Solubility and activity of oxygen in liquid indium and copper indium alloys

The solubility of oxygen in liquid indium in the temperature range 650–820 °C and in liquid copper-indium alloys at 1100 °C in equilibrium with indium sesquioxide has been measured by a phase equilibration technique. The solubility of oxygen in pure indium is given by the relation log(at.% O) = −4726/T + 3.73 (±0.08) Using the recently measured values for the standard free energy of formation of In2O3 and assuming that oxygen obeys Sievert's law up to saturation, the standard free energy of solution of molecular oxygen in liquid indium is calculated as View the MathML sourceΔG°= −51 440 + 8.07 T (±500) cal where the standard state for dissolved oxygen is an infinitely dilute solution in which activity is equal to atomic per cent. The effect of indium additions on the activity coefficient of oxygen dissolved in liquid copper was measured by a solid oxide galvanic cell. The interaction parameter ϵ0In is given by View the MathML source The experimentally determined variation of the activity coefficient of oxygen in dilute solution in Cu-In alloys is in fair agreement with that predicted by a quasichemical model in which each oxygen atom is assumed to be interstitially coordinated to four metal atoms and the nearest neighbour metal atoms are assumed to lose approximately half their metallic cohesive energies.

Solubility and activity of oxygen in liquid germanium and germanium copper alloys

The solubility of oxygen in liquid germanium in the temperature range 1233 to 1397 K, and in liquid germanium-copper alloys at 1373 K, in equilibrium with GeO2 has been measured by the phase equilibration technique. The solubility of oxygen in pure germanium is given by the relation R470 log(at. pct 0)=-6470/T+4.24 (±0.07). The standard free energy of solution of oxygen in liquid germanium is calculated from the saturation solubility, and recently measured values for the free energy of formation of GeO2, assuming that oxygen obeys Sievert’s law up to the saturation limit. For the reaction, 1/2 O2(g)→ OGe ΔG° =-39,000 + 3.21T (±500) cal = -163,200 + 13.43T (±2100) J. where the standard state for dissolved oxygen is that which makes the value of activity equal to the concentration (in at. pct), in the limit, as concentration approaches zero. The effect of copper on the activity of oxygen dissolved in liquid germanium is found to be in good agreement with that predicted by a quasichemical model in which each oxygen was assumed to be bonded to four metal atoms and the nearest neighbor metal atoms to an oxygen atom are assumed to lose approximately half of their metallic bonds.

Solubility and activity of oxygen in liquid antimony

The solubility limit of oxygen in liquid antimony has been measured by a novel isopiestic technique in the temperature range 995--1175 deg K. The results can be expressed by the equation log c = --5500/T + 3.754 ( plus/minus 0.04) with c in at.% O and T in deg K. The oxygen potential over Sb + O alloys equilibrium with Sb2O3 has been measured by a solid state cell using a fully stabilized CaO.ZrO2 electrolyte. The cell was designed to contain the Sb + Sb2O3 mixture in a closed volume, that the vaporization of the oxide can be minimized and true equilibrium attained. The Gibbs free energy of the reaction 2 Sb(s) + 3/2 O2 = Sb2O3(s) is Delta G deg = --719560 + 274.51 T( plus/minus 500) and Sb(l) + 3/2 O2 = Sb2O3(l), Delta G deg = --704711 + ( plus/minus 500) ( Delta G deg in J/mole, T in deg K). The combination of these results with Sieverts' law yields the standard free energy of solution of oxygen in liquid antimony according to the reaction 1/2 O2 = \O\Sb,at.% as Delta G deg = --129620 + 14.23 T ( plus/minus 950). The standard enthalopy and entropy of the solution of oxygen in Sb are compared with values for other metal- oyxgen systems, and with the standard enthalpies of formation of corresponding oxides. The resulting correlations permit the estimation of the standard free energy of solution of oxygen in pure metals for which experimental information is lacking. 24 ref.--AA

Novel Pentameric Structure of the Diarrhea-Inducing Region of the Rotavirus Enterotoxigenic Protein NSP4

