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Mahmoud GAE, Mayer P, Gaber DA, Ibrahim AB. Response to oxidative stress generation in Rhodotorula glutinis and Candida tropicalis by thallium dithiocarbamate complexes. INORG CHEM COMMUN 2023; 156:111283. [DOI: 10.1016/j.inoche.2023.111283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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2
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Lin LL, Lu BY, Chi MC, Huang YF, Lin MG, Wang TF. Activation and thermal stabilization of a recombinant γ-glutamyltranspeptidase from Bacillus licheniformis ATCC 27811 by monovalent cations. Appl Microbiol Biotechnol 2022; 106:1991-2006. [PMID: 35230495 DOI: 10.1007/s00253-022-11836-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/08/2022] [Accepted: 02/12/2022] [Indexed: 12/27/2022]
Abstract
The regulation of enzyme activity through complexation with certain metal ions plays an important role in many biological processes. In addition to divalent metals, monovalent cations (MVCs) frequently function as promoters for efficient biocatalysis. Here, we examined the effect of MVCs on the enzymatic catalysis of a recombinant γ-glutamyltranspeptidase (BlrGGT) from Bacillus licheniformis ATCC 27,811 and the application of a metal-activated enzyme to L-theanine synthesis. The transpeptidase activity of BlrGGT was enhanced by Cs+ and Na+ over a broad range of concentrations with a maximum of 200 mM. The activation was essentially independent of the ionic radius, but K+ contributed the least to enhancing the catalytic efficiency. The secondary structure of BlrGGT remained mostly unchanged in the presence of different concentrations of MVCs, but there was a significant change in its tertiary structure under the same conditions. Compared with the control, the half-life (t1/2) of the Cs+-enriched enzyme at 60 and 65 °C was shown to increase from 16.3 and 4.0 min to 74.5 and 14.3 min, respectively. The simultaneous addition of Cs+ and Mg2+ ions exerted a synergistic effect on the activation of BlrGGT. This was adequately reflected by an improvement in the conversion of substrates to L-theanine by 3.3-15.1% upon the addition of 200 mM MgCl2 into a reaction mixture comprising the freshly desalted enzyme (25 μg/mL), 250 mM L-glutamine, 600 mM ethylamine, 200 mM each of the MVCs, and 50 mM borate buffer (pH 10.5). Taken together, our results provide interesting insights into the complexation of MVCs with BlrGGT and can therefore be potentially useful to the biocatalytic production of naturally occurring γ-glutamyl compounds. KEY POINTS: • The transpeptidase activity of B. licheniformis γ-glutamyltranspeptidase can be activated by monovalent cations. • The thermal stability of the enzyme was profoundly increased in the presence of 200 mM Cs+. • The simultaneous addition of Cs+and Mg2+ions to the reaction mixture improves L-theanine production.
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Affiliation(s)
- Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan
| | - Bo-Yuan Lu
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan
| | - Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan
| | - Yu-Fen Huang
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Nangang District, Taipei City, 11529, Taiwan
| | - Tzu-Fan Wang
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City, 60004, Taiwan.
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3
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Cui J, Tcherkez G. Potassium dependency of enzymes in plant primary metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:522-530. [PMID: 34174657 DOI: 10.1016/j.plaphy.2021.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Potassium is a macroelement essential to many aspects of plant life, such as photosynthesis, phloem transport or cellular electrochemistry. Many enzymes in animals or microbes are known to be stimulated or activated by potassium (K+ ions). Several plant enzymes are also strictly K+-dependent, and this can be critical when plants are under K deficiency and thus intracellular K+ concentration is low. Although metabolic effects of low K conditions have been documented, there is presently no review focusing on roles of K+ for enzyme catalysis or activation in plants. In this mini-review, we compile the current knowledge on K+-requirement of plant enzymes and take advantage of structural data to present biochemical roles of K+. This information is instrumental to explain direct effects of low K+ content on metabolism and this is illustrated with recent metabolomics data.
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Affiliation(s)
- Jing Cui
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia; Institut de Recherche en Horticulture et Semences, INRAe Angers, Université d'Angers, 42 rue Georges Morel, 49070, Beaucouzé, France.
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4
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Dollins DE, Xiong JP, Endo-Streeter S, Anderson DE, Bansal VS, Ponder JW, Ren Y, York JD. A structural basis for lithium and substrate binding of an inositide phosphatase. J Biol Chem 2021; 296:100059. [PMID: 33172890 PMCID: PMC7948987 DOI: 10.1074/jbc.ra120.014057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/29/2020] [Accepted: 11/10/2020] [Indexed: 01/07/2023] Open
Abstract
Inositol polyphosphate 1-phosphatase (INPP1) is a prototype member of metal-dependent/lithium-inhibited phosphomonoesterase protein family defined by a conserved three-dimensional core structure. Enzymes within this family function in distinct pathways including inositide signaling, gluconeogenesis, and sulfur assimilation. Using structural and biochemical studies, we report the effect of substrate and lithium on a network of metal binding sites within the catalytic center of INPP1. We find that lithium preferentially occupies a key site involved in metal-activation only when substrate or product is added. Mutation of a conserved residue that selectively coordinates the putative lithium-binding site results in a dramatic 100-fold reduction in the inhibitory constant as compared with wild-type. Furthermore, we report the INPP1/inositol 1,4-bisphosphate complex which illuminates key features of the enzyme active site. Our results provide insights into a structural basis for uncompetitive lithium inhibition and substrate recognition and define a sequence motif for metal binding within this family of regulatory phosphatases.
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Affiliation(s)
- D Eric Dollins
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Jian-Ping Xiong
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Stuart Endo-Streeter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - David E Anderson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Vinay S Bansal
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University, St Louis, Missouri, USA
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - John D York
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
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5
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Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa. Sci Rep 2018; 8:11334. [PMID: 30054521 PMCID: PMC6063907 DOI: 10.1038/s41598-018-29535-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/12/2018] [Indexed: 01/30/2023] Open
Abstract
S-adenosyl-l-homocysteine hydrolase from Pseudomonas aeruginosa (PaSAHase) coordinates one K+ ion and one Zn2+ ion in the substrate binding area. The cations affect the enzymatic activity and substrate binding but the molecular mechanisms of their action are unknown. Enzymatic and isothermal titration calorimetry studies demonstrated that the K+ ions stimulate the highest activity and strongest ligand binding in comparison to other alkali cations, while the Zn2+ ions inhibit the enzyme activity. PaSAHase was crystallized in the presence of adenine nucleosides and K+ or Rb+ ions. The crystal structures show that the alkali ion is coordinated in close proximity of the purine ring and a 23Na NMR study showed that the monovalent cation coordination site is formed upon ligand binding. The cation, bound in the area of a molecular hinge, orders and accurately positions the amide group of Q65 residue to allow its interaction with the ligand. Moreover, binding of potassium is required to enable unique dynamic properties of the enzyme that ensure its maximum catalytic activity. The Zn2+ ion is bound in the area of a molecular gate that regulates access to the active site. Zn2+ coordination switches the gate to a shut state and arrests the enzyme in its closed, inactive conformation.
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6
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Bischof H, Rehberg M, Stryeck S, Artinger K, Eroglu E, Waldeck-Weiermair M, Gottschalk B, Rost R, Deak AT, Niedrist T, Vujic N, Lindermuth H, Prassl R, Pelzmann B, Groschner K, Kratky D, Eller K, Rosenkranz AR, Madl T, Plesnila N, Graier WF, Malli R. Novel genetically encoded fluorescent probes enable real-time detection of potassium in vitro and in vivo. Nat Commun 2017; 8:1422. [PMID: 29127288 PMCID: PMC5681659 DOI: 10.1038/s41467-017-01615-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/04/2017] [Indexed: 01/01/2023] Open
Abstract
Changes in intra- and extracellular potassium ion (K+) concentrations control many important cellular processes and related biological functions. However, our current understanding of the spatiotemporal patterns of physiological and pathological K+ changes is severely limited by the lack of practicable detection methods. We developed K+-sensitive genetically encoded, Förster resonance energy transfer-(FRET) based probes, called GEPIIs, which enable quantitative real-time imaging of K+ dynamics. GEPIIs as purified biosensors are suitable to directly and precisely quantify K+ levels in different body fluids and cell growth media. GEPIIs expressed in cells enable time-lapse and real-time recordings of global and local intracellular K+ signals. Hitherto unknown Ca2+-triggered, organelle-specific K+ changes were detected in pancreatic beta cells. Recombinant GEPIIs also enabled visualization of extracellular K+ fluctuations in vivo with 2-photon microscopy. Therefore, GEPIIs are relevant for diverse K+ assays and open new avenues for live-cell K+ imaging. K+ plays an important role in physiology and disease, but the lack of high specificity K+ sensors limits our understanding of its spatiotemporal dynamics. Here the authors develop genetically-encoded FRET-based probes able to quantify K+ concentration in body fluids, cells and specific organelles.
