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Mamot A, Sikorski PJ, Siekierska A, de Witte P, Kowalska J, Jemielity J. Ethylenediamine derivatives efficiently react with oxidized RNA 3' ends providing access to mono and dually labelled RNA probes for enzymatic assays and in vivo translation. Nucleic Acids Res 2021; 50:e3. [PMID: 34591964 PMCID: PMC8755103 DOI: 10.1093/nar/gkab867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/31/2021] [Accepted: 09/15/2021] [Indexed: 01/01/2023] Open
Abstract
Development of RNA-based technologies relies on the ability to detect, manipulate, and modify RNA. Efficient, selective and scalable covalent modification of long RNA molecules remains a challenge. We report a chemical method for modification of RNA 3′-end based on previously unrecognized superior reactivity of N-substituted ethylenediamines in reductive amination of periodate-oxidized RNA. Using this method, we obtained fluorescently labelled or biotinylated RNAs varying in length (from 3 to 2000 nt) and carrying different 5′ ends (including m7G cap) in high yields (70–100% by HPLC). The method is scalable (up to sub-milligrams of mRNA) and combined with label-facilitated HPLC purification yields highly homogeneous products. The combination of 3′-end labelling with 5′-end labelling by strain-promoted azide-alkyne cycloaddition (SPAAC) afforded a one-pot protocol for site-specific RNA bifunctionalization, providing access to two-colour fluorescent RNA probes. These probes exhibited fluorescence resonance energy transfer (FRET), which enabled real-time monitoring of several RNA hydrolase activities (RNase A, RNase T1, RNase R, Dcp1/2, and RNase H). Dually labelled mRNAs were efficiently translated in cultured cells and in zebrafish embryos, which combined with their detectability by fluorescent methods and scalability of the synthesis, opens new avenues for the investigation of mRNA metabolism and the fate of mRNA-based therapeutics.
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Affiliation(s)
- Adam Mamot
- Centre of New Technologies, University of Warsaw, Banacha 2c Street, 02-097 Warsaw, Poland.,Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c Street, 02-097 Warsaw, Poland
| | - Aleksandra Siekierska
- Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg, Herestraat 49, O&N II, 3000 Leuven, Belgium
| | - Peter de Witte
- Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg, Herestraat 49, O&N II, 3000 Leuven, Belgium
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c Street, 02-097 Warsaw, Poland
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Savio LEB, de Andrade Mello P, da Silva CG, Coutinho-Silva R. The P2X7 Receptor in Inflammatory Diseases: Angel or Demon? Front Pharmacol 2018; 9:52. [PMID: 29467654 PMCID: PMC5808178 DOI: 10.3389/fphar.2018.00052] [Citation(s) in RCA: 283] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
Under physiological conditions, adenosine triphosphate (ATP) is present at low levels in the extracellular milieu, being massively released by stressed or dying cells. Once outside the cells, ATP and related nucleotides/nucleoside generated by ectonucleotidases mediate a high evolutionary conserved signaling system: the purinergic signaling, which is involved in a variety of pathological conditions, including inflammatory diseases. Extracellular ATP has been considered an endogenous adjuvant that can initiate inflammation by acting as a danger signal through the activation of purinergic type 2 receptors-P2 receptors (P2Y G-protein coupled receptors and P2X ligand-gated ion channels). Among the P2 receptors, the P2X7 receptor is the most extensively studied from an immunological perspective, being involved in both innate and adaptive immune responses. P2X7 receptor activation induces large-scale ATP release via its intrinsic ability to form a membrane pore or in association with pannexin hemichannels, boosting purinergic signaling. ATP acting via P2X7 receptor is the second signal to the inflammasome activation, inducing both maturation and release of pro-inflammatory cytokines, such as IL-1β and IL-18, and the production of reactive nitrogen and oxygen species. Furthermore, the P2X7 receptor is involved in caspases activation, as well as in apoptosis induction. During adaptive immune response, P2X7 receptor modulates the balance between the generation of T helper type 17 (Th17) and T regulatory (Treg) lymphocytes. Therefore, this receptor is involved in several inflammatory pathological conditions. In infectious diseases and cancer, P2X7 receptor can have different and contrasting effects, being an angel or a demon depending on its level of activation, cell studied, type of pathogen, and severity of infection. In neuroinflammatory and neurodegenerative diseases, P2X7 upregulation and function appears to contribute to disease progression. In this review, we deeply discuss P2X7 receptor dual function and its pharmacological modulation in the context of different pathologies, and we also highlight the P2X7 receptor as a potential target to treat inflammatory related diseases.
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Affiliation(s)
- Luiz E B Savio
- Laboratory of Immunophysiology, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paola de Andrade Mello
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, MA, United States
| | - Cleide Gonçalves da Silva
- Division of Vascular Surgery, Department of Surgery, Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Robson Coutinho-Silva
- Laboratory of Immunophysiology, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Figliuolo VR, Chaves SP, Santoro GF, Coutinho CMLM, Meyer-Fernandes JR, Rossi-Bergmann B, Coutinho-Silva R. Periodate-oxidized ATP modulates macrophage functions during infection with Leishmania amazonensis. Cytometry A 2014; 85:588-600. [PMID: 24804957 DOI: 10.1002/cyto.a.22449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 11/30/2013] [Accepted: 01/27/2014] [Indexed: 12/11/2022]
Abstract
Previously, we showed that treating macrophages with ATP impairs the intracellular growth of Leishmania amazonensis, and that the P2X7 purinergic receptor is overexpressed during leishmaniasis. In the present study, we directly evaluated the effect of periodate-oxidized ATP (oATP) on parasite control in Leishmania-infected macrophages. We found that oATP impaired the attachment/entrance of L. amazonensis promastigotes to C57BL/6 mouse macrophages in a P2X7 receptor-independent manner, as macrophages from P2X7(-/-) mice were similarly affected. Although oATP directly inhibited the growth of axenic promastigotes in culture, promoted rapid ultrastructural alterations, and impaired Leishmania internalization by macrophages, it did not affect intracellular parasite multiplication. Upon infection, phagosomal acidification was diminished in oATP-treated macrophages, accompanied by reduced endosomal proteolysis. Likewise, MHC class II molecules expression and ectoATPase activity was decreased by oATP added to macrophages at the time of parasite infection. These inhibitory effects were not due to a cytotoxic effect, as no additional release of lactate dehydrogenase was detected in culture supernatants. Moreover, the capacity of macrophages to produce nitric oxide and reactive oxygen species was not affected by the presence of oATP during infection. We conclude that oATP directly affects extracellular parasite integrity and macrophage functioning.
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Affiliation(s)
- V R Figliuolo
- Laboratório de Imunofisiologia, Instituto de Biofísica Carlos Chagas Filho-IBCCF, Universidade Federal do Rio de Janeiro, RJ, Brazil; Instituto Nacional para Pesquisa Translacional em Saúde e Ambiente na Região Amazônica, Conselho Nacional de Desenvolvimento Científico e Tecnológico/MCT, Brasil
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P2X7 purinoceptors contribute to the death of Schwann cells transplanted into the spinal cord. Cell Death Dis 2013; 4:e829. [PMID: 24091672 PMCID: PMC3824653 DOI: 10.1038/cddis.2013.343] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/17/2013] [Accepted: 08/05/2013] [Indexed: 02/04/2023]
Abstract
The potential to use Schwann cells (SCs) in neural repair for patients suffering from neurotrauma and neurodegenerative diseases is well recognized. However, significant cell death after transplantation hinders the clinical translation of SC-based therapies. Various factors may contribute to the death of transplanted cells. It is known that prolonged activation of P2X7 purinoceptors (P2X7R) can lead to death of certain types of cells. In this study, we show that rat SCs express P2X7R and exposure of cultured SCs to high concentrations of ATP (3-5 mM) or a P2X7R agonist, 2'(3')-O-(4-benzoylbenzoyl)ATP (BzATP) induced significant cell death rapidly. High concentrations of ATP and BzATP increased ethidium uptake by SCs, indicating increased membrane permeability to large molecules, a typical feature of prolonged P2X7R activation. SC death, as well as ethidium uptake, induced by ATP was blocked by an irreversible P2X7R antagonist oxidized ATP (oxATP) or a reversible P2X7R antagonist A438079. oxATP also significantly inhibits the increase of intracellular free calcium induced by minimolar ATP concentrations. Furthermore, ATP did not cause death of SCs isolated from P2X7R-knockout mice. All these results suggest that P2X7R is responsible for ATP-induced SC death in vitro. When rat SCs were treated with oxATP before transplantation into uninjured rat spinal cord, 35% more SCs survived than untreated SCs 1 week after transplantation. Moreover, 58% more SCs isolated from P2X7R-knockout mice survived after being transplanted into rat spinal cord than SCs from wild-type mice. This further confirms that P2X7R is involved in the death of transplanted SCs. These results indicate that targeting P2X7R on SCs could be a potential strategy to improve the survival of transplanted cells. As many other types of cells, including neural stem cells, also express P2X7R, deactivating P2X7R may improve the survival of other types of transplanted cells.
