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Islas-Flores I, Villanueva MA. Inositol-1 (or 4)-monophosphatase from Glycine max embryo axes is a phosphatase with broad substrate specificity that includes phytate dephosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1770:543-50. [PMID: 17241743 DOI: 10.1016/j.bbagen.2006.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 12/05/2006] [Accepted: 12/06/2006] [Indexed: 10/23/2022]
Abstract
A phosphate-hydrolyzing activity from Glycine max embryo axes was purified by a series of chromatographic steps and electroelution from activity gels, and demonstrated to be an inositol-1 (or 4)-monophosphatase by partial internal amino acid sequence. This enzyme hydrolyzed ATP, sodium pyrophosphate (NaPPi), inositol hexakisphosphate, and inositol 1-monophosphate, but not p-nitrophenyl phosphate, ADP, AMP or glucose 6-P. Using NaPPi as substrate, the highly purified protein hydrolyzed up to 0.4 mmol phosphate min(-1) mg(-1) protein and had a Km(avg) of 235 microM for NaPPi. Since NaPPi is relatively inexpensive and readily available, we used this as substrate for the subsequent characterization. We observed the following: (a) specific inhibition by Li and NaF but not by butanedione monoxime, or orthovanadate; (b) activation by Cu(2+) and Mg(2+); (c) optimum activity at pH 7.4; and (d) temperature stability after 1-h incubations at 37-80 degrees C, with maximum activity at 37 degrees C. The partially purified protein was detected by in-gel activity assays and the band was electroeluted to yield a highly purified protein. Analysis by SDS-PAGE and native IEF-PAGE yielded a single major polypeptide of 29 kDa and pI approximately 5.9, respectively. In addition, in-gel activity from embryo axes and whole hypocotyls at early germination times revealed one high and one intermediate molecular weight isoform, but only the intermediate one corresponded to IMPase. Throughout the post-imbibition period, the activity of the high molecular weight isoform disappeared and IMPase increased, indicating an increasing expression of the enzyme as germination and growth proceeded. These data indicate that the inositol-1 (or 4)-monophosphatase present in the embryo axis of G. max has a wide phosphate substrate specificity, and may play an important role in phosphate metabolism during the germination process.
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177
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Samygina VR, Moiseev VM, Rodina EV, Vorobyeva NN, Popov AN, Kurilova SA, Nazarova TI, Avaeva SM, Bartunik HD. Reversible Inhibition of Escherichia coli Inorganic Pyrophosphatase by Fluoride: Trapped Catalytic Intermediates in Cryo-crystallographic Studies. J Mol Biol 2007; 366:1305-17. [PMID: 17196979 DOI: 10.1016/j.jmb.2006.11.082] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 11/29/2006] [Indexed: 11/22/2022]
Abstract
Here, we describe high-resolution X-ray structures of Escherichia coli inorganic pyrophosphatase (E-PPase) complexed with the substrate, magnesium, or manganese pyrophosphate. The structures correspond to steps in the catalytic synthesis of enzyme-bound pyrophosphate (PP(i)) in the presence of fluoride as an inhibitor of hydrolysis. The catalytic reaction intermediates were trapped applying a new method that we developed for initiating hydrolytic activity in the E-PPase crystal. X-ray structures were obtained for three consecutive states of the enzyme in the course of hydrolysis. Comparative analysis of these structures showed that the Mn2+-supported hydrolysis of the phosphoanhydride bond is followed by a fast release of the leaving phosphate from the P1 site. The electrophilic phosphate P2 is trapped in the "down" conformation. Its movement into the "up" position most likely represents the rate-limiting step of Mn2+-supported hydrolysis. We further determined the crystal structure of the Arg43Gln mutant variant of E-PPase complexed with one phosphate and four Mn ions.
