Crystal structure of Salmonella typhimurium 2-methylcitrate synthase: Insights on domain movement and substrate specificity

2-Methylcitric acid (2-MCA) cycle is one of the well studied pathways for the utilization of propionate as a source of carbon and energy in bacteria such as Salmonella typhimurium and Escherichia coli. 2-Methylcitrate synthase (2-MCS) catalyzes the conversion of oxaloacetate and propionyl-CoA to 2-methylcitrate and CoA in the second step of 2-MCA cycle. Here, we report the X-ray crystal structure of S. typhimurium 2-MCS (StPrpC) at 2.4 A resolution and its functional characterization. StPrpC was found to utilize propionyl-CoA more efficiently than acetyl-CoA or butyryl-CoA. The polypeptide fold and the catalytic residues of StPrpC are conserved in citrate synthases (CSs) suggesting similarities in their functional mechanisms. In the triclinic P1 cell, StPrpC molecules were organized as decamers composed of five identical dimer units. In solution, StPrpC was in a dimeric form at low concentrations and was converted to larger oligomers at higher concentrations. CSs are usually dimeric proteins. In Gram-negative bacteria, a hexameric form, believed to be important for regulation of activity by NADH, is also observed. Structural comparisons with hexameric E. coil CS suggested that the key residues involved in NADH binding are not conserved in StPrpC. Structural comparison with the ligand free and bound states of CSs showed that StPrpC is in a nearly closed conformation despite the absence of bound ligands. It was found that the Tyr197 and Leu324 of StPrpC are structurally equivalent to the ligand binding residues His and Val, respectively, of CSs. These substitutions might determine the specificities for acyl-CoAs of these enzymes. (C) 2010 Elsevier Inc. All rights reserved.

Effect of surfactant dispersed in oil on interaction force between an oil film and a steel substrate in water

The oil phase, in an oil-in-water emulsion on a steel substrate, is strongly repelled by the substrate. The oil in this situation does not wet the steel and steel/steel friction is high. In this work we disperse anionic surfactants in an oil film and study the effect of this dispersion on the force of interaction between a silica colloid probe (AFM) carrying the oil film and a steel substrate in water. It is observed that when the surfactant is oil insoluble and the interaction time is short the strong entropic repulsion (without the surfactant) is replaced by a strong attraction. The steel on steel sliding friction in this case is low compared to that what is achieved when the surfactant is soluble in oil. The rationale underlying these interactions is explored here. (C) 2011 Elsevier B.V. All rights reserved.

Modeling of a reacting nanofilm on a composite substrate

This article provides a detailed computational analysis of the reaction of dense nanofilms and the heat transfer characteristics on a composite substrate. Although traditional energetic compounds based on organic materials have similar energy per unit weight, non-organic material in nanofilm configuration offers much higher energy density and higher flame speed. The reaction of a multilayer thin film of aluminum and copper oxide has been studied by varying the substrate material and thicknesses. The numerical analysis of the thermal transport of the reacting film deposited on the substrate combined a hybrid approach in which a traditional two-dimensional black box theory was used in conjunction with the sandwich model to estimate the appropriate heat flux on the substrate accounting for the heat loss to the surroundings. A procedure to estimate this heat flux using stoichiometric calculations is provided. This work highlights two important findings. One is that there is very little difference in the temperature profiles between a single substrate of silica and a composite substrate of silicon silica. Secondly, with increase in substrate thickness, the quenching effect is progressively diminished at a given speed. These findings show that the composite substrate is effective and that the average speed and quenching of flames depend on the thickness of the silica substrate, and can be controlled by a careful choice of the substrate configuration. (C) 2011 Elsevier Ltd. All rights reserved.

Application of selective F-1 decoupled H-1 NMR for enantiomer resolution and accurate measurement of enantiomeric excess at low chiral substrate/auxiliary concentration

The higher substrate and chiral auxiliary concentration is a pre-requisite to obtain efficient separation of H-1 NMR signals of enantiomers. The higher concentration of chiral lanthanide shift reagents provides broadened spectral lines resulting in a severe loss of resolution between the enantiomer resonances. In order to circumvent such difficulties, herein we present the application and the usefulness of a selective F-1 decoupled correlation (COSY) experiment which yields proton decoupled proton spectra in the indirect dimension. The potentiality of the experiment is demonstrated on several chiral compounds possessing different functional groups, employing either a lanthanide shift reagent or a solvating reagent as chiral auxiliaries. (C) 2011 Elsevier B.V. All rights reserved.

High-Q, Ag-doped 123 resonator on unbuffered sapphire substrate

The microwave performance of an Ag-doped YBa2Cu3O7-x, thin-film X-band microstrip resonator on unbuffered sapphire substrate is reported. Q-values of 2400 and 1200 have been obtained al 15R and 77K, respectively, which correspond to R(s) values of 330 mu Omega and 680 mu Omega.

Effect of substrate on particle arrangement in arrays formed by self-assembly of polymer grafted nanoparticles

We show that the substrate affects the interparticle spacing in monolayer arrays with hexagonal order formed by self-assembly of polymer grafted nanoparticles. Remarkably, arrays with square packing were formed due to convective shearing at a liquid surface induced by miscibility of colloidal solution with the substrate.

