New structural insights and molecular-modelling studies of 4-methyl-5-beta-hydroxyethylthiazole kinase from Pyrococcus horikoshii OT3 (PhThiK)

4-Methyl-5-beta-hydroxyethylthiazole kinase (ThiK) catalyses the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole. This work reports the first crystal structure of an archaeal ThiK: that from Pyrococcus horikoshii OT3 (PhThiK) at 1.85 angstrom resolution with a phosphate ion occupying the position of the beta-phosphate of the nucleotide. The topology of this enzyme shows the typical ribokinase fold of an alpha/beta protein. The overall structure of PhThiK is similar to those of Bacillus subtilis ThiK (BsThiK) and Enterococcus faecalis V583 ThiK (EfThiK). Sequence analysis of ThiK enzymes from various sources indicated that three-quarters of the residues involved in interfacial regions are conserved. It also revealed that the amino-acid residues in the nucleotide-binding, magnesium ion-binding and substrate-binding sites are conserved. Binding of the nucleotide and substrate to the ThiK enzyme do not influence the quaternary association (trimer) as revealed by the crystal structure of PhThiK.

Structural studies of analgesics and their interactions. Part 4. Crystal structures of phenylbutazone and a 2 : 1 complex between phenylbutazone and piperazine

The X-ray crystal structures of 4-butyl-1,2-diphenylpyrazolidine-3,5-dione (phenylbutazone)(I). and its 2 : 1 complex (II) with piperazine have been determined by direct methods and the structures refined to R 0.096 (2 300 observed reflections measured by diffractometer) and 0.074 (2 494 observed reflections visuallyestimated). Crystals are monoclinic, space group P21/c; for (I)a= 21.695(4), b= 5.823(2), c= 27.881(4)Å, = 108.06 (10)°, Z= 8, and for (II)a= 8.048(4), b= 15.081(4), c= 15.583(7)Å, = 95.9(3)°, Z= 2. The two crystallographically independant molecules in the structure of (I) are similar except for the conformation of the butyl group, which is disordered in one of the molecules. In the pyrazolidinedione group, the two C–C bonds are single and the two C–O bonds double. The two nitrogen atoms in the five-membered ring are pyramidal with the attached phenyl groups lying on the opposite sides of the mean plane of the ring. The phenylbutazone molecule in (II) exists as a negative ion owing to deprotonation of C-4. C-4 is therefore trigonal and the orientation of the Bu group with respect to the pyrazolidinedione group is considerably different from that in (I); there is also considerable electron delocalization along the C–O and C–C bonds. These changes in geometry and electronic structure may relate to biological activity. The doubly charged cationic piperazine molecule exists in the chair form with the nitrogen atoms at the apices. The crystal structure of (II) is stabilized by ionic interactions and N–H O hydrogen bonds.

Unusual structural stability and ligand induced alterations in oligomerization of a galectin

Abstract L-14, a 14-kDa S-type lectin shows the jelly roll tertiary structural fold akin to legume lectins yet, unlike them, it does not dissociate on thermal unfolding. In the absence of ligand L-14 displays denaturation transitions corresponding to tetrameric and octameric entities. The presence of complementary ligand reduces the association of L-14, which is in stark contrast with legume lectins where no alterations in quaternary structures are brought about by saccharides. From the magnitude of the increase in denaturation temperature induced by disaccharides the binding constants calculated from differential scanning calorimetry are comparable with those extrapolated from titration calorimetry indicating that L-14 interacts with ligands essentially in the folded state.

Structural Modes of Stabilization of Permissive Phosphorylation Sites in Protein Kinases: Distinct Strategies in Ser/Thr and Tyr Kinases

Protein kinases phosphorylate several cellular proteins providing control mechanisms for various signalling processes. Their activity is impeded in a number of ways and restored by alteration in their structural properties leading to a catalytically active state. Most protein kinases are subjected to positive and negative regulation by phosphorylation of Ser/Thr/Tyr residues at specific sites within and outside the catalytic core. The current review describes the analysis on 3D structures of protein kinases that revealed features distinct to active states of Ser/Thr and Tyr kinases. The nature and extent of interactions among well-conserved residues surrounding the permissive phosphorylation sites differ among the two classes of enzymes. The network of interactions of highly conserved Arg preceding the catalytic base that mediates stabilization of the activation segment exemplifies such diverse interactions in the two groups of kinases. The N-terminal and the C-terminal lobes of various groups of protein kinases further show variations in their extent of coupling as suggested from the extent of interactions between key functional residues in activation segment and the N-terminal αC-helix. We observe higher similarity in the conformations of ATP bound to active forms of protein kinases compared to ATP conformations in the inactive forms of kinases. The extent of structural variations accompanying phosphorylation of protein kinases is widely varied. The comparison of their crystal structures and the distinct features observed are hoped to aid in the understanding of mechanisms underlying the control of the catalytic activity of distinct subgroups of protein kinases.

