyse key steps in the biosynthetic pathways of cofactors such as biotin, lipoate, thiamine, heme and the molybdenum cofactor. It will also include other examples to show the chemical logic which is emerging from the presently available data on this family of enzymes. The common step in all the (quite different) reactions described here is the monoelectronic reductive cleavage of SAM by a reduced [4Fe-4S](1+) cluster, producing methionine and a highly oxidising deoxyadenosyl radical, which can initiate chemically difficult reactions. This set of enzymes, which represent a means to perform oxidation under reductive conditions, are often present in anaerobic organisms. Some other, non-SAM-dependent, radical reactions obeying the same chemical logic are also covered.
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Affiliation(s)
- Andrée Marquet
- Université Pierre et Marie Curie-Paris 6, CNRS UMR 7613, (Synthèse, Structure et Fonction de Molécules Bioactives), Paris, France.
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