The Role of UPF0157 in the Folding of M-tuberculosis Dephosphocoenzyme A Kinase and the Regulation of the Latter by CTP

Background: Targeting the biosynthetic pathway of Coenzyme A (CoA) for drug development will compromise multiple cellular functions of the tubercular pathogen simultaneously. Structural divergence in the organization of the penultimate and final enzymes of CoA biosynthesis in the host and pathogen and the differences in their regulation mark out the final enzyme, dephosphocoenzyme A kinase (CoaE) as a potential drug target. Methodology/Principal Findings: We report here a complete biochemical and biophysical characterization of the M. tuberculosis CoaE, an enzyme essential for the pathogen's survival, elucidating for the first time the interactions of a dephosphocoenzyme A kinase with its substrates, dephosphocoenzyme A and ATP; its product, CoA and an intrinsic yet novel inhibitor, CTP, which helps modulate the enzyme's kinetic capabilities providing interesting insights into the regulation of CoaE activity. We show that the mycobacterial enzyme is almost 21 times more catalytically proficient than its counterparts in other prokaryotes. ITC measurements illustrate that the enzyme follows an ordered mechanism of substrate addition with DCoA as the leading substrate and ATP following in tow. Kinetic and ITC experiments demonstrate that though CTP binds strongly to the enzyme, it is unable to participate in DCoA phosphorylation. We report that CTP actually inhibits the enzyme by decreasing its Vmax. Not surprisingly, a structural homology search for the modeled mycobacterial CoaE picks up cytidylmonophosphate kinases, deoxycytidine kinases, and cytidylate kinases as close homologs. Docking of DCoA and CTP to CoaE shows that both ligands bind at the same site, their interactions being stabilized by 26 and 28 hydrogen bonds respectively. We have also assigned a role for the universal Unknown Protein Family 0157 (UPF0157) domain in the mycobacterial CoaE in the proper folding of the full length enzyme. Conclusions/Significance: In view of the evidence presented, it is imperative to assign a greater role to the last enzyme of Coenzyme A biosynthesis in metabolite flow regulation through this critical biosynthetic pathway.

High pressure studies on the electrical resistivity of As-Te-bond Si glasses and the effect of network topological thresholds

The variation of resistivity in an amorphous As30Te70-xSix system of glasses with high pressure has been studied for pressures up to 8 GPa. It is found that the electrical resistivity and the conduction activation energy decrease continuously with increase in pressure, and samples become metallic in the pressure range 1.0-2.0 GPa. Temperature variation studies carried out at a pressure of 0.92 GPa show that the activation energies lie in the range 0.16-0.18eV. Studies on the composition/average co-ordination number (r) dependence of normalized electrical resistivity at different pressures indicate that rigidity percolation is extended, the onset of the intermediate phase is around (r) = 2.44, and completion at (r) = 2.56, respectively, while the chemical threshold is at (r) = 2.67. These results compare favorably with those obtained from electrical switching and differential scanning calorimetric studies.

Analysis of texture evolution in pure magnesium and the magnesium alloy AM30 during rod and tube extrusion

The evolution of microstructure and texture during extrusion of pure magnesium and its single phase alloy AM30 has been studied experimentally as well as by crystal plasticity simulation. Microstructure and micro-texture were characterized by electron back scattered diffraction (EBSD), bulk-texture was measured using X-ray diffraction and deformation texture simulations were carried out using visco-plastic self consistent (VPSC) model. In spite of clear indications of the occurrence of dynamic recrystallization (DRX), simulations were able to reproduce the experimental textures successfully. This was attributed to the fact that the textures were c-type fibers with their axis of rotation parallel to the c-axis and DRX leads to simply rotate the texture around the c-axis. (C) 2011 Elsevier B.V. All rights reserved.

Stability of Filaments in Star-Forming Clouds and the Formation of Prestellar Cores in Them

The exact process(es) that generate(s) dense filaments which then form prestellar cores within them is unclear. Here we study the formation of a dense filament using a relatively simple set-up of a pressure-confined, uniform-density cylinder. We examine if its propensity to form a dense filament and further, to the formation of prestellar cores along this filament, bears on the gravitational state of the initial volume of gas. We report a radial collapse leading to the formation of a dense filamentary cloud is likely when the initial volume of gas is at least critically stable (characterised by the approximate equality between the mass line-density for this volume and its maximum value). Though self-gravitating, this volume of gas, however, is not seen to be in free-fall. This post-collapse filament then fragments along its length due to the growth of a Jeans-like instability to form prestellar cores. We suggest dense filaments in typical star-forming clouds classified as gravitationally super-critical under the assumption of: (i) isothermality when in fact, they are not, and (ii) extended radial profiles as against pressure-truncated, that significantly over-estimates their mass line-density, are unlikely to experience gravitational free-fall. The radial density and temperature profile derived for this post-collapse filament is consistent with that deduced for typical filamentary clouds mapped in recent surveys of nearby star-forming regions.