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178
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Carroll JD, Pastuszak I, Edavana VK, Pan YT, Elbein AD. A novel trehalase from Mycobacterium smegmatis − purification, properties, requirements. FEBS J 2007; 274:1701-14. [PMID: 17319935 DOI: 10.1111/j.1742-4658.2007.05715.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Trehalose is a nonreducing disaccharide of glucose (alpha,alpha-1,1-glucosyl-glucose) that is essential for growth and survival of mycobacteria. These organisms have three different biosynthetic pathways to produce trehalose, and mutants devoid of all three pathways require exogenous trehalose in the medium in order to grow. Mycobacterium smegmatis and Mycobacterium tuberculosis also have a trehalase that may be important in controlling the levels of intracellular trehalose. In this study, we report on the purification and characterization of the trehalase from M. smegmatis, and its comparison to the trehalase from M. tuberculosis. Although these two enzymes have over 85% identity throughout their amino acid sequences, and both show an absolute requirement for inorganic phosphate for activity, the enzyme from M. smegmatis also requires Mg(2+) for activity, whereas the M. tuberculosis trehalase does not require Mg(2+). The requirement for phosphate is unusual among glycosyl hydrolases, but we could find no evidence for a phosphorolytic cleavage, or for any phosphorylated intermediates in the reaction. However, as inorganic phosphate appears to bind to, and also to greatly increase the heat stability of, the trehalase, the function of the phosphate may involve stabilizing the protein conformation and/or initiating protein aggregation. Sodium arsenate was able to substitute to some extent for the sodium phosphate requirement, whereas inorganic pyrophosphate and polyphosphates were inhibitory. The purified trehalase showed a single 71 kDa band on SDS gels, but active enzyme eluted in the void volume of a Sephracryl S-300 column, suggesting a molecular mass of about 1500 kDa or a multimer of 20 or more subunits. The trehalase is highly specific for alpha,alpha-trehalose and did not hydrolyze alpha,beta-trelalose or beta,beta-trehalose, trehalose dimycolate, or any other alpha-glucoside or beta-glucoside. Attempts to obtain a trehalase-negative mutant of M. smegmatis have been unsuccessful, although deletions of other trehalose metabolic enzymes have yielded viable mutants. This suggests that trehalase is an essential enzyme for these organisms. The enzyme has a pH optimum of 7.1, and is active in various buffers, as long as inorganic phosphate and Mg(2+) are present. Glucose was the only product produced by the trehalase in the presence of either phosphate or arsenate.
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179
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Shishova EY, Di Costanzo L, Cane DE, Christianson DW. X-ray crystal structure of aristolochene synthase from Aspergillus terreus and evolution of templates for the cyclization of farnesyl diphosphate. Biochemistry 2007; 46:1941-51. [PMID: 17261032 PMCID: PMC2518937 DOI: 10.1021/bi0622524] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aristolochene synthase from Aspergillus terreus catalyzes the cyclization of the universal sesquiterpene precursor, farnesyl diphosphate, to form the bicyclic hydrocarbon aristolochene. The 2.2 A resolution X-ray crystal structure of aristolochene synthase reveals a tetrameric quaternary structure in which each subunit adopts the alpha-helical class I terpene synthase fold with the active site in the "open", solvent-exposed conformation. Intriguingly, the 2.15 A resolution crystal structure of the complex with Mg2+3-pyrophosphate reveals ligand binding only to tetramer subunit D, which is stabilized in the "closed" conformation required for catalysis. Tetramer assembly may hinder conformational changes required for the transition from the inactive open conformation to the active closed conformation, thereby accounting for the attenuation of catalytic activity with an increase in enzyme concentration. In both conformations, but especially in the closed conformation, the active site contour is highly complementary in shape to that of aristolochene, and a catalytic function is proposed for the pyrophosphate anion based on its orientation with regard to the presumed binding mode of aristolochene. A similar active site contour is conserved in aristolochene synthase from Penicillium roqueforti despite the substantial divergent evolution of these two enzymes, while strikingly different active site contours are found in the sesquiterpene cyclases 5-epi-aristolochene synthase and trichodiene synthase. Thus, the terpenoid cyclase active site plays a critical role as a template in binding the flexible polyisoprenoid substrate in the proper conformation for catalysis. Across the greater family of terpenoid cyclases, this template is highly evolvable within a conserved alpha-helical fold for the synthesis of terpene natural products of diverse structure and stereochemistry.
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180
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Singh NJ, Jun EJ, Chellappan K, Thangadurai D, Chandran RP, Hwang IC, Yoon J, Kim KS. Quinoxaline−Imidazolium Receptors for Unique Sensing of Pyrophosphate and Acetate by Charge Transfer. Org Lett 2007; 9:485-8. [PMID: 17249793 DOI: 10.1021/ol062849b] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] Quinoxaline derivatives (1-4) bearing two imidazolium moieties are found to strongly bind anions and show unique charge-transfer fluorescent responses to pyrophosphate and acetate, whereas they show excimer formation with other anions. Anion-binding studies are investigated with fluorescence and 1H NMR analysis, single-crystal X-ray analysis, and theoretical calculations.
