Sodium Malonate Research Articles

U1A RNA-binding domain at 1.8 A resolution.

The human U1A RNA-binding domain (RBD1) adopts one of the most common protein folds, the RNA-recognition motif, and is a paradigm for understanding RNA-protein interactions. A 2.8 A resolution structure of the unbound RBD1 has previously been determined [Nagai et al. (1990). Nature (London), 348, 515-520] and revealed a well defined alpha/beta core with disordered termini. Using a longer construct, a 1.8 A resolution structure of the unbound domain was determined that reveals an ordered C-terminal helix. The presence of this helix is consistent with a solution structure of the free domain [Avis et al. (1996). J. Mol. Biol. 257, 398-411]; however, in the solution structure the helix occludes the RNA-binding surface. In the present structure, the helix occupies a position similar to that seen in a 1.9 A resolution RNA-RBD1 complex structure [Oubridge et al. (1994). Nature (London), 372, 432-438]. The crystals in this study were grown from 2.2 M sodium malonate. It is possible that the high salt concentration helps to orient the C-terminal helix in the RNA-bound conformation by strengthening hydrophobic interactions between the buried face of the helix and the alpha/beta core of the protein. Alternatively, the malonate (several molecules of which are bound in the vicinity of the RNA-binding surface) may mimic RNA.

Expression and preliminary crystallographic studies of R1E, the large subunit of ribonucleotide reductase from Salmonella typhimurium.

The nrdE gene product R1E, the large subunit of the class 1b Salmonella typhimurium ribonucleotide reductase, has been overexpressed, purified and crystallized. Initially, the protein crystallized in two orthorhombic space groups, C222(1) and P2(1)2(1)2, using tartrate and PEG 6000 as precipitants, respectively. Better diffracting crystals belonging to the tetrahedral space group P4(3)2(1)2 were obtained using sodium malonate as precipitant. The P4(3)2(1)2 crystals could only be obtained after seeding from a drop containing C222(1) crystals grown in sodium tartrate. Thus, streak-seeding resulted in crystals of a supergroup to C222(1). Data to 2.8 A resolution have been collected on the P4(3)2(1)2 crystals which contained one R1E subunit in the asymmetric unit.

Study of the degradation of dyes by MnP of Phanerochaete chrysosporium produced in a fixed-bed bioreactor

The production of ligninolytic enzymes by the fungus Phanerochaete chrysosporium in a fixed-bed tubular bioreactor, filled with cubes of nylon sponge, operating in semi-solid-state conditions, was studied. Maximum individual manganese-dependent peroxidase (MnP) and lignin peroxidase (LiP) activities of 1293 and 225 U/l were detected. The in vitro decolourisation of two structurally different dyes (Poly R-478, crystal violet) by the extracellular liquid obtained in the above-mentioned bioreactor was monitored in order to determine its degrading capability. The concentration of some compounds (sodium malonate, manganese sulphate) from the reaction mixture was optimised in order to maximise the decolourisation levels. A percentage of Poly R-478 decolourisation of 24% after 15 min of dye incubation was achieved. On the other hand, a methodology for a long treatment of these dyes based on the continuous addition of MnP enzyme and H 2O 2 was developed. Moreover, this enzymatic treatment was compared with a photochemical decolourisation process. The former allowed to maintain the degradation rate almost constant for a long time, resulting in a decolourisation percentage of 70% and 30% for crystal violet and Poly R-478, respectively, after 2 h of treatment. As for the latter, it was not able to degrade Poly R-478, whereas crystal violet reached a degradation of 40% in 2 h.

Effect of sodium succinate on gas exchange in rats with barbiturate-induced coma.

Injection of sodium succinate in doses of 5 or 10 mmol/kg (but not 1 mmol/kg) intensified oxygen consumption in rats with sodium thiopental-induced coma. Injection of SDH inhibitor (sodium malonate) inhibited gas exchange and abolished the effect of sodium succinate. The effect of succinate on rat survival was positive, while that of malonate was negative, but manifested only as a trend. The critical role of succinate oxidation in preventing lethal complications of barbiturate-induced coma is proved.