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Boyarshin KS, Priss AE, Kriklivyi IA, Kovalenko OP, Yaremchuk AD, Tukalo MA. Role of tRNAPro in pretransfer editing of alanine by prolyl-tRNA synthetase. ACTA ACUST UNITED AC 2013. [DOI: 10.7124/bc.00082d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- K. S. Boyarshin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. E. Priss
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - I. A. Kriklivyi
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - O. P. Kovalenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. D. Yaremchuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - M. A. Tukalo
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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Hountondji C, Bulygin K, Woisard A, Tuffery P, Créchet JB, Pech M, Nierhaus KH, Karpova G, Baouz S. Lys53 of Ribosomal Protein L36AL and the CCA End of a tRNA at the P/E Hybrid Site Are in Close Proximity on the Human Ribosome. Chembiochem 2012; 13:1791-7. [DOI: 10.1002/cbic.201200208] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Ikawa Y, Moriyama S, Furuta H. Facile syntheses of BODIPY derivatives for fluorescent labeling of the 3′ and 5′ ends of RNAs. Anal Biochem 2008; 378:166-70. [DOI: 10.1016/j.ab.2008.03.054] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2008] [Revised: 03/19/2008] [Accepted: 03/24/2008] [Indexed: 10/22/2022]
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Gritsenko OM, Gromova ES. Dialdehyde-containing nucleic acids and their components: synthesis, properties and affinity modification of proteins. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1999v068n03abeh000489] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rodina EV, Vorobyeva NN, Kurilova SA, Belenikin MS, Fedorova NV, Nazarova TI. ATP as effector of inorganic pyrophosphatase of Escherichia coli. Identification of the binding site for ATP. BIOCHEMISTRY (MOSCOW) 2007; 72:93-9. [PMID: 17309442 DOI: 10.1134/s0006297907010117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interaction of Escherichia coli inorganic pyrophosphatase (E-PPase) with effector ATP has been studied. The E-PPase has been chemically modified with the dialdehyde derivative of ATP. It has been established that in the experiment only one molecule of effector ATP is bound to each subunit of the hexameric enzyme. Tryptic digestion of the adenylated protein followed by isolation of a modified peptide by HPLC and its mass-spectrometric identification has showed that it is an amino group of Lys146 that undergoes modification. Molecular docking of ATP to E-PPase indicates that the binding site for effector ATP is located in a cluster of positively charged amino acid residues proposed earlier on the basis of site-directed mutagenesis to participate in binding of effector pyrophosphate. Molecular docking also reveals several other amino acid residues probably involved in the interaction with effectors.
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Affiliation(s)
- E V Rodina
- Chemical Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.
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Tatarintsev NP, Malyan AN. Covalent Binding of 1,N 6-ethenoadenosine diphosphate to catalytic and noncatalytic sites of chloroplast ATP synthase. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906020138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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MacLeod TJ, Lunn FA, Bearne SL. The role of lysine residues 297 and 306 in nucleoside triphosphate regulation of E. coli CTP synthase: inactivation by 2',3'-dialdehyde ATP and mutational analyses. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1764:199-210. [PMID: 16427816 DOI: 10.1016/j.bbapap.2005.11.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 11/16/2005] [Accepted: 11/28/2005] [Indexed: 11/24/2022]
Abstract
Cytidine 5'-triphosphate synthase (CTPS) catalyzes the ATP-dependent formation of CTP from UTP using either NH3 or L-glutamine as the source of nitrogen. To identify the location of the ATP-binding site within the primary structure of E. coli CTPS, we used the affinity label 2',3'-dialdehyde adenosine 5'-triphosphate (oATP). oATP irreversibly inactivated CTPS in a first-order, time-dependent manner while ATP protected the enzyme from inactivation. In the presence of 10 mM UTP, the values of k(inact) and K(I) were 0.054 +/- 0.001 min(-1) and 3.36 +/- 0.02 mM, respectively. CTPS was labeled using (2,8-3H)oATP and subsequently subjected to trypsin-catalyzed proteolysis. The tryptic peptides were separated using reversed-phase HPLC, and two peptides were identified using N-terminal sequencing (S(492)GDDQLVEIIEVPNH(506) and Y(298)IELPDAY(K(306)) in a 5:1 ratio). The latter suggested that Lys 306 had been modified by oATP. Replacement of Lys 306 by alanine reduced the rate of oATP-dependent inactivation (k(inact) = 0.0058 +/- 0.0005 min(-1), K(I) = 3.7 +/- 1.3 mM) and reduced the apparent affinity of CTPS for both ATP and UTP by approximately 2-fold. The efficiency of K306A-catalyzed glutamine-dependent CTP formation was also reduced 2-fold while near wild-type activity was observed when NH3 was the substrate. These findings suggest that Lys 306 is not essential for ATP binding, but does play a role in bringing about the conformational changes that mediate interactions between the ATP and UTP sites, and between the ATP-binding site and the glutamine amide transfer domain. Replacement of the nearby, fully conserved Lys 297 by alanine did not affect NH3-dependent CTP formation, relative to wild-type CTPS, but reduced k(cat) for the glutaminase activity 78-fold. Our findings suggest that the conformational change associated with binding ATP may be transmitted through the L10-alpha11 structural unit (residues 297-312) and thereby mediate effects on the glutaminase activity of CTPS.
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Affiliation(s)
- Travis J MacLeod
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
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Villanueva RA, Guacucano M, Pizarro J, Sandino AM. Inhibition of virion-associated IPNV RNA polymerase, VP1, by radiolabeled nucleotide analogs. Virus Res 2005; 112:132-5. [PMID: 16022907 DOI: 10.1016/j.virusres.2005.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Revised: 10/19/2004] [Accepted: 02/23/2005] [Indexed: 11/21/2022]
Abstract
Infectious pancreatic necrosis virus (IPNV) is a bi-segmented, dsRNA virus of the Birnaviridae family. The structural protein VP1 has been postulated as the RNA-dependent RNA polymerase (RdRp), but its transcriptional activity has not been unequivocally identified from viral particles. Here, we assayed partially purified IPNV in an in vitro RNA synthesis system. To test the RdRp, dialdehyde-nucleotide analogs were used to covalently inhibit the polymerase-associated activity. Our results showed that dialdehyde-nucleotide analogs completely abrogated IPNV in vitro RNA synthesis. The protein involved in this process was identified as viral VP1, since: (a) after incubation of IPNV with [alpha-(32)P]2',3'-dialdehyde-UTP, labeled VP1 protein was identified and (b) VP1 was unable to bind [alpha-(32)P]GTP when particles were preincubated with 2',3'-dialdehyde-ATP. Thus, within viral particles, inhibition of the transcriptional activity is a result of the binding of 2',3'-dialdehyde-nucleotide analogs to the RdRp, VP1.
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Affiliation(s)
- Rodrigo A Villanueva
- Laboratorio de Virología, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, P.O. Box 40, Santiago 33, Chile.