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Affiliation(s)
- Helmut Bischof
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Markus Rehberg
- Ludwig-Maximilians University (LMU), Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Sarah Stryeck
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Katharina Artinger
- Clinical Division of Nephrology, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Emrah Eroglu
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Markus Waldeck-Weiermair
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Benjamin Gottschalk
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Rene Rost
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Andras T Deak
- Clinical Division of Nephrology, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Tobias Niedrist
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Nemanja Vujic
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Hanna Lindermuth
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010, Graz, Austria
| | - Ruth Prassl
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010, Graz, Austria
| | - Brigitte Pelzmann
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010, Graz, Austria
| | - Klaus Groschner
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010, Graz, Austria
| | - Dagmar Kratky
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Kathrin Eller
- Clinical Division of Nephrology, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Alexander R Rosenkranz
- Clinical Division of Nephrology, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Tobias Madl
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Nikolaus Plesnila
- Ludwig-Maximilians University (LMU), Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Wolfgang F Graier
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Roland Malli
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria. .,BioTechMed-Graz, Graz, Austria.
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7
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Roux M, Dosseto A. From direct to indirect lithium targets: a comprehensive review of omics data. Metallomics 2017; 9:1326-1351. [DOI: 10.1039/c7mt00203c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metal ions are critical to a wide range of biological processes.
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Affiliation(s)
| | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory
- School of Earth & Environmental Sciences
- University of Wollongong
- Wollongong
- Australia
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8
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Gohara DW, Di Cera E. Molecular Mechanisms of Enzyme Activation by Monovalent Cations. J Biol Chem 2016; 291:20840-20848. [PMID: 27462078 DOI: 10.1074/jbc.r116.737833] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Regulation of enzymes through metal ion complexation is widespread in biology and underscores a physiological need for stability and high catalytic activity that likely predated proteins in the RNA world. In addition to divalent metals such as Ca2+, Mg2+, and Zn2+, monovalent cations often function as efficient and selective promoters of catalysis. Advances in structural biology unravel a rich repertoire of molecular mechanisms for enzyme activation by Na+ and K+ Strategies range from short-range effects mediated by direct participation in substrate binding, to more distributed effects that propagate long-range to catalytic residues. This review addresses general considerations and examples.
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Affiliation(s)
- David W Gohara
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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9
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Manin N, da Silva MC, Zdravkovic I, Eliseeva O, Dyshin A, Yaşar O, Salahub DR, Kolker AM, Kiselev MG, Noskov SY. LiCl solvation in N-methyl-acetamide (NMA) as a model for understanding Li(+) binding to an amide plane. Phys Chem Chem Phys 2016; 18:4191-200. [PMID: 26784370 DOI: 10.1039/c5cp04847h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The thermodynamics of ion solvation in non-aqueous solvents remains of great significance for understanding cellular transport and ion homeostasis for the design of novel ion-selective materials and applications in molecular pharmacology. Molecular simulations play pivotal roles in connecting experimental measurements to the microscopic structures of liquids. One of the most useful and versatile mimetic systems for understanding biological ion transport is N-methyl-acetamide (NMA). A plethora of theoretical studies for ion solvation in NMA have appeared recently, but further progress is limited by two factors. One is an apparent lack of experimental data on solubility and thermodynamics of solvation for a broad panel of 1 : 1 salts over an appropriate temperature and concentration range. The second concern is more substantial and has to do with the limitations hardwired in the additive (fixed charge) approximations used for most of the existing force-fields. In this submission, we report on the experimental evaluation of LiCl solvation in NMA over a broad range of concentrations and temperatures and compare the results with those of MD simulations with several additive and one polarizable force-field (Drude). By comparing our simulations and experimental results to density functional theory computations, we discuss the limiting factors in existing potential functions. To evaluate the possible implications of explicit and implicit polarizability treatments on ion permeation across biological channels, we performed potential of mean force (PMF) computations for Li(+) transport through a model narrow ion channel with additive and polarizable force-fields.
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Affiliation(s)
- Nikolai Manin
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Mauricio C da Silva
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Igor Zdravkovic
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada
| | - Olga Eliseeva
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Alexey Dyshin
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Orhan Yaşar
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada
| | - Dennis R Salahub
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Arkadiy M Kolker
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Michael G Kiselev
- G.A. Krestov Institute for Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str, 1, Ivanovo, 153045, Russia.
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, BI-447, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada. and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T3A 2T3, Canada
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10
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Wheatley RW, Juers DH, Lev BB, Huber RE, Noskov SY. Elucidating factors important for monovalent cation selectivity in enzymes: E. coli β-galactosidase as a model. Phys Chem Chem Phys 2016; 17:10899-909. [PMID: 25820412 DOI: 10.1039/c4cp04952g] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many enzymes require a specific monovalent cation (M(+)), that is either Na(+) or K(+), for optimal activity. While high selectivity M(+) sites in transport proteins have been extensively studied, enzyme M(+) binding sites generally have lower selectivity and are less characterized. Here we study the M(+) binding site of the model enzyme E. coli β-galactosidase, which is about 10 fold selective for Na(+) over K(+). Combining data from X-ray crystallography and computational models, we find the electrostatic environment predominates in defining the Na(+) selectivity. In this lower selectivity site rather subtle influences on the electrostatic environment become significant, including the induced polarization effects of the M(+) on the coordinating ligands and the effect of second coordination shell residues on the charge distribution of the primary ligands. This work expands the knowledge of ion selectivity in proteins to denote novel mechanisms important for the selectivity of M(+) sites in enzymes.
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Affiliation(s)
- Robert W Wheatley
- Division of Biochemistry, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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11
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Sodium-Proton (Na+/H+) Antiporters: Properties and Roles in Health and Disease. Met Ions Life Sci 2016; 16:391-458. [DOI: 10.1007/978-3-319-21756-7_12] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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12
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Rodríguez-Mercado JJ, Hernández-de la Cruz H, Felipe-Reyes M, Jaramillo-Cruz E, Altamirano-Lozano MA. Evaluation of cytogenetic and DNA damage caused by thallium(I) acetate in human blood cells. ENVIRONMENTAL TOXICOLOGY 2015; 30:572-580. [PMID: 24318865 DOI: 10.1002/tox.21934] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/25/2013] [Indexed: 06/02/2023]
Abstract
Although thallium is detrimental to all living organisms, information regarding the mutagenic and genotoxic effects of this element and its compounds remains scarce. Therefore, we tested the genotoxic and cytotoxic effects of thallium(I) acetate on human peripheral blood cells in vitro using structural chromosomal aberrations (SCAs), sister chromatid exchanges (SCEs), and single-cell gel electrophoresis (at pH >13 or 12.1) analysis. Whole blood samples were incubated with 0.5, 1, 5, 10, 50, or 100 µg/mL thallium salt. Exposure to this metal compound resulted in a clear dose-dependent reduction in the mitotic and replicative indices. An increase in SCAs was evident in the treated group compared with the control group, and significant differences were observed in the percentage of cells with SCAs when metaphase cells were treated with 0.5-10 µg/mL of thallium(I). The SCE test did not reveal any significant differences. We observed that a 1-h treatment with thallium(I) at pH > 13 significantly increased the comet length for all the concentrations tested; however, at pH 12.1, only the two highest concentrations affected the comet length. These results suggested that thallium(I) acetate induces cytotoxic, cytostatic, and clastogenic effects, as well as DNA damage.
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Affiliation(s)
- Juan J Rodríguez-Mercado
- Unidad de Investigación en Genética y Toxicología Ambiental (UIGTA), Laboratorio L5 PA, Unidad Multidisciplinaria de Investigación Experimental (UMIE-Z), Facultad de Estudios Superiores-Zaragoza, Campus II, UNAM, AP 9-020, CP 15000, Ciudad de México, México
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13
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Wöhlert D, Kühlbrandt W, Yildiz O. Structure and substrate ion binding in the sodium/proton antiporter PaNhaP. eLife 2014; 3:e03579. [PMID: 25426802 PMCID: PMC4381880 DOI: 10.7554/elife.03579] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 11/25/2014] [Indexed: 11/29/2022] Open
Abstract
Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed
structures of antiporters with bound substrate ions are essential for understanding
how they work. We have resolved the substrate ion in the dimeric, electroneutral
sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2
Å, and have determined its structure in two different conformations at pH 8 and
pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine
and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the
deepest point of a negatively charged cytoplasmic funnel. A second narrow polar
channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP
is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent
allosteric coupling of protomers through two histidines at the dimer interface.