Influence of Hydrophilic Surface Specificity on the Structural Properties of Confined Water

The influence of chemical specificity of hydrophilic surfaces on the structure of confined water in the subnanometer regime is investigated using grand canonical Monte Carlo Simulations. The structural variations for water confined between hydroxylated silica surfaces are contrasted with water confined between mica surfaces. Although both surfaces are hydrophilic, our Study shows that hydration of potassium ions on the mica surface has a strong influence on the water Structure and solvation force response of confined water. In contrast to the disrupted hydrogen bond network observed for water confined between Mica Surfaces, water between silica surfaces retains its hydrogen bond network displaying bulklike structural features down to surface separations as small as 0.45 nm. Hydrogen bonding of all invariant contact water layer with the surface silanol groups aids in maintaining a constant number of hydrogen bonds per water molecule for the silica surfaces. As a consequence water depletion and rearrangement upon decreasing confinement is a strong function of the hydrophilic surface specificity, particularly at smaller separations. An oscillatory solvation force response is only observed for water confined between Silica surfaces, and bulklike features are observed for both Surfaces above a surface separation of about 1.2 nm. We evaluate and contrast the water density, dipole moment distributions, pi pair correlation functions, and solvation forces as a function of the surface separation.

Effect of oxygen partial pressure on the structural and optical properties of dc reactive magnetron sputtered molybdenum oxide films

Molybdenum oxide films (MoO3) were deposited on glass and crystalline silicon substrates by sputtering of molybdenum target under various oxygen partial pressures in the range 8 × 10−5–8 × 10−4 mbar and at a fixed substrate temperature of 473 K employing dc magnetron sputtering technique. The influence of oxygen partial pressure on the composition stoichiometry, chemical binding configuration, crystallographic structure and electrical and optical properties was systematically studied. X-ray photoelectron spectra of the films formed at 8 × 10−5 mbar showed the presence of Mo6+ and Mo5+ oxidation states of MoO3 and MoO3−x. The films deposited at oxygen partial pressure of 2 × 10−4 mbar showed Mo6+ oxidation state indicating the films were nearly stoichiometric. It was also confirmed by the Fourier transform infrared spectroscopic studies. X-ray diffraction studies revealed that the films formed at oxygen partial pressure of 2 × 10−4 mbar showed the presence of (0 k 0) reflections indicated the layered structure of α-phase MoO3. The electrical conductivity of the films decreased from 3.6 × 10−5 to 1.6 × 10−6 Ω−1 cm−1, the optical band gap of the films increased from 2.93 to 3.26 eV and the refractive index increased from 2.02 to 2.13 with the increase of oxygen partial pressure from 8 × 10−5 to 8 × 10−4 mbar, respectively.

Structural, dielectric, impedance and optical properties of CaBi2B2O7 glasses and glass-nanocrystal composites

Optically clear glasses were fabricated by quenching the melt of CaCO3-Bi2O3-B2O3 (in equimolecular ratio). The amorphous and glassy characteristics of the as-quenched samples were confirmed via the X-ray powder diffraction (XRD) and differential scanning calorimetric (DSC) studies These glasses were found to. have high thermal stability parameter (S). The optical transmission studies carried out in the 200-2500 nm wavelength range confirmed both the as-quenched and heat-treated samples to be transparent between 400 nm and 2500 nm. The glass-plates that were heat-treated just above the glass transition temperature (723 K) for 6 h retained approximate to 60% transparency despite having nano-crystallites (approximate to 50-100 nm) of CaBi2B2O7 (CBBO) as confirmed by both the XRD and transmission electron microscopy (TEM) studies. The dielectric properties and impedance characteristics of the as-quenched and heat-treated (723 K/6 h) samples were studied as a function of frequency at different temperatures. Cole-Cole equation was employed to rationalize the impedance data.

