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.

Permeability and consolidation behavior of fly ashes

A knowledge of permeability and consolidation is essential in a number of engineering problems such as settlement, seepage, and stability of the structures. Since fly ash is used very widely for several geotechnical applications, there is a need to understand its permeability and consolidation behavior. This paper presents a detailed study conducted on two Indian fly ashes. It brings out the role of chemical composition (free lime) on the permeability and consolidation behavior of fly ashes. It is found that the permeability values computed based on grain-size distribution agree well with those obtained based on test data.

Relaxation behavior of twin nonlinear optical chromophores: Effect of the spacer length

A new series of twin nonlinear optical (NLO) molecules, having two 4-nitrophenol chromophores that are linked via a flexible polymethylene spacer of varying length [(CH2)(n), n = 1-12], were synthesized. Powder second harmonic generation measurements of these twin samples indicated a pronounced odd-even oscillation, with the odd twins exhibiting a high SHG value while the even ones gave no measurable SH signal. This behavior reflects the crystal packing preferences in such twin NLO systems that have odd and even numbers of atoms linking them - the even ones appear to prefer a centrosymmetric packing arrangement. The orientational/disordering dynamics of these twin NLO molecules, doped in a polymer (poly(methyl methacrylate)) matrix, has also been studied using SHG in electric field poled samples. Interestingly, the maximum attainable SH signal, chi((2)), in, the poled samples also showed an odd-even oscillation; the odd ones again having a higher value of chi((2)) This unprecedented odd-even oscillation in such molecularly doped systems is rationalized as being due to the intrinsically greater ease of a parallel alignment of the two chromophores in the twins with an odd spacer than in those with an even one. Further, the temporal stability of the SHG intensity at 70 degrees C, after the removal of the applied corona, was also studied. The relaxation of all the twin chromophores followed a biexponential decay; the characteristic relaxation time (tau(2)) for the slow decay component suggests that while the twin with a single methylene unit relaxes relatively slowly, the relaxation is significantly faster in cases where n = 2 and 3. In the twins with even longer spacer segments, the relaxation again becomes slower and reaches a saturation value. The observed minimum appears to reflect the interplay of two competing factors that affect the chromophore alignment in such twin systems, namely, the electrostatic repulsion between neighboring oriented dipoles and the intrinsic flexibility of the spacer.

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.

California bearing ratio behavior of cement-stabilized fly ash-soil mixes

Thermal power stations using pulverized coal as fuel generate large quantities of fly ash as a byproduct, which has created environmental and disposal problems. Using fly ash for gainful applications will solve these problems. Among the various possible uses for fly ash, the most massive and effective utilization is in geotechnical engineering applications like backfill material, construction of embankments, as a subbase material, etc. A proper understanding of fly ash-soil mixes is likely to provide viable solutions for its large-scale utilization. Earlier studies initiated in the laboratory have resulted in a good understanding of the California Bearing Ratio (CBR) behavior of fly ash-soil mixes. Subsequently, in order to increase the CBR value, cement has been tried as an additive to fly ash-soil mixes. This paper reports the results.

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.

Fracture energy and softening behavior of high-strength concrete

An experimental investigation on the fracture properties of high-strength concrete (HSC) is reported. Three-point bend beam specimens of size 100 x 100 x 500 mm were used as per RILEM-FMC 50 recommendations. The influence of maximum size of coarse aggregate on fracture energy, fracture toughness, and characteristic length of concrete has been studied. The compressive strength of concrete ranged between 40 and 75 MPa. Relatively brittle fracture behavior was observed with the increase in compressive strength. The load-CMOD relationship is linear in the ascending portion and gradually drops off after the peak value in the descending portion. The length of the tail end portion of the softening curve increases as the size of coarse aggregate increases. The fracture energy increases as the maximum size of coarse aggregate and compressive strength of concrete increase. The characteristic length of concrete increases with the maximum size of coarse aggregate and decreases as the compressive strength increases, (C) 2002 Elsevier Science Ltd. All rights reserved.