Combined with comprehensive transport studies, the structures of PaNhaP offer unique
new insights into the transport mechanism of sodium/proton antiporters. DOI:http://dx.doi.org/10.7554/eLife.03579.001 Although the membrane that surrounds a cell is effective at separating the inside of
a cell from the outside environment, certain molecules must enter or leave the cell
for it to work correctly. One way this transport can occur is via proteins embedded
in the cell membrane, called transporters. Transporters that are found in all organisms include the sodium/proton antiporters,
which exchange protons from inside the cell with sodium ions from outside. However,
exactly how the antiporter works was unknown. Previous work suggested that the structure and activity of the sodium/proton
antiporter changes as the acidity of its environment changes, but the precise details
of how this occurs were unclear. Wöhlert et al. have now crystallised a
sodium/proton antiporter from a single-celled organism called Pyrococcus
abyssi, a species of archaea that has been found living in hydrothermal
vents deep in the Pacific Ocean. The structures the protein takes on in different
functional states were then deduced from these crystals using a technique called
X-ray crystallography. Using heavy thallium ions instead of sodium ions, which are
less visible to X-rays, Wöhlert et al. found the site in the antiporter where
the transported ion binds as it moves through the membrane. The antiporter has a funnel-shaped cavity that faces inwards (into the cell) in both
acidic and alkaline conditions, although a second narrow channel that is open in
alkaline conditions is blocked in acidic conditions by small protein rearrangements.
Wöhlert et al. suggest that the differences between both structures explain how
the antiporter tunes its ability to bind to the ions it transports. Wöhlert et al. further measured the activity of the antiporter and observed that
the transport of ions was most rapid under slightly acidic conditions. In more acidic
conditions, the sodium ion cannot bind to the antiporter, and in an alkaline
environment, the sodium ions bind too strongly to the antiporter; in both cases, the
ions cannot be transported. Comparing the findings presented here with separate work that uncovers the structure
of the sodium/proton antiporter in a different species of archaea revealed very
similar structures. Related transporters are also found in mammals, and defects in
these transporters can lead to problems with the heart and kidneys. A better
understanding of the sodium/proton antiporter structure could therefore help to
develop new treatments for these conditions. DOI:http://dx.doi.org/10.7554/eLife.03579.002
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Affiliation(s)
- David Wöhlert
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ozkan Yildiz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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14
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Dutta A, Bhattacharyya S, Dutta D, Das AK. Structural elucidation of the binding site and mode of inhibition of Li+and Mg2+in inositol monophosphatase. FEBS J 2014; 281:5309-24. [PMID: 25263816 DOI: 10.1111/febs.13070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/16/2014] [Accepted: 09/23/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Anirudha Dutta
- Department of Biotechnology; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
| | - Sudipta Bhattacharyya
- Department of Biotechnology; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
| | - Debajyoti Dutta
- Department of Biotechnology; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
| | - Amit Kumar Das
- Department of Biotechnology; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
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15
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Juers DH, Matthews BW, Huber RE. LacZ β-galactosidase: structure and function of an enzyme of historical and molecular biological importance. Protein Sci 2012; 21:1792-807. [PMID: 23011886 PMCID: PMC3575911 DOI: 10.1002/pro.2165] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 09/18/2012] [Indexed: 12/25/2022]
Abstract
This review provides an overview of the structure, function, and catalytic mechanism of lacZ β-galactosidase. The protein played a central role in Jacob and Monod's development of the operon model for the regulation of gene expression. Determination of the crystal structure made it possible to understand why deletion of certain residues toward the amino-terminus not only caused the full enzyme tetramer to dissociate into dimers but also abolished activity. It was also possible to rationalize α-complementation, in which addition to the inactive dimers of peptides containing the "missing" N-terminal residues restored catalytic activity. The enzyme is well known to signal its presence by hydrolyzing X-gal to produce a blue product. That this reaction takes place in crystals of the protein confirms that the X-ray structure represents an active conformation. Individual tetramers of β-galactosidase have been measured to catalyze 38,500 ± 900 reactions per minute. Extensive kinetic, biochemical, mutagenic, and crystallographic analyses have made it possible to develop a presumed mechanism of action. Substrate initially binds near the top of the active site but then moves deeper for reaction. The first catalytic step (called galactosylation) is a nucleophilic displacement by Glu537 to form a covalent bond with galactose. This is initiated by proton donation by Glu461. The second displacement (degalactosylation) by water or an acceptor is initiated by proton abstraction by Glu461. Both of these displacements occur via planar oxocarbenium ion-like transition states. The acceptor reaction with glucose is important for the formation of allolactose, the natural inducer of the lac operon.
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Affiliation(s)
- Douglas H Juers
- Department of Physics, Whitman CollegeWalla Walla, Washington 99362
| | - Brian W Matthews
- Institute of Molecular Biology, 1229 University of OregonEugene, Oregon 97403-1229
| | - Reuben E Huber
- Department of Biological Sciences, University of Calgary, 2500 University DriveNW, Calgary, Alberta, Canada T2N 1N4
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16
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Abstract
This review summarizes the current knowledge about the general toxicity of thallium (Tl) and its environmental sources, with special emphasis placed on its potential mutagenic, genotoxic, and cytotoxic effects on both eukaryotic and prokaryotic cells. Tl is a nonessential heavy metal that poses environmental and occupational threats as well as therapeutic hazards because of its use in medicine. It is found in two oxidation states, thallous (Tl(+)) and thallic (Tl(3+)), both of which are considered highly toxic to human beings and domestic and wild organisms. Many Tl compounds are colorless, odorless and tasteless, and these characteristics, combined with the high toxicity of TI compounds, have led to their use as poisons. Because of its similarity to potassium ions (K(+)), plants and mammals readily absorb Tl(+) through the skin and digestive and respiratory systems. In mammals, it can cross the placental, hematoencephalic, and gonadal barriers. Inside cells, Tl can accumulate and interfere with the metabolism of potassium and other metal cations, mimicking or inhibiting their action. The effects of Tl on genetic material have not yet been thoroughly explored, and few existing studies have focused exclusively on Tl(+). Both in vivo and in vitro studies indicate that Tl compounds can have a weak mutagenic effect, but no definitive effect on the induction of primary DNA damage or chromosomal damage has been shown. These studies have demonstrated that Tl compounds are highly toxic and lead to changes in cell-cycle progression.
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Affiliation(s)
- Juan José Rodríguez-Mercado
- Unidad de Investigación en Genética y Toxicología Ambiental (UIGTA), Laboratorio L5-PA, Unidad Multidisciplinaria de Investigación Experimental (UMIE-Z), Facultad de Estudios Superiores-Zaragoza, Cuidad de México, México.
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17
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Dudev T, Lim C. Competition between Li+ and Mg2+ in Metalloproteins. Implications for Lithium Therapy. J Am Chem Soc 2011; 133:9506-15. [DOI: 10.1021/ja201985s] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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18
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Dziewulska-Szwajkowska D, Dzugaj A. Kinetic properties of Pelophylax esculentus muscle FBPase. Comp Biochem Physiol B Biochem Mol Biol 2010; 157:294-300. [PMID: 20656052 DOI: 10.1016/j.cbpb.2010.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/13/2010] [Accepted: 07/18/2010] [Indexed: 10/19/2022]
Abstract
D-Fructose-1,6-bisphosphate 1-phosphohydrolase FBPase; [EC 3.1.3.11] was isolated from Pelophylax esculentus muscle in an electrophoretically homogeneous form with ca 30% yield. Its subunit molecular mass is ca 37 kDa. In this study, we determined the basic kinetic properties of the frog muscle enzyme. FBPase exhibited a maximum activity at pH 7.5. Like other FBPases the frog enzyme requires magnesium ions for its activity (K(a)=263 microM) and is activated by potassium ions (K(a)=63.6 microM). I(0.5) for calcium ion (91 microM) is 100 times higher than the corresponding value of mammalian muscle FBPase. K(s) for the substrate was 1.68 microM. Substrate excess inhibited the enzyme (K(si)=55 microM). AMP and fructose-2,6-bisphosphate (Fru-2,6P(2)) are potent inhibitors of frog muscle FBPase with I(0.5) of 0.2 microM and K(i) of 114 nM, respectively. Both inhibitors act synergistically on the frog muscle FBPase. In the presence of 0.05-0.5 microM of AMP, K(i) for Fru-2,6P(2) is 92 and 28 nM. I(0.5) for AMP for P. esculentus muscle FBPase is 55 times lower than the corresponding value for P. esculentus liver isozyme.
