Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 angstrom resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alpha beta alpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

The evolution of loop structures in flux rings within the solar convection zone

Choudhuri and Gilman (1987) considered certain implications of the hypothesis that the magnetic flux within the Sun is generated at the bottom of the convection zone and then rises through it. Taking flux rings symmetric around the rotation axis and using reasonable values of different parameters, they found that the Coriolis force deflects these flux rings into trajectories parallel to the rotation axis so that they emerge at rather high latitudes. This paper looks into the question of whether the action of the Coriolis force is subdued when the initial configuration of the flux ring has non-axisymmetries in the form of loop structures. The results depend dramatically on whether the flux ring with the loops lies completely within the convection zone or whether the lower parts of it are embedded in the stable layers underneath the convection zone. In the first case, the Coriolis force supresses the non-axisymmetric perturbations so that the flux ring tends to remain symmetric and the trajectories are very similar to those of Choudhuri and Gilman (1987). In the second case, however, the lower parts of the flux ring may remain anchored underneath the bottom of the convection zone, but the upper parts of the loops still tend to move parallel to the rotation axis and emerge at high latitudes. Thus the problem of the magnetic flux not being able to come out at the sunspot latitudes still persists after the non-axisymmetries in the flux rings are taken into account.

Time Domain Characteristics of Electrical Measures for a Piezoelectric Thin Film to Identify Defects in the Substrate

A reduced 3D continuum model of dynamic piezoelectricity in a thin-film surface-bonded to the substrate/host is presented in this article. While employing large area flexible thin piezoelectric films for novel applications in device/diagnostics, the feasibility of the proposed model in sensing the surface and/or sub-surface defects is demonstrated through simulations - which involve metallic beams with cracks and composite beam with delaminations of various sizes. We have introduced a set of electrical measures to capture the severity of the damage in the existing structures. Characteristics of these electrical measures in terms of the potential difference and its spatial gradients are illustrated in the time domain. Sensitivity studies of the proposed measures in terms of the defected areas and their region of occurence relative to the sensing film are reported. The simulations' results for electrical measures for damaged hosts/substrates are compared with those due to undamaged hosts/substrates, which show monotonicity with high degree of sensitivity to variations in the damage parameters.

A novel single pot synthesis of binuclear copper(II) complexes of macrocyclic and macroacyclic compartmental ligands: Structures and magnetic properties

Two binuclear copper(II) complexes one (complex 1) with a macrocyclic ligand (H(2)L1) and other (complex 2) with a macroacyclic (end-off type) compartmental ligand (HL2) have been synthesized from single pot template synthesis involving copper(II) nitrate, 1,2diaminoethane, 4-methyl-2,6-diformylphenol, and sodium azide. Structure analysis of complex I reveals that there are actually two half molecules present in the asymmetric unit and so two complexes (molecule-I and molecule-II) are present in unit cell, although they show slight differences. The two Cu(II) centers are in distorted square pyramidal coordination environment with two endogenous phenoxo bridges provided by the phenolate of H(2)L1 I having Cu-Cu separations of 2.9133(10) angstrom and 2.9103(10) in the two molecules. In complex 2 the coordination environments around two Cu(II) centers are asymmetric, Cu1 is in distorted square pyramidal environment whereas, the coordination environment around Cu2 is distorted octahedral. The two Cu(II) centers in complex 2 are connected by two different kinds of bridges, one is endogenous phenoxo bridge provided by the phenolate of the ligand HL2 and the other is exogenous azido bridge (mu-(1),(l) type) with Cu-Cu distance of 3.032(10) angstrom. Variable temperature magnetic studies show that two Cu(II) centers in both the complexes are strongly antiferromagnetically coupled with J = -625 +/- 5 cm(-1) and J = -188.6 +/- 1cm(-1) for complex 1 and 2, respectively. (C) 2006 Elsevier B.V. All rights reserved.