Mechanisms controlling the undrained strength behavior of remolded Ariake marine clays

The soft clay of Ariake Bay, in western Kyushu, Japan covers several hundred square kilometers. Ariake clay consists of the principal clay minerals namely, smectite, illite, kaolinite and vermiculite, and other minerals in lesser quantity. The percentage of the principal clay, mineral can vary significantly. The percent clay, size fraction and the salt concentration can also vary significantly. In view of the importance of undrained shear strength in geotechnical engineering practice, its behavior has been studied with respect to variation in salt concentration. Basically, two mechanisms control the undrained strength in clays, namely (a) cohesion or undrained strength is due to the net interparticle attractive forces, or (b) cohesion is due to the viscous nature of the double layer water. Concept (a) operates primarily for kaolinitic soil, and concept (b) dominates primarily for montmorillonitic soils. In Ariake clay, different clay minerals with different exchangeable cations and varying ion concentration in the pore water and varying nonclay size fraction are present. In view of this while both concepts (a) and (b) can coexist and operate simultaneously, one of the mechanisms dominates. For Isahaya clay, concept (a), factors responsible for an increase in level of flocculation and attractive forces result in higher undrained strength. Increase in salt concentration increases the remolded undrained strength at any moisture content. For Kubota and Kawazoe clays, concept (b) factors responsible for an expansion of diffuse double layer thickness, resulting in higher viscous resistance, increase the undrained shear strength, that is, as concentration decreases, the undrained strength increases at any moisture content.The liquid limit of Isahaya,a clay increases with increase in ion concentration and a marginal decrease is seen for both Kubota and Kawazoe clays, and their behavior has been explained satisfactorily,.

Metal-organic chemical vapour deposition of thin films of cobalt on different substrates: study of microstructure

We have investigated the microstructure of thin films grown by metal-organic chemical vapour deposition using a beta-diketonate complex of cobalt, namely cobalt (11) acetylacetonate. Films were deposited on three different substrates: Si(100), thermally oxidised silicon [SiO2/Si(100)] and glass at the same time. As-grown films were characterised by X-ray diffraction, scanning electron microscopy, scanning tunnelling microscopy, atomic force microscopy and secondary ion mass spectrometry. Electrical resistivity was measured for all the films as a function of temperature. We found that films have very fine grains, resulting in high electrical resistivity Further, film microstructure has a strong dependence on the nature of the substrate and there is diffusion of silicon and oxygen into cobalt from the substrate. (C) 2002 Elsevier Science B.V. All rights reserved.

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.

An assessment of creep deformation and fracture behavior of 2.25Cr-1Mo similar and dissimilar weld joints

The evaluation of the creep deformation and fracture behavior of a 2.25Cr-1Mo steel base metal, a 2.25Cr-1Mo/2.25Cr-1Mo similar weld joint, and a 2.25Cr-1Mo/Alloy 800 dissimilar weld joint at 823 K over a stress range of 90 to WO MPa has been carried out. The specimens for creep testing were taken from single-V weld pads fabricated by a shielded metal arc-welding process using 2.25Cr-1Mo steel (for similar-joint) and INCONEL 182 (for dissimilar-joint) electrodes. The weld pads were subsequently given a postweld hear treatment (PWHT) of 973 K for I hour. The microstructure and microhardness of the weld joints were evaluated in the as-welded, postweld heat-treated, and creep-tested conditions. The heat-affected zone (HAZ) of similar weld joint consisted of bainite in the coarse-prior-austenitic-grain (CPAG) region near the fusion line, followed by bainite in the fine-prior-austenitic-grain (FPAG) and intercritical regions merging with the unaffected base metal. In addition to the HAZ structures in the 2.25Cr-1Mo steel, the dissimilar weld joint displayed a definite INCONEL/2.25Cr-1Mo weld interface structure present either as a sharp line or as a diffuse region. A hardness trough was observed in the intercritical region of the HAZ in both weld joints, while a maxima in hardness was seen at the weld interface of the dissimilar weld joint. Both weld joints exhibited significantly lower rupture lives compared to the 2.25Cr-1Mo base metal. The dissimilar weld joint exhibited poor rupture life compared to the similar weld joint, at applied stresses lower than 130 MPa. In both weld joints, the strain distribution across the specimen gage length during creep testing varied significantly. During creep testing, localization of deformation occurred in the intercritical HAZ. In the similar weld joint, at all stress levels investigated, and in the dissimilar weld joint, at stresses greater than or equal to 150 MPa, the creep failure occulted in the intercritical HAZ. The fracture occurred by transgranular mode with a large number of dimples. At stresses below 150 MPa, the failure in the dissimilar weld joint occurred in the CPAG HAZ near to the weld interface. The failure occurred by extensive intergranular creep cavity formation.