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181
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Develay S, Tripier R, Bernier N, Le Baccon M, Patinec V, Serratrice G, Handel H. Complexation of the triphosphate anion: tuning the structure of cyclen based macrotricycles with 1,3-dimethylbenzene and 2,6-dimethylpyridine linkers. A potentiometric and NMR study. Dalton Trans 2007:1038-46. [PMID: 17325779 DOI: 10.1039/b616862k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The host-guest interaction between orthophosphate, pyrophosphate and triphosphate anions and three cyclen-based macrotricyclic ligands was investigated by potentiometric measurements and NMR spectroscopy. The ligands differ from one another by the nature of their spacers, which are 1,3-dimethylbenzene (TMC), 2,6-dimethylpyridine (TPyC) or a combination of the two (TMPyC). In aqueous solution, each ligand gave protonated species that further formed ternary complexes after binding with anions; these complexes were analyzed as a result of hydrogen bond formation and coulombic attraction between the organic host and the inorganic guest. The equilibrium constants found for all the detected species are reported and the selectivity, illustrated with species distribution diagrams, is discussed. The results unambiguously showed that the ligand possessing a single supplementary anchoring site (the pyridinyl spacer) exhibited the greatest affinity for the phosphate species in a large p[H] range.
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182
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Amorim CMPG, Albert-García JR, Montenegro MCBS, Araújo AN, Calatayud JM. Photo-induced chemiluminometric determination of Karbutilate in a continuous-flow Multicommutation assembly. J Pharm Biomed Anal 2007; 43:421-7. [PMID: 16930910 DOI: 10.1016/j.jpba.2006.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 06/29/2006] [Accepted: 07/02/2006] [Indexed: 11/29/2022]
Abstract
The present paper deals with the chemiluminescent determination of the herbicide Karbutilate on the basis of its previous photodegradation by using a low-pressure Hg lamp as UV source in a continuous-flow multicommutation assembly (a solenoid valves set). The pesticide solution was segmented by a solenoid valve and sequentially alternated with segments of the 0.001 mol l(-1) of NaOH solution, the suitable media for the formation of photo-fragments; then it passes through the photo-reactor and was lead to the flow-cell after being divided in small segments which were sequentially alternated with the oxidizing system; 2 x 10(-5) mol l(-1) of potassium permanganate in 0.2% pyrophosphoric acid. The studied calibration range, from 0.1 microg l(-1) to 65 mg l(-1), resulted in a linear behaviour over the range 20 microg l(-1)-20 mg l(-1) and fitting the linear equation: I=(1180+/-30)C+(15+/-5) with the correlation coefficient 0.9998. The limit of detection was 10 microg l(-1) and the sample throughput 17 h(-1). After testing the influence of a large series of potential interfering species, the method was applied to water and human urine samples.
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183
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Sitnik TS, Avaeva SM. Binding of substrate at the effector site of pyrophosphatase increases the rate of its hydrolysis at the active site. BIOCHEMISTRY (MOSCOW) 2007; 72:68-76. [PMID: 17309439 DOI: 10.1134/s0006297907010087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
It is shown that in addition to the active site, each subunit of Escherichia coli inorganic pyrophosphatase (E-PPase) contains an extra binding site for the substrate magnesium pyrophosphate or its non-hydrolyzable analog magnesium methylenediphosphonate. The occupancy of the extra site stimulates the substrate conversion. Binding affinity of this site decreased or disappeared upon the conversion of E-PPase into a trimeric form or introduction of point mutations. However, when the slowly hydrolyzed substrate, lanthanum pyrophosphate (LaPP(i)), is used, the extra site was revealed in all enzyme forms of E-PPase and of Y-PPase (Saccharomyces cerevisiae PPase), resulting in about 100-fold activation of hydrolysis. A hypothesis on the localization of the extra site and the mechanism of its effect in E-PPase is presented.
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184
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Hand CE, Honek JF. Phosphate transfer from inositol pyrophosphates InsP5PP and InsP4(PP)2: A semi-empirical investigation. Bioorg Med Chem Lett 2007; 17:183-8. [PMID: 17045478 DOI: 10.1016/j.bmcl.2006.09.066] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 09/20/2006] [Accepted: 09/21/2006] [Indexed: 11/17/2022]
Abstract
A novel phosphate transfer process involving the non-enzymatic transfer of a phosphate group from inositol pyrophosphates to serine residues in proteins has been recently reported. Semi-empirical calculations at the PM3/SM5.2 level were undertaken to explore the effect of inositol pyrophosphate structure and overall charge on the thermodynamics of this phosphate transfer.
