Solution nuclear magnetic resonance structure of the GATase subunit and structural Basis of the interaction between GATase and ATPPase subunits in a two-subunit-type GMPS from methanocaldococcus jannaschii

The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and N-15 backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 +/- 0.06 angstrom for backbone atoms and 0.8 +/- 0.06 angstrom for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed beta-sheet that is fenced by five alpha-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg2+ interaction has been found to be similar to 1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.

Increasing cleavage specificity and activity of restriction endonuclease KpnI

Restriction enzyme KpnI is a HNH superfamily endonuclease requiring divalent metal ions for DNA cleavage but not for binding. The active site of KpnI can accommodate metal ions of different atomic radii for DNA cleavage. Although Mg2+ ion higher than 500 mu M mediates promiscuous activity, Ca2+ suppresses the promiscuity and induces high cleavage fidelity. Here, we report that a conservative mutation of the metal-coordinating residue D148 to Glu results in the elimination of the Ca2+-mediated cleavage but imparting high cleavage fidelity with Mg2+. High cleavage fidelity of the mutant D148E is achieved through better discrimination of the target site at the binding and cleavage steps. Biochemical experiments and molecular dynamics simulations suggest that the mutation inhibits Ca2+-mediated cleavage activity by altering the geometry of the Ca2+-bound HNH active site. Although the D148E mutant reduces the specific activity of the enzyme, we identified a suppressor mutation that increases the turnover rate to restore the specific activity of the high fidelity mutant to the wild-type level. Our results show that active site plasticity in coordinating different metal ions is related to KpnI promiscuous activity, and tinkering the metal ion coordination is a plausible way to reduce promiscuous activity of metalloenzymes.

Multifunctional magnetic reduced graphene oxide dendrites: Synthesis, characterization and their applications

In this paper, for the first time, we have reported the novel synthesis of reduced graphene oxide (r-GO) dendrite kind of nanomaterial. The proposed r-GO dendrite possesses multifunctional properties in various fields of sensing and separation. The dendrite was synthesized by chemical reaction in different steps. Initially, the r-GO sheet was conjugated with silane group modified magnetic nanoparticle, resulting in nanoparticle decorated r-GO. The above r-GO sheet was further reacted with a new r-GO sheet, resulting in the formation of r-GO dendrite type of structure. Multifunctional behavior of this r-GO dendrite structure was studied by different methods. First, magnetic properties were studied by vibrating sample magnetometer (VSM) and it was found that dendrite structure shows good magnetic susceptibility (180.2 emu/g). The proposed r-GO dendrite also shows a very good antibacterial behavior for Escherichia coli and excellent electrochemical behavior towards ferrocyanide probe molecule. Along with these, it also acts as a substrate for the synthesis of molecularly imprinted polymer for europium metal ion, a lanthanide. The proposed imprinted sensor shows a very high selectivity and sensitivity for europium metal ion (limit of detection= 0.019 mu g L-1) in aqueous as well as real samples. (C) 2015 Elsevier B.V. All rights reserved.

SWEETENING OF BIOGAS IN SPRAY TOWERS FOR POWER GENERATION

This paper presents the experience of the new design of using impinging jet spray columns for scrubbing hydrogen sulfide from biogas that has been developed by Indian Institute of Science and patented. The process uses a chelated polyvalent metal ion which oxidizes the hydrogen sulfide to sulfur as a precipitate. The sulfur generated is filtered and the scrubbing liquid recycled after oxidation. The process involves in bringing contact the sour gas with chelated liquid in the spray columns where H2S reacts with chelated Fe3+ and precipitates as sulfur, whereas Fe3+ gets reduced to Fe2+. Fe2+ is regenerated to Fe3+ by reaction of oxygen in air in a separate packed column. The regenerated liquid is recirculated. Sulfur is filtered and separated as a byproduct. The paper presents the experience in using the spray towers for hydrogen sulfide removal and further use of the clean gas for generating power using gas engines. The maximum allowable limit of H2S for the gas engine is 200 ppm (v/v) in order to prevent any corrosion of engine parts and fouling of the lubricating oil. With the current ISET process, the hydrogen sulfide from the biogas is cleaned to less than 100 ppm (v/v) and the sweet gas is used for power generation. The system is designed for 550 NM3/hr of biogas and inlet H2S concentration of 2.5 %. The inlet concentration of the H2S is about 1 - 1.5 % and average measured outlet concentration is about 30 ppm, with an average gas flow of about 300 - 350 NM3/hr, which is the current gas production rate. The sweet gas is used for power generation in a 1.2 MWe V 12 engine. The average power generation is about 650 - 750 kWe, which is the captive load of the industry. The plant is a CHP (combined heat power) unit with heat from the cylinder cooling and flue being recovered for hot water and steam generation respectively. The specific fuel consumption is 2.29 kWh/m(3) of gas. The system has been in operation for more than 13,000 hours in last one year in the industry. About 8.4 million units of electricity has been generated scrubbing about 2.1 million m3 of gas. Performance of the scrubber and the engine is discussed at daily performance level and also the overall performance with an environment sustenance by precipitating over 27 tons of sulfur.