Synthesis, structural and ferromagnetic properties of La1-xKxMnO3 (0.0 <= x <= 0.25) phases by solution combustion method

We describe the solution combustion synthesis and characterization of La1-xKxMnO3 (0.0 <= x <= 0.25) perovskite phases, which is a low temperature initiated, rapid route to prepare metal oxides. As-synthesized compounds are amorphous in nature; crystallinity was observed on heating at 800 degrees C for 5 min. Structural parameters were determined by the Rietveld refinement method using powder XRD data. Parent LaMnO3 compound crystallizes in the orthorhombic structure (space group Pbnm, No. 62). Potassium substituted compounds were crystallized with rhombohedral symmetry (space group R-3c, No. 167). The ratio of the Mn3+/Mn4+ was determined by the iodometric titration. The Fourier transform infrared spectrum (FTIR) shows two absorption bands for Mn-O stretching vibration (v, mode), Mn-O-Mn deformation vibration (v(b) mode) around 600 cm(-1) and 400 cm(-1) for the compositions, x = 0.0, 0.05 and 0-10. Four-probe electrical resistivity measurements reveal a composition controlled metal to insulator transition (TM-1), the maximum TM-1 was observed for the composition La0.85K0.15MnO3 at 287 K. Room temperature vibrating sample magnetometer data indicate that for the composition up to x = 0-10, the compounds are paramagnetic whereas composition with x = 0.15, 0.20 and 0.25 show magnetic moments of 27, 29 and 30 emu/g, respectively.

Sol-Gel Template Synthesis, Structural Characterization and Growth Mechanism of Barium Zirconate Nanotubes

In this paper, we report the synthesis of barium zirconate, BaZrO3, (BZ) nanotubes fabricated by the modified sol-gel method within the nanochannels of anodic aluminum oxide (AAO) templates. The morphology, structure, and composition of as prepared nanotubes were characterized by means of X-ray diffraction (XRD), field emission scanning electron microscope (FE-SEM), transmission electron microscope (TEM), selected-area electron diffraction ( SAED), high resolution TEM (HRTEM) and energy-dispersive X-ray spectroscopy (EDX). The results of XRD and SAED indicated that postannealed (at 650 degrees C for 1 h) BZ nanotubes (BZNTs) exhibited a polycrystalline cubic perovskite crystal structure. SEM and TEM analysis revealed that BZNTs possessed a uniform length and diameter (similar to 200 nm) and the thickness of the wall of the BZNTs was about 20 nm. Y-junctions, multiple branching and typical T-junctions were also observed in some BZNTs. EDX analysis demonstrated that stoichiometric BaZrO3 was formed. HRTEM image confirmed that the obtained BZNTs were composed of nanoparticles in the range of 5-10 nm. The possible formation mechanism of BZNTs was discussed.

Vocalizations of wild Asian elephants (Elephas maximus): Structural classification and social context

Elephants use vocalizations for both long and short distance communication. Whereas the acoustic repertoire of the African elephant (Loxodonta africana) has been extensively studied in its savannah habitat, very little is known about the structure and social context of the vocalizations of the Asian elephant (Elephas maximus), which is mostly found in forests. In this study, the vocal repertoire of wild Asian elephants in southern India was examined. The calls could be classified into four mutually exclusive categories, namely, trumpets, chirps, roars, and rumbles, based on quantitative analyses of their spectral and temporal features. One of the call types, the rumble, exhibited high structural diversity, particularly in the direction and extent of frequency modulation of calls. Juveniles produced three of the four call types, including trumpets, roars, and rumbles, in the context of play and distress. Adults produced trumpets and roars in the context of disturbance, aggression, and play. Chirps were typically produced in situations of confusion and alarm. Rumbles were used for contact calling within and among herds, by matriarchs to assemble the herd, in close-range social interactions, and during disturbance and aggression. Spectral and temporal features of the four call types were similar between Asian and African elephants.

Pseudo-time marching schemes for inverse problems in structural health assessment and medical imaging

We propose a self-regularized pseudo-time marching strategy for ill-posed, nonlinear inverse problems involving recovery of system parameters given partial and noisy measurements of system response. While various regularized Newton methods are popularly employed to solve these problems, resulting solutions are known to sensitively depend upon the noise intensity in the data and on regularization parameters, an optimal choice for which remains a tricky issue. Through limited numerical experiments on a couple of parameter re-construction problems, one involving the identification of a truss bridge and the other related to imaging soft-tissue organs for early detection of cancer, we demonstrate the superior features of the pseudo-time marching schemes.