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185
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Miller DJ, Yu F, Young NJ, Allemann RK. Competitive inhibition of aristolochene synthase by phenyl-substituted farnesyl diphosphates: evidence of active site plasticity. Org Biomol Chem 2007; 5:3287-98. [PMID: 17912381 DOI: 10.1039/b713301b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analogues of farnesyl diphosphate (FPP, ) containing phenyl substituents in place of methyl groups have been prepared in syntheses that feature use of a Suzuki-Miyaura reaction as a key step. These analogues were found not to act as substrates of the sesquiterpene cyclase aristolochene synthase from Penicillium roqueforti (AS). However, they were potent competitive inhibitors of AS with K(I)-values ranging from 0.8 to 1.2 microM. These results indicate that the diphosphate group contributes the largest part to the binding of the substrate to AS and that the active sites of terpene synthases are sufficiently flexible to accommodate even substrate analogues with large substituents suggesting a potential way for the generation of non-natural terpenoids. Molecular mechanics simulations of the enzyme bound inhibitors suggested that small changes in orientations of active site residues and subtle alterations of the conformation of the backbones of the inhibitors are sufficient to accommodate the phenyl-farnesyl-diphosphates.
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186
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Boudreau MA, Vederas JC. Synthesis and biological evaluation of nucleoside dicarboxylates as potential mimics of nucleoside diphosphates. Org Biomol Chem 2007; 5:627-35. [PMID: 17285171 DOI: 10.1039/b615230a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of nucleotide analogues wherein the diphosphate moiety has been replaced by a dicarboxylate were synthesized and tested for inhibitory activity against nucleoside diphosphate (NDP) kinase as well as several pathogenic bacterial strains.
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187
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Zhao X, Liu Y, Schanze KS. A conjugated polyelectrolyte-based fluorescence sensor for pyrophosphate. Chem Commun (Camb) 2007:2914-6. [PMID: 17622429 DOI: 10.1039/b706629e] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new fluorescence turn-on sensor consisting of PPE-CO(2)(-)/Cu(2+) shows high selectivity for pyrophosphate over other anions and is used to develop a real-time assay for alkaline phosphatase.
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188
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Lee HN, Swamy KMK, Kim SK, Kwon JY, Kim Y, Kim SJ, Yoon YJ, Yoon J. Simple but Effective Way to Sense Pyrophosphate and Inorganic Phosphate by Fluorescence Changes. Org Lett 2006; 9:243-6. [PMID: 17217275 DOI: 10.1021/ol062685z] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new fluorescent chemosensor based on the acridine-Zn(II) derivative effectively recognizes pyrophosphate and inorganic phosphate at pH 7.4. Acridine derivative 1 displayed a fluorescent quenching effect with pyrophosphate; on the other hand, a large fluorescent enhancement was observed with inorganic phosphate. [structure: see text].
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189
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Ait Salah A, Jozwiak P, Zaghib K, Garbarczyk J, Gendron F, Mauger A, Julien CM. FTIR features of lithium-iron phosphates as electrode materials for rechargeable lithium batteries. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2006; 65:1007-13. [PMID: 16716657 DOI: 10.1016/j.saa.2006.01.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 01/18/2006] [Indexed: 05/09/2023]
Abstract
The essential structural features of lithium-metal phosphates (LMP) have been studied using FTIR spectroscopy which is a sensitive tool to probe the local environment in the solid materials. Various LMP materials where M is iron have been investigated including phospho-olivine LiFePO(4), diphosphate LiFeP(2)O(7), Nasicon-type phosphate Li(3)Fe(2)(PO(4))(3) and dihydrate FePO(4).2H(2)O. Vitreous and amorphous materials are also considered. Analysis of internal and external modes of vibration allows to distinguish between the different phases and the type of cationic environment in the framework. Results corroborate the contribution of the main factors which are responsible for the complexity of the spectra, i.e. departure from ideal symmetry, interactions between polyhedra, bridging atoms and lattice distortion.
