Characterization of the DNA-binding domain of beta protein, a component of phage lambda Red-pathway by UV catalyzed cross-linking

beta protein, a key component of Red-pathway of phage lambda is necessary for its growth and general genetic recombination in recombination-deficient mutants of Escherichia coli. To facilitate studies on structure-function relationships, we overexpressed beta protein and purified it to homogeneity. A chemical cross-linking reagent, glutaraldehyde, was used to stabilize the physical association of beta protein in solution. A 67-kDa band, corresponding to homodimer, was identified after separation by SDS-polyacrylamide gel electrophoresis. Stoichiometric measurements indicated a site-size of 1 monomer of beta protein/5 nucleotide residues. Electrophoretic gel mobility shift assays suggested that beta protein formed stable nucleoprotein complexes with 36-mer, but not with 27- or 17-mer DNA. Interestingly, the interaction of beta protein with DNA and the stability of nucleoprotein complexes was dependent on the presence of MgCl2, and the binding was abolished by 250 mM NaCl. The K-d of beta protein binding to 36-mer DNA was on the order of 1.8 x 10(-6) M. Photochemical cross-linking of native beta protein or its fragments, generated by chymotrypsin, to 36-mer DNA was performed to identify its DNA-binding domain. Characterization of the cross-linked peptide disclosed that amino acids required for DNA-binding specificity resided within a 20-kDa peptide at the N-terminal end. These findings provide a basis for further understanding oi the structure and function of beta protein.

Preparation of a soluble 58kDa-3-hydroxy-3-methylglutaryl CoA reductase from liver microsomes and its inhibition by ethoxysilatrane, a hypocholesterolemic compound

On repeated thawing at room temperature of frozen preparations of heavy microsomes from rat livers, HMGCoA reductase activity was solubilized due to limited proteolysis. This soluble enzyme was partially purified by fractionation with ammonium sulfate and filtration on Sephacryl S-200 column. The active enzyme was coeluted with a major 92 kDa-protein and was identified as a 58kDa-protein after separation by SDS-PAGE and immunoblotting. Ethoxysilatrane, a hypocholesterolemic compound, which decreased the liver-microsomal activity of HMGCoA reductase on intra-peritonial treatment of animals, showed little effect on the enzyme activity with isolated microsomes or the 50kDa-soluble enzyme when added in the assay. But it was able to inhibit the activity of the soluble 58kDa-enzyme in a concentration-dependent, reversible manner. Cholesterol and an oxycholesterol were without effect whereas chlorophenoxyisobutyrate and ubiquinone showed small inhibition under these conditions. The extra region that links the active site domain (50kDa protein) to the membrane, present in the 58kDa-protein appears to be involved in mediating the inhibition by silatrane.

Transmembrane domains participate in functions of integral membrane proteins

Integral membrane proteins have one or more transmembrane a-helical domains and carry out a variety of functions such as enzyme catalysis, transport across membranes, transducing signals as receptors of hormones and growth factors, and energy transfer in ATP synthesis. These transmembrane domains are not mere structural units anchoring the protein to the lipid bilayer but seem to-contribute in the overall activity. Recent findings in support of this are described using some typical examples-LDL receptor, growth factor receptor tyrosine kinase, HMG-CoA reductase, F-0-ATPase and adrenergic receptors. The trends in research indicate that these transmembrane domains participate in a variety of ways such as a linker, a transducer or an exchanger in the overall functions of these proteins in transfer of materials, energy and signals.

Cloning, expression, purification, crystallization and preliminary X-ray studies of the mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis

The mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis has been cloned, expressed, purified and crystallized and the crystals have been characterized using X-ray diffraction. The Matthews coefficient suggests the possibility of two lectin domains in the triclinic cell. The amino-acid sequence of the domain indicates structural similarity to well characterized beta-prism II fold lectins.