A novel pentameric structure which differs from the previously reported tetrameric form of the diarrhea-inducing region of the rotavirus enterotoxin NSP4 is reported here. A significant feature of this pentameric form is the absence of the calcium ion located in the core region of the tetrameric structures. The lysis of cells, the crystallization of the region spanning residues 95 to 146 of NSP4 (NSP4(95-146)) of strain ST3 (ST3: NSP4(95-146)) at acidic pH, and comparative studies of the recombinant purified peptide under different conditions by size-exclusion chromatography (SEC) and of the crystal structures suggested pH-, Ca(2+)-, and protein concentration-dependent oligomeric transitions in the peptide. Since the NSP4(95-146) mutant lacks the N-terminal amphipathic domain (AD) and most of the C-terminal flexible region (FR), to demonstrate that the pentameric transition is not a consequence of the lack of the N- and C-terminal regions, glutaraldehyde cross-linking of the Delta N72 and Delta N94 mutant proteins, which contain or lack the AD, respectively, but possess the complete C-terminal FR, was carried out. The results indicate the presence of pentamers in preparations of these longer mutants. Detailed SEC analyses of Delta N94 prepared under different conditions, however, revealed protein concentration-dependent but metal ion-and pH-independent pentamer accumulation at high concentrations which dissociated into tetramers and lower oligomers at low protein concentrations. While calcium appeared to stabilize the tetramer, magnesium in particular stabilized the dimer. Delta N72 existed primarily in the multimeric form under all conditions. These findings of a calcium-free NSP4 pentamer and its concentration-dependent and largely calcium-independent oligomeric transitions open up a new dimension in an understanding of the structural basis of its multitude of functions.

Conformational Basis for Substrate Recruitment in Protein Tyrosine Phosphatase 10D

The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate. While the role of conserved residues in the catalytic mechanism of PTPs has been extensively examined, the diversity in the mechanisms of substrate recognition and modulation of catalytic activity suggests that other, less conserved sequence and structural features could contribute to this process. Here we describe the crystal structures of Drosophila melanogaster PTP10D in the apo form as well as in a complex with a substrate peptide and an inhibitor. These studies reveal the role of aromatic ring stacking interactions at the boundary of the active site of PTPs in mediating substrate recruitment. We note that phenylalanine 76, of the so-called KNRY loop, is crucial for orienting the phosphotyrosine residue toward the nucleophilic cysteine. Mutation of phenylalanine 76 to leucine results in a 60-fold decrease in the catalytic efficiency of the enzyme. Fluorescence measurements with a competitive inhibitor, p-nitrocatechol sulfate, suggest that Phe76 also influences the formation of the enzyme-substrate intermediate. The structural and biochemical data for PTP10D thus highlight the role of relatively less conserved residues in PTP domains in both substrate recruitment and modulation of reaction kinetics.

Solubility and activity of oxygen in liquid manganese

The oxygen concentration of liquid manganese in equilibrium with MnAl2+2xO4+3x and α−Al2O3 has been determined in the temperature range 1520 to 1875 K. The oxygen content of quenched samples, wrapped in oxygen-free nickel foil, was determined by an inert gas fusion technique. The results are combined with accurate data now available on the Gibbs energies of formation of MnO and Al2O3−saturated MnAl2+2xO4+3x to derive the oxygen content of liquid manganese in equilibrium with MnO and the Gibbs energy of solution of diatomic oxygen gas in liquid manganese. The enthalpy and entropy of solution of oxygen in manganese are compared with similar data on other metal-oxygen systems.

Solubility and activity of oxygen in liquid nickel in equilibrium with -Al2O3 and NiO.(1+x)Al2O3

The limiting solubility of oxygen in liquid nickel in equilibrium withα-alumina and nickel aluminate has been measured by inert gas fusion analysis of suction samples in the temperature range 1730 to 1975 K. The corresponding oxygen potential has been monitored by a solid electrolyte cell consisting of calcia stabilized zirconia as the electrolyte and Mo + MoO2 as the reference electrode. The results can be summarized by the following equations: log(at. pct O) = \frac - 10,005T + 4.944 ( ±0.015)log(atpctO)=T−10005+4944(0015) % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn DmO2 /4.606RT = log P O2 1/2 = \frac - 13,550T + 4.411 ( ±0.009)O24606RT=logPO212=T−13550+4411(0009) From simultaneous measurements of the potential and concentration of oxygen in melts, not in thermodynamic equilibrium with alumina and aluminate phases, information on the composition dependence of the activity coefficient and the standard free energy of solution of oxygen is obtained. For the reaction, $\frac{1}{2} O_2 \to \underset{\raise0.3em\hbox{$Missing close brace ΔG o = -72,930 - 7.11T (±840) J gr.at.–1 = + 0.216 at. pct OlogfO=T−500+0216atpctO where the standard state for dissolved oxygen is that which makes the value of activity equal to the concentration (in at. pct) in the limit as concentration approaches zero. The oxygen solubility in liquid nickel in equilibrium with solid NiO, evaluated from thermodynamic data, is compared with information reported in the literature. Implications of the results to the deoxidation equilibria of aluminum in nickel are discussed.

