Important role of the amino acid attached to tRNA in formylation and in initiation of protein synthesis in Escherichia coli

In attempts to convert an elongator tRNA to an initiator tRNA, we previously generated a mutant elongator methionine tRNA carrying an anticodon sequence change from CAU to CUA along with the two features important for activity of Escherichia coli initiator tRNA in initiation. This mutant tRNA (Mi:2 tRNA) was active in initiation in vivo but only when aminoacylated with methionine by overproduction of methionyl-tRNA synthetase. Here we show that the Mi:2 tRNA is normally aminoacylated in vivo with lysine and that the tRNA aminoacylated with lysine is a very poor substrate for formylation compared with the same tRNA aminoacylated with methionine. By introducing further changes at base pairs 4:69 and 5:68 in the acceptor stem of the Mi:2 tRNA to those found in the E. coli initiator tRNA, we show that change of the U4:A69 base pair to G4:C69 and overproduction of lysyl-tRNA synthetase and methionyl-tRNA transformylase results in partial formylation of the mutant tRNA and activity of the formyllysyl-tRNAs in initiation of protein synthesis. Thus, the G4:C69 base pair contributes toward formylation of the tRNA and protein synthesis in E. coli can be initiated with formyllysine. We also discuss the implications of these and other results on recognition of tRNAs by E. coli lysyl-tRNA synthetase and on competition in cells among aminoacyl-tRNA synthetases.

p-Hydroxyphenylacetate-3-hydroxylase. A two-protein component enzyme

p-Hydroxyphenylacetate-3-hydroxylase, an inducible enzyme isolated from the soil bacterium Pseudomonas putida, catalyzes the conversion of p-hydroxyphenylacetate to 3,4-dihydroxyphenylacetate. The enzyme requires two protein components: a flavoprotein and a colorless protein referred to as the coupling protein. The flavoprotein alone in the presence of p-hydroxyphenylacetate and substrate analogs catalyzes the wasteful oxidation of NADH with the stoichiometric generation of H2O2. A 1:1 complex of the flavoprotein and coupling protein is required for stoichiometric product formation. Such complex formation also eliminates the nonproductive NADH oxidase activity of the flavoprotein. A new assay measuring the product formation activity of the enzyme was developed using homoprotocatechuate-2,3-dioxygenase, as monitoring the oxidation of NADH was not sufficient to demonstrate enzyme activity. The coupling protein does not seem to have any redox center in it. Thus, this 2-component flavin hydroxylase resembles the other aromatic hydroxylases in that the only redox chromophore present is FAD.

Modeling of a reacting nanofilm on a composite substrate

This article provides a detailed computational analysis of the reaction of dense nanofilms and the heat transfer characteristics on a composite substrate. Although traditional energetic compounds based on organic materials have similar energy per unit weight, non-organic material in nanofilm configuration offers much higher energy density and higher flame speed. The reaction of a multilayer thin film of aluminum and copper oxide has been studied by varying the substrate material and thicknesses. The numerical analysis of the thermal transport of the reacting film deposited on the substrate combined a hybrid approach in which a traditional two-dimensional black box theory was used in conjunction with the sandwich model to estimate the appropriate heat flux on the substrate accounting for the heat loss to the surroundings. A procedure to estimate this heat flux using stoichiometric calculations is provided. This work highlights two important findings. One is that there is very little difference in the temperature profiles between a single substrate of silica and a composite substrate of silicon silica. Secondly, with increase in substrate thickness, the quenching effect is progressively diminished at a given speed. These findings show that the composite substrate is effective and that the average speed and quenching of flames depend on the thickness of the silica substrate, and can be controlled by a careful choice of the substrate configuration. (C) 2011 Elsevier Ltd. All rights reserved.

Application of selective F-1 decoupled H-1 NMR for enantiomer resolution and accurate measurement of enantiomeric excess at low chiral substrate/auxiliary concentration

The higher substrate and chiral auxiliary concentration is a pre-requisite to obtain efficient separation of H-1 NMR signals of enantiomers. The higher concentration of chiral lanthanide shift reagents provides broadened spectral lines resulting in a severe loss of resolution between the enantiomer resonances. In order to circumvent such difficulties, herein we present the application and the usefulness of a selective F-1 decoupled correlation (COSY) experiment which yields proton decoupled proton spectra in the indirect dimension. The potentiality of the experiment is demonstrated on several chiral compounds possessing different functional groups, employing either a lanthanide shift reagent or a solvating reagent as chiral auxiliaries. (C) 2011 Elsevier B.V. All rights reserved.

