101
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Adhikari BR, Schraft H, Chen A. A high-performance enzyme entrapment platform facilitated by a cationic polymer for the efficient electrochemical sensing of ethanol. Analyst 2017; 142:2595-2602. [DOI: 10.1039/c7an00594f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient enzyme entrapment approach using a cationic polymer has been demonstrated for the development of a high-performance ethanol biosensor.
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Affiliation(s)
| | - Heidi Schraft
- Department of Biology
- Lakehead University
- Thunder Bay
- Canada
| | - Aicheng Chen
- Department of Chemistry
- Lakehead University
- Thunder Bay
- Canada
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102
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In vivo cytotoxicity, molecular docking and study of yeast alcohol dehydrogenase on polycarbazole-titanium dioxide nanocomposite. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.09.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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103
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Bhuiya S, Haque L, Pradhan AB, Das S. Inhibitory effects of the dietary flavonoid quercetin on the enzyme activity of zinc(II)-dependent yeast alcohol dehydrogenase: Spectroscopic and molecular docking studies. Int J Biol Macromol 2016; 95:177-184. [PMID: 27864057 DOI: 10.1016/j.ijbiomac.2016.11.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 12/01/2022]
Abstract
A multispectroscopic exploration was employed to investigate the interaction between the metallo-enzyme alcohol dehydrogenase (ADH) from yeast with bioflavonoid quercetin (QTN). Here, we have characterized the complex formation between QTN and Zn2+ in aqueous solution and then examined the effect of such complex formation on the enzymatic activity of a zinc(II)-dependent enzyme alcohol dehydrogenase from yeast. We have observed an inhibition of enzymatic activity of ADH in presence of QTN. Enzyme inhibition kinetic experiments revealed QTN as a non-competitive inhibitor of yeast ADH. Perturbation of Circular dichroic (CD) spectrum of ADH in presence of QTN is observed due to the structural changes of ADH on complexation with the above flavonoid. Our results indicate a conformational change of ADH due to removal of Zn2+ present in the enzyme by QTN. This was further established by molecular modeling study which shows that the flavonoid binds to the Zn2+ ion which maintains the tertiary structure of the metallo-enzyme. So, QTN abstracts only half of the Zn2+ ions present in the enzyme i.e. one Zn2+ ion per monomer. From the present study, the structural alteration and loss of enzymatic activity of ADH are attributed to the complex formation between QTN and Zn2+.
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Affiliation(s)
- Sutanwi Bhuiya
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Ankur Bikash Pradhan
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Suman Das
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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104
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Pfannebecker J, Schiffer-Hetz C, Fröhlich J, Becker B. Culture medium optimization for osmotolerant yeasts by use of a parallel fermenter system and rapid microbiological testing. J Microbiol Methods 2016; 130:14-22. [DOI: 10.1016/j.mimet.2016.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/18/2016] [Accepted: 08/20/2016] [Indexed: 12/25/2022]
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105
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Rodacka A, Gerszon J, Puchala M, Bartosz G. Radiation-induced inactivation of enzymes – Molecular mechanism based on inactivation of dehydrogenases. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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106
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Rasool A, Ahmed MS, Li C. Overproduction of squalene synergistically downregulates ethanol production in Saccharomyces cerevisiae. Chem Eng Sci 2016. [DOI: 10.1016/j.ces.2016.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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107
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Cheng C, Zhang M, Xue C, Bai F, Zhao X. Development of stress tolerant Saccharomyces cerevisiae strains by metabolic engineering: New aspects from cell flocculation and zinc supplementation. J Biosci Bioeng 2016; 123:141-146. [PMID: 27576171 DOI: 10.1016/j.jbiosc.2016.07.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/29/2016] [Indexed: 10/21/2022]
Abstract
Budding yeast Saccharomyces cerevisiae is widely studied for the production of biofuels from lignocellulosic biomass. However, economic production is currently challenged by the repression of cell growth and compromised fermentation performance of S. cerevisiae strains in the presence of various environmental stresses, including toxic level of final products, inhibitory compounds released from the pretreatment of cellulosic feedstocks, high temperature, and so on. Therefore, it is important to improve stress tolerance of S. cerevisiae to these stressful conditions to achieve efficient and economic production. In this review, the latest advances on development of stress tolerant S. cerevisiae strains are summarized, with the emphasis on the impact of cell flocculation and zinc addition. It was found that cell flocculation affected ethanol tolerance and acetic acid tolerance of S. cerevisiae, and addition of zinc to a suitable level improved stress tolerance of yeast cells to ethanol, high temperature and acetic acid. Further studies on the underlying mechanisms by which cell flocculation and zinc status affect stress tolerance will not only enrich our knowledge on stress response and tolerance mechanisms of S. cerevisiae, but also provide novel metabolic engineering strategies to develop robust yeast strains for biofuels production.