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Kalujnaia S, McVee J, Kasciukovic T, Stewart AJ, Cramb G. A role for inositol monophosphatase 1 (IMPA1) in salinity adaptation in the euryhaline eel (Anguilla anguilla). FASEB J 2010; 24:3981-91. [PMID: 20547660 DOI: 10.1096/fj.10-161000] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This study investigated the expression and tissue distribution of inositol monophosphatase (IMPA1) and characterized its role in salinity adaptation in the eel. The coding sequence of eel IMPA1 was determined and confirmed to be orthologous to the mammalian gene/enzyme by phylogenetic analysis and structural modeling. Quantitative real-time PCR and Western blot techniques indicated up to 17-fold increases in mRNA expression and 2-fold increases in protein abundance in major osmoregulatory tissues following transfer of fish to seawater (SW). This was accompanied by up to 5-fold increases in enzyme activity, and 1.8- and 3-fold increases in inositol contents within the gill and kidney, respectively. Immunohistological studies revealed that IMPA1 protein expression predominated in SW-acclimated fish within basal epithelial/epidermal layers of the gill, esophagus, intestine, skin, and fins. SW transfer also induced a 10-fold increase in inositol content in the fin. IMPA1 immunoreactivity was also identified in chondrocytes within the cartilagenous matrix of the gills and fins, as well as in clusters of interstitial cells surrounding the kidney tubules. The observed increases in expression of IMPA1 highlight a protective role for inositol within various eel tissues following SW acclimation. This constitutes an adaptive mechanism in teleost fish naturally exposed to hypertonic environments.
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Affiliation(s)
- Svetlana Kalujnaia
- School of Medicine, University of St Andrews, St Andrews, Fife, KY16 9TF, UK
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20
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Sequence Recognition of DNA by Protein-Induced Conformational Transitions. J Mol Biol 2010; 396:1145-64. [DOI: 10.1016/j.jmb.2009.12.050] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 12/23/2009] [Accepted: 12/25/2009] [Indexed: 11/21/2022]
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21
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The structure functional catalytic activity of rice bran lipase in the presence of selenium and lithium. Eur Food Res Technol 2009. [DOI: 10.1007/s00217-009-1195-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Kiser PD, Lorimer GH, Palczewski K. Use of thallium to identify monovalent cation binding sites in GroEL. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:967-71. [PMID: 19851000 PMCID: PMC2765879 DOI: 10.1107/s1744309109032928] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 08/18/2009] [Indexed: 11/10/2022]
Abstract
GroEL is a bacterial chaperone protein that assembles into a homotetradecameric complex exhibiting D(7) symmetry and utilizes the co-chaperone protein GroES and ATP hydrolysis to assist in the proper folding of a variety of cytosolic proteins. GroEL utilizes two metal cofactors, Mg(2+) and K(+), to bind and hydrolyze ATP. A K(+)-binding site has been proposed to be located next to the nucleotide-binding site, but the available structural data do not firmly support this conclusion. Moreover, more than one functionally significant K(+)-binding site may exist within GroEL. Because K(+) has important and complex effects on GroEL activity and is involved in both positive (intra-ring) and negative (inter-ring) cooperativity for ATP hydrolysis, it is important to determine the exact location of these cation-binding site(s) within GroEL. In this study, the K(+) mimetic Tl(+) was incorporated into GroEL crystals, a moderately redundant 3.94 A resolution X-ray diffraction data set was collected from a single crystal and the strong anomalous scattering signal from the thallium ion was used to identify monovalent cation-binding sites. The results confirmed the previously proposed placement of K(+) next to the nucleotide-binding site and also identified additional binding sites that may be important for GroEL function and cooperativity. These findings also demonstrate the general usefulness of Tl(+) for the identification of monovalent cation-binding sites in protein crystal structures, even when the quality and resolution of the diffraction data are relatively low.
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Hsiao C, Tannenbaum E, VanDeusen H, Hershkovitz E, Perng G, Tannenbaum AR, Williams LD. Complexes of Nucleic Acids with Group I and II Cations. NUCLEIC ACID–METAL ION INTERACTIONS 2008. [DOI: 10.1039/9781847558763-00001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Chiaolong Hsiao
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
| | | | - Halena VanDeusen
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
| | - Eli Hershkovitz
- School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA 30332–0250 USA
- School of Biomedical Engineering Georgia Institute of Technology Atlanta, GA 30332–0250 USA
| | - Ginger Perng
- School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA 30332–0250 USA
| | - Allen R. Tannenbaum
- School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA 30332–0250 USA
- School of Biomedical Engineering Georgia Institute of Technology Atlanta, GA 30332–0250 USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
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24
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Creation of salt-insensitive 3′(2′),5′-bisphosphate nucleotidase by modeling and mutagenesis approach. Arch Biochem Biophys 2008; 469:174-83. [DOI: 10.1016/j.abb.2007.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 10/17/2007] [Accepted: 10/19/2007] [Indexed: 01/11/2023]
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25
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Ganguly M, Wang F, Kaushik M, Stone MP, Marky LA, Gold B. A study of 7-deaza-2'-deoxyguanosine 2'-deoxycytidine base pairing in DNA. Nucleic Acids Res 2007; 35:6181-95. [PMID: 17855404 PMCID: PMC2094092 DOI: 10.1093/nar/gkm670] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The incorporation of 7-deazaguanine modifications into DNA is frequently used to probe protein recognition of H-bonding information in the major groove of DNA. While it is generally assumed that 7-deazaguanine forms a normal Watson–Crick base pair with cytosine, detailed thermodynamic and structural analyses of this modification have not been reported. The replacement of the 7-N atom on guanine with a C–H, alters the electronic properties of the heterocycle and eliminates a major groove cation-binding site that could affect the organization of salts and water in the major groove. We report herein the characterization of synthetic DNA oligomers containing 7-deazaguanine using a variety of complementary approaches: UV thermal melting, differential scanning calorimetry (DSC), circular dichroism (CD), chemical probing and NMR. The results indicate that the incorporation of a 7-deazaguanine modification has a significant effect on the dynamic structure of the DNA at the flanking residue. This appears to be mediated by changes in hydration and cation organization.
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Affiliation(s)
- Manjori Ganguly
- Eppley Institute for Research in Cancer, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE-68198-6025, Department of Chemistry, Vanderbilt University, Nashville, TN-37235 and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA-15261, USA
| | - Feng Wang
- Eppley Institute for Research in Cancer, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE-68198-6025, Department of Chemistry, Vanderbilt University, Nashville, TN-37235 and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA-15261, USA
| | - Mahima Kaushik
- Eppley Institute for Research in Cancer, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE-68198-6025, Department of Chemistry, Vanderbilt University, Nashville, TN-37235 and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA-15261, USA
| | - Michael P. Stone
- Eppley Institute for Research in Cancer, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE-68198-6025, Department of Chemistry, Vanderbilt University, Nashville, TN-37235 and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA-15261, USA
| | - Luis A. Marky
- Eppley Institute for Research in Cancer, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE-68198-6025, Department of Chemistry, Vanderbilt University, Nashville, TN-37235 and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA-15261, USA
| | - Barry Gold
- Eppley Institute for Research in Cancer, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE-68198-6025, Department of Chemistry, Vanderbilt University, Nashville, TN-37235 and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA-15261, USA
- *To whom correspondence should be addressed. +1 412 383 9593+1 412 383 7436
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26
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Gold B, Marky LM, Stone MP, Williams LD. A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns. Chem Res Toxicol 2007; 19:1402-14. [PMID: 17112226 PMCID: PMC2532758 DOI: 10.1021/tx060127n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Alkylating agents, including environmental and endogenous carcinogens and DNA targeting antineoplastic agents, that adduct DNA via intermediates with significant cationic charge show a sequence selectively in their covalent bonding to nucleobases. The resulting patterns of alkylation eventually contribute to the agent-dependent distributions and types of mutations. The origin of the regioselective modification of DNA by electrophiles has been attributed to steric and/or electronic factors, but attempts to mechanistically model and predict alkylation patterns have had limited success. In this review, we present data consistent with the role of the intrinsic sequence-dependent electrostatic landscape (SDEL) in DNA that modulates the equilibrium binding of cations and the bonding of reactive charged alkylating agents to atoms that line the floor of the major groove of DNA.
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Affiliation(s)
- Barry Gold
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
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27
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Zarzycki M, Maciaszczyk E, Dzugaj A. Glu 69 is essential for the high sensitivity of muscle fructose-1,6-bisphosphatase inhibition by calcium ions. FEBS Lett 2007; 581:1347-50. [PMID: 17350621 DOI: 10.1016/j.febslet.2007.02.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 02/15/2007] [Accepted: 02/22/2007] [Indexed: 11/18/2022]
Abstract
Muscle fructose-1,6-bisphosphatase (FBPase) is highly sensitive toward inhibition by AMP and calcium ions. In allosteric inhibition by AMP, a loop 52-72 plays a decisive role. This loop is a highly conservative region in muscle and liver FBPases. It is feasible that the same region is involved in the inhibition by calcium ions. To test this hypothesis, chemical modification, limited proteolysis and site directed mutagenesis Glu(69)/Gln were employed. The chemical modification of Lys(71-72) and the proteolytic cleavage of the loop resulted in the significant decrease of the muscle FBPase sensitivity toward inhibition by calcium ions. The mutation of Glu(69)-->Gln resulted in a 500-fold increase of muscle isozyme I(0.5) vs. calcium ions. These results demonstrate the key role that the 52-72 amino acid loop plays in determining the sensitivity of FBPase to inhibition by AMP and calcium ions.