The effect of sodium malonate on yeast thermotolerance

The study of the effect of malonate (an inhibitor of the succinate dehydrogenase complex of the respiratory chain of mitochondria) on the thermotolerance of the fermentative Saccharomyces cerevisiae and nonfermentative Rhodotorula rubra yeasts showed that malonate augmented the damaging effect of heat shock on the yeasts utilizing glucose (or other sugars) by means of oxidative phosphorylation. At the same time, malonate did not influence and sometimes even improved the thermotolerance of the yeasts utilizing glucose through fermentation. The suggestion is made that cell tolerance to heat shock depends on the normal functioning of mitochondria. On the other hand, their increased activity at elevated temperatures may accelerate the formation of cytotoxic reactive oxygen species and, hence, is not beneficial to cells.

Trapping of photochemical intermediates as a tool in organic synthesis. Preparation of spiroaziridinopyridones, a new heterocyclic system

Whereas alkyl lithium and Grignard reagents both at rt and at −80°C thermally react with 3-methylisoxazolo[5,4- b]pyridine giving alkylation and/or isoxazole ring opening products, sodium malonate and sodium boron hydride react only under UV irradiation. Selective trappings of ketenimine or azirine intermediates give an enaminopyridone or two diasteroisomeric spiroaziridinopirydones. Regioselective opening of the aziridine ring with perchloric acid gives 3(1-amino-ethyl)-1 H-pyridin-2-one.

Solvent extraction separation of rhodium(III) with N- n-octylaniline as an extractant

Solvent extraction separation method for the determination of rhodium(III) has been described. Selective and quantitative extraction of rhodium(III) by N- n-octylaniline, a high molecular weight amine (HMWA) into xylene takes place from aqueous sodium malonate medium. The effect of concentration of malonate, N- n-octylaniline, role of various diluents, stripping agents and foreign ions on the extraction of rhodium(III) has been studied. The procedure offers distinct improvements in need of real sample analysis and environmental safety as the extraction procedure carried out in weak organic acid media.

A 1,1’-ferrocenylene-bridged analogue of BIPNOR

At 170 °C, 1,1’-bis(3,4-dimethylphospholyl)ferrocene ( 7) isomerises through the corresponding 2 H-phospholes that are trapped by diphenylacetylene to give the 1,1’-ferrocenylene-bridged bis–1-phosphanorbornadiene ( 6). After resolution with an optically pure palladium complex, ( R, R)- and ( S, S)-( 6) are tested in the asymmetric hydrogenation of a dehydroaminoacid, hydroformylation of styrene, and allylation of sodium malonate.

Selective Organic Removal from the Alumina Industrial Liquor: Wet Oxidation and Catalytic Wet Oxidation of Disodium Malonate

The wet oxidation and catalytic wet oxidation of a key organic component, particularly disodium malonate (the salt of propanedioic acid) found in the alumina industrial liquor have been investigated. The wet oxidation and catalytic wet oxidation of the disodium malonate in highly alkaline media was carried out at 165 °C in a high-pressure reaction system. The main carbon-containing species detected as products from disodium malonate oxidation were sodium carbonate and sodium oxalate produced in similar quantities during wet oxidation and catalyzed wet oxidation. The amounts of ketomalonic acid hydrate detected during disodium malonate oxidation were up to 20 mg/L. Mechanisms for both wet oxidation and copper-catalyzed wet oxidation of disodium malonate are proposed, with ketomalonic acid (hydrate) as a key intermediate organic species.

Crystallization of Brome Mosaic Virus and T = 1 Brome Mosaic Virus Particles Following a Structural Transition

Brome mosaic virus (BMV), a T = 3 icosahedral plant virus, can be dissociated into coat protein subunits and subunit oligomers at pH 7.5 in the presence of concentrated salts. We have found that during the course of this treatment the coat protein subunits are cleaved, presumably by plant cell proteases still present in the preparation, between amino acids 35 and 36. The truncated protein subunits will then reorganize into T = 1 icosahedral particles and can be crystallized from sodium malonate. Quasi elastic light scattering and atomic force microscopy results suggest that the transition from T = 3 to T = 1 particles can occur by separate pathways, dissociation into coat protein subunits and oligomers and reassembly into T = 1 particles, or direct condensation of the T = 3 virions to T = 1 particles with the shedding of hexameric capsomeres. The latter process has been directly visualized using atomic force microscopy. Native T = 3 virions have been crystallized in several different crystal forms, but neither a rhombohedral form nor either of two orthorhombic forms diffract beyond about 3.4 A. Tetragonal crystals of the T = 1 particles, however, diffract to at least 2.5 A resolution. Evidence suggests that the T = 1 particles are more structurally uniform and ordered than are native T = 3 virions. A variety of anomalous virus particles having diverse sizes have been visualized in preparations of BMV used for crystallization. In some cases these aberrant particles are incorporated into growing crystals where they are frequently responsible for defect formation.