Investigations on the RNA binding and phosphorylation of groundnut bud necrosis virus nucleocapsid protein

Groundnut bud necrosis virus belongs to the genus Tospovirus, infects a wide range of crop plants and causes severe losses. To understand the role of the nucleocapsid protein in the viral life cycle, the protein was overexpressed in E. coli and purified by Ni-NTA chromatography. The purified N protein was well folded and was predominantly alpha-helical. Deletion analysis revealed that the C-terminal unfolded region of the N protein was involved in RNA binding. Furthermore, the N protein could be phosphorylated in vitro by Nicotiana benthamiana plant sap and by purified recombinant kinases such as protein kinase CK2 and calcium-dependent protein kinase. This is the first report of phoshphorylation of a nucleocapsid protein in the family Bunyaviridae. The possible implications of the present findings for the viral life cycle are discussed.

Morphology Dependence of Ag-Ni Solid Solubility

Electrodeposition produced features with a dendritic morphology and features with a branched wire like morphology made up of about 20 nm sized particles. Both the features contained Ag and Ni atoms in a solid solution arrangement. However, the feature made up of nanoparticles contained a greater concentration of Ni as compared to the Ni content in the dendritic feature. The greater Ni content in the Ag-Ni solid solution for the features with nanoparticles when compared to the dendritic morphology features strongly indicated the effect of curvature in increasing the extent of miscibility between bulk immiscible atoms. (C) 2011 The Electrochemical Society. [DOI: 10.1149/2.003202esl] All rights reserved.

Mycobacterium leprae RecA is structurally analogous but functionally distinct from Mycobacterium tuberculosis RecA protein

Mycobacterium leprae is closely related to Mycobacterium tuberculosis, yet causes a very different illness. Detailed genomic comparison between these two species of mycobacteria reveals that the decaying M. leprae genome contains less than half of the M. tuberculosis functional genes. The reduction of genome size and accumulation of pseudogenes in the M. leprae genome is thought to result from multiple recombination events between related repetitive sequences, which provided the impetus to investigate the recombination-like activities of RecA protein. In this study, we have cloned, over-expressed and purified M. leprae RecA and compared its activities with that of M. tuberculosis RecA. Both proteins, despite being 91% identical at the amino acid level, exhibit strikingly different binding profiles for single-stranded DNA with varying GC contents, in the ability to catalyze the formation of D-loops and to promote DNA strand exchange. The kinetics and the extent of single-stranded DNA-dependent ATPase and coprotease activities were nearly equivalent between these two recombinases. However, the degree of inhibition exerted by a range of ATP:ADP ratios was greater on strand exchange promoted by M. leprae RecA compared to its M. tuberculosis counterpart. Taken together, our results provide insights into the mechanistic aspects of homologous recombination and coprotease activity promoted by M. lepare RecA, and further suggests that it differs from the M. tuberculosis counterpart. These results are consistent with an emerging concept of DNA-sequence influenced structural differences in RecA nucleoprotein filaments and how these differences reflect on the multiple activities associated with RecA protein. (C) 2011 Elsevier B.V. All rights reserved.