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Affiliation(s)
- Marek Zarzycki
- Department of Animal Physiology, Zoological Institute, University of Wroclaw, Cybulskiego 30, 50-205 Wroclaw, Poland
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28
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An R, Chen QJ, Chai MF, Lu PL, Su Z, Qin ZX, Chen J, Wang XC. AtNHX8, a member of the monovalent cation: proton antiporter-1 family in Arabidopsis thaliana, encodes a putative Li/H antiporter. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:718-28. [PMID: 17270011 DOI: 10.1111/j.1365-313x.2006.02990.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The Arabidopsis monovalent cation:proton antiporter-1 (CPA1) family includes eight members, AtNHX1-8. AtNHX1 and AtNHX7/SOS1 have been well characterized as tonoplast and plasma membrane Na+/H+ antiporters, respectively. The proteins AtNHX2-6 have been phylogenetically linked to AtNHX1, while AtNHX8 appears to be related to AtNHX7/SOS1. Here we report functional characterization of AtNHX8. AtNHX8 T-DNA insertion mutants are hypersensitive to lithium ions (Li+) relative to wild-type plants, but not to the other metal ions such as sodium (Na+), potassium (K+) and caesium (Cs+). AtNHX8 overexpression in a triple-deletion yeast mutant AXT3 that exhibits defective Na+/Li+ transport specifically suppresses sensitivity to Li+, but does not affect Na+ sensitivity. Likewise, AtNHX8 overexpression complemented sensitivity to Li+, but not Na+, in sos1-1 mutant seedlings, and increased Li+ tolerance of both the sos1-1 mutant and wild-type seedlings. Results of Li+ and K+ measurement of loss-of-function and gain-of-function mutants indicate that AtNHX8 may be responsible for Li+ extrusion, and may be able to maintain K+ acquisition and intracellular ion homeostasis. Subcellular localization of the AtNHX8-enhanced green fluorescent protein (EGFP) fusion protein suggested that AtNHX8 protein is targeted to the plasma membrane. Taken together, our findings suggest that AtNHX8 encodes a putative plasma membrane Li+/H+ antiporter that functions in Li detoxification and ion homeostasis in Arabidopsis.
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Affiliation(s)
- Rui An
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100094, China
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29
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Abstract
Metal complexation is a key mediator or modifier of enzyme structure and function. In addition to divalent and polyvalent metals, group IA metals Na+and K+play important and specific roles that assist function of biological macromolecules. We examine the diversity of monovalent cation (M+)-activated enzymes by first comparing coordination in small molecules followed by a discussion of theoretical and practical aspects. Select examples of enzymes that utilize M+as a cofactor (type I) or allosteric effector (type II) illustrate the structural basis of activation by Na+and K+, along with unexpected connections with ion transporters. Kinetic expressions are derived for the analysis of type I and type II activation. In conclusion, we address evolutionary implications of Na+binding in the trypsin-like proteases of vertebrate blood coagulation. From this analysis, M+complexation has the potential to be an efficient regulator of enzyme catalysis and stability and offers novel strategies for protein engineering to improve enzyme function.
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Affiliation(s)
- Michael J Page
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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30
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Abstract
Enzymes activated by monovalent cations are abundantly represented in plants and the animal world. They have evolved to exploit Na+ and K+, readily available in biological environments, as major driving forces for substrate binding and catalysis. Recent progress in the structural biology of such enzymes has answered long standing questions about the molecular mechanism of activation and the origin of monovalent cation selectivity. That enables a simple classification of these functionally diverse enzymes and reveals unanticipated connections with ion transporters.
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Affiliation(s)
- Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
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31
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Abstract
Enzymes activated by monovalent cations are abundantly represented in plants and in the animal world. The mechanism, of activation involves formation of a ternary intermediate with the enzyme-substrate complex, or binding of the cation to an allosteric site in the protein. Thrombin is a Na+-activated enzyme with procoagulant, anticoagulant and signaling roles. The binding of Na+ influences allosterically thrombin function and offers a paradigm for regulatory control of protease activity and specificity. Here we review the molecular basis of thrombin allostery as recently emerged from mutagenesis and structural studies. The role of Na+ in blood coagulation and the evolution of serine proteases are also discussed.
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Affiliation(s)
- Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA.
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32
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Collins KD. Ion hydration: Implications for cellular function, polyelectrolytes, and protein crystallization. Biophys Chem 2005; 119:271-81. [PMID: 16213082 DOI: 10.1016/j.bpc.2005.08.010] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 08/30/2005] [Accepted: 08/31/2005] [Indexed: 11/25/2022]
Abstract
Only oppositely charged ions with matching absolute free energies of hydration spontaneously form inner sphere ion pairs in free solution [K.D.Collins, Ions from the Hofmeister series and osmolytes: effects on proteins in solution and in the crystallization process, Methods 34 (2004) 300-311.]. We approximate this with a Law of Matching Water Affinities which is used to examine the issues of (1) how ions are selected to be compatible with the high solubility requirements of cytosolic components; (2) how cytosolic components tend to interact weakly, so that association or dissociation can be driven by environmental signals; (3) how polyelectrolytes (nucleic acids) differ from isolated charges (in proteins); (4) how ions, osmolytes and polymers are used to crystallize proteins; and (5) how the "chelate effect" is used by macromolecules to bind ions at specific sites even when there is a mismatch in water affinity between the ion and the macromolecular ligands.
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Affiliation(s)
- Kim D Collins
- Department of Biochemistry and Molecular Biology, University of Maryland Medical School, 108 N. Greene Street, Baltimore, MD 21201-1503, USA.
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Gould TD, Quiroz JA, Singh J, Zarate CA, Manji HK. Emerging experimental therapeutics for bipolar disorder: insights from the molecular and cellular actions of current mood stabilizers. Mol Psychiatry 2004; 9:734-55. [PMID: 15136794 DOI: 10.1038/sj.mp.4001518] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bipolar disorder afflicts approximately 1-3% of both men and women, and is coincident with major economic, societal, medical, and interpersonal consequences. Current mediations used for its treatment are associated with variable rates of efficacy and often intolerable side effects. While preclinical and clinical knowledge in the neurosciences has expanded at a tremendous rate, recent years have seen no major breakthroughs in the development of novel types of treatment for bipolar disorder. We review here approaches to develop novel treatments specifically for bipolar disorder. Deliberate (ie not by serendipity) treatments may come from one of two general mechanisms: (1) Understanding the mechanism of action of current medications and thereafter designing novel drugs that mimics these mechanism(s); (2) Basing medication development upon the hypothetical or proven underlying pathophysiology of bipolar disorder. In this review, we focus upon the first approach. Molecular and cellular targets of current mood stabilizers include lithium inhibitable enzymes where lithium competes for a magnesium binding site (inositol monophosphatase, inositol polyphosphate 1-phosphatase, glycogen synthase kinase-3 (GSK-3), fructose 1,6-bisphosphatase, bisphosphate nucleotidase, phosphoglucomutase), valproate inhibitable enzymes (succinate semialdehyde dehydrogenase, succinate semialdehyde reductase, histone deacetylase), targets of carbamazepine (sodium channels, adenosine receptors, adenylate cyclase), and signaling pathways regulated by multiple drugs of different classes (phosphoinositol/protein kinase C, cyclic AMP, arachidonic acid, neurotrophic pathways). While the task of developing novel medications for bipolar disorder is truly daunting, we are hopeful that understanding the mechanism of action of current mood stabilizers will ultimately lead clinical trials with more specific medications and thus better treatments those who suffer from this devastating illness.
