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Mukherjee AJ, Zade SS, Singh HB, Sunoj RB. Organoselenium Chemistry: Role of Intramolecular Interactions. Chem Rev 2010; 110:4357-416. [PMID: 20384363 DOI: 10.1021/cr900352j] [Citation(s) in RCA: 390] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Anna J. Mukherjee
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India, and Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741252, Nadia, West Bengal, India
| | - Sanjio S. Zade
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India, and Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741252, Nadia, West Bengal, India
| | - Harkesh B. Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India, and Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741252, Nadia, West Bengal, India
| | - Raghavan B. Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India, and Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741252, Nadia, West Bengal, India
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52
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Chen Z, Li Q, Wang X, Wang Z, Zhang R, Yin M, Yin L, Xu K, Tang B. Potent Method for the Simultaneous Determination of Glutathione and Hydrogen Peroxide in Mitochondrial Compartments of Apoptotic Cells with Microchip Electrophoresis-Laser Induced Fluorescence. Anal Chem 2010; 82:2006-12. [DOI: 10.1021/ac902741r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Qingling Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Xu Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Zhiyuan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Ruirui Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Miao Yin
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Lingling Yin
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Kehua Xu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, and College of Life Sciences, Shandong Normal University, Jinan 250014, China
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53
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Dimastrogiovanni D, Anselmi M, Miele AE, Boumis G, Petersson L, Angelucci F, Nola AD, Brunori M, Bellelli A. Combining crystallography and molecular dynamics: The case ofSchistosoma mansoniphospholipid glutathione peroxidase. Proteins 2010; 78:259-70. [DOI: 10.1002/prot.22536] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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54
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Heverly-Coulson GS, Boyd RJ. Reduction of Hydrogen Peroxide by Glutathione Peroxidase Mimics: Reaction Mechanism and Energetics. J Phys Chem A 2009; 114:1996-2000. [DOI: 10.1021/jp910368u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
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55
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Bora RP, Ozbil M, Prabhakar R. Elucidation of insulin degrading enzyme catalyzed site specific hydrolytic cleavage of amyloid β peptide: a comparative density functional theory study. J Biol Inorg Chem 2009; 15:485-95. [DOI: 10.1007/s00775-009-0617-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 12/14/2009] [Indexed: 01/29/2023]
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56
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Rajapandian V, Hakkim V, Subramanian V. ONIOM Calculation on Azurin: Effect of Metal Ion Substitutions. J Phys Chem A 2009; 113:8615-25. [DOI: 10.1021/jp900451f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Hakkim
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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57
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Bayse CA, Antony S. Modeling the Oxidation of Ebselen and Other Organoselenium Compounds Using Explicit Solvent Networks. J Phys Chem A 2009; 113:5780-5. [DOI: 10.1021/jp901880n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Craig A. Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, Virginia 23529
| | - Sonia Antony
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, Virginia 23529
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58
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Margaritis I, Rousseau A, Marini J, Chopard A. Does antioxidant system adaptive response alleviate related oxidative damage with long term bed rest? Clin Biochem 2009; 42:371-9. [DOI: 10.1016/j.clinbiochem.2008.10.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 10/27/2008] [Accepted: 10/31/2008] [Indexed: 11/26/2022]
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59
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Singh R, Barman A, Prabhakar R. Computational Insights into Aspartyl Protease Activity of Presenilin 1 (PS1) Generating Alzheimer Amyloid β-Peptides (Aβ40 and Aβ42). J Phys Chem B 2009; 113:2990-9. [DOI: 10.1021/jp811154w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Rajiv Singh
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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60
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Bhabak KP, Mugesh G. A Synthetic Model for the Inhibition of Glutathione Peroxidase by Antiarthritic Gold Compounds. Inorg Chem 2009; 48:2449-55. [DOI: 10.1021/ic8019183] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Krishna P. Bhabak
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Govindasamy Mugesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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61
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The Oniom Method and its Applications to Enzymatic Reactions. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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62
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Melchers J, Diechtierow M, Fehér K, Sinning I, Tews I, Krauth-Siegel RL, Muhle-Goll C. Structural basis for a distinct catalytic mechanism in Trypanosoma brucei tryparedoxin peroxidase. J Biol Chem 2008; 283:30401-11. [PMID: 18684708 PMCID: PMC2662087 DOI: 10.1074/jbc.m803563200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 07/24/2008] [Indexed: 12/22/2022] Open
Abstract
Trypanosoma brucei, the causative agent of African sleeping sickness, encodes three cysteine homologues (Px I-III) of classical selenocysteine-containing glutathione peroxidases. The enzymes obtain their reducing equivalents from the unique trypanothione (bis(glutathionyl)spermidine)/tryparedoxin system. During catalysis, these tryparedoxin peroxidases cycle between an oxidized form with an intramolecular disulfide bond between Cys(47) and Cys(95) and the reduced peroxidase with both residues in the thiol state. Here we report on the three-dimensional structures of oxidized T. brucei Px III at 1.4A resolution obtained by x-ray crystallography and of both the oxidized and the reduced protein determined by NMR spectroscopy. Px III is a monomeric protein unlike the homologous poplar thioredoxin peroxidase (TxP). The structures of oxidized and reduced Px III are essentially identical in contrast to what was recently found for TxP. In Px III, Cys(47), Gln(82), and Trp(137) do not form the catalytic triad observed in the selenoenzymes, and related proteins and the latter two residues are unaffected by the redox state of the protein. The mutational analysis of three conserved lysine residues in the vicinity of the catalytic cysteines revealed that exchange of Lys(107) against glutamate abrogates the reduction of hydrogen peroxide, whereas Lys(97) and Lys(99) play a crucial role in the interaction with tryparedoxin.
