Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

Background: Disulphide bridges are well known to play key roles in stability, folding and functions of proteins. Introduction or deletion of disulphides by site-directed mutagenesis have produced varying effects on stability and folding depending upon the protein and location of disulphide in the 3-D structure. Given the lack of complete understanding it is worthwhile to learn from an analysis of extent of conservation of disulphides in homologous proteins. We have also addressed the question of what structural interactions replaces a disulphide in a homologue in another homologue. Results: Using a dataset involving 34,752 pairwise comparisons of homologous protein domains corresponding to 300 protein domain families of known 3-D structures, we provide a comprehensive analysis of extent of conservation of disulphide bridges and their structural features. We report that only 54% of all the disulphide bonds compared between the homologous pairs are conserved, even if, a small fraction of the non-conserved disulphides do include cytoplasmic proteins. Also, only about one fourth of the distinct disulphides are conserved in all the members in protein families. We note that while conservation of disulphide is common in many families, disulphide bond mutations are quite prevalent. Interestingly, we note that there is no clear relationship between sequence identity between two homologous proteins and disulphide bond conservation. Our analysis on structural features at the sites where cysteines forming disulphide in one homologue are replaced by non-Cys residues show that the elimination of a disulphide in a homologue need not always result in stabilizing interactions between equivalent residues. Conclusion: We observe that in the homologous proteins, disulphide bonds are conserved only to a modest extent. Very interestingly, we note that extent of conservation of disulphide in homologous proteins is unrelated to the overall sequence identity between homologues. The non-conserved disulphides are often associated with variable structural features that were recruited to be associated with differentiation or specialisation of protein function.

An Approximate Solution Of One-Dimensional Piston Problem

A new theory of shock dynamics has been developed in the form of a finite number of compatibility conditions along shock rays. It has been used to study the growth or decay of shock strength for accelerating or decelerating piston starting with a nonzero piston velocity. The results show good agreement with those obtained by Harten's high resolution TVD scheme.

Mössbauer studies of the corrosion products of iron formed in aqueous ammonium nitrate solution

The products of corrosion reaction of electrolytic iron in 45% ammonium nitrate solution formed under various conditions of time, temperature and pH have been analysed mainly by Mössbauer spectroscopy, in combination with X-ray diffraction, infrared absorption and electron microscopy techniques. γ-Fe00H is found to be the major product of hydrolytic precipitation at pH > 5.6 while only α-FeOOH is formed at pH < 3.0. In the pH range 3.0 < pH < 5.0, α-Fe00H and ferrihydrite are both formed. However, once the nuclei of α-Fe00H are formed under low pH conditions, their growth is favoured even in the otherwise unfavourable slightly acidic medium, resulting in a hydrous α-Fe00H which has two distinct hyperfine fields at the 57Fe nucleus. Magnetite is always formed in the vicinity of the metal and its rate of formation on the surface increases with temperature. α-Fe203 is the major product of hydrolytic precipitation at temperatures >80C. The possible mechanisms for the formation of each of the corrosion products are discussed.

Alfven surface waves along cylindrical plasma columns

The properties of Alfven surface waves along a cylindrical plasma column surrounded by vacuum or by another plasma medium are discussed. Both symmetric (m=0) and asymmetric (m=+or-1) modes are found to be dispersive in nature. The interfacial symmetric modes propagate in a certain frequency window ( omega A1, omega As), where omega As is the Alfven surface wave frequency along the interface of two semi-infinite media; when nu A1> nu A2 these modes propagate as backward waves and when nu A1< nu A2 as forward waves. The asymmetric modes change from backward to forward waves at a critical wave number kTr approximately=1.59/a when nu A1< nu A2 or vice versa when nu A1> nu A2.

Strain hardening during constrained deformation of metal foams - Effect of shear displacement

The crush bands that form during plastic deformation of closed-cell metal foams are often inclined at 11-20 degrees to the loading axis, allowing for shear displacement of one part of the foam with respect to the other. Such displacement is prevented by the presence of a lateral constraint. This was analysed in this study, which shows that resistance against shear by the constraint leads to the strain-hardening effect in the foam that has been reported in a recent experimental study. (C) 2009 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Identification of a class of non-linear systems

This paper considers the on-line identification of a non-linear system in terms of a Hammerstein model, with a zero-memory non-linear gain followed by a linear system. The linear part is represented by a Laguerre expansion of its impulse response and the non-linear part by a polynomial. The identification procedure involves determination of the coefficients of the Laguerre expansion of correlation functions and an iterative adjustment of the parameters of the non-linear gain by gradient methods. The method is applicable to situations involving a wide class of input signals. Even in the presence of additive correlated noise, satisfactory performance is achieved with the variance of the error converging to a value close to the variance of the noise. Digital computer simulation establishes the practicability of the scheme in different situations.

Presence of 2-methylthioribosyl-trans-zeatin in Azotobacter vinelandii tRNA.