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Beigi RD, Kertesy SB, Aquilina G, Dubyak GR. Oxidized ATP (oATP) attenuates proinflammatory signaling via P2 receptor-independent mechanisms. Br J Pharmacol 2004; 140:507-19. [PMID: 14522842 PMCID: PMC1574058 DOI: 10.1038/sj.bjp.0705470] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Periodate-oxidized ATP (oATP), which covalently modifies nucleotide-binding proteins, can significantly attenuate proinflammatory signaling. Although the P2X7 nucleotide receptor (P2X7R) is irreversibly antagonized by oATP, it is unclear whether anti-inflammatory actions of oATP are predominantly mediated via its actions on P2X7R. Here, we describe inhibitory effects of oATP on proinflammatory responses in three human cell types that lack expression of P2X7R: human umbilical vein endothelial cells (HUVEC), HEK293 cells, and 1321N1 astrocytes. oATP decreased by 40-70% the secretion of interleukin (IL)-8 stimulated by tumor necrosis factor-alpha (TNF-alpha) in all three cell types, by IL-1beta in HUVEC and 1321N1 cells, and by endotoxin in HUVEC. Attenuation of TNF-alpha-stimulated IL-8 secretion by oATP was similar in wild-type HEK cells or HEK cells stably expressing recombinant P2X7R. oATP also attenuated cytokine-stimulated expression of nuclear factor-kappaB-luciferase reporter genes expressed in HEK or 1321N1 cells, but did not affect the rapid downregulation of IkappaB. oATP had no effect on uridine triphosphate-induced activation of native P2Y2 receptors in HEK cells, but reduced the potency and efficacy of ADP as an agonist of native P2Y1 receptors. However, inhibition of P2Y1 receptors with the specific antagonist MRS2216 did not mimic the effects of oATP on TNF-alpha-stimulated IL-8 secretion. Although 1321N1 astrocytes lack expression of any known P2 receptor subtypes, oATP markedly inhibited ecto-ATPase activity in these cells, resulting in a significant accumulation of extracellular ATP. In summary, oATP can attenuate proinflammatory signaling by mechanisms independent of the expression or activation of known P2 receptor subtypes.
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Affiliation(s)
- Reza D Beigi
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, U.S.A
| | - Sylvia B Kertesy
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, U.S.A
| | - Gretchen Aquilina
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, U.S.A
| | - George R Dubyak
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, U.S.A
- Author for correspondence:
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15
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Shepel PN, Holden CP, Geiger JD. Ryanodine receptor modulation by diadenosine polyphosphates in synaptosomal and microsomal preparations of rat brain. Eur J Pharmacol 2003; 467:67-71. [PMID: 12706456 DOI: 10.1016/s0014-2999(03)01593-0] [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: 11/28/2022]
Abstract
Diadenosine polyphosphates (Ap(n)As) are transmitter-like substances that act intracellularly via unclear mechanisms. Here we tested hypotheses that diadenosine tetraphosphate (Ap(4)A) modulates ryanodine binding in microsomal and synaptosomal fractions of rat brain, and that Ap(4)A affects modulation of ryanodine binding by divalent cations and caffeine. Using [3H]ryanodine-binding assays, we showed that Ap(4)A produced significant and concentration-dependent increases in [3H]ryanodine binding in microsomes and these actions were reduced by Mg(2+) and potentiated by caffeine. In synaptosomal subfractions, effects of Ap(4)A on [3H]ryanodine binding were most profound in subfractions enriched in synaptic vesicle-associated protein synaptophysin. These results suggest that Ap(n)As and ryanodine receptors are well placed to modulate Ca(2+)-dependent synaptic processes.
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Affiliation(s)
- P Nickolas Shepel
- Department of Pharmacology and Therapeutics, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada R2H 2A6
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Thomas BC, Kazantsev AV, Chen JL, Pace NR. Photoaffinity cross-linking and RNA structure analysis. Methods Enzymol 2001; 318:136-47. [PMID: 10889985 DOI: 10.1016/s0076-6879(00)18049-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- B C Thomas
- Department of Plant and Microbial Biology, University of California, Berkeley 94720-3102, USA
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Labrou NE, Rigden DJ, Clonis YD. Characterization of the NAD+ binding site of Candida boidinii formate dehydrogenase by affinity labelling and site-directed mutagenesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:6657-64. [PMID: 11054119 DOI: 10.1046/j.1432-1327.2000.01761.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The 2',3'-dialdehyde derivative of ADP (oADP) has been shown to be an affinity label for the NAD+ binding site of recombinant Candida boidinii formate dehydrogenase (FDH). Inactivation of FDH by oADP at pH 7.6 followed biphasic pseudo first-order saturation kinetics. The rate of inactivation exhibited a nonlinear dependence on the concentration of oADP, which can be described by reversible binding of reagent to the enzyme (Kd = 0.46 mM for the fast phase, 0.45 mM for the slow phase) prior to the irreversible reaction, with maximum rate constants of 0.012 and 0.007 min-1 for the fast and slow phases, respectively. Inactivation of formate dehydrogenase by oADP resulted in the formation of an enzyme-oADP product, a process that was reversed after dialysis or after treatment with 2-mercaptoethanol (> 90% reactivation). The reactivation of the enzyme by 2-mercaptoethanol was prevented if the enzyme-oADP complex was previously reduced by NaBH4, suggesting that the reaction product was a stable Schiff's base. Protection from inactivation was afforded by nucleotides (NAD+, NADH and ADP) demonstrating the specificity of the reaction. When the enzyme was completely inactivated, approximately 1 mol of [14C]oADP per mol of subunit was incorporated. Cleavage of [14C]oADP-modified enzyme with trypsin and subsequent separation of peptides by RP-HPLC gave only one radioactive peak. Amino-acid sequencing of the radioactive tryptic peptide revealed the target site of oADP reaction to be Lys360. These results indicate that oADP inactivates FDH by specific reaction at the nucleotide binding site, with negative cooperativity between subunits accounting for the appearance of two phases of inactivation. Molecular modelling studies were used to create a model of C. boidinii FDH, based on the known structure of the Pseudomonas enzyme, using the MODELLER 4 program. The model confirmed that Lys360 is positioned at the NAD+-binding site. Site-directed mutagenesis was used in dissecting the structure and functional role of Lys360. The mutant Lys360-->Ala enzyme exhibited unchanged kcat and Km values for formate but showed reduced affinity for NAD+. The molecular model was used to help interpret these biochemical data concerning the Lys360-->Ala enzyme. The data are discussed in terms of engineering coenzyme specificity.
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Affiliation(s)
- N E Labrou
- Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, Greece
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Ermolinsky BS, Mikhailov SN. Periodate oxidation in chemistry of nucleic acids: Dialdehyde derivatives of nucleosides, nucleotides, and oligonucleotides (Review). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2000. [DOI: 10.1007/bf02758613] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mitterauer T, Nanoff C, Ahorn H, Freissmuth M, Hohenegger M. Metal-dependent nucleotide binding to the Escherichia coli rotamase SlyD. Biochem J 1999; 342 ( Pt 1):33-9. [PMID: 10432297 PMCID: PMC1220433 DOI: 10.1042/0264-6021:3420033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Upon expression and purification of the first catalytic domain of mammalian adenylate cyclase type 1 (IC1), a 27 kDa contaminant was observed, which was labelled by three radioactive ATP analogues (8-azido-ATP, 3'-O-(4-benzoyl)benzoyl-ATP and 2',3'-dialdehyde-ATP); the protein was purified separately and identified as Escherichia coli SlyD by N-terminal amino acid sequence determination. SlyD is the host protein required for lysis of E. coli upon infection with bacteriophage PhiX174 and has recently been shown to display rotamase (peptidylproline cis-trans-isomerase) activity. The covalent incorporation of ATP analogues into SlyD was promoted by bivalent transition metal ions (Zn(2+)>/=Ni(2+)>Co(2+)>Cu(2+)) but not by Mg(2+) or Ca(2+); this is consistent with the known metal ion specificity of SlyD. ATP, ADP, GTP and UTP suppressed labelling of SlyD with comparable potencies. Similarly, SlyD bound 2',3'-O-(-2,4, 6-trinitrophenyl)-ATP with an affinity in the range of 10 microM, as determined by fluorescence enhancement. This interaction was further augmented in the presence of Zn(2+) (K(d)= approximately 2 microM at saturating Zn(2+)) but not of Mg(2+). Irrespective of the assay conditions, hydrolysis of nucleotides by SlyD was not detected. Upon gel filtration on a Superose HR12 column, SlyD (predicted molecular mass=21 kDa) migrated with an apparent molecular mass of 44 kDa, indicating that the protein was a dimer. However, the migration of SlyD was not affected by the presence of Zn(2+) or of Zn(2+) and ATP. Thus we concluded that SlyD binds nucleotides in the presence of metal ions. These findings suggest that SlyD serves a physiological role that goes beyond that accounted for by its intrinsic rotamase activity, which is observed in the absence of metal ions.