Crystal Structures of a New Polymorphic Form of Gabapentin Monohydrate and the E and Z Isomers of 4-Tertiarybutylgabapentin

Gabapentin, a widely used antiepileptic drug, crystallizes in multiple polymorphic forms. A new crystal form of gabapentin monohydrate in the space group Pbca is reported and the packing arrangement compared with that of a previously reported polymorph in the space group P2(1)/c [Ibers, J.A. (2001) Acta Crystallogr; C57:641]. Gabapentin polymorphs can also occur from a selection of one of the two distinct chair forms of the 1,1-disubstituted cyclohexane. Crystal structures of the E and Z isomers of 4-tert-butylgabapentin provide models for analyzing anticipated packing modes in the conformational isomers of gabapentin. The E isomer crystallized in the space group Pca2(1), while the Z isomer crystallized in the space group P2(1)/c. The crystal structure of E-4-tert-butylgabapentin provides the only example of a structure in a non-centrosymmetric space group. Crystal structures of the hydrochloride and hydrobromide salts of 4-tert-butyl derivatives are reported. The results suggest that for gabapentin, a large 'polymorph-space' may be anticipated, in view of the multiple conformational states that are accessible to the molecule.

Conformation of di-n-propylglycine residues (Dpg) in peptides: crystal structures of a type I-turn forming tetrapeptide and an -helical tetradecapeptide

The crystal structures of two oligopeptides containing di-n-propylglycine (Dpg) residues, Boc-Gly-Dpg-Gly-Leu-OMe (1) and Boc-Val-Ala-Leu-Dpg-Val-Ala-Leu-Val-Ala-Leu-Dpg-Val-Ala-Leu-OMe (2) are presented. Peptide 1 adopts a type I-turn conformation with Dpg(2)-Gly(3) at the corner positions. The 14-residue peptide 2 crystallizes with two molecules in the asymmetric unit, both of which adopt -helical conformations stabilized by 11 successive 5 1 hydrogen bonds. In addition, a single 4 1 hydrogen bond is also observed at the N-terminus. All five Dpg residues adopt backbone torsion angles (, ) in the helical region of conformational space. Evaluation of the available structural data on Dpg peptides confirm the correlation between backbone bond angle NCC() and the observed backbone , values. For > 106° , helices are observed, while fully extended structures are characterized by < 106° . The mean values for extended and folded conformations for the Dpg residue are 103.6° ± 1.7° and 109.9° ± 2.6° , respectively.

Dynamics and control of buckling type devices using SMA wire integrated beam

An analysis and design study using Shape Memory Alloy (SMA) wire integrated beam and its buckling shape control are reported. The dynamical system performance is analyzed with a mathematical set-up involving nonlocal and rate sensitive kinetics of phase transformation in the SMA wire. A standard phenomenological constitutive model reported by Brinson (1993) is modified by considering certain consistency conditions in the material property tensors and by eliminating spurious singularity. Considering the inhomogeneity effects, a finite element model of the SMA wire is developed. Simulations are carried out to study the buckling shape control of a beam integrated with SMA wire.

The illustrative use of thiosulfate in the formation of new three-dimensional hybrid structures

Examples of 3D cadmium thiosulfate based inorganic-organic hybrid compounds have been shown to be active photocatalysts using sunlight.

Free vibration and wave propagation analysis of uniform and tapered rotating beams using spectrally formulated finite elements

This paper presents a formulation of an approximate spectral element for uniform and tapered rotating Euler-Bernoulli beams. The formulation takes into account the varying centrifugal force, mass and bending stiffness. The dynamic stiffness matrix is constructed using the weak form of the governing differential equation in the frequency domain, where two different interpolating functions for the transverse displacement are used for the element formulation. Both free vibration and wave propagation analysis is performed using the formulated elements. The studies show that the formulated element predicts results, that compare well with the solution available in the literature, at a fraction of the computational effort. In addition, for wave propagation analysis, the element shows superior convergence. (C) 2007 Elsevier Ltd. All rights reserved.

Genetic programming metamodel for rotating beams

This paper investigates the use of Genetic Programming (GP) to create an approximate model for the non-linear relationship between flexural stiffness, length, mass per unit length and rotation speed associated with rotating beams and their natural frequencies. GP, a relatively new form of artificial intelligence, is derived from the Darwinian concept of evolution and genetics and it creates computer programs to solve problems by manipulating their tree structures. GP predicts the size and structural complexity of the empirical model by minimizing the mean square error at the specified points of input-output relationship dataset. This dataset is generated using a finite element model. The validity of the GP-generated model is tested by comparing the natural frequencies at training and at additional input data points. It is found that by using a non-dimensional stiffness, it is possible to get simple and accurate function approximation for the natural frequency. This function approximation model is then used to study the relationships between natural frequency and various influencing parameters for uniform and tapered beams. The relations obtained with GP model agree well with FEM results and can be used for preliminary design and structural optimization studies.

