Unstructured N Terminus of the RNA Polymerase II Subunit Rpb4 Contributes to the Interaction of Rpb4·Rpb7 Subcomplex with the Core RNA Polymerase II of Saccharomyces cerevisiae

Two subunits of eukaryotic RNA polymerase II, Rpb7 and Rpb4, form a subcomplex that has counterparts in RNA polymerases I and III. Although a medium resolution structure has been solved for the 12-subunit RNA polymerase II, the relative contributions of the contact regions between the subcomplex and the core polymerase and the consequences of disrupting them have not been studied in detail. We have identified mutations in the N-terminal ribonucleoprotein-like domain of Saccharomyces cerevisiae Rpb7 that affect its role in certain stress responses, such as growth at high temperature and sporulation. These mutations increase the dependence of Rpb7 on Rpb4 for interaction with the rest of the polymerase. Complementation analysis and RNA polymerase pulldown assays reveal that the Rpb4 center dot Rbp7 subcomplex associates with the rest of the core RNA polymerase II through two crucial interaction points: one at the N-terminal ribonucleoprotein-like domain of Rpb7 and the other at the partially ordered N-terminal region of Rpb4. These findings are in agreement with the crystal structure of the 12-subunit polymerase. We show here that the weak interaction predicted for the N-terminal region of Rpb4 with Rpb2 in the crystal structure actually plays a significant role in interaction of the subcomplex with the core in vivo. Our mutant analysis also suggests that Rpb7 plays an essential role in the cell through its ability to interact with the rest of the polymerase.

Reliability assessment of internal stability of reinforced soil structures: A pseudo-dynamic approach

A methodology for reliability based optimum design of reinforced soil structures subjected to horizontal and vertical sinusoidal excitation based on pseudo-dynamic approach is presented. The tensile strength of reinforcement required to maintain the stability is computed using logarithmic spiral failure mechanism. The backfill soil properties, geometric and strength properties of reinforcement are treated as random variables. Effects of parameters like soil friction angle, horizontal and vertical seismic accelerations, shear and primary wave velocities, amplification factors for seismic acceleration on the component and system probability of failures in relation to tension and pullout capacities of reinforcement have been discussed. In order to evaluate the validity of the present formulation, static and seismic reinforcement force coefficients computed by the present method are compared with those given by other authors. The importance of the shear wave velocity in the estimation of the reliability of the structure is highlighted. The Ditlevsen's bounds of system probability of failure are also computed by taking into account the correlations between three failure modes, which is evaluated using the direction cosines of the tangent planes at the most probable points of failure. (c) 2009 Elsevier Ltd. All rights reserved.

An asymptotic analysis of a simple model for the structure and dynamics of the Ramdas layer

This paper presents a complete asymptotic analysis of a simple model for the evolution of the nocturnal temperature distribution on bare soil in calm clear conditions. The model is based on a simplified flux emissivity scheme that provides a nondiffusive local approximation for estimating longwave radiative cooling near ground. An examination of the various parameters involved shows that the ratio of the characteristic radiative to the diffusive timescale in the problem is of order 10(-3), and can therefore be treated as a small parameter (mu). Certain other plausible approximations and linearization lead to a new equation whose asymptotic solution as mu --> 0 can be written in closed form. Four regimes, consishttp://eprints.iisc.ernet.in/cgi/users/home?screen=EPrint::Edit&eprintid=27192&stage=core#tting of a transient at nominal sunset, a radiative-diffusive boundary ('Ramdas') layer on ground, a boundary layer transient and a radiative outer solution, are identified. The asymptotic solution reproduces all the qualitative features of more exact numerical simulations, including the occurrence of a lifted temperature minimum and its evolution during night, ranging from continuing growth to relatively sudden collapse of the Ramdas layer.

Exploring the interaction energies for the binding of hydroxydiphenyl ethers to enoyl-acyl carrier protein reductases

It is now well established that the potent anti-microbial compound, triclosan, interrupts the type II fatty acid synthesis by inhibiting the enzyme enoyl-ACP reductase in a number of organisms. Existence of a high degree of similarity between the recently discovered enoyl-ACP reductase from R falciparum and B. napus enzyme permitted building of a satisfactory model for the former enzyme that explained some of the key aspects of the enzyme such as its specificity for binding to the cofactor and the inhibitor. We now report the interaction energies between triclosan and other hydroxydiphenyl ethers with the enzymes from B. napus, E. coli and R falciparum. Examination of the triclosan-enzyme interactions revealed that subtle differences exist in the ligand binding sites of the enzymes from different sources i.e., B. napus, E. coli and P falciparum. A comparison of their binding propensities thus determined should aid in the design of effective inhibitors for the respective enzymes.