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Affiliation(s)
- Johannes Melchers
- Department of Structure and Biocomputing, EMBL, 69117 Heidelberg, Germany
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63
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Li GZ, Liang XF, Yao W, Liao WQ, Zhu WF. Molecular characterization of glutathione peroxidase gene from the liver of silver carp, bighead carp and grass carp. BMB Rep 2008; 41:204-9. [DOI: 10.5483/bmbrep.2008.41.3.204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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64
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Wessjohann LA, Schneider A, Abbas M, Brandt W. Selenium in chemistry and biochemistry in comparison to sulfur. Biol Chem 2008; 388:997-1006. [PMID: 17937613 DOI: 10.1515/bc.2007.138] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
What makes selenoenzymes--seen from a chemist's view--so special that they cannot be substituted by just more analogous or adapted sulfur proteins? This review compiles and compares physicochemical properties of selenium and sulfur, synthetic routes to selenocysteine (Sec) and its peptides, and comparative studies of relevant thiols and selenols and their (mixed) dichalcogens, required to understand the special role of selenium in selenoproteins on the atomic molecular level. The biochemically most relevant differences are the higher polarizability of Se- and the lower pKa of SeH. The latter has a strikingly different pH-dependence than thiols, with selenols being active at much lower pH. Finally, selected typical enzymatic mechanisms which involve selenocysteine are critically discussed, also in view of the authors' own results.
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Affiliation(s)
- Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle/Saale, Germany.
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65
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Dechancie J, Clemente FR, Smith AJT, Gunaydin H, Zhao YL, Zhang X, Houk KN. How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design. Protein Sci 2007; 16:1851-66. [PMID: 17766382 PMCID: PMC2206971 DOI: 10.1110/ps.072963707] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Quantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate-determining transition state plus the catalytic groups modeled by side-chain mimics was optimized using B3LYP/6-31G(d) or, in one case, HF/3-21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X-ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate-active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64 A from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 A. The implications for computational enzyme design are discussed.
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Affiliation(s)
- Jason Dechancie
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
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66
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Bayse CA, Antony S. Molecular modeling of bioactive selenium compounds. MAIN GROUP CHEMISTRY 2007. [DOI: 10.1080/10241220801994700] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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67
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Bayse CA. DFT study of the glutathione peroxidase-like activity of phenylselenol incorporating solvent-assisted proton exchange. J Phys Chem A 2007; 111:9070-5. [PMID: 17718544 DOI: 10.1021/jp072297u] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modeling of the glutathione peroxidase-like activity of phenylselenol has been accomplished using density-functional theory and solvent-assisted proton exchange (SAPE). SAPE is a modeling technique intended to mimic solvent participation in proton transfer associated with chemical reaction. Within this method, explicit water molecules incorporated into the gas-phase model allow relay of a proton through the water molecules from the site of protonation in the reactant to that in the product. The activation barriers obtained by SAPE for the three steps of the GPx-like mechanism of PhSeH fall within the limits expected for a catalytic system at physiological temperatures (DeltaG(1)++ = 19.1 kcal/mol; DeltaG(2)++= 6.6 kcal/mol; G(3)++ = 21.7 kcal/mol) and are significantly lower than studies which require direct proton transfer. The size of the SAPE network is also considered for the model of the reduction of the selenenic acid, step 2 of the GPx-like cycle. Use of a four-water network better accommodates the reaction pathway and reduces the activation barrier by 5 kcal/mol over the two-water model.