Hydroxylated cytokinin, 2-methylthio-N6-(4-hydroxy-3-methylbut-2-enyl) adenosine, was found in the tRNA of Azotobacter vinelandii. This cytokinin had the trans configuration, unlike the cis configuration reported for that from other bacteria. Culture-condition-dependent changes in the content of this thiocytokinin and a few other thionucleosides in the tRNA of this bacterium have been observed.

Determination of the thermodynamic stability of TiB2

The standard free energy of formation of titanium boride (TiB2) Was measured by the Electro Motive Force (EMF) method (by using yttria doped thoria (YDT) as the solid electrolyte). Two galvanic cells viz. Cell (I): Pt, TiB2 (s), TiO2 (s), B (s) vertical bar YDT vertical bar NiO (s), Ni (s), Pt and cell (II): Pt, TiB2 (s), TiO2 (s), B (s) vertical bar YDT vertical bar FeO (s). Fe (s), Pt were constructed in order to determine the Delta(f)G degrees, of TiB2. Enthalpy increments on TiB2 were measured by using inverse drop calorimetry over the temperature range 583-1769 K. The heat capacity, entropy and the free energy function have been derived from these experimental data in the temperature range 298-1800 K. The mean value of the standard enthalpy of formation of TiB2 (Delta H-f(298)degrees (TiB2)) was obtained by combining these Delta(f)G degrees, values and the free energy functions of TiB2 derived from the drop calorimetry data. The mean values of Delta H-f(298)degrees (TiB2) derived from the Delta(f)G degrees, data obtained from cell I and II were -322 +/- 1.2 kJ mol(-1) and -323.3 +/- 2.1 kJ mol(-1), respectively. These values were found to be in very good agreement with the assessed data. (C) 2009 Elsevier B.V. All rights reserved.

Parallelization of an unstructured data based cell centre finite volume code, HIFUN-3D

This work describes the parallelization of High Resolution flow solver on unstructured meshes, HIFUN-3D, an unstructured data based finite volume solver for 3-D Euler equations. For mesh partitioning, we use METIS, a software based on multilevel graph partitioning. The unstructured graph used for partitioning is associated with weights both on its vertices and edges. The data residing on every processor is split into four layers. Such a novel procedure of handling data helps in maintaining the effectiveness of the serial code. The communication of data across the processors is achieved by explicit message passing using the standard blocking mode feature of Message Passing Interface (MPI). The parallel code is tested on PACE++128 available in CFD Center

Photocytotoxicity and near-IR light DNA cleavage activity of oxovanadium(IV) Schiff base complexes having phenanthroline bases

Oxovanadium(IV) complexes VO(L)(B)] (1-3), where H2L is a Schiff base ligand 2-(2-hydroxybenzylideneamino) phenol and B is 1,10-phenanthroline (phen for 1), dipyrido3,2-d:2',3'-f]quinoxaline (dpq for 2) or dipyrido3,2-a:2',3'-c]phenazine (dppz for 3), have been prepared, characterized and their DNA binding property and photo-induced DNA cleavage activity studied. Complex 3 which is structurally characterized by X-ray crystallography shows the presence of an oxovanadium(IV) moiety in a six coordinate VO3N3 coordination geometry. The complexes show a d-d band within 800-850 nm in DMF. The complexes display an oxidative response near 0.7 V versus SCE for V(V)-V(IV) and a reductive response within -1.1 to -1.3 V due to V(IV)-V(III) couple in DMF-0.1 M TBAP. The complexes are avid binders to calf thymus DNA giving binding constant values of 4.2 x 10(4) to 1.2 x 10(5) M (1). The complexes do not show any ``chemical nuclease'' activity in dark. The dpq and dppz complexes are photocleavers of plasmid DNA in UV-A light of 365 nm via O-1(2) pathway and in near-IR light (752.5 to 799.3 nm IR optics) by HO* pathway. Complex 3 exhibits significant photocytotoxicity in visible light in HeLa cells giving IC50 value of 13 mu M, while it is less toxic in dark (IC50 = 97 mu M). (C) 2010 Elsevier B.V. All rights reserved.

Representation of thermodynamic properties of ternary systems and its application to the system silver-gold-copper at 1350 K

The article presents a generalized analytical expression for description of the integral excess Gibbs free energy of mixing of a ternary system. Twelve constants of the equation are assessed by the least mean squares regressional analysis of the experimental integral excess data of the constituent binaries; three ternary parameters are evaluated by a regressional analysis based on the partial experimental data of a component of the ternary system. The assessed values of the ternary parameters describe the nature of the ternary interaction in the system. Activities and isoactivities of the components in the Ag-Au-Cu system at 1350 K are calculated and found to be in good agreement with the experimental data. This analytical treatment is particularly useful to ternary systems where the thermodynamic data are available from different sources.