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Affiliation(s)
- Cheng Cheng
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Mingming Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Chuang Xue
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Fengwu Bai
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China; State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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108
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Östberg LJ, Persson B, Höög JO. Computational studies of human class V alcohol dehydrogenase - the odd sibling. BMC BIOCHEMISTRY 2016; 17:16. [PMID: 27455956 PMCID: PMC4960878 DOI: 10.1186/s12858-016-0072-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/12/2016] [Indexed: 02/25/2023]
Abstract
Background All known attempts to isolate and characterize mammalian class V alcohol dehydrogenase (class V ADH), a member of the large ADH protein family, at the protein level have failed. This indicates that the class V ADH protein is not stable in a non-cellular environment, which is in contrast to all other human ADH enzymes. In this report we present evidence, supported with results from computational analyses performed in combination with earlier in vitro studies, why this ADH behaves in an atypical way. Results Using a combination of structural calculations and sequence analyses, we were able to identify local structural differences between human class V ADH and other human ADHs, including an elongated β-strands and a labile α-helix at the subunit interface region of each chain that probably disturb it. Several amino acid residues are strictly conserved in class I–IV, but altered in class V ADH. This includes a for class V ADH unique and conserved Lys51, a position directly involved in the catalytic mechanism in other ADHs, and nine other class V ADH-specific residues. Conclusions In this study we show that there are pronounced structural changes in class V ADH as compared to other ADH enzymes. Furthermore, there is an evolutionary pressure among the mammalian class V ADHs, which for most proteins indicate that they fulfill a physiological function. We assume that class V ADH is expressed, but unable to form active dimers in a non-cellular environment, and is an atypical mammalian ADH. This is compatible with previous experimental characterization and present structural modelling. It can be considered the odd sibling of the ADH protein family and so far seems to be a pseudoenzyme with another hitherto unknown physiological function. Electronic supplementary material The online version of this article (doi:10.1186/s12858-016-0072-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Linus J Östberg
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Bengt Persson
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jan-Olov Höög
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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109
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Wilcox AE, LoConte MA, Slade KM. Effects of Macromolecular Crowding on Alcohol Dehydrogenase Activity Are Substrate-Dependent. Biochemistry 2016; 55:3550-8. [PMID: 27283046 DOI: 10.1021/acs.biochem.6b00257] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymes operate in a densely packed cellular environment that rarely matches the dilute conditions under which they are studied. To better understand the ramifications of this crowding, the Michaelis-Menten kinetics of yeast alcohol dehydrogenase (YADH) were monitored spectrophotometrically in the presence of high concentrations of dextran. Crowding decreased the maximal rate of the reaction by 40% for assays with ethanol, the primary substrate of YADH. This observation was attributed to slowed release of the reduced β-nicotinamide adenine dinucleotide product, which is rate-limiting. In contrast, when larger alcohols were used as the YADH substrate, the rate-limiting step becomes hydride transfer and crowding instead increased the maximal rate of the reaction by 20-40%. This work reveals the importance of considering enzyme mechanism when evaluating the ways in which crowding can alter kinetics.