Transcriptional activation of the Escherichia coli bgl operon: negative regulation by DNA structural elements near the promoter

The bgl operon of Escherichia coil is transcriptionally inactive in wild-type cells. DNA insertion sequences (IS) constitute a major class of spontaneous mutations that activate the cryptic bgl promoter. In an attempt to study the molecular mechanism of activation mediated by insertion sequences, transcription of the bgl promoter was carried out in vitro. Stimulation of transcription is observed when a plasmid containing an insertionally activated bgl promoter is used as a template in the absence of proteins other than RNA polymerase. Deletions that remove sequences upstream of the bgl promoter, and insertion of a 1.2 kb DNA fragment encoding resistance to kanamycin, activate the promoter. Point mutations within a region of dyad symmetry upstream of the promoter, which has the potential to extrude into a cruciform structure under torsional stress, also lead to activation, Introduction of a sequence with dyad symmetry, upstream of an activated bgl promoter carrying a deletion of upstream sequences, results in a fourfold reduction in transcription, These results suggest that the cryptic nature of the bgl promoter is because of the presence of DNA structural elements near the promoter that negatively affect transcription.

Two highly unsymmetrical tetradentate (N3O) Schiff base copper(II) complexes: Template synthesis, structural characterization, magnetic and computational studies

Two new copper(II) complexes, [Cu-2(L-1)(2)](ClO4)(2) (1) and [Cu(L-2)(ClO4)] (2), of the highly unsymmetrical tetradentate (N3O) Schiff base ligands HL1 and HL2 (where HL1 = N-(2-hydroxyacetophenone)-bis-3-aminopropylamine and HL2 = N-(salicyldehydine)-bis-3-aminopropylamine) have been synthesised using a template method. Their single crystal X-ray structures show that in complex 1 two independent copper(II) centers are doubly bridged through sphenoxo-O atoms (O1A and O1B) of the two ligands and each copper atom is five-coordinated with a distorted square pyramidal geometry. The asymmetric unit of complex 2 consists of two crystallographically independe N-(salicylidene) bis(aminopropyl)amine-copper(II) molecules, A and B, with similar square pyramidal geometries. Cryomagnetic susceptibility measurements (5-300 K) on complex 1 reveal a distinct antiferromagnetic interaction with J=-23.6 cm(-1), which is substantiated by a DFT calculation (J=-27.6 cm(-1)) using the B3LYP functional. Complex 1, immobilized over highly ordered hexagonal mesoporous silica, shows moderate catalytic activity for the epoxidation of cyclohexene and styrene in the presence of TBHP as an oxidant.

Structural Investigation of Activated Lattice Oxygen in Ce1-xSnxO2 and Ce1-x-ySnxPdyO2-delta by EXAFS and DFT calculation

Substitution of Sn4+ ion in CeO2 creates activated oxygen in Ce0.8Sn0.2O2 leading to higher oxygen storage capacity compared to Ce0.8Zr0.2O2. With Pd ion substitution in Ce0.8Sn0.2O2,activation of oxygen is further enhanced as observed from the H-2/TPR study. Both EXAFS analysis and DFT calculation reveal that in the solid solution Ceexhibits 4 + 4 coordination, Sri exhibits 4 + 2 + 2 coordination and Pd has 4 + 3 coordination. While the oxygen in the First four coordination with short M-O bonds are strongly held in the lattice, the oxygens in the second and higher coordinations with long M-O bonds are weakly bound, and they are the activated oxygen ill the lattice. Bond valence analysis shows that oxygen with valencies as low its 1.65 are created by the Sn and Pd ion Substitution. Another interesting observation is that H-2/TPR experiment of Ce1-xSnxO2 shows a broad peak starting from 200 to 500 degrees C, while the same reduction is achieved in a single step at similar to 110 degrees C in presence Pd2+ on. Substitution of Pd2+ ion thus facilitates synergistic reduction of the catalyst at lower temperature. We have shown that simultaneous reduction of the Ce4+ and Sr4+ ions by Pd-0 is the synergistic interaction leading to high oxygen storage capacity at low temperature.

Bi4Ti3O12-5BiFeO(3) Aurivillius intergrowth: Structural and ferroelectric properties

Aurivillus intergrowth Bi4Ti3O12-5BiFeO(3) was demonstrated to be ferroelectric that evoked the possibility of achieving high temperature magnetoelectric property in this family of compounds. X-ray diffraction studies confirmed its structure to be orthorhombic [Fmm2; a=5.5061(11) A degrees, b=5.4857(7) A degrees, c=65.742(12) A degrees]. However, transmission electron microscopy established the random incidence of intergrowth at nanoscale corresponding to n=6 and n=7 members of the Aurivillius family. Diffuse ferroelectric orthorhombic to paraelectric tetragonal phase transition around 857 K was confirmed by dielectric and high temperature x-ray diffraction studies. Polarization versus electric field hysteresis loops associated with 2P(r) of 5.2 mu C/cm(2) and coercive field of 42 kV/cm were obtained at 300 K.