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190
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Sen SE, Hitchcock JR, Jordan JL, Richard T. Juvenile hormone biosynthesis in M. sexta: substrate specificity of insect prenyltransferase utilizing homologous diphosphate analogs. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2006; 36:827-34. [PMID: 17046596 DOI: 10.1016/j.ibmb.2006.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 08/04/2006] [Indexed: 05/12/2023]
Abstract
Analogs of dimethylallyl diphosphate (DMAPP) and geranyl diphosphate (GPP) were prepared and tested as potential substrates of prenyltransferase of the tobacco hornworm, Manduca sexta, and of a sesquiterpene synthase derived from pig liver. Enzyme derived from corpora allata homogenates of both the larval and adult stage of M. sexta coupled each of the DMAPP analogs to produce homologous geranyl and farnesyl diphosphate products in the order (Z)-3-ethyl>(Z)-3-n-propyl>(Z)-3-methyl (DMAPP)>(Z)-3-i-propyl(Z)-3-n-butyl. In competition studies, the ethyl and n-propyl analogs either enhanced or had no effect on DMAPP coupling, whereas the larger analogs were inhibitors. (Z)-7-ethyl and (2Z,6Z)-3,7-diethyl analogs of GPP were as good, if not better substrates of larval prenyltransferase, while the C-3 ethyl analog of GPP, which is precursor to an isomeric form of juvenile hormone (JH) that is not typically found in insects, was poorly coupled by the enzyme. While similarities were seen for whole-cell extracts derived from adult and larval M. sexta, adult prenyltransferase derived from cytosolic and 16,000xg pellet fractions displayed distinct competitive coupling of GPP and its homologs, suggesting differences in substrate specificity as a result of enzyme localization. In contrast to M. sexta, the pig liver enzyme poorly coupled each of the homologous DMAPP derivatives, and the homologous derivatives of GPP were less efficiently coupled than GPP. These results indicate that prenyltransferase in M. sexta possesses high steric latitude at the (Z)-C-3 and C-7 alkyl positions of DMAPP and GPP, respectively, in contrast to other animal prenyltransferases but in keeping with the enzyme's presumptive role in homologous JH metabolism.
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191
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Novak JM, Watts DW. Phosphorus sorption by sediments in a southeastern coastal plain in-stream wetland. JOURNAL OF ENVIRONMENTAL QUALITY 2006; 35:1975-82. [PMID: 17071865 DOI: 10.2134/jeq2006.0077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A close relationship has been reported between sediment organic C (SedOC) content and its P sorption capacity (P(max)) and total P (TP) concentration. Phosphorus sorbed to organically complexed cations is a proposed explanation for this relationship. The objectives of this study were (i) to determine relationships between in-stream wetland SedOC content and both the sediment's P(max) and TP concentrations, and (ii) to ascertain the role of both organically complexed and oxalate-extractable cations on the sediment P(max) and TP values. The sediment's oxalate-extractable Fe (Fe(ox)) and Al (Al(ox)) contents were determined using acidified ammonium oxalate, while sodium pyrophosphate was used to extract organically complexed cations (Al(pryo), Ca(pyro), Fe(pyro), Mg(pyro), and Mn(pyro)). Both the sediment's P(max) and TP contents were strongly correlated with its SedOC concentration (r(2) > 0.90, P < 0.001). Only the Al(ox) contents were significantly correlated with TP and P(max), suggesting that amorphous Al forms have an important role in P sorption. All five pyrophosphate-extracted cations were significantly correlated with SedOC contents. Regression analyses showed that the Al(pyro) accounted for 88% of the variation in sediment P(max) values, whereas a combination of Al(pyro) and Ca(pyro) accounted for 98% of the variation in sediment TP concentrations. Additionally, Al and Ca chelated by SedOC compounds also have an important role in P binding and indicate that a linkage exists between the wetlands SedOC and P(max) content and its ability to accumulate TP. This study identified that two different mechanisms have significant roles in regulating P sorption by sediments in a southeastern Coastal Plain in-stream wetland.
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192
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Nielsen KL, Høgh AL, Emmersen J. DeepSAGE--digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Res 2006; 34:e133. [PMID: 17028099 PMCID: PMC1636492 DOI: 10.1093/nar/gkl714] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Digital transcriptomics with pyrophosphatase based ultra-high throughput DNA sequencing of di-tags provides high sensitivity and cost-effective gene expression profiling. Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE). We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato. The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest. Importantly, many transcripts were detected that cannot be matched to known genes, but is likely to be part of the abiotic stress-response in potato.