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Affiliation(s)
- A E Wilcox
- Department of Chemistry, Hobart and William Smith Colleges , Geneva, New York 14456, United States
| | - Micaela A LoConte
- Department of Chemistry, Hobart and William Smith Colleges , Geneva, New York 14456, United States
| | - Kristin M Slade
- Department of Chemistry, Hobart and William Smith Colleges , Geneva, New York 14456, United States
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110
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Lebrun V, Ravanat JL, Latour JM, Sénèque O. Near diffusion-controlled reaction of a Zn(Cys) 4 zinc finger with hypochlorous acid. Chem Sci 2016; 7:5508-5516. [PMID: 30034691 PMCID: PMC6021785 DOI: 10.1039/c6sc00974c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/14/2016] [Indexed: 11/22/2022] Open
Abstract
Reaction rate constants of HOCl with zinc-bound cysteines are determined, demonstrating that zinc fingers are potent targets for HOCl and may serve as HOCl sensors.
Hypochlorous acid (HOCl) is one of the strongest oxidants produced in mammals to kill invading microorganisms. The bacterial response to HOCl involves proteins that are able to sense HOCl using methionine, free cysteines or zinc-bound cysteines of zinc finger sites. Although the reactivity of methionine or free cysteine with HOCl is well documented at the molecular level, this is not the case for zinc-bound cysteines. We present here a study that aims at filling this gap. Using a model peptide of the Zn(Cys)4 zinc finger site of the chaperone Hsp33, a protein involved in the defence against HOCl in bacteria, we show that HOCl oxidation of this model leads to the formation of two disulfides. A detailed mechanistic and kinetic study of this reaction, relying on stopped-flow measurements and competitive oxidation with methionine, reveals very high rate constants: the absolute second-order rate constants for the reaction of the model zinc finger with HOCl and its conjugated base ClO– are (9.3 ± 0.8) × 108 M–1 s–1 and (1.2 ± 0.2) × 104 M–1 s–1, the former approaching the diffusion limit. Revised values of the second-order rate constants for the reaction of methionine with HOCl and ClO– were also determined to be (5.5 ± 0.8) × 108 M–1 s–1 and (7 ± 5) × 102 M–1 s–1, respectively. At physiological pH, the zinc finger site reacts faster with HOCl than methionine and glutathione or cysteine. This study demonstrates that zinc fingers are potent targets for HOCl and confirms that they may serve as HOCl sensors as proposed for Hsp33.
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Affiliation(s)
- Vincent Lebrun
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France . ;
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes , INAC-SyMMES , F-38000 Grenoble , France.,CEA , INAC-SyMMES , F-38000 Grenoble , France
| | - Jean-Marc Latour
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France . ;
| | - Olivier Sénèque
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France . ;
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111
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Lederer F, Vignaud C, North P, Bodevin S. Trifluorosubstrates as mechanistic probes for an FMN-dependent l-2-hydroxy acid-oxidizing enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1215-1221. [PMID: 27155230 DOI: 10.1016/j.bbapap.2016.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/17/2016] [Accepted: 05/03/2016] [Indexed: 11/29/2022]
Abstract
A controversy exists with respect to the mechanism of l-2-hydroxy acid oxidation by members of a family of FMN-dependent enzymes. A so-called carbanion mechanism was initially proposed, in which the active site histidine abstracts the substrate α-hydrogen as a proton, followed by electron transfer from the carbanion to the flavin. But an alternative mechanism was not incompatible with some results, a mechanism in which the active site histidine instead picks up the substrate hydroxyl proton and a hydride transfer occurs. Even though more recent experiments ruling out such a mechanism were published (Rao & Lederer (1999) Protein Science 7, 1531-1537), a few authors have subsequently interpreted their results with variant enzymes in terms of a hydride transfer. In the present work, we analyse the reactivity of trifluorolactate, a substrate analogue, with the flavocytochrome b2 (Fcb2) flavodehydrogenase domain, compared to its reactivity with an NAD-dependent lactate dehydrogenase (LDH), for which this compound is known to be an inhibitor (Pogolotti & Rupley (1973) Biochem. Biophys. Res. Commun, 55, 1214-1219). Indeed, electron attraction by the three fluorine atoms should make difficult the removal of the α-H as a hydride. We also analyse the reactivity of trifluoropyruvate with the FMN- and NAD-dependent enzymes. The results substantiate a different effect of the fluorine substituents on the two enzymes compared to their normal substrates. In the discussion we analyse the conclusions of recent papers advocating a hydride transfer mechanism for the family of l-2-hydroxy acid oxidizing FMN-dependent enzymes.