Roughness generated in surface grinding of metals

When a metal is surface ground the roughness generated is the summation of a function of the wheel roughness and the roughness due to wheel attrition and damage to the workpiece. We identify this function here as a maximum em,elope profile, which is fractal within certain cut off wavelengths determined by the dressing conditions of the wheel. Estimating the global displacement of the binder-grit-workpiece system from the maximum envelope power spectra, we determine the plastic indentation of the workpiece at characteristic length scales using simple contact-mechanical calculation. The estimated roughness corresponds well with that recorded experimentally for hard steel, copper; titanium and aluminium.

Ecological Assessment of Lentic Water Bodies of Bangalore

The restoration, conservation and management of water resources require a thorough understanding of what constitutes a healthy ecosystem. Monitoring and assessment provides the basic information on the condition of our waterbodies. The present work details the study carried out at two waterbodies, namely, the Chamarajasagar reservoir and the Madiwala Lake. The waterbodies were selected on the basis of their current use and locations. Chamarajasagar reservoir serves the purpose of supplying drinking water to Bangalore city and is located on the outskirts of the city surrounded by agricultural and forest land. On the other hand, Madiwala lake is situated in the heart of Bangalore city receiving an influx of pollutants from domestic and industrial sewage. Comparative assessment of the surface water quality of both were carried out by instituting the various physico–chemical and biological parameters. The physico-chemical analyses included temperature, transparency, pH, electrical conductivity, dissolved oxygen, alkalinity, total hardness, calcium hardness, magnesium hardness, nitrates, phosphates, sodium, potassium and COD measurements of the given waterbody. The analysis was done based on the standard methods prescribed (or recommended) by (APHA) and NEERI. The biological parameter included phytoplankton analysis. The detailed investigations of the parameters, which are well within the tolerance limits in Chamarajasagar reservoir, indicate that it is fairly unpolluted, except for the pH values, which indicate greater alkalinity. This may be attributed to the natural causes and the agricultural runoff from the catchment. On the contrary, the limnology of Madiwala lake is greatly influenced by the inflow of sewage that contributes significantly to the dissolved solids of the lake water, total hardness, alkalinity and a low DO level. Although, the two study areas differ in age, physiography, chemistry and type of inflows, they still maintain a phytoplankton distribution overwhelmingly dominated by Cyanophyceae members,specifically Microcystis aeruginosa. These blue green algae apparently enter the waterbodies from soil, which are known to harbour a rich diversity of blue green flora with several species common to limnoplankton, a feature reported to be unique to the south Indian lakes.Chamarajasagar water samples revealed five classes of phytoplankton, of which Cyanophyceae (92.15 percent) that dominated other algal forms comprised of one single species of Microcystis aeruginosa. The next major class of algae was Chlorophyceae (3.752 percent) followed by Dinophyceae (3.51 percent), Bacillariophyceae (0.47 percent) and a sparsely available and unidentified class (0.12 percent).Madiwala Lake phytoplankton, in addition to Cyanophyceae (26.20 percent), revealed a high density of Chlorophyceae members (73.44 percent) dominated by Scenedesmus sp.,Pediastrum sp., and Euglena sp.,which are considered to be indicators of organic pollution. The domestic and industrial sewage, which finds its way into the lake, is a factor causing organic pollution. As compared to the other classes, Euglenophyceae and Bacillariophyceae members were the lowest in number. Thus, the analysis of various parameters indicates that Chamarajasagar reservoir is relatively unpolluted except for the high percentage of Microcystis aeruginosa, and a slightly alkaline nature of water. Madiwala lake samples revealed eutrophication and high levels of pollution, which is clarified by the physico–chemical analysis, whose values are way above the tolerance limits. Also, the phytoplankton analysis in Madiwala lake reveals the dominance of Chlorophyceae members, which indicate organic pollution (sewage being the causative factor).

Hydrothermal synthesis and characterization of bis(4,4 `-bipyridinium) dodecatungstosilicate dihydrate

Hydrothermal synthesis and structural characterization of a new organic polyoxometalate, namely, bis(4,4'-bipyridinium) dodecatungstosilicate dihydrate, 4,4'-bipyH(2)](2)SiW12O40]center dot 2H(2)O (1) is reported. The crystal structure of (1) consists of a SiW12O40](4-) Keggin anion situated on a two-fold axis, two unique 4,4'-bipyridinium cations, one of which is situated on a two-fold axis, and two independent lattice water molecules. The cations and anions are linked by H-bonding.

Fabrication and characterization of sub 100 nm period polymer gratings for photonics applications

We report on the fabrication of polymethylmethacrylate (PMMA) nanogratings on silicon (Si) and glass substrates using electron beam lithography technique. Various aspects of proximity corrections using Monte Carlo simulation have been discussed. The fabrication process parameters such as proximity gap of exposure, exposure dosage and developing conditions have been optimized for high-density PMMA nanogratings structure on Si and glass substrates. Electron beam exposure is adjusted in such a way that PMMA acts as a negative tone resist and at the same time resolution loss due to proximity effect is minimum. Both reflection and transmission-type, nanometre period gratings have been fabricated and their diffraction characteristics are evaluated.