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Affiliation(s)
- T D Gould
- Laboratory of Molecular Pathophysiology, National Institute of Mental Health, Bethesda, MD 20892, USA
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Pineda AO, Carrell CJ, Bush LA, Prasad S, Caccia S, Chen ZW, Mathews FS, Di Cera E. Molecular dissection of Na+ binding to thrombin. J Biol Chem 2004; 279:31842-53. [PMID: 15152000 DOI: 10.1074/jbc.m401756200] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Na(+) binding near the primary specificity pocket of thrombin promotes the procoagulant, prothrombotic, and signaling functions of the enzyme. The effect is mediated allosterically by a communication between the Na(+) site and regions involved in substrate recognition. Using a panel of 78 Ala mutants of thrombin, we have mapped the allosteric core of residues that are energetically linked to Na(+) binding. These residues are Asp-189, Glu-217, Asp-222, and Tyr-225, all in close proximity to the bound Na(+). Among these residues, Asp-189 shares with Asp-221 the important function of transducing Na(+) binding into enhanced catalytic activity. None of the residues of exosite I, exosite II, or the 60-loop plays a significant role in Na(+) binding and allosteric transduction. X-ray crystal structures of the Na(+)-free (slow) and Na(+)-bound (fast) forms of thrombin, free or bound to the active site inhibitor H-d-Phe-Pro-Arg-chloromethyl-ketone, document the conformational changes induced by Na(+) binding. The slow --> fast transition results in formation of the Arg-187:Asp-222 ion pair, optimal orientation of Asp-189 and Ser-195 for substrate binding, and a significant shift of the side chain of Glu-192 linked to a rearrangement of the network of water molecules that connect the bound Na(+) to Ser-195 in the active site. The changes in the water network and the allosteric core explain the thermodynamic signatures linked to Na(+) binding and the mechanism of thrombin activation by Na(+). The role of the water network uncovered in this study establishes a new paradigm for the allosteric regulation of thrombin and other Na(+)-activated enzymes involved in blood coagulation and the immune response.
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Affiliation(s)
- Agustin O Pineda
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Abstract
Lithium is an effective drug for both the treatment and prophylaxis of bipolar disorder. However, the precise mechanism of lithium action is not yet well understood. Extensive research aiming to elucidate the molecular mechanisms underlying the therapeutic effects of lithium has revealed several possible targets. The behavioral and physiological manifestations of the illness are complex and are mediated by a network of interconnected neurotransmitter pathways. Thus, lithium's ability to modulate the release of serotonin at presynaptic sites and modulate receptor-mediated supersensitivity in the brain remains a relevant line of investigation. However, it is at the molecular level that some of the most exciting advances in the understanding of the long-term therapeutic action of lithium will continue in the coming years. The lithium cation possesses the selective ability, at clinically relevant concentrations, to alter the PI second-messenger system, potentially altering the activity and dynamic regulation of receptors that are coupled to this intracellular response. Subtypes of muscarinic receptors in the limbic system may represent particularly sensitive targets in this regard. Likewise, preclinical data have shown that lithium regulates arachidonic acid and the protein kinase C signaling cascades. It also indirectly regulates a number of factors involved in cell survival pathways, including cAMP response element binding protein, brain-derived neurotrophic factor, bcl-2 and mitogen-activated protein kinases, and may thus bring about delayed long-term beneficial effects via under-appreciated neurotrophic effects. Identification of the molecular targets for lithium in the brain could lead to the elucidation of the pathophysiology of bipolar disorder and the discovery of a new generation of mood stabilizers, which in turn may lead to improvements in the long-term outcome of this devastating illness (1).
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Affiliation(s)
- B Corbella
- 1Clinical Institute of Psychiatry and Psychology, University of Barcelona, Barcelona, Spain
| | - E Vieta
- 1Clinical Institute of Psychiatry and Psychology, University of Barcelona, Barcelona, Spain
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36
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Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter K, Vajda S. Identification of substrate binding sites in enzymes by computational solvent mapping. J Mol Biol 2003; 332:1095-113. [PMID: 14499612 DOI: 10.1016/j.jmb.2003.08.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Enzyme structures determined in organic solvents show that most organic molecules cluster in the active site, delineating the binding pocket. We have developed algorithms to perform solvent mapping computationally, rather than experimentally, by placing molecular probes (small molecules or functional groups) on a protein surface, and finding the regions with the most favorable binding free energy. The method then finds the consensus site that binds the highest number of different probes. The probe-protein interactions at this site are compared to the intermolecular interactions seen in the known complexes of the enzyme with various ligands (substrate analogs, products, and inhibitors). We have mapped thermolysin, for which experimental mapping results are also available, and six further enzymes that have no experimental mapping data, but whose binding sites are well characterized. With the exception of haloalkane dehalogenase, which binds very small substrates in a narrow channel, the consensus site found by the mapping is always a major subsite of the substrate-binding site. Furthermore, the probes at this location form hydrogen bonds and non-bonded interactions with the same residues that interact with the specific ligands of the enzyme. Thus, once the structure of an enzyme is known, computational solvent mapping can provide detailed and reliable information on its substrate-binding site. Calculations on ligand-bound and apo structures of enzymes show that the mapping results are not very sensitive to moderate variations in the protein coordinates.
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Prasad S, Wright KJ, Banerjee Roy D, Bush LA, Cantwell AM, Di Cera E. Redesigning the monovalent cation specificity of an enzyme. Proc Natl Acad Sci U S A 2003; 100:13785-90. [PMID: 14612565 PMCID: PMC283499 DOI: 10.1073/pnas.2333109100] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2003] [Indexed: 11/18/2022] Open
Abstract
Monovalent-cation-activated enzymes are abundantly represented in plants and in the animal world. Most of these enzymes are specifically activated by K+, whereas a few of them show preferential activation by Na+. The monovalent cation specificity of these enzymes remains elusive in molecular terms and has not been reengineered by site-directed mutagenesis. Here we demonstrate that thrombin, a Na+-activated allosteric enzyme involved in vertebrate blood clotting, can be converted into a K+-specific enzyme by redesigning a loop that shapes the entrance to the cation-binding site. The conversion, however, does not result into a K+-activated enzyme.
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Affiliation(s)
- Swati Prasad
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110, USA
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38
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Lah N, Lah J, Zegers I, Wyns L, Messens J. Specific potassium binding stabilizes pI258 arsenate reductase from Staphylococcus aureus. J Biol Chem 2003; 278:24673-9. [PMID: 12682056 DOI: 10.1074/jbc.m303194200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arsenate reductase (ArsC) from Staphylococcus aureus plasmid pI258 catalyzes the reduction of arsenate to arsenite and plays a role in bacterial heavy metal resistance. The high resolution x-ray structure of ArsC reveals the atomic details of the K+ binding site situated next to the catalytic P-loop structural motif of this redox enzyme. A full thermodynamic study of the binding characteristics of a series of monovalent cations (Li+, Na+, K+, Rb+, and Cs+) and their influence on the thermal stability of ArsC was performed with isothermal titration calorimetry, circular dichroism spectroscopy, and differential scanning calorimetry. Potassium has the largest affinity with a Ka of 3.8 x 10(3) m(-1), and the effectiveness of stabilization of ArsC by monovalent cations follows the binding affinity order: K+ > Rb+ > Cs+ > Na+ > Li+. A mutagenesis study on the K+ binding side chains showed that Asn-13 and Asp-65 are essential for potassium binding, but the impact on the stability of ArsC was the most extreme when mutating Ser-36. Additionally, the thermal stabilization by K+ is significantly reduced in the case of the ArsC E21A mutant, showing the importance of a Glu-21-coordinated water molecule in its contact with K+. Although potassium is not essential for catalysis, in its presence the kcat/KM increases with a factor of 5. Altogether, the interaction of K+ with specific residues in ArsC is an enthalpydriven process that stabilizes ArsC and increases the specific activity of this redox enzyme.
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Affiliation(s)
- Nina Lah
- Department Ultrastructure, Vlaams interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Pleinlaan 2, Belgium.
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39
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Ramírez-Silva L, Oria-Hernández J. Selectivity of pyruvate kinase for Na+ and K+ in water/dimethylsulfoxide mixtures. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:2377-85. [PMID: 12755692 DOI: 10.1046/j.1432-1033.2003.03605.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In aqueous media, muscle pyruvate kinase is highly selective for K+ over Na+. We now studied the selectivity of pyruvate kinase in water/dimethylsulfoxide mixtures by measuring the activation and inhibition constants of K+ and Na+, i.e. their binding to the monovalent and divalent cation binding sites of pyruvate kinase, respectively [Melchoir J.B. (1965) Biochemistry 4, 1518-1525]. In 40% dimethylsulfoxide the K0.5 app for K+ and Na+ were 190 and 64-fold lower than in water. Ki app for K+ and Na+ decreased 116 and 135-fold between 20 and 40% dimethylsulfoxide. The ratios of Ki app/K0.5 app for K+ and Na+ were 34-3.5 and 3.3-0.2, respectively. Therefore, dimethylsulfoxide favored the partition of K+ and Na+ into the monovalent and divalent cation binding sites of the enzyme. The kinetics of the enzyme at subsaturating concentrations of activators show that K+ and Mg2+ exhibit high selectivity for their respective cation binding sites, whereas when Na+ substitutes K+, Na+ and Mg2+ bind with high affinity to their incorrect sites. This is evident by the ratio of the affinities of Mg2+ and K+ for the monovalent cation binding site, which is close to 200. For Na+ and Mg2+ this ratio is approximately 20. Therefore, the data suggest that K+ induces conformational changes that prevent the binding of Mg2+ to the monovalent cation binding site. Circular dichroism spectra of the enzyme and the magnitude of the transfer and apparent binding energies of K+ and Na+ indicate that structural arrangements of the enzyme induced by dimethylsulfoxide determine the affinities of pyruvate kinase for K+ and Na+.