Synthesis, spectral and structural studies on metal complexes of Schiff bases involving vitamin B6 and histamine

Six metal complexes of Schiff bases involving Vitamin B6 and the decarboxylated amino acid histamine have been synthesised and characterized. Crystal structures have been determined for [CuL1(H2O)Br]-NO31(L1= pyridoxylidenehistamine) and [Cu2L22(NO3)2]·6H2O 2(L2= 5′-phosphopyridoxylidenehistaminate). The crystal structure of complex 1[space group P[1 with combining macron], a= 8.161(2), b= 10.368(2), c= 11.110(2)Å, α= 105.18(1), β= 102.12(1), γ= 72.10(1)° and Z= 2; R= 0.072, R′= 0.083] consists of square-pyramidally co-ordinated copper with the tridentate Schiff base in the zwitterionic form, whereas in 2[space group P[1 with combining macron], a= 8.727(1), b= 10.308(1), c= 12.845(2)Å, α= 110.00(1), β= 78.94(1), γ= 114.35(1)° and Z= 1; R= 0.035, R′= 0.034] the copper has the same co-ordination geometry but the tetradentate Schiff-base ligand exists as a monoanion. The conformational parameters deduced from such structures are important for understanding the stereochemical aspects of Vitamin B6-catalysed model reactions involving histidine.

Dendritic encapsulation of amino acid-metal complexes. Synthesis and studies of dendron-functionalized L-tyrosine-metal (Zn-II, Co-II) complexes

This paper describes the synthesis, characterization and studies of dendrimers possessing an amino acid-metal complex as the core. Using Frechet-type polyaryl ether dendrons, L-tyrosine-metal (Zn-II and Co-II) complex cored dendrimers of 0-4 generations were synthesized. The metal complexation of the tyrosine unit at the focal point of these dendrons took place smoothly, in excellent yields, even though the sizes of the dendrons increase as the generations advance. Spectrophotometric titrations with CoII metal ion confirmed the formation of a 2 : 1 dendritic ligand to metal complex and the existence of a pseudotetrahedral geometry at the metal centre is also inferred. Cyclic voltammetric studies of dendrimer-Co-II complexes showed that while the electron transfer of Co-II to Co-I was facile for generations 0-2, such a process was difficult with generations 3 and 4, indicating a rigid encapsulation of the metal ion centre by proximal dendron groups. Further reduction of Co-I to Co-0 and the corresponding oxidation processes appear to be limited by adsorption at the surfaces of the electrodes.

Interface capturing simulations of acoustically driven bubble dynamics in and near tissue

Tissue injury during therapeutic ultrasound or lithotripsy is thought, in cases, to be due to the action of cavitation bubbles. Assessing this and mitigating it is challenging since bubble dynamics in the complex confinement of tissues or in small blood vessels are challenging to predict. Simulations tools require specialized algorithms to simultaneously represent strong acoustic waves and shocks, topologically complex liquid‐vapor phase boundaries, and the complex viscoelastic material dynamics of tissue. We discuss advances in a simulation tool for such situations. A single‐mesh Eulerian solver is used to solve the governing equations. Special sharpening terms maintain the liquid‐vapor interface in face of the finite numerical dissipation included in the scheme to accurately capture shocks. A recent enhancement to this formulation has significantly improved this interface capturing procedure, which is demonstrated for simulation of the Rayleigh collapse of a bubble. The solver also transports elastic stresses and can thus be used to assess the effects of elastic properties on bubble dynamics. A shock‐induced bubble collapse adjacent to a model elastic tissue is used to demonstrate this and draw some conclusions regarding the injury suppressing role that tissue elasticity might play.

The influence of esterification of carboxyl groups of ribonuclease-a on its structure and immunological activity

The effect of modification of carboxyl groups of Ribonuclease-Aa on the enzymatic activity and the antigenic structure of the protein has been studied. Modification of four of the eleven free carboxyl groups of the protein by esterification in anhydrous methanol/0.1 M hydrochloric acid resulted in nearly 80% loss in enzymatic activity but had very little influence on the antigenic structure of the protein. Further increases in the modification of the carboxyl groups caused a progressive loss in immunological activity, and the fully methylated RNase-A exhibited nearly 30% immunological activity. Concomitant with this change in the antigenic structure of the protein, the ability of the molecule to complement with RNase-S-protein increased, clearly indicating the unfolding of the peptide "tail" from the remainder of the molecule. The susceptibility to proteolysis, accessibility of methionine residues for orthobenzoquinone reaction and the loss in immunological activity of the more extensively esterified derivatives of RNase-A are suggestive of the more flexible conformation of these derivatives as compared with the compact native conformation. The fact that even the fully methylated RNase-A retains nearly 30% of its immunological activity suggested that the modified protein contained antibody recognizable residual native structure, which presumably accommodates some antigenic determinants.

