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.

Twist phase in Gaussian-beam optics

The recently discovered twist phase is studied in the context of the full ten-parameter family of partially coherent general anisotropic Gaussian Schell-model beams. It is shown that the nonnegativity requirement on the cross-spectral density of the beam demands that the strength of the twist phase be bounded from above by the inverse of the transverse coherence area of the beam. The twist phase as a two-point function is shown to have the structure of the generalized Huygens kernel or Green's function of a first-order system. The ray-transfer matrix of this system is exhibited. Wolf-type coherent-mode decomposition of the twist phase is carried out. Imposition of the twist phase on an otherwise untwisted beam is shown to result in a linear transformation in the ray phase space of the Wigner distribution. Though this transformation preserves the four-dimensional phase-space volume, it is not symplectic and hence it can, when impressed on a Wigner distribution, push it out of the convex set of all bona fide Wigner distributions unless the original Wigner distribution was sufficiently deep into the interior of the set.

Determination of diffusion parameters and activation energy of diffusion in V3Si phase with A15 crystal structure

Diffusion such is the integrated diffusion coefficient of the phase, the tracer diffusion coefficient of species at different temperatures and the activation energy for diffusion, are determined in V3Si phase with A15 crystal structure. The tracer diffusion coefficient of Si Was found to be negligible compared to the tracer diffusion coefficient of V. The calculated diffusion parameters will help to validate the theoretical analysis of defect structure of the phase, which plays an important role in the superconductivity.

Phase transitions and rare-earth magnetism in hexagonal and orthorhombic $DyMnO_{3}$ single crystals

The floating-zone method with different growth ambiences has been used to selectively obtain hexagonal or orthorhombic DyMnO3 single crystals. The crystals were characterized by x-ray powder diffraction of ground specimens and a structure refinement as well as electron diffraction. We report magnetic susceptibility, magnetization and specific heat studies of this multiferroic compound in both the hexagonal and the orthorhombic structure. The hexagonal DyMnO3 shows magnetic ordering of Mn3+ (S = 2) spins on a triangular Mn lattice at T-N(Mn) = 57 K characterized by a cusp in the specific heat. This transition is not apparent in the magnetic susceptibility due to the frustration on the Mn triangular lattice and the dominating paramagnetic susceptibility of the Dy3+ (S = 9/2) spins. At T-N(Dy) = 3 K, a partial antiferromagnetic order of Dy moments has been observed. In comparison, the magnetic data for orthorhombic DyMnO3 display three transitions. The data broadly agree with results from earlier neutron diffraction experiments, which allows for the following assignment: a transition from an incommensurate antiferromagnetic ordering of Mn3+ spins at T-N(Mn) = 39 K, a lock-in transition at Tlock-in = 16 K and a second antiferromagnetic transition at T-N(Dy) = 5 K due to the ordering of Dy moments. Both the hexagonal and the orthorhombic crystals show magnetic anisotropy and complex magnetic properties due to 4f-4f and 4f-3d couplings.

High-Temperature Phase Transition Studies in a Novel Fast Ion Conductor, Na2Cd(SO4)2, Probed by Raman Spectroscopy

Temperature-dependent Raman spectroscopic studies were carried out on Na2Cd(SO4)(2) from room temperature to 600 degrees C. We observe two transitions at around 280 and 565 degrees C. These transitions are driven by the change in the SO4 ion. On the basis of these studies, one can explain the changes in the conductivity data observed around 280 and 565 degrees C. At 280 degrees C, spontaneous tilting of the SO4 ion leads to restriction of Na+ mobility. Above 565 degrees C, the SO4 ion starts to rotate freely, leading to increased mobility of Na+ ion in the channel.

Phase Equilibria in the System $Al_{2}O_{3}-CaO-CoO$ and Gibbs Energy of Formation of $Ca_{3}CoAl_{4}O_{10}$

The floating-zone method with different growth ambiences has been used to selectively obtain hexagonal or orthorhombic DyMnO3 single crystals. The crystals were characterized by x-ray powder diffraction of ground specimens and a structure refinement as well as electron diffraction. We report magnetic susceptibility, magnetization and specific heat studies of this multiferroic compound in both the hexagonal and the orthorhombic structure. The hexagonal DyMnO3 shows magnetic ordering of Mn3+ (S = 2) spins on a triangular Mn lattice at T-N(Mn) = 57 K characterized by a cusp in the specific heat. This transition is not apparent in the magnetic susceptibility due to the frustration on the Mn triangular lattice and the dominating paramagnetic susceptibility of the Dy3+ (S = 9/2) spins. At T-N(Dy) = 3 K, a partial antiferromagnetic order of Dy moments has been observed. In comparison, the magnetic data for orthorhombic DyMnO3 display three transitions. The data broadly agree with results from earlier neutron diffraction experiments, which allows for the following assignment: a transition from an incommensurate antiferromagnetic ordering of Mn3+ spins at T-N(Mn) = 39 K, a lock-in transition at Tlock-in = 16 K and a second antiferromagnetic transition at T-N(Dy) = 5 K due to the ordering of Dy moments. Both the hexagonal and the orthorhombic crystals show magnetic anisotropy and complex magnetic properties due to 4f-4f and 4f-3d couplings.