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Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, Virginia 23529, USA
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68
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Koh CS, Didierjean C, Navrot N, Panjikar S, Mulliert G, Rouhier N, Jacquot JP, Aubry A, Shawkataly O, Corbier C. Crystal Structures of a Poplar Thioredoxin Peroxidase that Exhibits the Structure of Glutathione Peroxidases: Insights into Redox-driven Conformational Changes. J Mol Biol 2007; 370:512-29. [PMID: 17531267 DOI: 10.1016/j.jmb.2007.04.031] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 04/06/2007] [Accepted: 04/09/2007] [Indexed: 01/29/2023]
Abstract
Glutathione peroxidases (GPXs) are a group of enzymes that regulate the levels of reactive oxygen species in cells and tissues, and protect them against oxidative damage. Contrary to most of their counterparts in animal cells, the higher plant GPX homologues identified so far possess cysteine instead of selenocysteine in their active site. Interestingly, the plant GPXs are not dependent on glutathione but rather on thioredoxin as their in vitro electron donor. We have determined the crystal structures of the reduced and oxidized form of Populus trichocarpaxdeltoides GPX5 (PtGPX5), using a selenomethionine derivative. PtGPX5 exhibits an overall structure similar to that of the known animal GPXs. PtGPX5 crystallized in the assumed physiological dimeric form, displaying a pseudo ten-stranded beta sheet core. Comparison of both redox structures indicates that a drastic conformational change is necessary to bring the two distant cysteine residues together to form an intramolecular disulfide bond. In addition, a computer model of a complex of PtGPX5 and its in vitro recycling partner thioredoxin h1 is proposed on the basis of the crystal packing of the oxidized form enzyme. A possible role of PtGPX5 as a heavy-metal sink is also discussed.
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Affiliation(s)
- Cha San Koh
- LCM3B, Equipe Biocristallographie, UMR 7036 CNRS-UHP, Faculté des Sciences et Techniques, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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69
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70
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Soujanya Y, Narahari Sastry G. Theoretical elucidation of the antioxidant mechanism of 1,3-dihydro-1-methyl-2H-imidazole-2-selenol (MSeI). Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.01.131] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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71
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Navrot N, Collin V, Gualberto J, Gelhaye E, Hirasawa M, Rey P, Knaff DB, Issakidis E, Jacquot JP, Rouhier N. Plant glutathione peroxidases are functional peroxiredoxins distributed in several subcellular compartments and regulated during biotic and abiotic stresses. PLANT PHYSIOLOGY 2006; 142:1364-79. [PMID: 17071643 PMCID: PMC1676047 DOI: 10.1104/pp.106.089458] [Citation(s) in RCA: 227] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We provide here an exhaustive overview of the glutathione (GSH) peroxidase (Gpx) family of poplar (Populus trichocarpa). Although these proteins were initially defined as GSH dependent, in fact they use only reduced thioredoxin (Trx) for their regeneration and do not react with GSH or glutaredoxin, constituting a fifth class of peroxiredoxins. The two chloroplastic Gpxs display a marked selectivity toward their electron donors, being exclusively specific for Trxs of the y type for their reduction. In contrast, poplar Gpxs are much less specific with regard to their electron-accepting substrates, reducing hydrogen peroxide and more complex hydroperoxides equally well. Site-directed mutagenesis indicates that the catalytic mechanism and the Trx-mediated recycling process involve only two (cysteine [Cys]-107 and Cys-155) of the three conserved Cys, which form a disulfide bridge with an oxidation-redox midpoint potential of -295 mV. The reduction/formation of this disulfide is detected both by a shift on sodium dodecyl sulfate-polyacrylamide gel electrophoresis or by measuring the intrinsic tryptophan fluorescence of the protein. The six genes identified coding for Gpxs are expressed in various poplar organs, and two of them are localized in the chloroplast, with one colocalizing in mitochondria, suggesting a broad distribution of Gpxs in plant cells. The abundance of some Gpxs is modified in plants subjected to environmental constraints, generally increasing during fungal infection, water deficit, and metal stress, and decreasing during photooxidative stress, showing that Gpx proteins are involved in the response to both biotic and abiotic stress conditions.