Electrochemical and spectroscopic studies on dicarboxylato niobocene complexes

Reaction of sodium oxalate or malonate onto the niobocene dichloride Nb(η 5-C 5H 4SiMe 3)Cl 2 ( 1) yields the dicarboxylato complexes Nb(η 5-C 5H 4SiMe 3) 2( O, O′-OCOOCO) ( 4a) and Cp′ 2Nb( O, O′-OCOCH 2OCO) ( 5a) where the dicarboxylato ligand is proved to be chelating. An alternative way to yield the dicarboxylato niobium (IV) complexes consists in the electrochemical reduction of 1 in the presence of the corresponding carboxylic acid followed by the oxidation of the electrogenerated complex. In addition to 4a and 5a the latter method has been shown to yield the succinato and orthophtalato analogs Nb(η 5-C 5H 4SiMe 3) 2( O, O′-OCOCH 2CH 2OCO) ( 6a) and Nb(η 5-C 5H 4SiMe 3) 2( O, O′-OCOC 6H 4OCO) ( 7a). The structure of the complexes as well as the mechanism of their formation is discussed above electrochemical and spectroscopic data. A special emphasis is made on the ESR data which strongly depends on the length of the dicarboxylato chain.

Rapid solvent extraction of gold(III) with high molecular weight amine from organic acid solution

A novel solvent extraction separation method has been developed for the determination of gold in real samples. It involves selective and quantitative extraction of gold by N-n-octylaniline, a high molecular weight amine (HMWA), in xylene from aqueous sodium malonate medium at pH 1.0. The effects of concentration of malonate, extractant, metal ion, and pH and of various diluents, stripping agents and other substances on the quantitative extraction of gold have been assessed. The applicability of the method to binary mixtures, synthetic mixtures, alloys and pharmaceutical samples is discussed.

The water cycles of water-soluble organic salts of atmospheric importance

In this study, the water cycles of nine water-soluble organic salts of atmospheric interest were studied using an electrodynamic balance (EDB) at 25°C. Sodium formate, sodium acetate, sodium succinate, sodium pyruvate and sodium methanesulfonate (Na-MSA) particles crystallize as the relative humidity (RH) decreases and they deliquesce as the RH increases. Sodium oxalate and ammonium oxalate form supersaturated particles at low RH before crystallization but they do not deliquesce even at RH=90%. Sodium malonate and sodium maleate particles neither crystallize nor deliquesce. These two salts absorb and evaporate water reversibly without hysteresis. In most cases, the solid states of single particles resulting from the crystallization of supersaturated droplets do not form the most thermodynamically stable state found in bulk studies. Sodium formate, sodium oxalate, ammonium oxalate, sodium succinate, sodium pyruvate and Na-MSA form anhydrous particles after crystallization. Sodium acetate forms particles with a water/salt molar ratio of 0.5 after crystallization. In salts with several hydrated states including sodium formate and sodium acetate, the particles deliquesce at the lowest deliquescence relative humidity (DRH) of the hydrates. Except sodium oxalate and ammonium oxalate, all the salts studied here are as hygroscopic as typical inorganic hygroscopic aerosols. The hygroscopic organic salts have a growth factor of 1.76–2.18 from RH=10–90%, comparable to that of typical hygroscopic inorganic salts such as NaCl and (NH 4) 2SO 4. Further study of other atmospheric water-soluble organic compounds and their mixtures with inorganic salts is needed to explain the field observations of the hygroscopic growth of ambient aerosols.

Carotenoid accumulation in Haematococcus pluvialis in mixotrophic growth

The microalga Haematococcus pluvialis was cultured with NaNO3 from 0 to 1 g l−1 and optimal growth was obtained at 0.15 g l−1. Sodium acetate and malonate (from 0 to 2% w/v) enhanced the accumulation of astaxanthin three and five times higher, respectively, than in autotrophic control cultures. However, high concentration of those compounds strongly inhibited growth. The ratio chlorophyll a/total carotenoids was a good indicator of the extent of nitrogen deficiency in the cells.