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Affiliation(s)
- Florence Lederer
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France; Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
| | - Caroline Vignaud
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Paul North
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Sabrina Bodevin
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
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112
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Varga MJ, Schwartz SD. Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations. J Chem Theory Comput 2016; 12:2047-54. [PMID: 26949835 DOI: 10.1021/acs.jctc.5b01169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems.
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Affiliation(s)
- Matthew J Varga
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
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113
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Plapp BV, Charlier HA, Ramaswamy S. Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol. Arch Biochem Biophys 2016; 591:35-42. [PMID: 26743849 DOI: 10.1016/j.abb.2015.12.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 11/27/2022]
Abstract
Yeast alcohol dehydrogenase I is a homotetramer of subunits with 347 amino acid residues, catalyzing the oxidation of alcohols using NAD(+) as coenzyme. A new X-ray structure was determined at 3.0 Å where both subunits of an asymmetric dimer bind coenzyme and trifluoroethanol. The tetramer is a pair of back-to-back dimers. Subunit A has a closed conformation and can represent a Michaelis complex with an appropriate geometry for hydride transfer between coenzyme and alcohol, with the oxygen of 2,2,2-trifluoroethanol ligated at 2.1 Å to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. Subunit B has an open conformation, and the coenzyme interacts with amino acid residues from the coenzyme binding domain, but not with residues from the catalytic domain. Coenzyme appears to bind to and dissociate from the open conformation. The catalytic zinc in subunit B has an alternative, inverted coordination with Cys-43, Cys-153, His-66 and the carboxylate of Glu-67, while the oxygen of trifluoroethanol is 3.5 Å from the zinc. Subunit B may represent an intermediate in the mechanism after coenzyme and alcohol bind and before the conformation changes to the closed form and the alcohol oxygen binds to the zinc and displaces Glu-67.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA.
| | - Henry A Charlier
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA.
| | - S Ramaswamy
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA.
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114
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Rodacka A. The effect of radiation-induced reactive oxygen species (ROS) on the structural and functional properties of yeast alcohol dehydrogenase (YADH). Int J Radiat Biol 2015; 92:11-23. [DOI: 10.3109/09553002.2015.1106022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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115
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Choi H, Kim HJ, Matsuura A, Mikami B, Yoon HJ, Lee HH. Structural and functional studies of a metallo-β-lactamase unveil a new type of structurally encoded nickel-containing heterodinuclear site. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2054-65. [PMID: 26457429 DOI: 10.1107/s1399004715014807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 08/06/2015] [Indexed: 11/10/2022]
Abstract
The selection of correct metal ions with high fidelity against competing cellular cations is crucial for the function of many metalloenzymes; however, the understanding of the principles that govern metal selectivity is still incomplete. In this study, the crystal structure of the Tm1162 protein from Thermotoga maritima, a metallo-β-lactamase, is reported. Several crystal structures of wild-type Tm1162 and its mutants were solved. Homologues of Tm1162 are widely distributed in bacteria and archaea, including several human pathogens. The monomer possesses an αβ/βα fold, with the core β-strands having the β-sheet sandwich structure common to the metallo-β-lactamase superfamily. Tm1162 exists as a trimer in the crystal and this trimeric unit is likely to be present in solution. In the trimer, three active sites reside at the interface between subunits, suggesting that the oligomeric assembly is crucial for catalysis. A new type of structurally encoded heterodinuclear site has been identified by confirming the identity of nickel-containing heteronuclear sites in Tm1162 via X-ray absorption spectroscopy and anomalous difference Fourier maps. The second coordination sphere, including His8 and Glu73, maintains the side-chain orientations of histidines and stabilizes the metal-binding site. Nickel coordination was crucial for the oligomerization of Tm1162. The nickel-dependent and manganese-dependent β-lactamase and phosphodiesterase activities of Tm1162 have also been characterized.