Dependence of giant magnetoresistance on oxygen stoichiometry and magnetization in polycrystalline La0.67Ba0.33MnOz

We have studied resistivity, magnetization, and magnetoresistance in polycrystalline La0.67Ba0.33MnOz by reducing the oxygen stoichiometry from z=2.99 to 2.80. As the oxygen content decreases, the resistivity of La0.67Ba0.33 MnOz increases and the magnetic transition temperature shifts to lower temperature. A large magnetoresistance effect was observed over a wide temperature range for all samples except the insulating z=2.80 sample. The similarity between our results on oxygen-deficient polycrystalline La0.67 Ba0.33MnOz and films previously reported to have a very large intrinsic magnetoresistance is discussed. At low temperature the magnetoresistance was observed to be strongly dependent on the magnetization. A possible mechanism for this effect is discussed.

Elasticity of DNA and the effect of dendrimer binding

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic properties of short double-stranded DNA (dsDNA) and the effect of dendrimer binding using fully atomistic molecular dynamics and numerical simulations. In equilibrium at room temperature, the contour length distribution P(L) and the end-to-end distance distribution P(R) are nearly Gaussian, the former gives an estimate of the stretch modulus gamma(1) of dsDNA in quantitative agreement with the literature value. The bend angle distribution P(.) of the dsDNA also has a Gaussian form and allows to extract a persistence length, L-p of 43 nm. When the dsDNA is compacted by positively charged dendrimer, the stretch modulus stays invariant but the effective bending rigidity estimated from the end-to-end distance distribution decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We support our observations with numerical solutions of the worm-like-chain (WLC) model as well as using non-equilibrium dsDNA stretching simulations. These results are helpful in understanding the dsDNA elasticity at short length scales as well as how the elasticity is modulated when dsDNA binds to a charged object such as a dendrimer or protein.

Conformation of antibiotic X-537A (lasalocid-A) and its calcium complex in acetonitrile solvent using circular dichroism spectroscopy

The calcium binding characteristics of antibiotic X-537A (lasalocid-A) in a lipophilic solvent, acetonitrile (CH3CN), have been studied using circular dichroism (CD) spectroscopy. The analysis of the data indicated that in this medium polar solvent, X-537A forms predominantly the charged complexes of stoichiometries 2:1 and 1:1, the relative amounts of the two being dependent on [Ca2+]. The conformation of the complexes, arrived at on the basis of the data, seem to indicate a rigid part encompassing Ca2+, liganded to 3 oxygens of the molecule, viz., the carbonyl, the substituted tetrahydrofuran ring and the substituted pyran ring oxygens (apart from possibly, the liganding provided by nitrogen atoms of the solvent molecules), and a flexible part consisting of the salicylic acid group of the molecule.

Velocity and acceleration analysis of complex mechanisms by graphical iteration

A simple graphical method is presented for velocity and acceleration analysis of complex mechanisms possessing low or high degree of complexity. The method is iterative in character and generally yields the solution within a few iterations. Several examples have been worked out to illustrate the method.

Complex carbohydrates: 2. The modes of binding of complex carbohydrates to concanavalin A - a computer modelling approach

The probable modes of binding of some complex carbohydrates, which have the trimannosidic core structure (Man3GlcNAc2), to concanavalin A (Con A) have been determined using a computer modelling technique. These studies show that Con a can bind to the terminal mannose residues of the trimannosidic core structure and to the internal mannosyl as well as to the terminal N-acetylglucosamine residues of the N-acetylglucosamine substituted trimannosidic core structure. The oligosaccharide with terminal mannose residues can bind in its minimum energy conformers, whereas the oligosaccharide with internal mannosyl and terminal N-acetylglucosamine residues can bind only in higher energy conformers. In addition the former oligosaccharide forms more hydrogen bonds with Con A than the latter. These results suggest that, for these oligosaccharides, the terminal mannose residue has a much higher probability of reaching the binding site than either the internal mannosyl or the terminal N-acetylglucosamine residues. The substitution of a bisecting N-acetylglucosamine residue on these oligosaccharides, affects significantly the accessibility of the residues which bind to Con A and thereby reduces their binding affinity. It thus seems that the binding affinity of an oligosaccharide to Con A depends not only on the number of sugar residues which possess free 3-, 4- and 6-hydroxyl groups but also on the accessibility of these sugar residues to Con A. This study also reveals that the sugar binding site of Con A is small and that the interactions between Con A and carbohydrates are extended slightly beyond the single sugar residue that is placed in the binding site.

A Convenient Route for the Synthesis of Complex Metal Oxides Employing Solid-Solution Precursors

Synthesis of complex metal oxides by the thermal decomposition of solid-solution precursors (formed by isomorphous compounds of component metals) has been investigated since the method enables mixing of cations on an atomic scale and drastically reduces diffusion distances to a few angstroms. Several interesting oxides such as Ca2Fe03,5C, aCoz04,C a2C0205a, nd Ca,FeCo05 have been prepared by this technique starting from carbonate solid solutions of the type Ca,-,Fe,C03, Cal-,Co,C03, and Ca,-,,M,M'yC03 (M, M' = Mn, Fe, Co). The method has been extended to oxalate solid-solution precursors, and the possibility of making use of other kinds of precursor solid solutions is indicated.