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193
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Anand VS, Patel SS. Transient state kinetics of transcription elongation by T7 RNA polymerase. J Biol Chem 2006; 281:35677-85. [PMID: 17005565 DOI: 10.1074/jbc.m608180200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The single subunit DNA-dependent RNA polymerase (RNAP) from bacteriophage T7 catalyzes both promoter-dependent transcription initiation and promoter-independent elongation. Using a promoter-free substrate, we have dissected the kinetic pathway of single nucleotide incorporation during elongation. We show that T7 RNAP undergoes a slow conformational change (0.01-0.03 s(-1)) to form an elongation competent complex with the promoter-free substrate (dissociation constant (Kd) of 96 nM). The complex binds to a correct NTP (Kd of 80 microM) and incorporates the nucleoside monophosphate (NMP) into RNA primer very efficiently (220 s(-1) at 25 degrees C). An overall free energy change (-5.5 kcal/mol) and internal free energy change (-3.7 kcal/mol) of single NMP incorporation was calculated from the measured equilibrium constants. In the presence of inorganic pyrophosphate (PPi), the elongation complex catalyzes the reverse pyrophosphorolysis reaction at a maximum rate of 0.8 s(-1) with PPi Kd of 1.2 mM. Several experiments were designed to investigate the rate-limiting step in the pathway of single nucleotide addition. Acid-quench and pulse-chase kinetics indicated that an isomerization step before chemistry is rate-limiting. The very similar rate constants of sequential incorporation of two nucleotides indicated that the steps after chemistry are fast. Based on available data, we propose that the preinsertion to insertion isomerization of NTP observed in the crystallographic studies of T7 RNAP is a likely candidate for the rate-limiting step. The studies here provide a kinetic framework to investigate structure-function and fidelity of RNA synthesis and to further explore the role of the conformational change in nucleotide selection during RNA synthesis.
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194
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Wang GM, Chen CH, Ho HO, Wang SS, Sheu MT. Novel design of osmotic chitosan capsules characterized by asymmetric membrane structure for in situ formation of delivery orifice. Int J Pharm 2006; 319:71-81. [PMID: 16701971 DOI: 10.1016/j.ijpharm.2006.03.041] [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: 09/02/2005] [Revised: 03/24/2006] [Accepted: 03/28/2006] [Indexed: 11/15/2022]
Abstract
In this study, chitosan capsules with asymmetric membrane to induce osmotic effects and in situ formation of the delivery orifice were optimally prepared and characterized. Chitosan capsules were formed on stainless steel mold pins by dipping the pins into a chitosan solution followed by forming asymmetric structure by dipping into a quenching solution containing tripolyphosphate (TPP) to cause an ionic cross-linking reaction between the outer layer of chitosan and TPP. Factors influencing the properties of the capsule membrane, such as the molecular weight of chitosan, the dipping solution and dipping time, and the quenching solution and time, were optimized to successfully produce osmotic chitosan capsules with asymmetric membrane using chitosans that possessed different viscosities. In situ formation of a delivery orifice on the asymmetric membrane of the chitosan capsule was proven by the observation of a jet stream of chlorophyll being released from the capsule. Drugs with different solubility were selected, and a linear correlation between drug solubility and the initial drug release rate calculated from the slope of the drug release profile was used to verify that the delivery orifices that were in situ formed on the asymmetric membrane of the chitosan capsules induced by osmotic effect was responsible for the drug release. Water permeability across the optimally produced asymmetric membrane of the capsule from chitosan of 500 cps (300-700 cps) quenched with TPP for 30 min (C500/TPP30) was determined to be 1.40 x 10(-6)cm(2)h(-1)atm(-1) at 37.0+/-0.5 degrees C. The encapsulation of poorly water-soluble drugs, felodipine (FE) and nifedipine (NF), in such an asymmetric chitosan capsule was capable of creating a sufficient osmotic effect to activate the release of the drug with the addition of SLS and HPMC. The multiple regression equations of maximal release percent at 24h for FE and NF confirmed that both sodium lauryl sulfate (SLS) and hydroxypropyl methylcellulose (HPMC) positively influenced this response factor, and the effect of SLS was greater than that of HPMC.
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Potrzebowski MJ, Bujacz GD, Bujacz A, Olejniczak S, Napora P, Heliński J, Ciesielski W, Gajda J. Study of molecular dynamics and the solid state phase transition mechanism for unsymmetrical thiopyrophosphate using X-ray diffraction, DFT calculations and NMR spectroscopy. J Phys Chem B 2006; 110:761-71. [PMID: 16471600 DOI: 10.1021/jp0547459] [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] [Indexed: 11/28/2022]
Abstract
Differential scanning calorimetry (DSC) and low-temperature X-ray diffraction studies showed that 2-thio-(5,5-dimethyl-1,3,2-dioxaphosphorinanyl)2'-oxo-dineopentyl-thiophosphate (compound 1) undergoes reversible phase transition at 203 K related to the change of symmetry of the crystallographic unit. Solid state NMR spectroscopy was used to establish the dynamic processes of aliphatic groups and the phosphorus skeleton. 13C and 31P variable temperature NMR studies as well as T1 and T1rho measurements of relaxation times revealed the different mode of molecular motion for each neopentyl residue directly bonded to phosphorus. It is concluded that molecular dynamics of aliphatic groups causes different van der Waals interactions in the crystal lattice and is the driving force of phase transition for compound 1. Finally, we showed that very sharp phase transition temperature makes compound 1 an excellent candidate as a low-temperature NMR thermometer in the solid phase.