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Affiliation(s)
- Leticia Ramírez-Silva
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México.
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40
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Choe JY, Nelson SW, Fromm HJ, Honzatko RB. Interaction of Tl+ with product complexes of fructose-1,6-bisphosphatase. J Biol Chem 2003; 278:16008-14. [PMID: 12595529 DOI: 10.1074/jbc.m212394200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fructose-1,6-bisphosphatase requires divalent cations (Mg2+, Mn2+, or Zn2+) for catalysis, but a diverse set of monovalent cations (K+, Tl+, Rb+, or NH(4)(+)) will further enhance enzyme activity. Here, the interaction of Tl+ with fructose-1,6-bisphosphatase is explored under conditions that support catalysis. On the basis of initial velocity kinetics, Tl+ enhances catalysis by 20% with a K(a) of 1.3 mm and a Hill coefficient near unity. Crystal structures of enzyme complexes with Mg2+, Tl+, and reaction products, in which the concentration of Tl+ is 1 mm or less, reveal Mg2+ at metal sites 1, 2, and 3 of the active site, but little or no bound Tl+. Intermediate concentrations of Tl+ (5-20 mm) displace Mg2+ from site 3 and the 1-OH group of fructose 6-phosphate from in-line geometry with respect to bound orthophosphate. Loop 52-72 appears in a new conformational state, differing from its engaged conformation by disorder in residues 61-69. Tl+ does not bind to metal sites 1 or 2 in the presence of Mg2+, but does bind to four other sites with partial occupancy. Two of four Tl+ sites probably represent alternative binding sites for the site 3 catalytic Mg2+, whereas the other sites could play roles in monovalent cation activation.
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Affiliation(s)
- Jun-Yong Choe
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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41
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Howerton SB, Nagpal A, Williams LD. Surprising roles of electrostatic interactions in DNA-ligand complexes. Biopolymers 2003; 69:87-99. [PMID: 12717724 DOI: 10.1002/bip.10319] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The positions of cations in x-ray structures are modulated by sequence, conformation, and ligand interactions. The goal here is to use x-ray diffraction to help resolve structural and thermodynamic roles of specifically localized cations in DNA-anthracycline complexes. We describe a 1.34 A resolution structure of a CGATCG(2)-adriamycin(2) complex obtained from crystals grown in the presence of thallium (I) ions. Tl(+) can substitute for biological monovalent cations, but is readily detected by distinctive x-ray scattering, obviating analysis of subtle differences in coordination geometry and x-ray scattering of water, sodium, potassium, and ammonium. Six localized Tl(+) sites are observable adjacent to each CGATCG(2)-adriamycin(2) complex. Each of these localized monovalent cations are found within the G-tract major groove of the intercalated DNA-drug complex. Adriamycin appears to be designed by nature to interact favorably with the electrostatic landscape of DNA, and to conserve the distribution of localized cationic charge. Localized inorganic cations in the major groove are conserved upon binding of adriamycin. In the minor groove, inorganic cations are substituted by a cationic functional group of adriamycin. This partitioning of cationic charge by adriamycin into the major groove of CG base pairs and the minor groove of AT base pairs may be a general feature of sequence-specific DNA-small molecule interactions and a potentially useful important factor in ligand design.
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Affiliation(s)
- Shelley B Howerton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta 30332-0400, USA
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42
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Stieglitz KA, Johnson KA, Yang H, Roberts MF, Seaton BA, Head JF, Stec B. Crystal structure of a dual activity IMPase/FBPase (AF2372) from Archaeoglobus fulgidus. The story of a mobile loop. J Biol Chem 2002; 277:22863-74. [PMID: 11940584 DOI: 10.1074/jbc.m201042200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Several hyperthermophilic organisms contain an unusual phosphatase that has dual activity toward inositol monophosphates and fructose 1,6-bisphosphate. The structure of the second member of this family, an FBPase/IMPase from Archaeoglobus fulgidus (AF2372), has been solved. This enzyme shares many kinetic and structural similarities with that of a previously solved enzyme from Methanococcus jannaschii (MJ0109). It also shows some kinetic differences in divalent metal ion binding as well as structural variations at the dimer interface that correlate with decreased thermal stability. The availability of different crystal forms allowed us to investigate the effect of the presence of ligands on the conformation of a mobile catalytic loop independently of the crystal packing. This conformational variability in AF2372 is compared with that observed in other members of this structural family that are sensitive or insensitive to submillimolar concentrations of Li(+). This analysis provides support for the previously proposed mechanism of catalysis involving three metal ions. A direct correlation of the loop conformation with strength of Li(+) inhibition provides a useful system of classification for this extended family of enzymes.
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Affiliation(s)
- Kimberly A Stieglitz
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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43
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Abstract
Lithium is highly effective in the treatment of bipolar disorder and also has multiple effects on embryonic development, glycogen synthesis, hematopoiesis, and other processes. However, the mechanism of lithium action is still unclear. A number of enzymes have been proposed as potential targets of lithium action, including inositol monophosphatase, a family of structurally related phosphomonoesterases, and the protein kinase glycogen synthase kinase-3. These potential targets are widely expressed, require metal ions for catalysis, and are generally inhibited by lithium in an uncompetitive manner, most likely by displacing a divalent cation. Thus, the challenge is to determine which target, if any, is responsible for a given response to lithium in cells. Comparison of lithium effects with genetic disruption of putative target molecules has helped to validate these targets, and the use of alternative inhibitors of a given target can also lend strong support for or against a proposed mechanism of lithium action. In this review, lithium sensitive enzymes are discussed, and a number of criteria are proposed to evaluate which of these enzymes are involved in the response to lithium in a given setting.
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Affiliation(s)
- C J Phiel
- Department of Medicine and Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104. USA.
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44
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Abstract
Many RNAs, including the ribosome, RNase P, and the group II intron, explicitly require monovalent cations for activity in vitro. Although the necessity of monovalent cations for RNA function has been known for more than a quarter of a century, the characterization of specific monovalent metal sites within large RNAs has been elusive. Here we describe a biochemical approach to identify functionally important monovalent cations in nucleic acids. This method uses thallium (Tl+), a soft Lewis acid heavy metal cation with chemical properties similar to those of the physiological alkaline earth metal potassium (K+). Nucleotide analog interference mapping (NAIM) with the sulfur-substituted nucleotide 6-thioguanosine in combination with selective metal rescue of the interference with Tl+ provides a distinct biochemical signature for monovalent metal ion binding. This approach has identified a K+ binding site within the P4-P6 domain of the Tetrahymena group I intron that is also present within the X-ray crystal structure. The technique also predicted a similar binding site within the Azoarcus group I intron where the structure is not known. The approach is applicable to any RNA molecule that can be transcribed in vitro and whose function can be assayed.
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Affiliation(s)
- S Basu
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
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45
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De Wall SL, Meadows ES, Barbour LJ, Gokel GW. Synthetic receptors as models for alkali metal cation-pi binding sites in proteins. Proc Natl Acad Sci U S A 2000; 97:6271-6. [PMID: 10841532 PMCID: PMC18592 DOI: 10.1073/pnas.97.12.6271] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The alkali metal cations Na(+) and K(+) have several important physiological roles, including modulating enzyme activity. Recent work has suggested that alkali metal cations may be coordinated by pi systems, such as the aromatic amino acid side chains. The ability of K(+) to interact with an aromatic ring has been assessed by preparing a family of synthetic receptors that incorporate the aromatic side chains of phenylalanine, tyrosine, and tryptophan. These receptors are constructed around a diaza-18-crown-6 scaffold, which serves as the primary binding site for an alkali metal cation. The ability of the aromatic rings to coordinate a cation was determined by crystallizing each of the receptors in the presence of K(+) and by solving the solid state structures. In all cases, complexation of K(+) by the pi system was observed. When possible, the structures of the unbound receptors also were determined for comparison. Further proof that the aromatic ring makes an energetically favorable interaction with the cation was obtained by preparing a receptor in which the arene was perfluorinated. Fluorination of the arene reverses the electrostatics, but the aromaticity is maintained. The fluorinated arene rings do not coordinate the cation in the solid state structure of the K(+) complex. Thus, the results of the predicted electrostatic reversal were confirmed. Finally, the biological implications of the alkali metal cation-pi interaction are addressed.