Phase conversions in calcium manganites with changing Ca/Mn ratios and their influence on the electrical transport properties

The phase-interconversions between the spinel-, brownmillerite-, defect rocksalt and perovskite-type structures have been investigated by way of (i) introducing deficiency in A-sites in CaxMn2-xO3 (0.05 <= x <= 1) i.e., by varying Ca/Mn ratio from 0.025 to 1 and (ii) nonstoichiometric CaMnO3-delta (CMO) with 0.02 <= delta <= 1. The temperature dependence of resistivity (rho-T) have been investigated on nonstoichiometric CaMnO3-delta (undoped) as well as the CMO substituted with donor impurities such as La3+, Y3+, Bi3+ or acceptor such as Na1+ ion at the Ca-site. The rho-T characteristics of nonstoichiometric CaMnO3-delta is strongly influenced by oxygen deficiency, which controls the concentration of Mn3+ ions and, in turn, affects the resistivity, rho. The results indicated that the substitution of aliovalent impurities at Ca-site in CaMnO3 has similar effects as of CaMnO3-delta ( undoped) annealed in atmospheres of varying partial pressures whereby electron or hole concentration can be altered, yet the doped samples can be processed in air or atmospheres of higher P-O2. The charge transport mechanisms of nonstoichiometric CaMnO3-delta as against the donor or acceptor doped CaMnO3 (sintered in air, P-O2 similar to 0.2 atm) have been predicted. The rho (T) curves of both donor doped CaMnO3 as well as non-stoichiometric CaMnO3-delta, is predictable by the small polaron hopping (SPH) model, which changes to the variable range hopping (VRH) at low temperatures whereas the acceptor doped CaMnO3 exhibited an activated semiconducting hopping ( ASH) throughout the measured range of temperature (10-500 K).

Single 2×1 domain orientation on Si(001) surfaces using aperiodic Bi line arrays

Studies of Bi heteroepitaxy on Si(001) have shown that lines grow to lengths of up to 500nm if the substrate is heated to above the Bi desorption temperature (500°C) during or after Bi deposition. Unlike many other nanoline systems, the lines formed by this nonequilibrium growth process have no detectable width dispersion. Although much attention has been given to the atomic geometery of the line, in this paper, we focus on how the lines can be used to create a majority 2×1 domain orientation. It is demonstrated that the Bi lines can be used to produce a single-domain orientation on Si(001) if the lines are grown on Si(001) surfaces with a regular distribution of single height steps. This is a compelling example of how a nanoscale motif can be used to modify mesoscopic surface structure on Si(001).

IFN-gamma inhibits growth of WISH cells in a cell cycle phase-specific manner

Treatment of WISH (human amnion) cells with interferon-gamma (IFN-gamma) inhibits their growth. Release of the cells from IFN-gamma-mediated growth inhibition led to a rapid and significant increase in DNA synthesis, followed by doubling of cell numbers. The DNA synthesis profile was strikingly similar to that shown by WISH cells released from growth arrest by the G(1)/S phase inhibitor, aphidicolin, This strongly suggested that IFN-gamma treatment leads to growth inhibition of WISH cells at the G(1)/S boundary of the cell cycle. In contrast, IFN-alpha blocked growth of these cells at the G(0)/G(1) boundary.

Mechanical processing and microstructural control in hot working of hot isostatically pressed P/M IN-100 superalloy

The hot deformation behavior of hot isostatically pressed (HIPd) P/M IN-100 superalloy has been studied in the temperature range 1000-1200 degrees C and strain rate range 0.0003-10 s(-1) using hot compression testing. A processing map has been developed on the basis of these data and using the principles of dynamic materials modelling. The map exhibited three domains: one at 1050 degrees C and 0.01 s(-1), with a peak efficiency of power dissipation of approximate to 32%, the second at 1150 degrees C and 10 s(-1), with a peak efficiency of approximate to 36% and the third at 1200 degrees C and 0.1 s(-1), with a similar efficiency. On the basis of optical and electron microscopic observations, the first domain was interpreted to represent dynamic recovery of the gamma phase, the second domain represents dynamic recrystallization (DRX) of gamma in the presence of softer gamma', while the third domain represents DRX of the gamma phase only. The gamma' phase is stable upto 1150 degrees C, gets deformed below this temperature and the chunky gamma' accumulates dislocations, which at larger strains cause cracking of this phase. At temperatures lower than 1080 degrees C and strain rates higher than 0.1 s(-1), the material exhibits flow instability, manifested in the form of adiabatic shear bands. The material may be subjected to mechanical processing without cracking or instabilities at 1200 degrees C and 0.1 s(-1), which are the conditions for DRX of the gamma phase.