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Affiliation(s)
- Hwajung Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hee Jung Kim
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Atsushi Matsuura
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Bunzo Mikami
- Laboratory of Quality Design and Exploitation, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto 611-0011, Japan
| | - Hye Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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116
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Schneider SH, Lockwood SP, Hargreaves DI, Slade DJ, LoConte MA, Logan BE, McLaughlin EE, Conroy MJ, Slade KM. Slowed Diffusion and Excluded Volume Both Contribute to the Effects of Macromolecular Crowding on Alcohol Dehydrogenase Steady-State Kinetics. Biochemistry 2015; 54:5898-906. [DOI: 10.1021/acs.biochem.5b00533] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Samuel H. Schneider
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Schuyler P. Lockwood
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Dominique I. Hargreaves
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - David J. Slade
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Micaela A. LoConte
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Bridget E. Logan
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Erin E. McLaughlin
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Michael J. Conroy
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Kristin M. Slade
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
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117
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Gómez-Anquela C, García-Mendiola T, Abad JM, Pita M, Pariente F, Lorenzo E. Scaffold electrodes based on thioctic acid-capped gold nanoparticles coordinated Alcohol Dehydrogenase and Azure A films for high performance biosensor. Bioelectrochemistry 2015; 106:335-42. [PMID: 26152878 DOI: 10.1016/j.bioelechem.2015.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 06/19/2015] [Accepted: 06/21/2015] [Indexed: 10/23/2022]
Abstract
Nanometric size gold nanoparticles capped with thiotic acid are used to coordinate with the Zn (II) present in the catalytic center of Alcohol Dehydrogenase (ADH). In combination with the NADH oxidation molecular catalyst Azure A, electrografted onto carbon screen-printed electrodes, they are used as scaffold electrodes for the construction of a very efficient ethanol biosensor. The final biosensing device exhibits a highly efficient ethanol oxidation with low overpotential of -0.25 V besides a very good analytical performance with a detection limit of 0.14±0.01 μM and a stable response for more than one month.
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Affiliation(s)
- C Gómez-Anquela
- Department of Analytical Chemistry, Universidad Autónoma de Madrid, 28049, Spain.
| | - T García-Mendiola
- Department of Analytical Chemistry, Universidad Autónoma de Madrid, 28049, Spain.
| | - José M Abad
- Department of Analytical Chemistry, Universidad Autónoma de Madrid, 28049, Spain.
| | - M Pita
- Instituto de Catalisis y Petroleoquimica, CSIC. C/ Marie Curie, 2, L10., 28049 Madrid, Spain.
| | - F Pariente
- Department of Analytical Chemistry, Universidad Autónoma de Madrid, 28049, Spain.
| | - E Lorenzo
- Department of Analytical Chemistry, Universidad Autónoma de Madrid, 28049, Spain; IMDEA Nanociencia, Madrid, Spain.
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118
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Benavente R, Esteban-Torres M, Kohring GW, Cortés-Cabrera Á, Sánchez-Murcia PA, Gago F, Acebrón I, de las Rivas B, Muñoz R, Mancheño JM. Enantioselective oxidation of galactitol 1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli. ACTA ACUST UNITED AC 2015; 71:1540-54. [PMID: 26143925 DOI: 10.1107/s1399004715009281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/15/2015] [Indexed: 11/11/2022]
Abstract
Galactitol-1-phosphate 5-dehydrogenase (GPDH) is a polyol dehydrogenase that belongs to the medium-chain dehydrogenase/reductase (MDR) superfamily. It catalyses the Zn(2+)- and NAD(+)-dependent stereoselective dehydrogenation of L-galactitol 1-phosphate to D-tagatose 6-phosphate. Here, three crystal structures of GPDH from Escherichia coli are reported: that of the open state of GPDH with Zn(2+) in the catalytic site and those of the closed state in complex with the polyols Tris and glycerol, respectively. The closed state of GPDH reveals no bound cofactor, which is at variance with the conformational transition of the prototypical mammalian liver alcohol dehydrogenase. The main intersubunit-contacting interface within the GPDH homodimer presents a large internal cavity that probably facilitates the relative movement between the subunits. The substrate analogue glycerol bound within the active site partially mimics the catalytically relevant backbone of galactitol 1-phosphate. The glycerol binding mode reveals, for the first time in the polyol dehydrogenases, a pentacoordinated zinc ion in complex with a polyol and also a strong hydrogen bond between the primary hydroxyl group and the conserved Glu144, an interaction originally proposed more than thirty years ago that supports a catalytic role for this acidic residue.