Metallophosphoesterases: structural fidelity with functional promiscuity

Calcineurin-like metallophosphoesterases (MPEs) form a large superfamily of binuclear metal-ion-centre-containing enzymes that hydrolyse phosphomono-, phosphodi-or phosphotri-esters in a metal-dependent manner. The MPE domain is found in Mre11/SbcD DNA-repair enzymes, mammalian phosphoprotein phosphatases, acid sphingomyelinases, purple acid phosphatases, nucleotidases and bacterial cyclic nucleotide phosphodiesterases. Despite this functional diversity, MPEs show a remarkably similar structural fold and active-site architecture. In the present review, we summarize the available structural, biochemical and functional information on these proteins. We also describe how diversification and specialization of the core MPE fold in various MPEs is achieved by amino acid substitution in their active sites, metal ions and regulatory effects of accessory domains. Finally, we discuss emerging roles of these proteins as non-catalytic protein-interaction scaffolds. Thus we view the MPE superfamily as a set of proteins with a highly conserved structural core that allows embellishment to result in dramatic and niche-specific diversification of function.

High aspect ratio, processable coordination polymer gel nanotubes based on an AIE-active LMWG with tunable emission

A new TPE based low molecular weight gelator (LMWG) which displays both AIE and MCIE phenomena in gel state has been synthesized. LMWG self-assembles to form 1D nanofibers which undergo morphology transformation to coordination polymer gel (CPG) nanotubes upon metal ion coordination. CPG shows enhanced mechanical stability along with tunable emission properties.

Characterization of silver-kaolinite (AgK): an adsorbent for long-lived I-129 species

Bentonite is a preferred buffer and backfill material for deep geological disposal of high-level nuclear waste (HLW). Bentonite does not retain anions by virtue of its negatively charged basal surface. Imparting anion retention ability to bentonite is important to enable the expansive clay to retain long-lived I-129 (iodine-129; half-life = 16 million years) species that may escape from the HLW geological repository. Silver-kaolinite (AgK) material is prepared as an additive to improve the iodide retention capacity of bentonite. The AgK is prepared by heating kaolinite-silver nitrate mix at 400 degrees C to study the kaolinite influence on the transition metal ion when reacting at its dehydroxylation temperature. Thermo gravimetric-Evolved Gas Detection analysis, X-ray diffraction analysis, X-ray photo electron spectroscopy and electron probe micro analysis indicated that silver occurs as AgO/Ag2O surface coating on thermally reacting kaolinite with silver nitrate at 400 degrees C.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Ensaios dinâmicos de biossorção de cobre com macroalgas em leitos-fixos contendo materiais adsorventes de natureza não-biológica

A biossorção é o termo aplicado à tecnologia de adsorção de íons metálicos em solução, por meio de materiais de natureza biológica inativa, comparável à adsorção utilizando-se adsorventes convencionais. A biossorção depende da temperatura, pH, concentração inicial do íon metálico, e tipo de biosorvente. O objetivo principal dessa dissertação é estudar e comparar os processos de adsorção de cobre iônico a partir de soluções aquosas utilizando Sargassum sp., alginato de cálcio úmido e desidratado e carvão ativo em pó e granular, em regime de batelada e contínuo. O alginato de cálcio foi preparado através de uma solução 4% (m/v) de alginato de sódio gotejada em solução 37% (m/v) de cloreto de cálcio dihidratado. O alginato de cálcio apresentou uma umidade de 89% após secagem em estufa a 100C por 24 horas. Os parâmetros da biossorção foram fixados em: a dose de adsorventes de 2 g/L; a temperatura em 30C; pH da solução em 5,0; e velocidade de rotação da chapa rotatória em 150 rpm. Para os estudos de cinética e equilíbrio, os ensaios foram feitos em regime de batelada. Nos ensaios cinéticos para duas concentrações medias (0,16 e 3,15 mmol/L) variou-se o tempo de contato (1 a 120 min) para se atingir o equilíbrio. Nos ensaios de equilíbrio variou-se as concentrações (0,16 a 15,72 mmol/L) utilizando o tempo de equilíbrio determinado nos ensaios cinéticos. Foram utilizadas duas modelagens cinéticas (a de pseudo-primeira ordem e a de segunda ordem) e duas modelagens do equilíbrio (Langmuir e Freundlich). O modelo cinético de segunda ordem ajustou melhor os resultados. O tempo de equilíbrio para adsorção do cobre foi de 60 minutos para Sargassum sp. e pellets de alginatos de cálcio úmido e desidratado. Para os carvões ativos os tempos de equilíbrio para a adsorção do cobre foram mais rápidos, mas a capacidade de remoção do cobre foram muito baixas. Com base nos resultados desfavoráveis obtidos para os carvões ativos eles foram descartados para se prosseguir com os ensaios de equilíbrio. A isoterma de Freundlich melhor ajusta os dados experimentais para Sargassum sp. e alginato de cálcio úmido. A capacidade de adsorção máxima calculada pelo modelo de Freundlich: na concentração de equilíbrio de 11,66 0,06 mmol/L foi de 1,97 0,07 mmol/g para Sargassum sp.; e na concentração de equilíbrio de 12,12 0,03 mmol/L foi de 1,69 0,04 mmol/g para alginato de cálcio úmido. O processo de biossorção em regime contínuo, com alturas de leito variável de 10 a 40 cm, teve melhor desempenho com a altura de 40 cm. Em regime de batelada, o desempenho da Sargassum sp. foi superior ao dos alginatos de cálcio (úmido melhor que o desidratado), que por sua vez foram superiores ao desempenho dos carvões ativos em pó e granular (em pó melhor que o granular). O sistema contínuo com concentração inicial de cobre de 8,5 mmol/L deve ser operado com altura de leito igual ou superior a 40 cm, ou com sistemas multicolunas para soluções mais concentradas

