Structural studies of protein unfolding

Methods for macromolecular structure determination (NMR and crystallography) are now being used to get structural information on partially folded and unfolded states of proteins. These techniques, in combination with proton hydrogen exchange studies are powerful tools to extract information on non-native states of proteins. This review discusses progress In this area of protein folding.

Studies on structural and electrical properties of barium strontium titanate thin films developed by metallo-organic decomposition

Thin films of barium strontium titanate (BST) including BaTiO3 and SrTiO3 end members were deposited using the metallo-organic decomposition (MOD) technique. Processing parameters such as nonstoichiometry, annealing temperature and time, film thickness and doping concentration were correlated with the structural and electrical properties of the films. A random polycrystalline structure was observed for all MOD films under the processing conditions in this study. The microstructures of the films showed multi-grains structure through the film thickness. A dielectric constant of 563 was observed for (Ba0.7Sr0.3)TiO3 films rapid thermal annealed at 750 degrees C for 60 s. The dielectric constant increased with annealing temperature and film thickness, while the dielectric constant could reach the bulk values for thicknesses as thin as similar to 0.3 mu m. Nonstoichiometry and doping in the films resulted in a lowering of the dielectric constant. For near-stoichiometric films, a small dielectric dispersion obeying the Curie-von Schweidler type dielectric response was observed. This behavior may be attributed to the presence of the high density of disordered grain boundaries. All MOD processed films showed trap-distributed space-charge limited conduction (SCLC) behavior with slope of similar to 7.5-10 regardless of the chemistry and processing parameter due to the presence of main boundaries through the film thickness. The grain boundaries masked the effect of donor-doping, so that all films showed distributed-trap SCLC behavior without discrete-traps. Donor-doping could significantly improve the time-dependent dielectric breakdown behavior of BST thin films, mostly likely due to the lower oxygen vacancy concentration resulted from donor-doping. From the results of charge storage density, leakage current and time-dependent dielectric breakdown behavior, BST thin films are found to be promising candidates for 64 and 256Mb ULSI DRAM applications. (C) 1997 Elsevier Science S.A.

Magneto-structural correlation in (mu-alkoxo/hydroxo)(mu-carboxylato)dicopper(II) systems: Synthesis, X-ray structure and magnetic properties of aquo(mu-hydroxo) (mu-arylcarboxylato)bis(N,N,N ',N '-tetramethylethane-1,2-diamine)dicopper(II) diperchlorate

Asymmetrically dibridged dicopper(II) complexes, [Cu-2(OH)(O2CC6H4-p-Me)(tmen)(2)(H2O)](ClO4)(2) (1) and [Cu-2(OH)(O2CC6H4-p-OMe)(tmen)(2)(H2O)](ClO4)(2) (2) (tmen = N,N,N',N'-tetramethylethane-1,2-diamine), were prepared and structurally characterized. Complex 1 crystallizes in the monoclinic space group P2(1)/a with a = 17.718(2), b = 9.869(1), c = 19.677(2) Angstrom, beta = 115.16(1)degrees, V = 3114.3(6) Angstrom(3) and Z = 4. The structure was refined to R(wR(2)) = 0.067(0.178). Complex 2 crystallizes in the monoclinic space group P2(1)/a with a = 17.695(3), b = 9.574(4), c = 20.104(2) Angstrom, beta = 114.18(1)degrees, V = 3107(1) Angstrom(3) and Z = 4. The final residuals are R(wR(2)) = 0.067(0.182). The complexes have a [Cu-2(mu-OH)(mu-OH)(mu-O2CAr)](2+) core with tmen Ligands occupying the terminal sites of the core. In addition, one copper is axially bound to a water molecule. The Cu ... Cu distances and the Cu-OH Cu angles in the core are 3.394(1) Angstrom, 124.4(2)degrees for 1 and 3.374(1) Angstrom, 123.3(3)degrees for 2. The complexes show axial X-band EPR spectral features in methanol glass at 77 K giving g(perpendicular to) = 2.02, g(parallel to) = 2.3 (A(parallel to) = 165 x 10(-4) cm(-1)) and a visible band near similar to 630 nm in methanol. The complexes are weakly antiferromagnetic. A theoretical fit of the magnetic susceptibility data in the temperature range 40-295 K gives -J = 10 cm(-1), g = 2.05 for 1 and -J = 10 cm(-1), g = 2.0 for 2. Plots of -2J versus the Cu-OH-Cu angle (phi) in this class of asymmetrically dibridged dicopper(II) complexes having d(x2-y2)-d(x2-y2) magnetic orbitals show a linear magneto-structural correlation: -2J(cm(-1)) = 11.48 phi(deg) - 1373.

Structural characterization and chain dynamics of poly(alpha-methylstyrene peroxide) by NMR spectroscopy

Poly(alpha-methylstyrene peroxide) has been synthesized and characterized spectroscopically. The H-1 and C-13 NMR spectra are shown to reveal the stereochemical features and the endgroups in the peroxide chain. The preliminary studies on the chain dynamics of the polyperoxide chain has been done by measuring the spin-lattice relaxation times (T-1) of the main chain as well as the side chain carbons. It has been shown from the dependence of the spin-lattice relaxation times that the polyperoxide chain is more flexible compared to the corresponding hydrocarbon-backbone analog.

Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics

Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The H-1 resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T-12 and U-15 nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T-14 stacks upon both T-12 and U-15 while T-13 partially stacks upon T-14. Very weak stacking interaction is observed between T-13 and T-12. All the individual nucleotide bases adopt 'anti' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T-13 and T-14. The stereochemistry of U-15 mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously.

Structural, dielectric and optical properties of lithium borate-bismuth tungstate glass-ceramicsc

Glasses in the system (1 - x)Li2B4O7-xBi(2)WO(6) (0.1 less than or equal to x less than or equal to 0.35) were prepared by splat quenching technique. Powder X-ray diffraction (XRD) and differential thermal analysis (DTA) were employed to characterize the as-quenched glasses. High-resolution transmission electron microscopy (HR TEM) revealed the presence of fine, nearly spherical crystallites of Bi2WO6 varying from 1.5 to 20 nm in size, depending on x in the as-quenched glasses. The glasses (corresponding to x = 0.3) heat-treated at 723 K for 6 h gave rise to a clear crystalline phase of Bi2WO6 embedded in the Li2B4O7 glass matrix, as observed by X-ray studies. The dielectric constants of the as-quenched glasses as well as the glass-ceramics decreased with increase in frequency (40Hz-100 kHz) at 300 K, and the value obtained for the glass-ceramic (x = 0.2) is in agreement with the values predicted using Maxwell's model and the logarithmic mixture rule. The dielectric constants for both the as-quenched glass and the glass-ceramic increased with increase in temperature (300 - 873 K) and exhibited anomalies close to the onset of the crystallization temperature of the host glass matrix. The optical transmission properties:of these glass-ceramics were found to be compositional dependant. (C) 2000 Elsevier Science Ltd.

Structural dielectric and optical properties of SrB4O7-BaO-TiO2 glasses

Glass samples with compositions (100-2x)SrB4O7-xBaO-xTiO(2) (10 less than or equal to x less than or equal to 40) were prepared by conventional melt quenching and the influence of the addition of BaO-TiO2 on the structural, dielectric and optical properties of SBO glasses was studied The molar volume, glass transition temperature and the optical polarisability of the glass samples were found to decrease with increase in BaO-TiO2 content while the refractive index and optical band gap increase with increase in BaO-TiO2 content.

Structural instability of the charge ordered compound Nd0.5Sr0.5MnO3 under a magnetic field

We report an anomalous magnetostriction behavior of the charge ordered compound Nd0.5Sr0.5MnO3. We have found that the applied magnetic field not only gives rise to a large negative magnetoresistance but also produces a huge positive magnetovolume effect. This unusual effect is explained considering that the applied magnetic field induces a structural transition at which the volume drastically increases. This effect is also seen in the anisotropic magnetostriction which shows clear anomalies at the field induced transition.

Structural phase transitions in Bi2V1-xGexO5.5-x/2 (x=0.2, 0.4, and 0.6) single crystals: X-ray crystallographic study

Single crystals of Bi2V1-xGexO5.5-x/2 (x = 0.2, 0.4, and 0.6) were grown by slow cooling of melts. Bismuth vanadate transforms from an orthorhombic to a tetragonal structure and subsequently to an orthorhombic system when the Ge4+ concentration was varied from x = 0.2 to x = 0.6. All of these compositions crystallized in polar space groups (Aba2, F4mm, and Fmm2 for x = 0.2, 0.4, and 0.6, respectively). The structures were fully determined by single crystal X-ray diffraction studies, (C) 1999 Elsevier Science Ltd.

Stress-strain Curves and Corresponding Structural Parameters in Mulberry and Non-mulberry Silk Fibers

Mulberry fiber (Bivoltine) and non-mulberry fiber (Tassar) were subjected to stress-strain studies and the corresponding samples were examined using wide angle X-ray scattering studies. Here we have two different characteristic stress-strain curves and this has been correlated with changes in crystallite shape ellipsoids in all the fibers. Exclusive crystal structure studies of Tassar fibers show interesting feature of transformation from antiparallel chains to parallel chains.

The studies on micro-structural defects in deformed composite matrix of Al-Si-Mg and SiC

Detailed Fourier line shape analysis has been performed on three different compositions of the composite matrix of Al-Si-Mg and SiC. The alloy composition in wt% is Al-7%Si, 0.35%Mg, 0.14%Fe and traces of copper and titanium (similar to 0.01%) with SiC varying from 0 to 30wt% in three steps i.e., 0, 10 and 30wt%. The line shift analysis has been performed by considering 111, 200, 220, 311 and 222 reflections after estimating their relative shift. Peak asymmetry analysis has been performed considering neighbouring 111 and 200 reflections and Fourier line shape analysis has been performed after considering the multiple orders 111 and 222, 200 and 400 reflections. Combining all these three analyses it has been found that the deformation stacking faults both intrinsic alpha' and extrinsic alpha " are absent in this alloy system whereas the deformation twin beta has been found to be positive and increases with the increase of SiC concentration. So, like other Al-base alloys this ternary alloy also shows high stacking fault energy, and the addition of SiC introduces deformation twin which increases with its concentration in the deformed lattices.