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Affiliation(s)
- T Mitterauer
- Institute of Pharmacology, University of Vienna, Währinger Str. 13a, A-1090 Vienna, Austria
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20
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Mitterauer T, Hohenegger M, Tang WJ, Nanoff C, Freissmuth M. The C2 catalytic domain of adenylyl cyclase contains the second metal ion (Mn2+) binding site. Biochemistry 1998; 37:16183-91. [PMID: 9819210 DOI: 10.1021/bi981441m] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane-bound mammalian adenylyl cyclase isoforms contain two internally homologous cytoplasmic domains (C1 and C2). When expressed separately, C1 and C2 are catalytically inactive, but conversion of ATP to cAMP is observed if C1 and C2 are combined. By analogy with DNA polymerases, adenylyl cyclases are thought to require two divalent metal ions for nucleotide binding and phosphodiester formation; however, only one Mg2+ ion (liganded to C1) has been visualized in the recently solved crystal structure of a C1-C2 complex [Tesmer, J. J. G., Sunahara, R. K., Gilman, A. G., and Sprang, S. R. (1997) Science 278, 1907-1916]. Here, we have studied the binding of ATP to IIC2 (from type II adenylyl cyclase) using ATP analogues [2',3'-dialdehyde ATP (oATP), a quasi-irreversible inhibitor that is covalently incorporated via reduction of a Schiff base, the photoaffinity ligand 8-azido-ATP (8N3-ATP), and trinitrophenyl-ATP (TNP-ATP), a fluorescent analogue] and fluorescein isothiocyanate (FITC). [alpha-32P]oATP and 8N-[alpha-32P]ATP are specifically incorporated into IIC2. Labeling of IIC2 by [alpha-32P]oATP and by FITC is greatly enhanced by Mn2+ and to a much lesser extent by Mg2+. Similarly, TNP-ATP binds to IIC2 as determined by fluorescence enhancement, and this binding is promoted by Mn2+. Thus, a second metal ion binding site (preferring Mn2+) is contained within the C2 domain, and this finding highlights the analogy in the reaction catalyzed by DNA polymerases and adenylyl cyclases.
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Affiliation(s)
- T Mitterauer
- Institute of Pharmacology, University of Vienna, Austria
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21
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Henke W, Hagen T, Jung K, Loening SA. Periodate-oxidized ATP stimulates the permeability transition of rat liver mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1363:209-16. [PMID: 9518617 DOI: 10.1016/s0005-2728(97)00103-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Periodate-oxidized ADP (oADP)2 and periodate-oxidized ATP (oATP) stimulate the permeability transition in energized rat liver mitochondria measured as the Ca2+-efflux induced by Ca2+ and Pi. In the presence of Mg2+ and Pi, mitochondria lose intramitochondrial adenine nucleotides at a slow rate. oATP induces a strong decrease of the matrix adenine nucleotides which is inhibited by carboxyatractyloside. Under these conditions, Mg2+ prevents the opening of the permeability transition pore. EGTA prevents the Pi-induced slow efflux of adenine nucleotides, but is without effect on the oATP-induced strong decrease of adenine nucleotides. This oATP-induced strong adenine nucleotide efflux is inhibited by ADP. oATP reduces the increase of matrix adenine nucleotides occurring when the mitochondria are incubated with Mg2+ and ATP. This effect of oATP is also prevented by carboxyatractyloside. oATP is not taken up by the mitochondria. It is suggested that oATP induces a strong efflux of matrix adenine nucleotides by the interaction with the ADP/ATP carrier from the cytosolic side. The induction of the mitochondrial permeability transition by oADP and oATP is attributed to two mechanisms-a strong decrease in the intramitochondrial adenine nucleotide content, especially that of ADP, and a stabilization of the c-conformation of the ADP/ATP carrier.
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Affiliation(s)
- W Henke
- Research Division, Department of Urology, University Hospital Charité, Humboldt University, Schumannstrasse 20/21, D-10098 Berlin, Germany.
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22
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Richards OC, Ehrenfeld E. One of two NTP binding sites in poliovirus RNA polymerase required for RNA replication. J Biol Chem 1997; 272:23261-4. [PMID: 9287335 DOI: 10.1074/jbc.272.37.23261] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The poliovirus RNA-dependent RNA polymerase (3Dpol) has been shown to contain two NTP binding sites by chemical cross-linking of oxidized nucleotide to the intact protein. Only one site (Lys-61) was shown to be essential for RNA chain elongation activity by purified enzyme; however, a full-length viral RNA, coding for an altered lysine residue (K276L) in the second site, generated virus with a minute plaque phenotype that rapidly reverted to a wild-type phenotype with Arg-276 replacing Leu-276 in 3D. Viruses with lysine to leucine substitutions in other positions of the second binding site of their polymerase proteins grew with wild-type phenotype. To test the significance of the second binding site, poliovirus 3Dpol was generated with lysine (wild-type), leucine, or arginine at residue 276 and tested for NTP cross-linking using 32P-oxidized GTP. Analysis of cyanogen bromide peptides of each 3D preparation showed that the second NTP binding site had severely reduced NTP binding in mu276(Leu) but not in the revertant mu276(Arg), despite the reported requirement for lysine in the cross-linking reaction. To eliminate the possibility that 32P-oxidized GTP cross-linked to Arg at residue 276, a model system was designed with unmodified amino acid or acetylated (alpha-amino) amino acid and 32P-oxidized GTP. Cross-linking to lysine, but not leucine or arginine, was observed thus eliminating the possibility that NTP could be cross-linked to residue 276 in 3D. We conclude that NTP binding at the second site in poliovirus 3D is at lysine residues at positions other than 276 (278 or 283), and nucleotide binding at these sites has no bearing on elongation activity or replication of the virus. Nucleotide binding only at the site including Lys-61 is essential for RNA replication.
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Affiliation(s)
- O C Richards
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.
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23
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Li Z, Phillips NF. Involvement and identification of a lysine in the PPi-site of pyrophosphate-dependent phosphofructokinase from Giardia lamblia. Biochimie 1997; 79:221-7. [PMID: 9242987 DOI: 10.1016/s0300-9084(97)83509-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The substrate binding and/or catalytic site of the pyrophosphate-dependent phosphofructokinase (PPi-PFK) of Giardia lamblia was investigated using an ATP affinity label, 2',3'-dialdehyde of ATP, oxidized ATP (oATP), for the involvement of lysine residues. The enzyme, which uses PPi rather than ATP as a substrate was inhibited by low concentrations of oATP. Oxidized ATP behaves as an affinity label for the substrate binding site as evidenced by saturation kinetics with the formation of reversible complex prior to inactivation, and the observation that the inactivation was stoichiometric with the amount of oATP incorporated which extrapolated to 1 mol per mol of monomeric PPi-PFK. The critical lysine modified by oATP is proposed to be located at the PPi-binding site since complete protection is afforded by PPi; and under steady-state, PPi was competitive with the inhibitor. Other substrates of the reaction in either the forward or reverse direction did not completely protect against inactivation. This is further confirmed by the non-competitive inhibition displayed by either Pi or fructose 1,6, bisphosphate. Furthermore, the Km values for Pi and fructose 1,6 bisphosphate of the oATP-modified enzyme were not altered. The oATP-modified peptides were analyzed by HPLC peptide mapping, and the profile showed a major peak absorbing at 258 nm, which was absent when the modification was carried out in the presence of MgPPi. This peptide was sequenced and found to contain Lys-497. These results suggest that the essential lysine-497 modified by oATP is involved in the binding and/or catalysis of PPi and that an ATP-type of binding domain, with reference to the phosphoryl groups, is present in the PPi-dependent phosphofructokinase of Giardia.