绞股蓝离体培养中影响皂甙产量的几个因素研究

绞股蓝(Gynostemma pentaphyllum)系葫芦科绞股蓝属植物，药用价值广泛，但其野生资源日趋减少，绞股蓝主要药效成分为绞股 蓝皂甙。利用组织和细胞培养生产绞股蓝皂甙是合理开发利用和保护绞股蓝资源的可能途径之一。本文对绞股蓝组织培养中培养基 的蔗糖和激素的组成以及各种胁迫条件：渗透压、重金属离子、真菌诱导物等对皂苷产量的影响进行了初步研究。其中，渗透压、 重金属离子、真菌诱导物对绞股蓝愈伤组织皂甙产量的影响尚未见报道。1. 蔗糖对绞股蓝愈伤组织之生长影响显著，2,4-D对绞股 蓝愈伤组织皂甙含量、产量影响显著。增加蔗糖用量，减少2，4-D的用量可提高皂甙产量。2. Mn++ 用量的提高抑制绞股蓝愈伤组 织的生长，但可促进皂甙含量、产量的提高。Mn++用量提高至MS培养基的20-30倍时可使皂甙产量增加近一倍，而提高Cu++浓度的 作用不明显。3. 甘露醇用量增加抑制绞股蓝愈伤组织的生长，但可使皂甙含量、产量提高。0.680mol·l-1甘露醇可使皂甙产量提 高83%，而Nacl较大抑制愈伤组织的生长并使皂甙产量降低。4. 米曲霉粗提物对绞股蓝愈伤组织生长先略微促进，然后抑制，而根 霉粗提物则使愈伤组织生长受抑制；两者对皂甙含量、产量的作用相似：在较低浓度范围内升高，然后下降。米曲霉粗提物可提高 产量一倍，根霉粗提物可提高42%。这些结果为高产细胞系的筛选和生长、生产培养条件的优化积累了资料。在综述部分，对植物 细胞培养中组织和器官分化、细胞结构变化、生化水平的变化与次生物合成和积累的关系作了讨论。Gynostemma pentaphyllum blongs to Gynostemma, Cucurbitaccae. It has a wide medical use, but its wild resource is threatened by people's excessive use. Its effective medical components are gypenosides. For reasonable use and protect its resource, it is a possible way to product gypenosides by plant tissue and cell culture. This paper has a primary study on the components of sucrose and hormones and a variety of stress conditions: osmostic pressure, heavy metal ion, fungal elicitors in the medium for the calli culture. The effects of osmostic pressure, heavy metal ion and fungal elicitors on the calli of Gynostemma pentaphyllum have not been reported. 1. Sucrose had a significant effect on the growth of the calli, 2,4 D had notable effects on the gypenosides content and production of the calli. Increased the concentration of sucrose and decreased the concentration of 2,4 D improved the production of gypenosides. 2. Increased the concentration of Mn++ inhibited the growth of the calli, but improved the content and production of gypenosides. The optimum concentration was 20-30 times as MS medium which improved the production 100%. Increased the concentration of Cu++ had not a notable effect. 3. Increased the concentration of mannitol inhibited the growth of the calli, but improved the content and production of gypenosides. The optimum concentration was 0.680mol·l-1 which improved the production 83%. Nacl apparently inhibited the growth of the calli and decreased the production of gypenosides. 4. The crude preparation of Aspergillus oryzae inhibited the growth of the calli that in low concentration. The crude praparation of Rhizopus formosensis inhibited the growth of the calli throughout. Their effects on the content and production of gypenosides are alike, but the former is higher than the latter. On the optimum concentration, each crude preparation improved the production 100% (Aspergillus oryzae), 42%(Rhizopus formosensis). These results has accumulated some informantion on the select of high yield cell strains and choose the best culture conditons for the growth and gypenosides product of the calli. In the review, it is discussed that the differentiation on tissue-organal, cellular and biochemical levels related to the synthesis and accumulation of secondary metabolites in plant culuture.