Influence of growth below and above T-c on the morphology and domain structure in flux-grown KTP crystals

KTP crystals have been grown below and above the ferroelectric transition temperature by flux method employing both spontaneous and top-seeded solution growth techniques. A slight morphological difference has been observed in these crystals when grown below and above the T-c. Ferroelectric domains are studied in these crystals by selective domain etching. It is seen that the ferroelectric domains in crystals grown spontaneously below T, show a complicated structure. A systematic investigation of the factors influencing domain structure has been carried out. Stress to some extent has been shown to affect the domain structure. Finally, a convenient way of converting the multidomain crystals into monodomain ones is described.

Synthesis and vesicle formation from novel pseudoglyceryl dimeric lipids. Evidence of formation of widely different membrane organizations with exceptional thermotropic properties

Eight new bis-cationic dimeric lipids 2a-h have been synthesized; TEM of their aqueous dispersions confirmed the vesicle formation and from the thermal, spectroscopic, DLS and XRD studies it has been revealed that they form three different kinds of membranous aggregate depending on the m-value.

Effect of convection on domain growth during demixing transitions in fluids

Current analytical work on the effect of convection on the late stages of spinodal decomposition in liquids is briefly described. The morphology formed during the spinodal decomposition process depends on the relative composition of the two species. Droplet spinodal decomposition occurs when the concentration of one of the species is small. Convective transport has a significant effect on the scaling laws in the late-stage coarsening of droplets in translational or shear flows. In addition, convective transport could result in an attractive interaction between non-Brownian droplets which could lead to coalescence. The effect of convective transport for the growth of random interfaces in a near-symmetric quench was analysed using an area distribution function, which gives the distribution of surface area of the interface in curvature space. It was found that the curvature of the interface decreases proportional to time t in the late stages of spinodal decomposition, and the surface area also decreases proportional to t.

Stability of fluid flow past a membrane

The stability of fluid flow past a membrane of infinitesimal thickness is analysed in the limit of zero Reynolds number using linear and weakly nonlinear analyses. The system consists of two Newtonian fluids of thickness R* and H R*, separated by an infinitesimally thick membrane, which is flat in the unperturbed state. The dynamics of the membrane is described by its normal displacement from the flat state, as well as a surface displacement field which provides the displacement of material points from their steady-state positions due to the tangential stress exerted by the fluid flow. The surface stress in the membrane (force per unit length) contains an elastic component proportional to the strain along the surface of the membrane, and a viscous component proportional to the strain rate. The linear analysis reveals that the fluctuations become unstable in the long-wave (alpha --> 0) limit when the non-dimensional strain rate in the fluid exceeds a critical value Lambda(t), and this critical value increases proportional to alpha(2) in this limit. Here, alpha is the dimensionless wavenumber of the perturbations scaled by the inverse of the fluid thickness R*(-1), and the dimensionless strain rate is given by Lambda(t) = ((gamma) over dot* R*eta*/Gamma*), where eta* is the fluid viscosity, Gamma* is the tension of the membrane and (gamma) over dot* is the strain rate in the fluid. The weakly nonlinear stability analysis shows that perturbations are supercritically stable in the alpha --> 0 limit.

The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations

Background: Phosphorylation by protein kinases is central to cellular signal transduction. Abnormal functioning of kinases has been implicated in developmental disorders and malignancies. Their activity is regulated by second messengers and by the binding of associated domains, which are also influential in translocating the catalytic component to their substrate sites, in mediating interaction with other proteins and carrying out their biological roles. Results: Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. A set of 448 sequences, which show significant similarity to protein kinases and contain the critical residues essential for kinase function, have been selected for an analysis of domain combinations after classifying the kinase domains into subfamilies. The unusual domain combinations in particular kinases suggest their involvement in ubiquitination pathways and alternative modes of regulation for mitogen-activated protein kinase kinases (MAPKKs) and cyclin-dependent kinase (CDK)-like kinases. Previously unexplored kinases have been implicated in osteoblast differentiation and embryonic development on the basis of homology with kinases of known functions from other organisms. Kinases potentially unique to vertebrates are involved in highly evolved processes such as apoptosis, protein translation and tyrosine kinase signaling. In addition to coevolution with the kinase domain, duplication and recruitment of non-catalytic domains is apparent in signaling domains such as the PH, DAG-PE, SH2 and SH3 domains. Conclusions: Expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations. Experimental verification of the predicted implications of these kinases could enhance our understanding of their biological roles.