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Affiliation(s)
- Z Li
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4983, USA
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24
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Ramos A, Rotllán P. Specific dinucleoside polyphosphate cleaving enzymes from chromaffin cells: a fluorimetric study. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1253:103-11. [PMID: 7492590 DOI: 10.1016/0167-4838(95)00154-m] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This article presents a fluorimetric study of the main properties of the enzymes dinucleoside tetraphosphate (asymmetrical) hydrolase or dinucleoside tetraphosphatase (Ap4Aase, EC 3.6.1.17) and dinucleoside triphosphate hydrolase or dinucleoside triphosphatase (Ap3Aase, EC 3.6.1.29), both present in adrenal medulla cytosolic extracts. Diethenoadenosine polyphosphates, epsilon-(ApnA), are used as artificial fluorogenic substrates. Ap4Aase exhibits a molecular mass around 20 kDa and neutral optimum pH (7.0-7.5). It requires Mg2+ and preferentially hydrolyzes substrates with four phosphate groups. Km for epsilon-(Ap4A) is 1.3 microM and Ki for Ap4A and Gp4G are 1 and 0.2 microM respectively. Km for Ap4A determined by HPLC is 1.6 microM. epsilon-(Ap5A) and epsilon-(Ap6A) are hydrolyzed at reduced rates. This enzyme is inhibited by Zn2+, F- and very strongly by Ap4 and epsilon-Ap4. Ca2+ cannot replace Mg2+, but behaves as inhibitor in its presence. The substrate analogs dinucleoside triphosphates Ap3A, G;3G, m7Gp3G and m7Gp3A and the periodate-oxidized nucleotides o-(Ap4A), o epsilon-(Ap4A), o-Ap4 and o epsilon-Ap4 behave as inhibitors. Ap3Aase exhibits a molecular mass around 30 kDa and neutral optimum pH (7.0-7.5). It requires Mg2+ or Ca2+, but retains a low measurable activity around 10% in the absence of these divalent cations. It only hydrolyzes substrates with three phosphate groups. Km for epsilon-(Ap3A) is 11 microM and Ki for Ap3A and Gp3G are 20 and 22 microM, respectively. Km for Ap3A determined by HPLC is 16 microM. m7Gp3G and m7Gp3A are also good substrates for triphosphatase.
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Affiliation(s)
- A Ramos
- Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna, Tenerife, Canary Islands, Spain
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25
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Hilden I, Hove-Jensen B, Harlow KW. Inactivation of Escherichia coli phosphoribosylpyrophosphate synthetase by the 2',3'-dialdehyde derivative of ATP. Identification of active site lysines. J Biol Chem 1995; 270:20730-6. [PMID: 7657655 DOI: 10.1074/jbc.270.35.20730] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The enzyme 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP) synthetase from Escherichia coli was irreversibly inactivated on exposure to the affinity analog 2',3'-dialdehyde ATP (oATP). The reaction displayed complex saturation kinetics with respect to oATP with an apparent KD of approximately 0.8 mM. Reaction with radioactive oATP demonstrated that complete inactivation of the enzyme corresponded to reaction at two or more sites with limiting stoichiometries of approximately 0.7 and 1.3 mol of oATP incorporated/mol of PRPP synthetase subunit. oATP served as a substrate in the presence of ribose-5-phosphate, and the enzyme could be protected against inactivation by ADP or ATP. Isolation of radioactive peptides from the enzyme modified with radioactive oATP, followed by automated Edman sequencing allowed identification of Lys181, Lys193, and Lys230 as probable sites of reaction with the analog. Cysteine 229 may also be labeled by oATP. Of these four residues, Lys193 is completely conserved within the family of PRPP synthetases, and Lys181 is found at a position in the sequence where the cognate amino acid (Asp181) in human isozyme I PRPP synthetase has been previously implicated in the regulation of enzymatic activity. These results imply a functional role for at least two of the identified amino acid residues.
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Affiliation(s)
- I Hilden
- Center for Enzyme Research, University of Copenhagen, Denmark
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26
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Hohenegger M, Herrmann-Frank A, Richter M, Lehmann-Horn F. Activation and labelling of the purified skeletal muscle ryanodine receptor by an oxidized ATP analogue. Biochem J 1995; 308 ( Pt 1):119-25. [PMID: 7755553 PMCID: PMC1136851 DOI: 10.1042/bj3080119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have tested the periodate-oxidized ATP analogue 2',3'-dialdehyde adenosine triphosphate (oATP) as a ligand for the skeletal muscle ryanodine receptor/Ca(2+)-release channel. Ca2+ efflux from passively loaded heavy sarcoplasmic reticulum vesicles of skeletal muscle is biphasic. oATP stimulates the initial phase of Ca2+ release in a concentration-dependent manner (EC50 160 microM), and the efflux proceeds with a half-time in the range 100-200 ms. This oATP-modulated initial rapid Ca2+ release was specifically inhibited by millimolar concentrations of Mg2+ and micromolar concentrations of Ruthenium Red, indicating that the effect of oATP was mediated via the ryanodine receptor. The purified Ca(2+)-release channel was incorporated into planar lipid bilayers, and single-channel recordings were carried out to verify a direct interaction of oATP with the ryanodine receptor. Addition of oATP to the cytoplasmic side activated the channel with an EC50 of 76 microM, which is roughly 30-fold higher than the apparent affinity of ATP. The oATP-induced increase in the open probability of the ryanodine receptor displays a steep concentration-response curve with a Hill coefficient of approximately 2, which suggests a co-operativity of the ATP binding sites in the tetrameric protein. oATP binds to the ryanodine receptor in a quasi-irreversible manner via Schiff base formation between the aldehyde groups of oATP and amino groups in the nucleotide binding pocket. This allows for the covalent specific incorporation of [alpha-32P]oATP by borhydride reduction. A typical adenine nucleotide binding site cannot be identified in the primary sequence of the ryanodine receptor. Our results demonstrate that oATP can be used to probe the structure and function of the nucleotide binding pocket of the ryanodine receptor and presumably of other ATP-regulated ion channels.
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Affiliation(s)
- M Hohenegger
- Institute of Pharmacology, University of Vienna, Austria
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27
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Structural and functional characterization of the interaction between 2‘,3‘-dialdehyde guanine nucleotide analogues and the stimulatory G protein alpha-subunit. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)31795-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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28
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Abstract
Ribonuclease P, which contains a catalytic RNA subunit, cleaves 5' precursor-specific sequences from pre-tRNAs. It was previously shown that the RNase P RNA optimally cleaves substrates which contain the mature, 3'-terminal CCA of tRNA. In order to determine the contributions of those individual 3'-terminal nucleotides to the interaction, pre-tRNAs that have CCA, only CC or C or are without CCA at the 3'-end were synthesized by run-off transcription, tested as substrates for cleavage by RNase P RNA and used in photoaffinity crosslinking experiments to examine contact sites in the ribozyme. In order to generalize the results, analyses were carried out using three different bacterial RNase P RNAs, from Escherichia coli, Bacillus subtilis and Thermotoga maritima. At optimal (Kcat/Km) ionic strength (1 M NH4+/25 mM Mg2+), Km increases incrementally 3- to 10-fold upon stepwise removal of each nucleotide from the 3'-end. At high ionic strength (2 M NH4+/50 mM Mg2+), which suppresses conformational effects, removal of the 3'-terminal A had little effect on Km, indicating that it is not a specific contact. Analysis of the deletion and substitution mutants indicated that the C residues act specially; their contribution to binding energy at high ionic strength (approximately 1 kcal/mol) is consistent with a non-Watson-Crick interaction, possibly irregular triple-strand formation with some component of the RNase P RNA. In agreement with previous studies, we find that the RNase P holoenzyme in vitro does not discriminate between tRNAs containing or lacking CCA. The structural elements of the three RNase P RNAs in proximity to the 3'-end of tRNA were examined by photoaffinity crosslinking. Photoagent-labeled tRNAs with 3'-terminal CCA, only CC or C, or lacking all these nucleotides were covalently conjugated to the three RNase P RNAs by irradiation and the sites of crosslinks were mapped by primer extension. The main crosslink sites are located in a highly conserved loop (probably an irregular helix) that is part of the core of the RNase P RNA secondary structure. The crosslinking results orient the CCA of tRNA with respect to that region of the RNase P RNA.
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Affiliation(s)
- B K Oh
- Department of Chemistry, Indiana University, Bloomington 47405
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29
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Thomson GJ, Coggins JR, Price NC. The reaction of GroEL (cpn 60) with the ATP analogue 2',3' dialdehyde ATP. FEBS Lett 1993; 336:19-22. [PMID: 7903255 DOI: 10.1016/0014-5793(93)81600-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The reaction of the E. coli chaperonin GroEL (cpn 60) with the ATP analogue 2',3' oxidised ATP (oATP) has been studied. Treatment with the reagent leads to loss of the ATPase activity of GroEL in a pseudo-first-order fashion; this can be prevented by inclusion of ATP in the reaction mixture. Measurements of the stoichiometry of the reaction indicate that the loss of activity corresponds to the incorporation of about one oATP per subunit of GroEL. From analysis of the sequences of modified peptides it is proposed that the reaction probably occurs with one or both of the two cysteines Cys-457 and Cys-518, although the instability of the adduct(s) makes a definite identification of the site(s) of reaction difficult. The involvement of Cys side chains in the reaction with oATP was confirmed by using Nbs2 (5,5'-dithiobis(2-nitrobenzoate)) to estimate thiol groups in both modified and unmodified GroEL.