全永磁ECR离子源研究进展

Electron Cyclotron Resonance (ECR) ion source is regarded as the most efficient machine to produce stable multiple charge state ion beams. Because of the special characteristics, all-permanent magnet ECR ion sources have been widely adopted around the world to produce stable ion beams of multiple charge state with good repetition have been widely adopted around the world to produce stable ion beams of multiple charge state with good repetition and high duty factor for compact research platforms and ion beam implanters. In this paper, all-permanent magnet ECR ion sources developed at IMP are presented, and typical parameters and performances are discussed. The high charge state source, LAPECR2, is mainly used to produce intense high charge state ion beams, and the LAPECR1 source is designed to produce intense ion beams of medium and low charge state. An improved LAPECR1-M is specially designed to produce heavy metal ion beams of low charge state. These ECR ion sources have been adopted by different experimental terminals at IMP and, with their nice performance, many experimental studies could be possible. 中文文摘：ECR(电子回旋共振)离子源是产生稳定的强流多电荷态离子束流最有效装置。全永磁ECR 离子源因其独特的特点为很多中小型多电荷态离子束流实验平台与离子注入机等系统所采用，为后者产生重复性好、稳定性强的多电荷态离子束流。本文着重论述了中国科学院近代物理研究所研制的几台全永磁多电荷态ECR 离子源及其特性与典型性能，如能产生强流高电荷态离子束流的高性能全永磁离子源LAPECR2，能产生强流中 低电荷态离子束流的LAPECR1，能产生多电荷态重金属离子束流的LAPECR1-M 等。这些性能稳定的离子源为提高近代物理研究所相关试验平台的性能提供了关键的束流品质保障。

Flow-through room temperature phosphorescence optosensing for the determination of lead in sea water

The chelates formed between the heavy metal ion Pb(II) and the reagents 8-hydroxy-5-quinolinesulphonic acid, 8-hydroxy-7-quinolinesulphonic acid and 8-hydroxy-7-iodo-5-quinolinesulphonic acid exhibit strong room temperature phosphorescence (RTP) if retained on the surface of anion exchange resin beads. Based on the on-line formation, in a flow-injection system, of such RTP lead chelates and their transient immobilization on an anion exchange resin, three flow-through optosensing systems are investigated for lead in sea water. Optimum experimental conditions and the analytical performance characteristics of the three optosensors are discussed. Relative standard deviations (RSDs) of the order of 3% are typical at 100 ng ml−1 Pb(II) and the active sensing phases can easily be regenerated by passing 500 μl of 6 M hydrochloric acid. A lead(II) detection limit of 0.1 ng ml−1 (3×background SD, for 2 ml sample injection volumes) was achieved for the optosensor based on 8-hydroxy-7-quinolinesulphonic acid. Possible interferences present in sea water, including cations and anions which could affect the sensor response, are discussed in detail. Finally, the selected RTP flow-through optical sensor has been successfully tested for the determination of lead in sea water at a few ng ml−1.

Assembly of the highest connectivity Wells-Dawson polyoxometalate coordination polymer: the use of organic ligand flexibility

Through tuning the length of flexible bis(triazole) ligands and different metal ion coordination geometries, four Wells-Dawson polyoxoanion-based hybrid compounds, [Cu-6(btp)(3)(P2W18O62)] center dot 3H(2)O (1) (btp = 1,3-bis(1,2,4-triazol-1-yl)propane), [Cu-6(btb)(3)((P2W18O62) center dot 2H(2)O (2), [Cu-3(btb)(6)(P2W18O62)] center dot 6H(2)O (btb = 1,4-bis(1,2,4-triazol-1-yl)butane) (3), and [Cu-3(btx)(5.5)((P2W18O62) center dot 4H(2)O (btx = 1,6-bis(1,2,4-triazol-1-yl)hexane) (4), were synthesized and structurally characterized. in compound 1, the metal-organic motif exhibits a ladder-like chain, which is further fused by the ennead-dentate [P2W18O62](6-) anions to construct a 3D structure. In compound 2, the metal-organic motif exhibits an interesting Cu-btb grid layer, and the ennead-dentate polyoxoanions are sandwiched by two Cu-btb layers to construct a 3D structure