Expression of the extracellular domain of the human heat-stable enterotoxin receptor in Escherichia coli and generation of neutralizing antibodies

The entire extracellular domain of the human heat-stable enterotoxin (ST) receptor as well as a truncated N-terminal domain were cloned as glutathione S-transferase fusion proteins and expressed in Escherichia coli. The recombinant fusion proteins were purified from both the cytosol and the inclusion body fractions by selective detergent extraction followed by glutathione-agarose affinity chromatography. The purified protein, corresponding to the entire extracellular domain, bound the stable toxin peptide with an affinity comparable to that of the native receptor characterized from the human colonic T84 cell line. No binding was observed with the N-terminal truncated fragment of the receptor under similar conditions, Polyclonal antibodies were raised to the entire extracellular domain fusion protein as well as the truncated extracellular domain fusion protein, and the antibodies were purified by affinity chromatography. Addition of the purified antibodies to T84 cells inhibited ST binding and abolished ST-mediated cGMP production, indicating that critical epitopes involved in ligand interaction are present in the N-terminal fragment of the receptor, Purified antibodies recognized a single protein of M(r) 160,000 Da on Western blotting with T84 membranes, corresponding to a size of the native glycosylated receptor in T84 cells. These studies are the first report of the expression, purification, and characterization of any member of the guanylyl cyclase family of receptors in E. coli and show that binding of the toxin to the extracellular domain of the receptor is possible in the absence of any posttranslational modifications such as glycosylation. The recombinant fusion proteins as well as the antibodies that we have generated could serve as useful tools in the identification of critical residues of the extracellular domain involved in ligand interaction.

Constraining the low-energy pion electromagnetic form factor with space-like and phase of time-like data

The Taylor coefficients c and d of the EM form factor of the pion are constrained using analyticity, knowledge of the phase of the form factor in the time-like region, 4m(pi)(2) <= t <= t(in) and its value at one space-like point, using as input the (g - 2) of the muon. This is achieved using the technique of Lagrange multipliers, which gives a transparent expression for the corresponding bounds. We present a detailed study of the sensitivity of the bounds to the choice of time-like phase and errors present in the space-like data, taken from recent experiments. We find that our results constrain c stringently. We compare our results with those in the literature and find agreement with the chiral perturbation-theory results for c. We obtain d similar to O(10) GeV-6 when c is set to the chiral perturbation-theory values.

Oxidation of aqueous sulfur dioxide catalyzed by poly-4-vinylpyridine-Cu(II) complex. Part 1: Homogeneous phase oxidation

The oxidation of aqueous sulfur dioxide in the presence of polymer-supported copper(II) catalyst is also accompanied by homogeneous oxidation of aqueous sulfur dioxide catalyzed by leached copper(II) ions. Aqueous phase oxidation of sulfur dioxide of low concentrations by oxygen in the presence of dissolved copper(II) has therefore been studied. The solubility of SO2 in aqueous solutions is not affected by the concentration of copper(II) in the solution. In the oxidation reaction, only HSO3- is the reactive S(IV) species. Based on this observation a rate model which also incorporates the effect of sulfuric acid on the solubility of SO2 is developed. The rate model includes a power-law type term for the rate of homogeneous phase reaction obtained from a proposed free-radical chain mechanism for the oxidation. Experiments are conducted at various levels of concentrations of SO2 and O-2 in the gas phase and Cu(II) in the liquid phase. The observed orders are one in each of O-2, Cu(II) and HSO3-. This suggests a first-order termination of the free radicals of bisulfite ions.

Multiphase models for simulating hot and slightly miscible DNAPL (dense non-aqueous phase fluids) in a saturated rock fracture under deformation

In the present study a two dimensional model is first developed to show the behaviour of dense non-aqueous phase liquids (DNAPL) within a rough fracture. To consider the rough fracture, the fracture is imposed with variable apertures along its plane. It is found that DNAPL follows preferential pathways. In next part of the study the above model is further extended for non-isothermal DNAPL flow and DNAPL-water interphase mass transfer phenomenon. These two models are then coupled with joint deformation due to normal stresses. The primary focus of these models is specifically to elucidate the influence of joint alteration due to external stress and fluid pressures on flow driven energy transport and interphase mass transfer. For this, it is assumed that the critical value for joint alteration is associated with external stress and average of water and DNAPL pressures in multiphase system and the temporal and spatial evolution of joint alteration are determined for its further influence on energy transport and miscible phase transfer. The developed model has been studied to show the influence of deformation on DNAPL flow. Further this preliminary study demonstrates the influence of joint deformation on heat transport and phase miscibility via multiphase flow velocities. It is seen that the temperature profile changes and shows higher diffusivity due to deformation and although the interphase miscibility value decreases but the lateral dispersion increases to a considerably higher extent.

Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations

Background: Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result: The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion: Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.