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Affiliation(s)
- G J Thomson
- Department of Biochemistry, University of Glasgow, Scotland, UK
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30
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Craig DB, Wallace CJ. ATP binding to cytochrome c diminishes electron flow in the mitochondrial respiratory pathway. Protein Sci 1993; 2:966-76. [PMID: 8391357 PMCID: PMC2142400 DOI: 10.1002/pro.5560020610] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Eukaryotic cytochrome c possesses an ATP-binding site of substantial specificity and high affinity that is conserved between highly divergent species and which includes the invariant residue arginine91. Such evolutionary conservatism strongly suggests a physiological role for ATP binding that demands further investigation. We report the preparation of adducts of the protein and the affinity labels 8-azido adenosine 5'-triphosphate, adenosine 5'-triphosphate-2',3'-dialdehyde, and 5'-p-fluorosulfonylbenzoyladenosine. The two former reagents were seen to react at the arginine91-containing site, yet the reaction of the latter, although specific, occurred elsewhere, suggesting caution is necessary in its use. None of the adducts displayed significant modification of global structure, stability, or physicochemical properties, leading us to believe that the 8-N3-ATP and oATP adducts are good stabilized models of the noncovalent interaction; yet modification led to significant, and sometimes pronounced, effects on biological activity. We therefore propose that the role of ATP binding to this site, which we have shown to occur when the phosphorylation potential of the system is high under the equivalent of physiological conditions, is to cause a decrease in electron flow through the mitochondrial electron transport chain. Differences in the degree of inhibition produced by differences in adduct chemistry suggest that this putative regulatory role is mediated primarily by electrostatic effects.
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Affiliation(s)
- D B Craig
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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31
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Murgia M, Hanau S, Pizzo P, Rippa M, Di Virgilio F. Oxidized ATP. An irreversible inhibitor of the macrophage purinergic P2Z receptor. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53082-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Klinger E, Aviram I. Involvement of GTP in cell-free activation of neutrophil NADPH oxidase. Studies with GTP analogues. Biochem J 1992; 285 ( Pt 2):635-9. [PMID: 1637353 PMCID: PMC1132836 DOI: 10.1042/bj2850635] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Activation of superoxide-producing NADPH oxidase of neutrophils requires the presence of cell membranes, cytosolic components and arachidonate and is markedly enhanced by non-hydrolysable analogues of guanine nucleotides, i.e. guanosine 5'-[gamma-thio]triphosphate and guanosine 5'[beta gamma-imido]triphosphate (p[NH]ppG). Gel filtration and ultrafiltration of the cytosol decreased the basal activity of NADPH oxidase. Activity could be restored by GTP, suggesting participation of the nucleotide in basal activation. Preincubation of neutrophil cytosol with periodate-oxidized p[NH]ppG (ox-p[NH]ppG) followed by gel filtration resulted in a time-dependent enhancement of basal oxidase activity. The presence of GDP or GTP, but not ATP, during the incubation with ox-p[NH]ppG abolished this enhancement. These data are consistent with a stable association of ox-p[NH]ppG with an oxidase-linked cytosolic protein. SDS/PAGE of neutrophil cytosol preincubated with [3H]ox-p[NH]ppG revealed radioactivity in bands migrating as 100, 70, 47, 34 and 22 kDa proteins. Evidence for covalent labelling of the cytosolic protein p47-phox with [3H]ox-p[NH]ppG is presented. Heterogeneity of cytosolic GTP-binding sites and possible participation of protein p47-phox in functional interaction with GTP analogues during cell-free activation are suggested.
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Affiliation(s)
- E Klinger
- Department of Biochemistry, Faculty of Life Sciences, Tel-Aviv University, Israel
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33
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Morii H, Makinose M. Adenosine(5')hexaphospho(5')adenosine stimulation of a Ca(2+)-induced Ca(2+)-release channel from skeletal muscle sarcoplasmic reticulum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 205:979-84. [PMID: 1374335 DOI: 10.1111/j.1432-1033.1992.tb16864.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stimulation of a Ca(2+)-induced Ca(2+)-release channel from skeletal muscle sarcoplasmic reticulum by various adenosine(5')oligophospho(5')adenosines (ApnA, n = 2-6) by a rapid quenching technique using radioactive calcium was studied. Ap4A, Ap5A and Ap6A, as well as adenosine 5'-[beta, gamma-methylene]triphosphate (AdoPP [CH2]P), a non-hydrolyzable ATP analogue, stimulated the Ca(2+)-release channel, whereas Ap2A and Ap3A had no effect. At a concentration of 0.5 mM, the order of stimulation was AdoPP[CH2]P less than Ap4A less than Ap5A much less than Ap6A. As well as having the highest affinity (0.44 mM for half-maximal stimulation), Ap6A showed an extraordinarily high Hill coefficient of 3.3 (1.9 for AdoPP[CH2]P, 2.1 for Ap5A). The stimulating effect of Ap6A was reversible, yet its dissociation proceeded very slowly. Stimulation of Ca2+ release by Ap6A was counteracted by Mg2+ and ruthenium red. A 2',3'-dialdehyde derivative of Ap6A, which is a chemical probe for amino groups, stimulated irreversibly the Ca(2+)-release channel and modified some high-molecular-mass sarcoplasmic reticulum proteins, possibly including the channel protein. Our data suggest that Ap6A stimulates the Ca2+ channel by binding to the activation site of the channel subunit and simultaneously preventing the spontaneous decay of the Ca2+ channel by keeping together two of the four channel subunits by bridging them with its two adenosine groups.
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Affiliation(s)
- H Morii
- Max-Planck-Institute for Medical Research, Heidelberg, Federal Republic of Germany
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34
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Hohenegger M, Makinose M. 2',3'-Dialdehyde ATP analog labels the Ca(2+)-ATPase of sarcoplasmic reticulum via the catalytic adenosine-nucleotide-binding site. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 205:173-9. [PMID: 1532553 DOI: 10.1111/j.1432-1033.1992.tb16765.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The 2',3'-dialdehyde ATP analog (oATP) was synthesized and its ability to activate the Ca(2+)-ATPase of skeletal muscle sarcoplasmic reticulum via the adenosine-nucleotide-binding site was investigated. After reduction by sodium borohydride, oATP binds covalently to the catalytic adenosine-nucleotide-binding site of the enzyme, resulting in 85% loss of acetyl-phosphate-driven Ca2+ uptake and ATP-hydrolysing ability. In the absence of a reducing agent, oATP serves as a substrate for the Ca(2+)-ATPase, as indicated by Pi formation (hydrolysis) and Ca(2+)-uptake ability. oATP binding to the intact light sarcoplasmic reticulum is observed in the absence and presence of the competitive adenosine nucleotide inhibitor, fluorescein isothiocyanate with apparent affinity constants of 1.2 mM and 2.2 mM, respectively. Autoradiography of tryptic fragments from partially purified Ca(2+)-ATPase labeled with [alpha-32P]oATP or [gamma-32P]oATP locates the covalent binding site to the A1 fragment, even in the fluorescein-isothiocyanate-labeled pump protein. With high probability, a lysine residue in the tryptic A1 fragment is labeled by the ribose-modified ATP analog close to the phosphorylation site at Asp351.