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Yao B, Petrova RV, Vanfleet RR, Coffey KR. A modified back-etch method for preparation of plan-view high-resolution transmission electron microscopy samples. JOURNAL OF ELECTRON MICROSCOPY 2006; 55:209-14. [PMID: 17040930 DOI: 10.1093/jmicro/dfl027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A modified back-etch method is described that has been successfully used to prepare samples of thin films and nanoparticles on Si wafer substrates for examination by high-resolution transmission electron microscopy (HRTEM). This process includes ultrasonic cutting, abrasive pre-thinning and a two-stage etching procedure. Unlike previous reports of back-etching methods, tetramethyl ammonium hydroxide, which has a very high-etching selectivity of Si to SiO(2), is used for the final etching to allow removal of the Si without degradation of the SiO(2) membrane. An innovative wrapping method is also described. This novel approach reduces the preparation time for HRTEM samples to <1 h per sample for groups of 10 or more samples. As an example, the preparation of FePt nanoparticle samples for HRTEM imaging is described.
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Wright SF, Nichols KA, Schmidt WF. Comparison of efficacy of three extractants to solubilize glomalin on hyphae and in soil. CHEMOSPHERE 2006; 64:1219-24. [PMID: 16403563 DOI: 10.1016/j.chemosphere.2005.11.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 11/02/2005] [Accepted: 11/08/2005] [Indexed: 05/06/2023]
Abstract
Glomalin, a glycoprotein produced by arbuscular mycorrhizal (AM) fungi, is a major component of the humus fraction of soil organic matter. Glomalin is extracted from soil and hyphae of AM fungi by using sodium citrate at 121 degrees C in multiple 1-h cycles, but extensive extraction does not solubilize all glomalin in all soils. Efficacies of 100 mM sodium salts of citrate, borate or pyrophosphate (pH 9.0, 121 degrees C) were tested for two 1-h cycles for hyphae from four AM fungal isolates and four 1-h cycles for seven soils from four US geographic regions. Residual soil glomalin was examined by pyrophosphate extraction of soils previously extracted with citrate or borate followed by extraction of all soils after treatment with NaOH. Hyphal extracts were compared using Bradford-reactive total protein (BRTP) values, and extracts from soils were compared using BRTP, percentage C and C weight. No difference among extractants was detected for AM fungal isolates or across soils. The residual glomalin across soils for extractants contained the following percentages of the total BRTP: pyrophosphate, 14%; borate, 17%; and citrate, 22%. Comparisons among individual soils indicated that pyrophosphate extracted significantly more BRTP (10-53%) than borate or citrate in six soils and borate was equal to pyrophosphate in one soil. Extraction with borate should be compared with pyrophosphate before initiating an experiment. For routine extractions of ca. 85% of the glomalin across a variety of soils, sodium pyrophosphate appears to be equal to or better than borate and better than citrate.
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Tanaka H, Futaoka M, Hino R, Kandori K, Ishikawa T. Structure of synthetic calcium hydroxyapatite particles modified with pyrophosphoric acid. J Colloid Interface Sci 2006; 283:609-12. [PMID: 15721940 DOI: 10.1016/j.jcis.2004.09.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Accepted: 09/09/2004] [Indexed: 11/21/2022]
Abstract
Synthetic colloidal calcium hydroxyapatite (Ca(10)(PO(4))(6)(OH)(2): CaHap) was treated with pyrophosphoric acid (H(4)P(2)O(7): PP) in acetone and the materials were characterized by XRD, TEM, FTIR, and N(2) and H(2)O adsorption measurements. XRD patterns and morphology of CaHap particles were essentially not changed by the modification. The additional amount of PO(4) of CaHap was increased with an increase of PP concentration and the Ca/P molar ratio of the particles decreased from 1.62 to 0.81. IR results indicated that the isolated surface POH band developed with increasing the PP concentration up to 6.0 mmol dm(-3) by the reaction of isolated surface POH groups of CaHap and pyrophosphoric acids. Above 10.2 mmol dm(-3), a hydrogen-bonding surface POH band appeared at 2913 cm(-1) and enlarged with increasing the PP concentration, while the isolated surface POH band was weakened. The results of N(2) and H(2)O adsorption measurements revealed that the modified particles aggregated compared to the unmodified ones, which would be due to the formation of hydrogen-bonding surface POH groups among the particles.