Catabolite repression of phosphoenolpyruvate carboxykinase by a zinc finger protein under biotin- and pyruvate carboxylase-deficient conditions in Pichia pastoris

We have identified a methanol- and biotin-starvation-inducible zinc finger protein named ROP [repressor of phosphoenolpyruvate carboxykinase (PEPCK)] in the methylotrophic yeast Pichia pastoris. When P. pastoris strain GS115 (wild-type, WT) is cultured in biotin-deficient, glucose-ammonium (Bio(-)) medium, growth is suppressed due to the inhibition of anaplerotic synthesis of oxaloacetate, catalysed by the biotin-dependent enzyme pyruvate carboxylase (PC). Deletion of ROP results in a strain (Delta ROP) that can grow under biotin-deficient conditions due to derepression of a biotin- and PC-independent pathway of anaplerotic synthesis of oxaloacetate. Northern analysis as well as microarray expression profiling of RNA isolated from WT and Delta ROP strains cultured in Bio(-) medium indicate that expression of the phosphoenolpyruvate carboxykinase gene (PEPCK) is induced in Delta ROP during biotin- or PC-deficiency even under glucose-abundant conditions. There is an excellent correlation between PEPCK expression and growth of Delta ROP in Bio(-) medium, suggesting that ROP-mediated regulation of PEPCK may have a crucial role in the biotin- and PC-independent growth of the Delta ROP strain. To our knowledge, ROP is the first example of a zinc finger transcription factor involved in the catabolite repression of PEPCK in yeast cells cultured under biotin- or PC-deficient and glucose-abundant conditions.

Structure and dynamics of protein excited states with millisecond lifetimes

An in-depth understanding of biological processes often requires detailed atomic resolution structures of the molecules involved. However in solution where most of these processes occur the conformation of biomolecules like RNA, DNA and proteins is not static but fluctuates. Routinely used structural techniques like X-ray crystallography, NMR spectroscopy and cryo-electron microscopy have almost always been used to determine the structure of the dominant conformation or obtain an average structure of the biomolecule in solution with very little detailed information regarding the dynamics of these molecules in solution. Over the last few years, NMR based methods have been developed to study the dynamics of these biomolecules in solution in a site-specific manner with the aim of generating structures of the different conformations that these molecules can adopt in solution. One powerful technique is the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiment, which can be used to detect and characterize protein excited states that are populated for as less as 0.5% of the time with ∼0.5–10 millisecond lifetimes. Due to recent advances in NMR pulse sequences and labeling methodology, it is now possible to determine the structures of these transiently populated excited states with millisecond lifetimes by obtaining accurate chemical shifts, residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) of these excited states. In these excited states the dynamics of some methyl containing residues can also be studied.

Nonspecific Interaction between DNA and Protein allows for Cooperativity: A Case Study with Mycobacterium DNA Binding Protein

Different DNA-binding proteins have different interaction modes with DNA. Sequence-specific DNA protein interaction has been mostly associated with regulatory processes inside a cell, and as such extensive studies have been made. Adequate data is also available on nonspecific DNA protein interaction, as an intermediate to protein's search for its cognate partner. Multidomain nonspecific DNA protein interaction involving physical sequestering of DNA has often been implicated to regulate gene expression indirectly. However, data available on this type of interaction is limited. One such interaction is the binding of DNA with mycobacterium DNA binding proteins. We have used the Langmuir-Blodgett technique to evaluate for the first time the kinetics and thermodynamics of Mycobacterium smegmatis Dps 1 binding to DNA. By immobilizing one of the interacting partners, we have shown that, when a kinetic bottleneck is applied, the binding mechanism showed cooperative binding (n = 2.72) at lower temperatures, but the degree of cooperativity gradually reduces (n = 1.38) as the temperature was increased We have also compared the kinetics and thermodynamics of sequence-specific and nonspecific DNA protein interactions under the same set of conditions.

Functional regulation of PVBV Nuclear Inclusion protein-a protease activity upon interaction with Viral Protein genome-linked and phosphorylation

Regulation of NIa-Pro is crucial for polyprotein processing and hence, for successful infection of potyviruses. We have examined two novel mechanisms that could regulate NIa-Pro activity. Firstly, the influence of VPg domain on the proteolytic activity of NIa-Pro was investigated. It was shown that the turnover number of the protease increases when these two domains interact (as: two-fold; trans: seven-fold) with each other. Secondly, the protease activity of NIa-Pro could also be modulated by phosphorylation at Ser129. A mutation of this residue either to aspartate (phosphorylation-mimic) or alanine (phosphorylation-deficient) drastically reduces the protease activity. Based on these observations and molecular modeling studies, we propose that interaction with VPg as well as phosphorylation of Ser129 could relay a signal through Trp143 present at the protein surface to the active site pocket by subtle conformational changes, thus modulating protease activity of NIa-Pro. (C) 2011 Elsevier Inc. All rights reserved.