Ru(II)-CO complexes of thioarylazoimidazoles: Syntheses, structures, spectroscopy and DFT calculation

The complexes, cis-(CO)-trans-(Cl)-[Ru(SRaaiNR)(CO)(2)Cl-2] (2) and trans-(Cl)-[Ru(SRaaiNR)(CO)Cl-2] (3) (SRaaiNR = 1-alkyl-2-{(o-thioalkyl)phenylazo}imidazoles; R = Me (1a) and Et (1b)) have been synthesized and characterized. The structural confirmation is achieved by single crystal X-ray structure determinations. The complexes show Ru(III)/Ru(II) couple and ligand reductions. Electronic structure and spectral properties of the complexes have been explained with the DFT and TDDFT calculation. (C) 2009 Elsevier B.V. All rights reserved.

Ion pairs in non-redundant protein structures

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 angstrom and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.

Experimental Demonstration of H{infty} Control based Active Vibration Suppression in Composite Fin-tip of Aircraft using Optimally Placed Piezoelectric Patch Actuators

The goal of this study is the multi-mode structural vibration control in the composite fin-tip of an aircraft. Structural model of the composite fin-tip with surface bonded piezoelectric actuators is developed using the finite element method. The finite element model is updated experimentally to reflect the natural frequencies and mode shapes accurately. A model order reduction technique is employed for reducing the finite element structural matrices before developing the controller. Particle swarm based evolutionary optimization technique is used for optimal placement of piezoelectric patch actuators and accelerometer sensors to suppress vibration. H{infty} based active vibration controllers are designed directly in the discrete domain and implemented using dSpace® (DS-1005) electronic signal processing boards. Significant vibration suppression in the multiple bending modes of interest is experimentally demonstrated for sinusoidal and band limited white noise forcing functions.

Modeling and analysis of a tunable piezoelectric structure for transverse shear wave generation

An analytical investigation of the transverse shear wave mode tuning with a resonator mass (packing mass) on a Lead Zirconium Titanate (PZT) crystal bonded together with a host plate and its equivalent electric circuit parameters are presented. The energy transfer into the structure for this type of wave modes are much higher in this new design. The novelty of the approach here is the tuning of a single wave mode in the thickness direction using a resonator mass. First, a one-dimensional constitutive model assuming the strain induced only in the thickness direction is considered. As the input voltage is applied to the PZT crystal in the thickness direction, the transverse normal stress distribution induced into the plate is assumed to have parabolic distribution, which is presumed as a function of the geometries of the PZT crystal, packing mass, substrate and the wave penetration depth of the generated wave. For the PZT crystal, the harmonic wave guide solution is assumed for the mechanical displacement and electric fields, while for the packing mass, the former is solved using the boundary conditions. The electromechanical characteristics in terms of the stress transfer, mechanical impedance, electrical displacement, velocity and electric field are analyzed. The analytical solutions for the aforementioned entities are presented on the basis of varying the thickness of the PZT crystal and the packing mass. The results show that for a 25% increase in the thickness of the PZT crystal, there is ~38% decrease in the first resonant frequency, while for the same change in the thickness of the packing mass, the decrease in the resonant frequency is observed as ~35%. Most importantly the tuning of the generated wave can be accomplished with the packing mass at lower frequencies easily. To the end, an equivalent electric circuit, for tuning the transverse shear wave mode is analyzed.

Structures and molecular-dynamics studies of three active-site mutants of bovine pancreatic phospholipase A(2)

Phospholipase A(2) hydrolyzes phospholipids at the sn-2 position to cleave the fatty-acid ester bond of L-glycerophospholipids. The catalytic dyad (Asp99 and His48) along with a nucleophilic water molecule is responsible for enzyme hydrolysis. Furthermore, the residue Asp49 in the calcium-binding loop is essential for controlling the binding of the calcium ion and the catalytic action of phospholipase A2. To elucidate the structural role of His48 and Asp49, the crystal structures of three active-site single mutants H48N, D49N and D49K have been determined at 1.9 angstrom resolution. Although the catalytically important calcium ion is present in the H48N mutant, the crystal structure shows that proton transfer is not possible from the catalytic water to the mutated residue. In the case of the Asp49 mutants, no calcium ion was found in the active site. However, the tertiary structures of the three active-site mutants are similar to that of the trigonal recombinant enzyme. Molecular-dynamics simulation studies provide a good explanation for the crystallographic results.