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Salim S, Santini A, Husham A. An In-Vitro Study of Microleakage Around Class V Cavities Bonded with a Self-Etching Material Versus a Conventional Two-Bottle System. ACTA ACUST UNITED AC 2006; 13:107-11. [PMID: 16836814 DOI: 10.1308/135576106777795545] [Citation(s) in RCA: 3] [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
Objective To evaluate the microleakage around class V restorations restored with either a self-etching adhesive system or a conventional two-bottle adhesive system used with ‘total etch’ technique, and their recommended resin-based composites (RBC). Methods Two types of adhesive systems were used. A self-etching adhesive, Etch and Prime 3.0 (Degussa AG, Hanau, Germany), and a conventional two-bottle adhesive, Gluma Solid Bond (Heraeus Kulzer, Dormagen, Germany). The bonding systems were used in strict accordance with the manufacturers’ instructions, except that, with the two-bottle adhesive system, the cavities were filled with either a ‘wet’ or a ‘dry’ bonding technique, subsequent to acid-etching with 20% phosphoric acid. Etch & Prime 3.0 was used in conjunction with Degufill Mineral (Degussa, Hanau, Germany) RBC and Gluma Solid Bond with Flow Line RBC (Heraeus Kulzer, Dormagen, Germany). Standardised bucco-cervical cavities were prepared on the buccal and lingual surfaces of 15 extracted maxillary first premolar teeth; all cavity margins were in enamel. Ten of the resulting cavities (Group A) were restored using Etch & Prime 3.0 and Degufill Mineral, ten (Group B) using Gluma Solid Bond (Wet Bond), and ten (Group C) using Gluma Solid Bond (Dry Bond). Leakage scores at occlusal and gingival margins were calculated after thermocycling 500 times between baths, held at 5°C and 55°C, respectively, with 30 seconds dwell time in both. Data were analysed by the Fisher Exact Test. Results There was no statistically significant difference between the self-etching adhesive and conventional two-bottle adhesive systems at either the occlusal or the gingival margins. With the self-etching adhesive, there was no statistically significant difference in leakage scores between occlusal and gingival margins. There was a statistically significant difference between the occlusal and the gingival margins when a ‘wet’ or ‘dry’ bonding technique was used with the conventional two-bottle adhesive system. Conclusions The results suggest that the application of a conventional two-bottle bonding system used with a ‘total etch’ technique is better than that of a self-etching adhesive system. With the former, the use of a ‘wet’ bonding does not give better results than a ‘dry’ bonding technique.
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Zsila F, Nadolski G, Lockwood SF. Association studies of aggregated aqueous lutein diphosphate with human serum albumin and α1-acid glycoprotein in vitro: Evidence from circular dichroism and electronic absorption spectroscopy. Bioorg Med Chem Lett 2006; 16:3797-801. [PMID: 16678417 DOI: 10.1016/j.bmcl.2006.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 04/12/2006] [Accepted: 04/12/2006] [Indexed: 11/25/2022]
Abstract
Water-dispersible C40 carotenoid derivatives, with increased utility in mammalian therapeutic applications, include natural stereoisomer-based (3R,3'R,6'R)-lutein (beta,epsilon-carotene-3,3'-diol) derivatives. Esterification with inorganic phosphate and conversion to the sodium salt produced compounds (lutein diphosphate sodium salt; 'LdP') capable of forming red-orange aqueous suspensions after addition to USP-purified water. The aqueous dispersibility of this diphosphate salt reached 29 mg/mL without the addition of heat, detergents, co-solvents, or other additives, and was a potent direct scavenger of superoxide anion (by EPR spectroscopy) in an isolated human neutrophil assay. In the current study, preliminary evidence of the aqueous aggregation of this compound in EPR studies was confirmed using circular dichroism (CD) and electronic absorption (UV-vis) spectroscopy. Evidence for H-type ('card-pack') and J-type ('head-to-tail') self-assemblies was obtained. In vitro analysis of the potential binding interaction between LdP and human serum albumin (HSA) and alpha1-acid glycoprotein (AGP) revealed only non-specific binding with HSA (and none with AGP), contrasting with previous reports of direct interaction between astaxanthin-based soft drugs and the major plasma protein albumin. The rapid in vivo cleavage of this phosphodiester by promiscuous mammalian phosphatases may overcome the aqueous aggregation of the formulated compound. This difference in potential plasma protein interaction with prior reports reflects the subtle structural differences inherent in either the parent carotenoid scaffolds and/or the esterifying moieties.
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