Structural and optical properties of nonpolar (11-20) a-plane GaN grown on (1-102) r-plane sapphire substrate by plasma-assisted molecular beam epitaxy

We report the structural and optical properties of a-plane GaN film grown on r-plane sapphire substrate by plasma-assisted molecular beam epitaxy. High resolution X-ray diffraction was used to determine the out-of-plane and in-plane epitaxial relation of a-plane GaN to r-plane sapphire. Low-temperature photoluminescence emission was found to be dominated by basal stacking faults along with near-band emission. Raman spectroscopy shows that the a-GaN film is of reasonably good quality and compressively strained. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Ultrasonic wave characteristics of a monolayer graphene on silicon substrate

The present work deals with an ultrasonic type of wave propagation characteristics of monolayer graphene on silicon (Si) substrate. An atomistic model of a hybrid lattice involving a hexagonal lattice of graphene and surface atoms of diamond lattice of Si is developed to identify the carbon-silicon bond stiffness. Properties of this hybrid lattice model is then mapped into a nonlocal continuum framework. Equivalent force constant due to Si substrate is obtained by minimizing the total potential energy of the system. For this equilibrium configuration, the nonlocal governing equations are derived to analyze the ultrasonic wave dispersion based on spectral analysis. From the present analysis we show that the silicon substrate affects only the flexural wave mode. The frequency band gap of flexural mode is also significantly affected by this substrate. The results also show that, the silicon substrate adds cushioning effect to the graphene and it makes the graphene more stable. The analysis also show that the frequency bang gap relations of in-plane (longitudinal and lateral) and out-of-plane (flexural) wave modes depends not only on the y-direction wavenumber but also on nonlocal scaling parameter. In the nonlocal analysis, at higher values of the y-directional wavenumber, a decrease in the frequency band gap is observed for all the three fundamental wave modes in the graphene-silicon system. The atoms movement in the graphene due to the wave propagation are also captured for all the tree fundamental wave modes. The results presented in this work are qualitatively different from those obtained based on the local analysis and thus, are important for the development of graphene based nanodevices such as strain sensor, mass and pressure sensors, atomic dust detectors and enhancer of surface image resolution that make use of the ultrasonic wave dispersion properties of graphene. (C) 2011 Elsevier Ltd. All rights reserved.

Crystallization of SrCO3 on a self-assembled monolayer substrate: an in-situ synchrotron X-ray study

Self-assembled monolayers (SAMs) of alkanethiols on gold surfaces show great promise in controlling the nucleation and growth of inorganic minerals from solution. In doing so, they mimic the role of some biogenic macromolecules in natural biomineralisation processes. Crystallization on SAM surfaces is usually monitored ex-situ; by allowing the process to commence and to evolve for some time, removing the substrate from the mother solution, and then examining it using microscopy, diffraction etc. We present here for the first time, the use of high energy monochromatic synchrotron X-radiation in conjunction with a two dimensional detector to monitor in situ, in a time resolved fashion, the growth of SrCO3 (strontianite) crystals on a SAM substrate.

Synthesis and Microstructure of Laser Surface Alloyed Al–Sn–Si Layer on Commercial Aluminum Substrate

A new type of bearing alloy containing ultrafine sized tin and silicon dispersions in aluminum was designed using laser surface alloying and laser remelting techniques. The microstructures of these non-equilibrium processed alloys were studied in detail using scanning and transmission electron microscopy. The microstructures revealed three distinct morphologies of tin particles namely elongated particles co-existing with silicon, globular particles, and very fine particles. Our detailed analyses using cellular growth theories showed that the formation of these globular tin particles was due to the pinching off of the tin rich liquid in the inter-cellular space by the growth of aluminum secondary dendrite arms. Evidence of fine recrystallized aluminum grains at the top layer due to constrained solidification was shown. Thermal analyses suggested that melting of the spherical shaped tin particles was controlled by the binary aluminum-tin eutectic reaction, whereas non-spherical tin particles melted via the tin-silicon eutectic reaction.

Ellipsometry as a Sensitive Technique to Probe film -Substrate Interfaces: Al2O3 on Si(100)

An attempt has been made to study the film-substrate interface by using a sensitive, non- conventional tool. Because of the prospective use of gate oxide in MOSFET devices, we have chosen to study alumina films grown on silicon. Film-substrate interface of alumina grown by MOCVD on Si(100) was studied systematically using spectroscopic ellipsometry in the range 1.5-5.0 eV, supported by cross-sectional SEM, and SIMS. The (ε1,ε2) versus energy data obtained for films grown at 600°C, 700°C, and 750°C were modeled to fit a substrate/interface/film “sandwich”. The experimental results reveal (as may be expected) that the nature of the substrate -film interface depends strongly on the growth temperature. The simulated (ε1,ε2) patterns are in excellent agreement with observed ellipsometric data. The MOCVD precursors results the presence of carbon in the films. Theoretical simulation was able to account for the ellipsometry data by invoking the presence of “free” carbon in the alumina films.

Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis

Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the C alpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses a, b elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase

Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug an application that has been actively pursued for a variety of therapeutic strategies. The catalytic mechanism of this enzyme is governed by a conserved histidine that coordinates a magnesium ion at the active site. Despite substantial structural and biochemical information on NDK, the mechanistic feature of the phospho-transfer that leads to auto-phosphorylation remains unclear. While the role of the histidine residue is well documented, the other active site residues, in particular the conserved serine remains poorly characterized. Studies on some homologues suggest no role for the serine residue at the active site, while others suggest a crucial role for this serine in the regulation and quaternary association of this enzyme in some species. Here we report the biochemical features of the Staphylococcus aureus NDK and the mutant enzymes. We also describe the crystal structures of the apo-NDK, as a transition state mimic with vanadate and in complex with different nucleotide substrates. These structures formed the basis for molecular dynamics simulations to understand the broad substrate specificity of this enzyme and the role of active site residues in the phospho-transfer mechanism and oligomerization. Put together, these data suggest that concerted changes in the conformation of specific residues facilitate the stabilization of nucleotide complexes thereby enabling the steps involved in the ping-pong reaction mechanism without large changes to the overall structure of this enzyme. (C) 2011 Elsevier B.V. All rights reserved.