Electron diffraction structure analysis: structural research with low-quality diffraction data

Electron Diffraction Structure Analysis (EDSA) with data from standard selected-area electron diffraction (SAED) is still the method of choice for structure determination of nano-sized single crystals. The recently determined heavy atom structure α-Ti2Se (Albe & Weirich, 2003) is used as an example to illustrate the developed procedure for structure determination from two-dimensionally SAED data via direct methods and kinematical least-squares refinement. Despite the investigated crystallite had a relatively large effective thickness of about 230 Å as determined from dynamical calculations, the obtained structural model from SAED data was found in good agreement with the result from an earlier single crystal X-ray study (Weirich, Pöttgen & Simon, 1996). Arguments, which support the validity of the used quasi-kinematical approach, are given in the text. The influences of dynamical and secondary scattering on the quality of the data and the structure solution are discussed. Moreover, the usefulness of first-principles calculations for verifying the results from EDSA is demonstrated by two examples, whereas one of the structures was unattainable by conventional X-ray diffraction.

Design and structural analysis of hairpin-TFO for transcriptional activation of genes in S-cerevisiae

Triplex forming oligonucleotides (TFOs) have the potential to modulate gene expression. While most of the experiments are directed towards triplex mediated inhibition of gene expression the strategy potentially could be used for gene specific activation. In an attempt to design a strategy for gene specific activation in vivo applicable to a large number of genes we have designed a TFO based activator-target system which may be utilized in Saccharomyces cerevisiae or any other system where Gal4 protein is ectopically expressed. The total genome sequence of Saccharomyces cerevisiae and expression profiles were used to select the target genes with upstream poly (pu/py) sequences. We have utilized the paradigm of Gal4 protein and its binding site. We describe here the selection of target genes and design of hairpin-TFO including the targeting sequences containing polypurine stretch found in the upstream promoter regions of weakly expressed genes. We demonstrate, the formation of hairpin-TFO, its binding to Gal4 protein, its ability to form triplex with the target duplex in vitro, the effect of polyethylenimine on complex formation and discuss the implication on in vivo transcription activation.

Organometallic chemistry of chiral diphosphazane ligands: Synthesis and structural characterisation

The diphosphazane ligands of the type, (C20H12O2)PN(R)P(E)Y2 (R = CHMe2 or (S)-*CHMePh; E = lone pair or S; Y2 = O2C20H12 or Y = OC6H5 or OC6H4Me-4 or OC6H4OMe-4 or OC6H4But-4 or C6H5) bearing axially chiral 1,1'-binaphthyl-2,2′-dioxy moiety have been synthesised. The structure and absolute configuration of a diastereomeric palladium complex, [PdCl2{ηsu2}-((O2C20H12)PN((S)-*CHMePh)PPh2] has been determined by X-ray crystallography. The reactions of [CpRu(PPh3)2Cl] with various symmetrical and unsymmetrical diphosphazanes of the type, X2PN(R)PYY′ (R = CHMe2 or (S)-*CHMePh; X = C6H5 or X2 = O2C20H12; Y=Y′= C6H5 or Y = C6H5, Y′ = OC6H4Me-4 or OC6H3Me2-3,5 or N2C3HMe2-3,5) yield several diastereomeric neutral or cationic half-sandwich ruthenium complexes which contain a stereogenic metal center. In one case, the absolute configuration of a trichiral ruthenium complex, viz. [Cp*Ruη2-Ph2PN((S)-*CHMePh)*PPh (N2C3HMe2-3,5)Cl] is established by X-ray diffraction. The reactions of Ru3(CO)12 with the diphosphazanes (C20H12O2)PN(R)PY2 (R = CHMe2orMe; Y2=O2C20H12or Y= OC6H5 or OC6H4Me-4 or OC6H4OMe-4 or OC6H4But-4 or C6H5) yield the triruthenium clusters [Ru3(CO)10{η-(O2C20H12)PN(R)PY2}], in which the diphosphazane ligand bridges two metal centres. Palladium allyl chemistry of some of these chiral ligands has been investigated. The structures of isomeric η3-allyl palladium complexes, [Pd(η3-l,3-R′2-C3H3){η2-(rac)-(02C20H12)PN(CHMe2)PY2}](PF6) (R′ = Me or Ph; Y = C6H5 or OC6H5) have been elucidated by high field two-dimensional NMR spectroscopic and X-ray crystallographic studies.

Orthometalation in calixarenes: Synthesis and structural characterization of a novel orthopalladated calix[4]arene bisphosphite

The treatment of a symmetrically bridged p-Bu-t-calix[4] arene bisphosphite with PdCl2(NCPh)(2) yields a novel orthopalladated derivative by a C-C bond scission of a t-butyl group attached to an aryl ring. The structure of this orthopalladated calix[4]arene derivative has been established by X-ray crystallography.