Amino acid interaction preferences in helical membrane proteins

Membrane proteins are involved in a number of important biological functions. Yet, they are poorly understood from the structure and folding point of view. The external environment being drastically different from that of globular proteins, the intra-protein interactions in membrane proteins are also expected to be different. Hence, statistical potentials representing the features of inter-residue interactions based exclusively on the structures of membrane proteins are much needed. Currently, a reasonable number of structures are available, making it possible to undertake such an analysis on membrane proteins. In this study we have examined the inter-residue interaction propensities of amino acids in the membrane spanning regions of the alpha-helical membrane (HM) proteins. Recently we have shown that valuable information can be obtained on globular proteins by the evaluation of the pair-wise interactions of amino acids by classifying them into different structural environments, based on factors such as the secondary structure or the number of contacts that a residue can make. Here we have explored the possible ways of classifying the intra-protein environment of HM proteins and have developed scoring functions based on different classification schemes. On evaluation of different schemes, we find that the scheme which classifies amino acids to different intra-contact environment is the most promising one. Based on this classification scheme, we also redefine the hydrophobicity scale of amino acids in HM proteins.

A new parallel overlapped domain decomposition method for nonlinear dynamic finite element analysis

In this paper a new parallel algorithm for nonlinear transient dynamic analysis of large structures has been presented. An unconditionally stable Newmark-beta method (constant average acceleration technique) has been employed for time integration. The proposed parallel algorithm has been devised within the broad framework of domain decomposition techniques. However, unlike most of the existing parallel algorithms (devised for structural dynamic applications) which are basically derived using nonoverlapped domains, the proposed algorithm uses overlapped domains. The parallel overlapped domain decomposition algorithm proposed in this paper has been formulated by splitting the mass, damping and stiffness matrices arises out of finite element discretisation of a given structure. A predictor-corrector scheme has been formulated for iteratively improving the solution in each step. A computer program based on the proposed algorithm has been developed and implemented with message passing interface as software development environment. PARAM-10000 MIMD parallel computer has been used to evaluate the performances. Numerical experiments have been conducted to validate as well as to evaluate the performance of the proposed parallel algorithm. Comparisons have been made with the conventional nonoverlapped domain decomposition algorithms. Numerical studies indicate that the proposed algorithm is superior in performance to the conventional domain decomposition algorithms. (C) 2003 Elsevier Ltd. All rights reserved.

Transmission electron microscopy study of domain structures in ferroelectric SrBi2Nb2O9 ceramics

A transmission electron microscopy study has been carried out on the domain structures of SrBi2Nb2O9 (SBN) ferroelectric ceramics which belong to the Aurivillius family of bismuth layered perovskite oxides. SBN is a potential candidate for Ferroelectric Random access memory (FeRAM) applications. The 90° ferroelectric domains and antiphase boundaries (APBs) were identified with dark field imaging techniques using different superlattice reflections which arise as a consequence of octahedral rotations and cationic shifts. The 90° domain walls are irregular in shape without any faceting. The antiphase boundaries are less dense compared to that of SrBi2Ta2O9(SBT). The electron microscopy observations are correlated with the polarization fatigue nature of the ceramic where the domain structures possibly play a key role in the fatigue- free behavior of the Aurivillius family of ferroelectric oxides.

Electrical and optical characterization of conducting polymers by THz time-domain spectroscopy

The absorption and index of refraction of polypyrrole (PPy) and poly-3-methylthiophene (PMeT), from low frequencies up to 4 THz, have been measured by tera-Herz (THz) time-domain spectroscopy. The complex conductance was obtained over this range of frequency. Highly conducting metallic samples follow the Drude model, whereas less conducting ones fit the localization-modified Drude model. The carrier scattering time and mobility in conducting polymers can be directly determined from these measurements.