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Affiliation(s)
- Nicolas Navrot
- Unité Mixte de Recherche Institut National de la Recherche Agronomique-Université Henri Poincaré 1136, Université Henri Poincaré, 54506 Vandoeuvre cedex, France
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72
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Prabhakar R, Morokuma K, Musaev DG. A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): Role of the active site cysteine-6 residue in the oxidative half-reaction. J Comput Chem 2006; 27:1438-45. [PMID: 16804959 DOI: 10.1002/jcc.20455] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the present DFT study, the catalytic mechanism of H2O2 formation in the oxidative half-reaction of NiSOD, E-Ni(II) + O2- + 2H+ --> E-Ni(III) + H2O2, has been investigated. The main objective of this study is to investigate the source of two protons required in this half-reaction. The proposed mechanism consists of two steps: superoxide coordination and H2O2 formation. The effect of protonation of Cys6 and the proton donating roles of side chains (S) and backbones (B) of His1, Asp3, Cys6, and Tyr9 residues in these two steps have been studied in detail. For protonated Cys6, superoxide binding generates a Ni(III)-O2H species in a process that is exothermic by 17.4 kcal/mol (in protein environment using the continuum model). From the Ni(III)-O2H species, H2O2 formation occurs through a proton donation by His1 via Tyr9, which relative to the resting position of the enzyme is exothermic by 4.9 kcal/mol. In this pathway, a proton donating role of His1 residue is proposed. However, for unprotonated Cys6, a Ni(II)-O2- species is generated in a process that is exothermic by 11.3 kcal/mol. From the Ni(II)-O2- species, the only feasible pathway for H2O2 formation is through donation of protons by the Tyr9(S)-Asp3(S) pair. The results discussed in this study elucidate the role of the active site residues in the catalytic cycle and provide intricate details of the complex functioning of this enzyme.
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Affiliation(s)
- Rajeev Prabhakar
- Cherry L. Emerson Center for Scientific Computation, and Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, Georgia 30322, USA
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73
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Sarma BK, Mugesh G. Biomimetic Studies on Selenoenzymes: Modeling the Role of Proximal Histidines in Thioredoxin Reductases. Inorg Chem 2006; 45:5307-14. [PMID: 16813393 DOI: 10.1021/ic052033r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The roles of built-in thiol cofactors and the basic histidine (His) residues in the active site of mammalian thioredoxin reductases (TrxRs) are described with the help of experimental and density functional theory calculations on small-molecule model compounds. The reduction of selenenyl sulfides by thiols in selenoenzymes such as glutathione peroxidase (GPx) and TrxR is crucial for the regeneration of the active site. Experimental as well as theoretical studies were carried out with model selenenyl sulfides to probe their reactivity toward incoming thiols. We have shown that the nucleophilic attack of thiols takes place at the selenium center in the selenenyl sulfides. These thiol exchange reactions would hamper the regeneration of the active species selenol. Therefore, the basic His residues are expected to play crucial roles in the selenenyl sulfide state of TrxR. Our model study with internal amino groups in the selenenyl sulfide state reveals that the basic His residues may play important roles by deprotonating the thiol moiety in the selenenic acid state and by interacting with the sulfur atom in the selenenyl sulfide state to facilitate the nucleophilic attack of thiol at sulfur rather than at selenium, thereby generating the catalytically active species selenol. This model study also suggests that the enzyme may use the internal cysteines as cofactors to overcome the thiol exchange reactions.
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Affiliation(s)
- Bani Kanta Sarma
- Department of Inorganic & Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
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Prabhakar R, Vreven T, Frisch MJ, Morokuma K, Musaev DG. Is the Protein Surrounding the Active Site Critical for Hydrogen Peroxide Reduction by Selenoprotein Glutathione Peroxidase? An ONIOM Study. J Phys Chem B 2006; 110:13608-13. [PMID: 16821888 DOI: 10.1021/jp0619181] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this ONIOM(QM:MM) study, we evaluate the role of the protein surroundings in the mechanism of H2O2 reduction catalyzed by the glutathione peroxidase enzyme, using the whole monomer (3113 atoms in 196 amino acid residues) as a model. A new optimization scheme that allows the full optimization of transition states for large systems has been utilized. It was found that in the presence of the surrounding protein the optimized active site structure bears a closer resemblance to the one in the X-ray structure than that without the surrounding protein. H2O2 reduction occurs through a two-step mechanism. In the first step, the selenolate anion (E-Se(-)) formation occurs with a barrier of 16.4 kcal/mol and is endothermic by 12.0 kcal/mol. The Gln83 residue plays the key role of the proton abstractor, which is in line with the experimental suggestion. In the second step, the O-O bond is cleaved, and selenenic acid (R-Se-OH) and a water molecule are formed. The calculated barrier for this process is 6.0 kcal/mol, and it is exothermic by 80.9 kcal/mol. The overall barrier of 18.0 kcal/mol for H2O2 reduction is in reasonable agreement with the experimentally measured barrier of 14.9 kcal/mol. The protein surroundings has been calculated to exert a net effect of only 0.70 kcal/mol (in comparison to the "active site only" model including solvent effects) on the overall barrier, which is most likely due to the active site being located at the enzyme surface.
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Affiliation(s)
- Rajeev Prabhakar
- Cherry Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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75
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