Avirulent mutants ofMacrophomina phaseolina andAspergillus fumigatus initiate infection inPhaseolus mungo in the presence of phaseolinone; levamisole gives protection

To evaluate the role of phaseolinone, a phytotoxin produced by Macrophomina phaseolina, in disease initiation, three nontoxigenic avirulent mutants of the fungus were generated by UV-mutagenesis. Two of them were able to initiate infection in germinating Phaseolus mungo seeds only in the presence of phaseolinone. The minimum dose of phaseoli-none required for infection in 30% seedlings was 2 5 mg/ml. A human pathogen, Aspergillus fumigatus was also able to infect germinating seeds of P. mungo in the presence of 5 mg/ml concentration of phaseolinone. Phaseolinone seemed to facilitate infection by A. fumigatus, which is not normally phytopathogenic, by reducing the immunity of germinating seedlings in a nonspecific way. Levamisole, a non-specific immunopotentiator gave protection against infection induced by A. fumigatus at an optimum dose of 50 mg/ml. Sodium malonate prevented the effects of levamisole.

Efficient Palladium-Catalyzed Substitution in Enantiomerically Pure Allyl Carbonates – A Stereodivergent Access to β-Aryl-Substituted γ-Lactones and γ-Hydroxy Amides

Allyl carbonates (Z)-8 and (E)-9 are available from the addition of the chiral alkenyllithium reagent 5b to aromatic aldehydes 6. When sujected to a palladium-catalyzed substitution by sodium malonate, (Z)-carbonates 8 give diesters 10 and 11, whereas (E)-carbonate 9 predominantly leads to the diastereomeric product 12. The latter is converted into (S)-γ-butyrolactone 13 in a three step sequence. When the same protocol is applied to the isomeric diesters 10 and 11, (R)-lactones 13 result. A rationale for the stereochemical outcome of the allylic substitutions in the carbonates 10-12 is offered, based on π-σ-π interconversions of the palladium complexes 20-23.

Efficient Palladium-Catalyzed Substitution in Enantiomerically Pure Allyl Carbonates – A Stereodivergent Access to β-Aryl-Substituted γ-Lactones and γ-Hydroxy Amides

Allyl carbonates (Z)-8 and (E)-9 are available from the addition of the chiral alkenyllithium reagent 5b to aromatic aldehydes 6. When sujected to a palladium-catalyzed substitution by sodium malonate, (Z)-carbonates 8 give diesters 10 and 11, whereas (E)-carbonate 9 predominantly leads to the diastereomeric product 12. The latter is converted into (S)-γ-butyrolactone 13 in a three step sequence. When the same protocol is applied to the isomeric diesters 10 and 11, (R)-lactones 13 result. A rationale for the stereochemical outcome of the allylic substitutions in the carbonates 10-12 is offered, based on π-σ-π interconversions of the palladium complexes 20-23.

Oxidative decomposition of malonic acid as basis for the action of manganese peroxidase in the absence of hydrogen peroxide

Manganese peroxidase (MnP) from the ligninolytic basidiomycetes Phlebia radiata and Nematoloma frowardii was found to decompose malonate oxidatively in the absence of H 2O 2 in a reaction system consisting of the enzyme, sodium malonate and MnCl 2. The enzymatic oxidation resulted in a substantial decrease in malonate concentration and the formation of CO 2, oxalate, glyoxylate and formate. Simultaneously with the decomposition of malonate, Mn(II) was oxidized to Mn(III) leading to high transient concentrations of the latter. MnP action in the absence of H 2O 2 started slowly after a lag period of 3 h. The lag period was considerably shortened after a single addition of Mn(III). Superoxide dismutase and catalase inhibited the enzymatic reaction partly, ascorbate completely. ESR studies demonstrated the formation of a carbon-centered radical during the course of the reaction. We propose that the latter generates peroxides that can be used by MnP to oxidize Mn(II) to Mn(III).

Chemo-enzymic synthesis of protected cyano derivatives of glutamate

(2S,4RS)-Boc-4-cyanoglutamate γ-methyl ester (ee = 95%) and (2S)-Boc-2-amino-4-bis(cyano)butyrate (ee = 96%) were synthesised in respectively 43% and 40% overall yields by addition of sodium malonate derivatives onto Boc-dehydroalanine methyl ester followed by regio- and stereoselective hydrolysis of α-methyl ester by α-chymotrypsin. These regio-and stereoselectivities were strongly dependent on the nature of the γ-substituents.

New homochiral amino-phosphine ligands: application in asymmetric palladium catalyzed allylic alkylation

A new series of homochiral amino-phosphine ligands was prepared. The use of these ligands in the palladium catalyzed allylic alkylation of 1,3-diphenyl-1-acetoxy-2-propene with sodium malonate gave substitution products with up to 76% e.e. The enantioselectivity was largely dependent on the nitrogen substituent.