Mineralogical changes and geotechnical properties of an expansive soil interacted with caustic solution

The type and amount of clay mineral plays an important role in the behaviour of fine-grained soils. Clay minerals are the primary source and moisture is often the external agent of swelling in soils. Also soils may exhibit increased/reduced swelling due to interaction with chemicals. Alkalis used in industrial operations are one such example. Concentrations of alkali and mineral type are the key factors in such interactions. The present paper reports the changes in the properties of an expansive Black Cotton soil containing a mixed layer mineral, rectorite upon interaction with high concentration caustic solutions. X-ray diffraction studies have shown that the rectorite present in the soil undergoes changes with increase in the concentration of alkali. Saponite gets transformed to nantronite. Small amount of kaolinitic mineral present in the soil also reacts with alkali producing some changes in its mineralogy. Many hydroxides are produced. Differential thermal analysis studies have been supportive of these changes. Consequent of these changes, the soil-specific surface increases, changes its Atterberg limits and free swell volume increases. The results have been supported by the characteristics and behaviour of samples contaminated in the field with alkali from an alumina extraction plant.

Effect of fuel on the formation structure, transport and magnetic properties of LaMnO3+nanopowders

Single-step low-temperature solution combustion (LCS) synthesis was adopted for the preparation of LaMnO3+ (LM) nanopowders. The powders were well characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS),surface area and Fourier transform infrared spectroscopy (FTIR). The PXRD of as-formed LM showed a cubic phase but, upon calcination (900degrees C, 6 h), it transformed into a rhombohedral phase. The effect of fuel on the formation of LM was examined, and its structure and magnetoresistance properties were investigated. Magnetoresistance (MR) measurements on LM were carried out at 0, 1, 4 and 7 T between 300 and 10 K. LM (fuel-to-oxidizer ratio; = 1) showed an MR of 17% at 1 T, whereas, for 4 and 7 T, it exhibited an MR of 45 and 55%, respectively, near the TM-I. Metallic resistivity data below TM-I showed that the double exchange interaction played a major role in this compound. It was interesting to observe that the sample calcined at 1200 degrees C for 3 h exhibited insulator behavior.

Crystal structure of an intermolecular 2:1 complex between adenine and thymine.Evidence for both Hoogsteen and `quasi-Watson-Crick' interactions

The titled complex, obtained by co-crystallization (EtOH/25 degrees C),is apparently the only known complex of the free bases. Its crystal structure, as determined by X-ray diffraction at both 90 K and 313 K, showed that one A-T pair involves a Hoogsteen interaction, and the other a Watson-Crick interaction but only with respect to the adenine unit. The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix. (C) 2010 Elsevier Ltd. All rights reserved.

A particle filtering approach for structural system identification in vehicle–structure interaction problems

The problem of identification of parameters of a beam-moving oscillator system based on measurement of time histories of beam strains and displacements is considered. The governing equations of motion here have time varying coefficients. The parameters to be identified are however time invariant and consist of mass, stiffness and damping characteristics of the beam and oscillator subsystems. A strategy based on dynamic state estimation method, that employs particle filtering algorithms, is proposed to tackle the identification problem. The method can take into account measurement noise, guideway unevenness, spatially incomplete measurements, finite element models for supporting structure and moving vehicle, and imperfections in the formulation of the mathematical models. Numerical illustrations based on synthetic data on beam-oscillator system are presented to demonstrate the satisfactory performance of the proposed procedure.

Folding a Polymer via Two-Point Interaction with an External Folding Agent: Use of H-Bonding and Charge-Transfer Interactions

A polymer containing electron-rich aromatic donors (1,5-dialkoxynaphthalene (DAN)) was coerced into a folded state by an external folding agent that contained an electron-deficient aromatic acceptor (pyromellitic diimide (PM)) unit. The donor-containing polymer was designed to carry a tertiary amine moiety in the linking segment, which served as an H-bonding site for reinforcing the interaction with the acceptor containing folding agent that also bore a carboxylic acid group. The H-bonding interaction of the carboxylic acid and the tertiary amine brings the PDI unit between two adjacent DAN units along the polymer backbone to induce charge-transfer (C-T) interactions, and this in turn causes the polymer chain to form a pleated structure. Evidence for the formation of such a pleated structure was obtained from NMR titration studies and also by monitoring the C-T band in their UV-visible spectra. By varying the length of the segment that links the PDI acceptor to the carboxylic acid group, we showed that the most effective folding agent was the one that had a single carbon spacer, as evident from the highest value of the association constant. Control experiments with propionic acid clearly demonstrated the importance of the additional C-T interactions for venerating the folded structures. Further, solution viscosity measurements in the presence of varying amounts of the folding agent revealed a gradual stiffening of the chain in the case of the PDI carrying carboxylic acid, whereas no such affect was seen in the case of simple propionic acid. These observations were supported by D FT calculations of the interactions of a dimeric model of the polymer with the various folding agents; here too the stability of the complex was seen to be highest in the case of the single carbon spacer.

Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study

ingle tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G(7)) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. There quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Angstrom from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Nai counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. in the absence of any coordinated ion. due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.

Role of the environment in the interaction of nonintercalators with Z-DNA

Interaction of the DNA binding nonintercalators Netropsin, Distamycin and the mPD derivative with Z-DNA has been studied. It has been found that environmental factors like the solvent and added cations significantly modulate the interaction of these ligands with Z-DNA. However no definite Z to B transition in presence of these ligands was found in any case, in contrast to previously reported results (Ch. Zimmer, C. Marck and W. Guschlbauer, FEBS Lett. 154, 156-160 (1983)).

Inelastic Torsional Response of a Single-Story Framed Structure

In this paper, a single-story, bilinear-hysteretic structure, square in plan and supported on four columns, subjected to two horizontal ground motions is studied. The model is assumed to possess three degrees of freedom, viz., translational displacements along the two horizontal orthogonal directions and a rotation about the vertical axis. Interaction of the bending moments in the two perpendicular directions has been considered.

Crystal structure of L-lysyl-L-glutamic acid dihydrate

L-Lysyl-L-glutamic acid dihydrate, C11N3O5H21·2H2O, crystallizes in the monoclinic space group P21 with a = 12.474(2), b = 5.020(1), c = 13.157(2) Å, β= 114.69(1)° and Z = 2. The crystal structure was solved by direct methods and refined to an R value of 0.037 using full matrix least-squares method. The molecule exists as a double zwitterion with both the amino and carboxyl groups ionised. The peptide has a folded conformation with its Lys residue trans and Glu residue gauche−gauche+. The side chains of the Lys and Glu residues correspond to all trans and folded (g−g−g−) conformations respectively. The terminal carboxyl group forms hydrogen bonds with the ξ-amino group of the lysine side chain. The head-to-tail interaction often seen in peptide crystals is absent in the present structure. In the extended crystal structure water molecules form channels along the b direction and are enclosed within helically arranged hydrogen bonds formed by the lysine side chain and the peptide backbone.

Spectroscopic, microscopic and first rheological investigations in charge-transfer interaction induced organogels

This article describes two-component charge-transfer interaction mediated organogels (CT-gels) derived from anthracene carboxamides obtained from 2-amino 2-hydroxymethyl-1,3-propanediol (TRIS), and 2,3-dialkoxyanthracenes as donors, with 2,4,7-trinitrofluorenone (TNF) as the common acceptor. We demonstrate the versatility of TNF as an electron acceptor in the formation of these gels. The effect of subtle changes in the donor structure on the gelation ability has been investigated by varying the alkyl chain length in the dialkoxyanthracene donors, and by varying the position of the TRIS substituent in the anthracene carboxamide donors. Distinct differences have been observed in the nature of the CT-gels based on these two kinds of anthracene donors. It has been reported in the literature that 2,3-dialkoxyanthracenes form gels on their own in various aliphatic hydrocarbons and alcohols for linear alkyl chains bearing at least 6mcarbon atoms (C-6). In the present study, it is shown that themCT-complex of these molecules with TNF is able to gel many alcoholic and a few hydrocarbon solvents. Also, in the presence of TNF, the 2,3-dialkoxyanthracenes (C-4-C-5) which were non-gelators on their own at ambient temperatures, form CT-gels in a number of alcohols. The other series of gelators discussed, the anthracene carboxamides, require the mandatory presence of TNF to form gels. This donor-acceptor complex forms gels in various aliphatic alcohols. Interestingly, the formation of these CT-gels requires rapid cooling in most of the cases. Thermal stability studies with both types of CT-gels indicate an optimum stoichiometry of 1 : 1 between the donor and the acceptor. Dynamic rheological experiments reveal these gels as viscoelastic soft materials, with the mechanical strength of these gels depending on the amount of TNF present. This provides a means to tune the strength of the gel by varying the doping concentration of the acceptor.

Electronic structure of high-Tc superconductors from core-level spectroscopies

Using the configuration-interaction approach, we show that various core-level spectroscopic observations on the high-Tc superconducting oxides can be consistently described in terms of mixing between d9 and d10 configurations, with a negligible amount of the d8 (Cu3+) state. From our analysis of the existing experimental data, we provide evidence of a wide and continuous valence transition in these systems as a function of temperature. The changes in the hybridization strengths deduced here are indicative of structural modifications of the square-planar CuO4 clusters with decreasing temperature.