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35
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Hayes BK, Varki A. The synthesis of high-specific-activity UDP-[6-3H]galactose, UDP-N-[6-3H]acetylgalactosamine, and their corresponding monosaccharides. Anal Biochem 1992; 201:140-5. [PMID: 1621952 DOI: 10.1016/0003-2697(92)90186-b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Tritiated uridine-5'-diphosphogalactose (UDP-[3H]Gal) has been widely used to study oligosaccharide biosynthesis and structure. It can be synthesized either chemically or enzymatically using galactose oxidase to oxidize the hydroxyl moiety at C-6 to an aldehyde (6-aldo-UDP-Gal), which is then reduced back to the alcohol with tritiated sodium borohydride. Although the enzymatic approach is simple and efficient, there are several problems associated with it. First, incomplete oxidation to the aldehyde reduces the final specific activity. Second, if the galactose oxidase is not removed from the 6-aldo-UDP-Gal prior to reduction, the resulting UDP-[6-3H]Gal can be reoxidized to 6-aldo-UDP-[6-3H]Gal. We present evidence for the occurrence of this compound in one commercially obtained preparation of UDP-[6-3H]Gal. Finally, if an excess of 6-aldo-UDP-Gal is used for good yield, it is necessary to quench the reduction with nonradioactive borohydride, again reducing the final specific activity. We have devised a rapid, inexpensive, and efficient synthesis of UDP-[6-3H]Gal that circumvents all of these problems. Galactose oxidase is used to produce 6-aldo-UDP-Gal and the completeness of this reaction is confirmed on polyethyleneimine (PEI) cellulose TLC plates. The 6-aldo-UDP-Gal is purified on silica gel 60 TLC plates. This purified compound is then reduced with tritiated sodium borohydride, with the aldehyde present in excess. Unreacted 6-aldo-UDP-Gal is then purified away from the product UDP-[6-3H]Gal by chromatography on PEI cellulose. Radiochemically pure UDP-[6-3H]Gal with a specific activity of 10 Ci/mmol was obtained using the above scheme.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- B K Hayes
- Department of Medicine, UCSD Cancer Center, San Diego, La Jolla 92093
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36
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Rao GS, Cook PF, Harris BG. Modification of the ATP inhibitory site of the Ascaris suum phosphofructokinase results in the stabilization of an inactive T state. Biochemistry 1991; 30:9998-10004. [PMID: 1832959 DOI: 10.1021/bi00105a026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Treatment of the Ascaris suum phosphofructokinase (PFK) with 2',3'-dialdehyde ATP (oATP) results in an enzyme form that is inactive. The conformational integrity of the active site, however, is preserved, suggesting that oATP modification locks the PFK into an inactive T state that cannot be activated. A rapid, irreversible first-order inactivation of the PFK is observed in the presence of oATP. The rate of inactivation is saturable and gives a KoATP of 1.07 +/- 0.27 mM. Complete protection against inactivation is afforded by high concentrations of ATP, and the dependence of the inactivation rate on the concentration of ATP gives a Ki of 326 +/- 26 microM for ATP which is 22-fold higher than the Km for ATP at the catalytic site but close to the binding constant for ATP to the inhibitory site. Fructose 6-phosphate, fructose 2,6-bisphosphate, and AMP provide only partial protection against modification. The pH dependence of the inactivation rate gives a pKa of 8.4 +/- 0.1. Approximately 2 mol of [3H]oATP is incorporated into a subunit of PFK concomitant with 90% loss of activity, and ATP prevents the derivatization of 1 mol/subunit. The oATP-modified enzyme is not activated by AMP or fructose 2,6-bisphosphate. oATP has no effect on the activity of a desensitized form of PFK in which the ATP inhibitory site is modified with diethyl pyrocarbonate but with the active site intact [Rao, G.S.J., Wariso, B.A., Cook, P.F., Hofer, H.W., & Harris, B.G. (1987) J. Biol. Chem. 262, 14068-14073].(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- G S Rao
- Department of Biochemistry and Molecular Biology, Texas College of Osteopathic Medicine/University of North Texas, Fort Worth 76107
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37
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Klinger E, Aviram I. Dialdehyde-GDP blocks activity of cytosolic components of neutrophil NADPH oxidase. Biochem Biophys Res Commun 1991; 177:504-10. [PMID: 2043136 DOI: 10.1016/0006-291x(91)92012-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Superoxide production by neutrophil NADPH oxidase activated in a cell-free system consisting of plasma membranes, cytosol and arachidonate is enhanced by nonhydrolyzable analogs of GTP and reduced by GDP. To characterize the interaction of guanine nucleotides with the system, dialdehyde analogs of GTP and GDP (oGTP and oGDP) were employed. oGDP or oGTP caused an irreversible and dose dependent inactivation of NADPH oxidase-supporting cytosolic activity. Cytosol was fractionated on S and Q Sepharose ion exchange columns into three fractions, combinations of which synergistically supported activation of NADPH oxidase. Two fractions shown by immunoblotting to contain the oxidase-linked p47 and p67 proteins were inactivated by oGDP. Labeling with [alpha-32P]-oGTP lead to incorporation of the label into several proteins.
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Affiliation(s)
- E Klinger
- Department of Biochemistry, Faculty of Life Sciences, Tel-Aviv University, Israel
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38
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Kinzy TG, Merrick WC. Characterization of a limited trypsin digestion form of eukaryotic elongation factor 1 α. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(20)64291-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Anthony DD, Kinzy TG, Merrick WC. Affinity labeling of eukaryotic initiation factor 2 and elongation factor 1 alpha beta gamma with GTP analogs. Arch Biochem Biophys 1990; 281:157-62. [PMID: 2383020 DOI: 10.1016/0003-9861(90)90426-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
As part of an attempt to understand the specific function and role of each subunit in multisubunit protein synthesis factors, we have attempted to identify the nucleotide binding peptides of eukaryotic initiation factor 2 (eIF-2). To ensure that the interactions were of a specific nature, two general controls were used: first, other protein factors with characterized GTP binding activity were tested; second, all affinity labeling was checked for nucleotide specificity by protection with the authentic nucleotide at a 10-fold molar excess over the affinity reagent. Results with a number of GTP modifying reagents ([alpha-32P]GTP, [alpha-32P]GDP, oxidized [alpha-32P]GTP, 3'-p-azidobenzoyl-[alpha-32P]GTP, 3'-p-azidobenzoyl-[alpha-32P]GDP, and 5'-p-[8-3H]fluorosulfonylbenzoyl guanosine) indicate that appropriate conditions for both nucleotide and subunit specific labeling have been achieved. Under these conditions all reagents modified the beta subunit of eIF-2. Complementary studies with subunit-deficient forms of eIF-2 also suggest that the beta subunit of eIF-2 is involved with GTP binding. Coupled with other data suggesting that the gamma subunit of eIF-2 might be involved in GTP binding and amino acid sequence data of eIF-2 gamma from which a part of a GTP binding consensus sequence can be localized, support is provided for the concept of alternate GTP binding domains or a GTP binding domain shared between different subunits of eIF-2.
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Affiliation(s)
- D D Anthony
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
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Mignaco J, Scofano HM, Barrabin H. Inhibition and labeling of the Ca2(+)-ATPase from sarcoplasmic reticulum by periodate oxidized ATP. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1039:305-12. [PMID: 2143085 DOI: 10.1016/0167-4838(90)90263-f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The analog of ATP obtained by oxidation of the ribose ring of ATP with periodate (oxATP) was used as a reagent for the inhibition and labeling of the Ca2(+)-ATPase purified from sarcoplasmic reticulum membranes. The substrate concentration dependence for hydrolysis showed a biphasic pattern for both ATP and oxATP as substrates. Preincubation of Ca2(+)-ATPase in the presence of 0.05 mM CaCl2, 5 mM MgCl2, 100 mM KCl and oxATP led to an irreversible inhibition. This inhibition occurred faster at alkaline pH. The presence of ADP, adenyl-5'-imidodiphosphate (AMP-PNP) or EGTA in the preincubation medium decreased the rate of inhibition. OxATP covalently labels the enzyme: the labeling was decreased by ADP. This ADP-protected labeling increased with time until it reached approx. 1 mol [3H]oxATP per mol ATPase. The rate of labeling of the ADP-protected group correlated with the rate of loss of ADP-protected activity. Trypsin digestion of oxATP-labeled ATPase followed by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate showed that fragment A1 contained a high degree of label that is displaced by ADP. We propose that the A1 fragment is situated close to the ribose ring when the adenosine moiety of ATP is bound to the catalytic site of the Ca2(+)-ATPase.