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Affiliation(s)
- S L De Wall
- Bioorganic Chemistry Program and Department of Molecular Biology and Pharmacology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
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46
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Tasevski V, Benn D, King M, Luttrell B, Simpson A. Mitogenic effect of lithium in FRTL-5 cells can be reversed by blocking de novo cholesterol synthesis and subsequent signal transduction. Thyroid 2000; 10:305-11. [PMID: 10807058 DOI: 10.1089/thy.2000.10.305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Lithium therapy is the therapeutic mainstay for bipolar disorder and has been associated in the thyroid with euthymic goiter, hyper and hypothyroidism as well as thyroid autoimmune disease. The FRTL-5 cell line is a well known model of thyroid cell physiology, where lithium has been shown to increase 3H-thymidine uptake at concentrations of 2 mM. This mitogenic effect was not associated with adenylate cyclase as measured by cyclic adenosine monophosphate (cAMP) production. The de novo synthesis of cholesterol is an important signal transduction pathway in FRTL-5 cells, where newly synthesized Rho GTPase is geranylgeranylated, enabling membrane localization of the G-protein and subsequent G1 to S-phase transition, resulting from extracellular stimulation. Here we confirm lithium mitogenicity at therapeutically relevant concentrations (1 mM) and demonstrate a lithium-associated accumulation of FRTL-5 cells in S-phase of the cell cycle. These effects could be abolished by Pravastatin, a potent inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA), the rate-limiting enzyme in the formation of intermediates (de novo cholesterol synthesis) required for G-protein prenylation. Pravastatin, similar to lithium, showed no effect on cAMP production either under basal or thyroid stimulating hormone (TSH)-stimulated conditions indicating that de novo cholesterol synthesis is not involved with adenylate cyclase. The inhibitory effect of pravastatin could be overcome by reinitiating de novo cholesterol synthesis. This was achieved by the addition of the cell permeable, first metabolite (mevalonate) after HMG-CoA, which allowed the cycle to continue, leading eventually to protein prenylation, despite the presence of Pravastatin. These novel findings demonstrate lithium involvement in de novo cholesterol synthesis and G-protein prenylation, an important signal transduction pathway in FRTL-5 cells.
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Affiliation(s)
- V Tasevski
- Department of Endocrinology, Royal North Shore Hospital, St. Leonards, NSW, Australia.
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47
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Lin T, Kornblatt MJ. The binding of Na(+) to apo-enolase permits the binding of substrate. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1476:279-86. [PMID: 10669792 DOI: 10.1016/s0167-4838(99)00233-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Enolase from rabbit muscle (betabeta-enolase) is inactivated by NaClO(4). Enolase free of divalent cations is more susceptible to inactivation by NaClO(4) than is enolase in the presence of Mg(2+). We find that substrate protects apo-enolase against inactivation, indicating that substrate can bind to enolase in the absence of a divalent cation. This binding is not due to contamination by trace levels of divalent cations since (1) it occurs even in the presence of EDTA or EGTA and (2) metal analysis by ICP (inductively coupled plasma) mass spectrometry did not reveal sufficient contamination to account for the protection. The binding of PGA to apo-enolase did require Na(+). When TMAClO(4) was used instead of NaClO(4), there was no protection by PGA. Protection was restored when TMAClO(4) plus NaCl were used. The inactivation of apo-enolase by NaClO(4) is due to dissociation into inactive monomers. We conclude that Na(+) binds to apo-enolase, permitting substrate to then bind. Of the three known Me(2+) binding sites on enolase, we believe the most likely binding site for Na(+) is the carboxylate cluster of site 1, the highest affinity site of enolase.
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Affiliation(s)
- T Lin
- Enzyme Research Group, Department of Chemistry and Biochemistry, Concordia University, 1455 de Maisonneuve Boulevard W., Montreal, Que., Canada
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48
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Ludwig HC, Herrera R, Reyes AM, Hubert E, Slebe JC. Suppression of kinetic AMP cooperativity of fructose-1,6-bisphosphatase by carbamoylation of lysine 50. JOURNAL OF PROTEIN CHEMISTRY 1999; 18:533-45. [PMID: 10524771 DOI: 10.1023/a:1020647116022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Selective treatment of pig kidney fructose 1,6-bisphosphatase with cyanate leads to the formation of an active carbamoylated derivative that shows no cooperative interaction between the AMP-binding sites, but completely retains the sensitivity to the inhibitor. By an exhaustive carbamoylation of the enzyme a derivative is formed that has a complete loss of cooperativity and a decrease of sensitivity to AMP. It was proposed that the observed changes of allosteric properties were due to the chemical modification of two lysine residues per enzyme subunit [Slebe et al. (1983), J. Protein Chem. 2, 437-443]. Studies of the temperature dependence of AMP sensitivity and the interaction with Cibacron Blue Sepharose of carbamoylated fructose 1,6-bisphosphatase derivatives indicate that the lysine residue involved in AMP sensitivity is located at the allosteric AMP site, while the lysine residue involved in AMP cooperativity is at a distinct location. Using [14C]cyanate, we identified both lysine residues in the primary structure of the enzyme; Lys50 is essential for AMP cooperativity and Lys112 appears to be the reactive residue involved in the AMP sensitivity. According to the fructose 1,6-bisphosphatase crystal structure, Lys50 is strategically positioned at the C1-C2 interface, near the molecular center of the tetramer, and Lys112 is in the AMP-binding site. The results reported here, combined with the structural data of the enzyme, strongly suggest that the C1-C2 interface is critical for the propagation of the allosteric signal among the AMP sites on different subunits.
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Affiliation(s)
- H C Ludwig
- Instituto de Bioquímica, Facultad de Ciencias, Universidad Austral de Chile, Valdivia
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49
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Spiegelberg BD, Xiong JP, Smith JJ, Gu RF, York JD. Cloning and characterization of a mammalian lithium-sensitive bisphosphate 3'-nucleotidase inhibited by inositol 1,4-bisphosphate. J Biol Chem 1999; 274:13619-28. [PMID: 10224133 DOI: 10.1074/jbc.274.19.13619] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Discovery of a structurally conserved metal-dependent lithium-inhibited phosphomonoesterase protein family has identified several potential cellular targets of lithium as used to treat manic depression. Here we describe identification of a novel family member using a "computer cloning" strategy. Human and murine cDNA clones encoded proteins sharing 92% identity and were highly expressed in kidney. Native and recombinant protein harbored intrinsic magnesium-dependent bisphosphate nucleotidase activity (BPntase), which removed the 3'-phosphate from 3'-5' bisphosphate nucleosides and 3'-phosphoadenosine 5'-phosphosulfate with Km and Vmax values of 0.5 microM and 40 micromol/min/mg. Lithium uncompetitively inhibited activity with a Ki of 157 microM. Interestingly, BPntase was competitively inhibited by inositol 1,4-bisphosphate with a Ki of 15 microM. Expression of mammalian BPntase complemented defects in hal2/met22 mutant yeast. These data suggest that BPntase's physiologic role in nucleotide metabolism may be regulated by inositol signaling pathways. The presence of high levels of BPntase in the kidney are provocative in light of the roles of bisphosphorylated nucleotides in regulating salt tolerance, sulfur assimilation, detoxification, and lithium toxicity. We propose that inhibition of human BPntase may account for lithium-induced nephrotoxicity, which may be overcome by supplementation of current therapeutic regimes with inhibitors of nucleotide biosynthesis, such as methionine.
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Affiliation(s)
- B D Spiegelberg
- Departments of Pharmacology & Cancer Biology and Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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50
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Dionisi HM, Alvarez CV, Viale AM. Alkali metal ions protect mitochondrial rhodanese against thermal inactivation. Arch Biochem Biophys 1999; 361:202-6. [PMID: 9882447 DOI: 10.1006/abbi.1998.0944] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Incubation of bovine liver mitochondrial rhodanese in dilute, reducing solutions at temperatures ranging between 30 and 45 degreesC conduced to a rapid loss of enzymatic activity. This inactivation was substantially reduced in the presence of millimolar concentrations of alkali metal ions, divalent cations (including Mg2+, Ca2+, and Ba2+) were ineffective. The extent of protection afforded by monovalent cations was highly dependent on their ionic radii, with K+ and Na+ ions being the most effective protective agents. The protection afforded by a number of anions, including thiosulfate, could be totally ascribed to the presence of the accompanying monovalent cation. The overall results indicate that K+ and Na+, at concentrations and temperatures within the physiological range, substantially contribute to the stabilization of the functional structure of rhodanese.
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Affiliation(s)
- H M Dionisi
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
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