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Affiliation(s)
- Rocío Benavente
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - María Esteban-Torres
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Gert-Wieland Kohring
- Microbiology, Saarland University, Campus Gebäude A1.5, 66123 Saarbruecken, Germany
| | - Álvaro Cortés-Cabrera
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Pedro A Sánchez-Murcia
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Federico Gago
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Iván Acebrón
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Blanca de las Rivas
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Rosario Muñoz
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - José M Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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Andreatta ME, Levine JA, Foy SG, Guzman LD, Kosinski LJ, Cordes MHJ, Masel J. The Recent De Novo Origin of Protein C-Termini. Genome Biol Evol 2015; 7:1686-701. [PMID: 26002864 PMCID: PMC4494051 DOI: 10.1093/gbe/evv098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Protein-coding sequences can arise either from duplication and divergence of existing sequences, or de novo from noncoding DNA. Unfortunately, recently evolved de novo genes can be hard to distinguish from false positives, making their study difficult. Here, we study a more tractable version of the process of conversion of noncoding sequence into coding: the co-option of short segments of noncoding sequence into the C-termini of existing proteins via the loss of a stop codon. Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes. We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic. We find one putative gene fusion that turns out, on close inspection, to be the product of replicated assembly errors, further highlighting the issue of false positives in the study of rare events. Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure.
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Affiliation(s)
- Matthew E Andreatta
- Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN
| | - Joshua A Levine
- Department of Ecology & Evolutionary Biology, University of Arizona
| | - Scott G Foy
- Department of Ecology & Evolutionary Biology, University of Arizona
| | - Lynette D Guzman
- Department of Ecology & Evolutionary Biology, University of Arizona Present address: Program in Mathematics Education, Michigan State University, MI
| | - Luke J Kosinski
- Biochemistry and Molecular & Cellular Biology Graduate Program, University of Arizona
| | | | - Joanna Masel
- Department of Ecology & Evolutionary Biology, University of Arizona
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120
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Uygun DA, Akduman B, Uygun M, Akgöl S, Denizli A. Immobilization of alcohol dehydrogenase onto metal-chelated cryogels. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2015; 26:446-57. [PMID: 25715869 DOI: 10.1080/09205063.2015.1023241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this presented work, poly(HEMA-GMA) cryogel was synthesized and used for the immobilization of alcohol dehydrogenase. For this, synthesized cryogels were functionalized with iminodiacetic acid and chelated with Zn(2+). This metal-chelated cryogels were used for the alcohol dehydrogenase immobilization and their kinetic parameters were compared with free enzyme. Optimum pH was found to be 7.0 for both immobilized and free enzyme preparations, while temperature optima for free and immobilized alcohol dehydrogenase was 25 °C. Kinetic constants such as K(m), V(max), and k(cat) for free and immobilized form of alcohol dehydrogenase were also investigated. k(cat) value of free enzyme was found to be 3743.9 min(-1), while k(cat) for immobilized enzyme was 3165.7 min(-1). Thermal stability of the free and immobilized alcohol dehydrogenase was studied and stability of the immobilized enzyme was found to be higher than free form. Also, operational stability and reusability profile of the immobilized alcohol dehydrogenase were investigated. Finally, storage stability of the free and immobilized alcohol dehydrogenase was studied, and at the end of the 60 days storage, it was demonstrated that, immobilized alcohol dehydrogenase was exhibited high stability than that of free enzyme.
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