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Affiliation(s)
- J Mignaco
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Cidade Universitaira, Brasil
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41
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Miziorko HM, Brodt CA, Krieger TJ. Affinity labeling of spinach leaf phosphoribulokinase by ATP analogs. Modification of an active site lysine. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39641-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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42
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Rabinkov AG, Amontov SV. Affinity labelling of rat liver acetyl-CoA carboxylase by a 2',3'-dialdehyde derivative of ATP. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1037:216-20. [PMID: 1968347 DOI: 10.1016/0167-4838(90)90170-k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The interaction of rat liver acetyl-CoA carboxylase with a 2',3'-dialdehyde derivative of ATP (oATP) has been studied. The degree of the enzyme inactivation has been found to depend on the oATP concentration and the incubation time. ATP was proved to be the only substrate which protected the inactivation. Acetyl-CoA did not effect inactivation, while HCO3- accelerated the process. Ki values for oATP in the absence and presence of HCO3- were 0.35 +/- 0.04 and 0.5 +/- 0.06 mM, and those of the modification constant (kmod) were 0.11 and 0.26 min-1 respectively. oATP completely inhibited the [14C]ADP in equilibrium ATP exchange and did not effect the [14C]acetyl-CoA in equilibrium malonyl-CoA exchange. Incorporation of approximately 1 equivalent of [3H]oATP per acetyl-CoA carboxylase subunit has been shown. No recovery of the modified enzyme activity has been observed in Tris or beta-mercaptoethanol containing buffers, and treatment with NaB3H4 has not led to 3H incorporation. The modification elimination of the ATP triphosphate chain. The results indicated the affinity modification of acetyl-CoA carboxylase by oATP. It was shown that the reagent apparently interacted selectively with the epsilon-amino group of lysine in the ATP-binding site to form a morpholine-like structure.
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Affiliation(s)
- A G Rabinkov
- V.A. Engelhardt Institute of Molecular Biology, U.S.S.R. Academy of Sciences, Moscow
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44
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Structure and Function of Human Hemoglobin Covalently Labeled with Periodate-oxidized Adenosine Triphosphate. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)60419-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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45
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Bidwai AP, Morjana NA, Scarborough GA. Studies on the active site of the Neurospora crassa plasma membrane H+-ATPase with periodate-oxidized nucleotides. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)80135-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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46
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Schraw WP, Post RL. Inhibition and labeling of sodium, potassium ATPase by the dialdehyde derivative of ATP. Arch Biochem Biophys 1989; 269:327-38. [PMID: 2537059 DOI: 10.1016/0003-9861(89)90114-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Canine renal Na,K-ATPase was treated with ATP dialdehyde, "oxATP" (20 microM), as described by G. Ponzio, B. Rossi, and M. Lazdunski (1983, J. Biol. Chem. 258, 8201-8205). In this system, a by-product, formaldehyde, was the inactivator. We modified the system to minimize such inhibition and to speed up the reaction. oxATP itself inactivated the enzyme at a rate that was slow at first and later speeded up. We fitted a precursor-product model to the data. Labeling with [3H]oxATP indicated about three sites per alpha beta protomer at complete inactivation. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the labeled enzyme showed radioactivity in many components, in the alpha and beta subunits and in small molecules at the tracker dye region. ATP (20 mM) prevented all labeling and inactivation. Ponzio et al. concluded that oxATP labels covalently an ATP binding site. Our experiments did not support this conclusion. Ouabain did not affect labeling. Sodium stimulated both inhibition and labeling more than potassium did, indicating a high-affinity ATP binding site, if any. But nucleotide specificity for preventing or producing inhibition did not correspond to nucleotide specificity for binding of ATP to the native enzyme. Blocking the ATP binding center with fluorescein isothiocyanate or fluorosulfonyl benzoyl adenosine had no effect on [3H]oxATP labeling. ATP also prevented [3H]oxATP labeling of bovine serum albumin or of integral-membrane proteins.
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Affiliation(s)
- W P Schraw
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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Smith RM, Curnutte JT, Babior BM. Affinity Labeling of the Cytosolic and Membrane Components of the Respiratory Burst Oxidase by the 2′,3′-Dialdehyde Derivative of NADPH. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)94127-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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48
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Inano H, Kurihara S. Affinity labeling of cofactor-binding region of human placental estradiol 17 beta-dehydrogenase by periodate-oxidized NADP+ (o-NADP+). Biochem Biophys Res Commun 1989; 158:617-23. [PMID: 2537079 DOI: 10.1016/s0006-291x(89)80094-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Periodate-oxidized NADP+ (o-NADP+), an analogue of the cofactors, is a reversible inhibitor of estradiol 17 beta-dehydrogenase in human placenta. Mode of the inhibition by o-NADP+ appeared to be competitive type (Ki = 0.84 microM) against NAD+ and non-competitive type (Ki = 1.13 microM) against estradiol, respectively. Treatment of the estradiol 17 beta-dehydrogenase with o-NADP+ resulted in time-dependent loss of the enzyme activity. The inactivation exhibited pseudo-first order kinetics (t1/2 = 15 min) and was protected by NAD+ and NADP+. On the other hand, periodate-oxidized ATP inactivated slightly the estradiol 17 beta-dehydrogenase. These results indicate that the residue(s) of lysines is located near the cofactor-binding region of estradiol 17 beta-dehydrogenase of human placenta.
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Affiliation(s)
- H Inano
- National Institute of Radiological Sciences, Chiba-shi, Japan
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49
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Saavedra C, Araneda S, Cardemil E. Affinity labeling of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase with the 2',3'-dialdehyde derivative of ATP. Arch Biochem Biophys 1988; 267:38-45. [PMID: 3058040 DOI: 10.1016/0003-9861(88)90005-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase [ATP:oxaloacetate carboxy-lyase (transphosphorylating), EC 4.1.1.49] is completely inactivated by the 2',3'-dialdehyde derivative of ATP (oATP) in the presence of Mn2+. The dependence of the pseudo-first-order rate constant on reagent concentration indicates the formation of a reversible complex with the enzyme (Kd = 60 +/- 17 microM) prior to covalent modification. The maximum inactivation rate constant at pH 7.5 and 30 degrees C is 0.200 +/- 0.045 min-1. ATP or ADP plus phosphoenolpyruvate effectively protect the enzyme against inactivation. oATP is a competitive inhibitor toward ADP, suggesting that oATP interacts with the enzyme at the substrate binding site. The partially inactivated enzyme shows an unaltered Km but a decreased V as compared with native phosphoenolpyruvate carboxykinase. Analysis of the inactivation rate at different H+ concentrations allowed estimation of a pKa of 8.1 for the reactive amino acid residue in the enzyme. Complete inactivation of the carboxykinase can be correlated with the incorporation of about one mole of [8-14C]oATP per mole of enzyme subunit. The results indicate that oATP can be used as an affinity label for yeast phosphoenolpyruvate carboxykinase.
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Affiliation(s)
- C Saavedra
- Departamento de Química, Facultad de Ciencia, Universidad de Santiago de Chile
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Basu S, Basu M, Das KK, Daussin F, Schaeper RJ, Banerjee P, Khan FA, Suzuki I. Solubilized glycosyltransferases and biosynthesis in vitro of glycolipids. Biochimie 1988; 70:1551-63. [PMID: 3149522 DOI: 10.1016/0300-9084(88)90291-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The assembly of most of the ceramide-linked glycolipids (GSLs) in eukaryotic cells occurs in Golgi bodies. At least 18 different glycolipid:glycosyltransferases (GSL:GLTs) have been characterized, 10 of which have been solubilized. These GLTs can be classified into 2 distinct groups: 1) GLTs dedicated to either Dol-P-P-sugar(s) or ceramide-linked sugar(s); and 2) GLTs with dual loyalties (i.e., they compete with glycolipid- and glycoprotein-bound oligosaccharides). Studies with solubilized and purified GalNAcT-1 and GalNAcT-2 from embryonic chicken brains prove that GalNAcT-1 (UDP-GalNAc:GM3 beta 1-4GalNAcT) is specific for GSL, whereas GalNAcT-2 (UDP-GalNAc:Gb3 beta 1-3GalNAcT) can transfer to an oligosaccharide containing the alpha-linked terminal galactose. Similarly, GalT-3 (UDP-Gal:GM2 beta 1-3GalT) is more specific for ganglio-oligosaccharide and GalT-4 (UDP-Gal:Lc3 beta 1-4GalT) can transfer galactose to N-acetylglucosamine linked to p-nitrophenol, glycolipid or glycoprotein. Both GalT-3 and GalT-4 have been separated and purified from embryonic chicken brains. Studies with solubilized SAT-4 and SAT-3, from bovine spleen and embryonic chicken brains, respectively, suggest the existence of 2 different gene-expressed alpha 2-3SATs. The newly discovered FucT-3 (GDP-Fuc:NeuGc-iLc6-alpha 1-3FucT) from human colon carcinoma (Colo-205) has also been solubilized and separated from other GSL:GLTs. Using a new activity gel-Western blot combined technique, the molecular mass of this FucT-3 was determined to be 105 kDa.
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Affiliation(s)
- S Basu
- Department of Chemistry, University of Notre Dame, IN 46556
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