Structural investigation of combustion synthesized Cu/CeO2 catalysts by EXAFS and other physical techniques: Formation of a Ce1-xCuxO2-delta solid solution

The structure and chemical environment of Cu in Cu/CeO2 catalysts synthesized by the solution combustion method have been investigated by X-ray diffraction (XRD), transmission electron microscopy (TEM), electron paramagnetic resonance (EPR) spectroscopy, X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), and extended X-ray fine structure (EXAFS) spectroscopy. High-resolution XRD studies of 3 and 5 atom % Cu/CeO2 do not show CuO lines in their respective patterns. The structure could be refined for the composition Ce1-xCuxO2-delta (x = 0.03 and 0.05; delta similar to 0.13 and 0.16) in the fluorite structure with 5-8% oxide ion vacancy. High-resolution TEM did not show CuO particles in 5 atom % Cu/CeO2. EPR as well as XPS studies confirm the presence of Cu2+ species in the CeO2 matrix. Redox potentials of Cu species in the CeO2 matrix are lower than those in CuO. EXAFS investigations of these catalysts show an average coordination number of 3 around the Cu2+ ion in the first shell at a distance of 1.96 Angstrom, indicating the O2- ion vacancy around the Cu2+ ion. The Cu-O bond length also decreases compared to that in CuO. The second and third shell around the Cu2+ ion in the catalysts are attributed to -Cu2+-O2--Cu2+ - at 2.92 Angstrom and -Cu2+-O2--Ce4+- at the distance of 3.15 Angstrom, respectively. The present results provide direct evidence for the formation of a Ce1-xCuxO2-delta type of solid solution phase having -square-Cu2+-O-Ce4+- kind of linkages.

An assessment of creep deformation and fracture behavior of 2.25Cr-1Mo

The evaluation of the creep deformation and fracture behavior of a 2.25Cr-1Mo steel base metal, a 2.25Cr-1Mo/2.25Cr-1Mo similar weld joint, and a 2.25Cr-1Mo/Alloy 800 dissimilar weld joint at 823 K over a stress range of 90 to WO MPa has been carried out. The specimens for creep testing were taken from single-V weld pads fabricated by a shielded metal arc-welding process using 2.25Cr-1Mo steel (for similar-joint) and INCONEL 182 (for dissimilar-joint) electrodes. The weld pads were subsequently given a postweld hear treatment (PWHT) of 973 K for I hour. The microstructure and microhardness of the weld joints were evaluated in the as-welded, postweld heat-treated, and creep-tested conditions. The heat-affected zone (HAZ) of similar weld joint consisted of bainite in the coarse-prior-austenitic-grain (CPAG) region near the fusion line, followed by bainite in the fine-prior-austenitic-grain (FPAG) and intercritical regions merging with the unaffected base metal. In addition to the HAZ structures in the 2.25Cr-1Mo steel, the dissimilar weld joint displayed a definite INCONEL/2.25Cr-1Mo weld interface structure present either as a sharp line or as a diffuse region. A hardness trough was observed in the intercritical region of the HAZ in both weld joints, while a maxima in hardness was seen at the weld interface of the dissimilar weld joint. Both weld joints exhibited significantly lower rupture lives compared to the 2.25Cr-1Mo base metal. The dissimilar weld joint exhibited poor rupture life compared to the similar weld joint, at applied stresses lower than 130 MPa. In both weld joints, the strain distribution across the specimen gage length during creep testing varied significantly. During creep testing, localization of deformation occurred in the intercritical HAZ. In the similar weld joint, at all stress levels investigated, and in the dissimilar weld joint, at stresses greater than or equal to 150 MPa, the creep failure occulted in the intercritical HAZ. The fracture occurred by transgranular mode with a large number of dimples. At stresses below 150 MPa, the failure in the dissimilar weld joint occurred in the CPAG HAZ near to the weld interface. The failure occurred by extensive intergranular creep cavity formation.

Structural Transitions of Nitrogen Confined in Slit Graphite Pores

The structure of ordered phases that are formed when nitrogen is confined in slit graphite pores of height h is investigated using Monte Carlo simulations. The pore wall consists of a single-structured graphite sheet. Canonical ensemble simulations are carried out for temperatures ranging from 15 to 70Kwith layer density distributions, in-plane, out-of-plane angular distributions and snapshots evaluated at different temperatures. At each pore height the pore densities are obtained from independent grand ensemble simulations. At the smallest pore height studied (h)7 Å), where a single layer of molecules is accommodated at the center of the pore, the orientations are predominantly wall parallel, forming a biaxially incommensurate herringbone structure.Whentwo or more fluid layers are formed in the slit pore, the orientation of molecules adsorbed next to the wall can exist in either the herringbone or hexagonal phases. In all the multilayered cases studied, with the exception of the h ) 10 Å pore, where both wall layers form a commensurate herringbone structure, the low-temperature wall structures are incommensurate, possessing 6-fold hexagonal symmetry. The presence of the pinwheel structures, which were observed at low temperatures in the h ) 12 Å and h ) 14 Å pores, is determined by the pore height or the proximity and/or density of the adjacent fluid layers when inner layers are present.