Some aspects of information processing in biological vision

An attempt is made to present some challenging problems (mainly to the technically minded researchers) in the development of computational models for certain (visual) processes which are executed with, apparently, deceptive ease by the human visual system. However, in the interest of simplicity (and with a nonmathematical audience in mind), the presentation is almost completely devoid of mathematical formalism. Some of the findings in biological vision are presented in order to provoke some approaches to their computational models, The development of ideas is not complete, and the vast literature on biological and computational vision cannot be reviewed here. A related but rather specific aspect of computational vision (namely, detection of edges) has been discussed by Zucker, who brings out some of the difficulties experienced in the classical approaches.Space limitations here preclude any detailed analysis of even the elementary aspects of information processing in biological vision, However, the main purpose of the present paper is to highlight some of the fascinating problems in the frontier area of modelling mathematically the human vision system.

Thiol/disulphide exchange reaction: A key regulatory process in biological systems

Cysteine residues in proteins serve many important functions such as stabilizing and maintaining the three-dimensional conformation of many proteins(1), in enzyme catalysis, as a residue undergoing post-translational 2 and in the formation of DNA-binding modification domain of a class of transcriptional activators(3), It is also involved in biological redox coupling(4) and xenobiotic metabolism(5). Disulphide bonds formed by xenobiotic metabolism oxidation of cysteine residues have been used as a probe to study the structure/function relationships of proteins, Introducing novel disulphide bonds in proteins to increase their thermal stability and, therefore, the shelf life is an important goal of protein engineering(6,7), In addition, the thiol group of cysteine residue participates in a reaction termed as thiol/disulphide exchange reaction, the biological significance of this reaction being the theme of this review.

High-Q, Ag-doped 123 resonator on unbuffered sapphire substrate

The microwave performance of an Ag-doped YBa2Cu3O7-x, thin-film X-band microstrip resonator on unbuffered sapphire substrate is reported. Q-values of 2400 and 1200 have been obtained al 15R and 77K, respectively, which correspond to R(s) values of 330 mu Omega and 680 mu Omega.

Effect of substrate on particle arrangement in arrays formed by self-assembly of polymer grafted nanoparticles

We show that the substrate affects the interparticle spacing in monolayer arrays with hexagonal order formed by self-assembly of polymer grafted nanoparticles. Remarkably, arrays with square packing were formed due to convective shearing at a liquid surface induced by miscibility of colloidal solution with the substrate.

Modeling of angiogenin-3 '-NMP complex

Angiogenin belongs to the Ribonuclease superfamily and has a weak enzymatic activity that is crucial for its biological function of stimulating blood vessel growth. Structural studies on ligand bound Angiogenin will go a long way in understanding the mechanism of the protein as well as help in designing drugs against it. In this study we present the first available structure of nucleotide ligand bound Angiogenin obtained by computer modeling. The importance of this study in itself notwithstanding, is a precursor to modeling a full dinucleotide substrate onto Angiogenin. Bovine Angiogenin, the structure of which has been solved at a high resolution, was earlier subjected to Molecular Dynamics simulations for a nanosecond. The MD structures offer better starting points for docking as they offer lesser obstruction than the crystal structure to ligand binding. The MD structure with the least serious short contacts was modeled to obtain a steric free Angiogenin - 3' mononucleotide complex structure. The structures were energetically minimized and subjected to a brief spell of Molecular Dynamics. The results of the simulation show that all the li,ligand-Angiogenin interactions and hydrogen bonds are retained, redeeming the structure and docking procedure. Further, following ligand - protein interactions in the case of the ligands 3'-CMP and 3'-UMP we were able to speculate on how Angiogenin, a predominantly prymidine specific ribonuclease prefers Cytosine to Uracil in the first base position.

Structural and optical properties of nonpolar (11-20) a-plane GaN grown on (1-102) r-plane sapphire substrate by plasma-assisted molecular beam epitaxy

We report the structural and optical properties of a-plane GaN film grown on r-plane sapphire substrate by plasma-assisted molecular beam epitaxy. High resolution X-ray diffraction was used to determine the out-of-plane and in-plane epitaxial relation of a-plane GaN to r-plane sapphire. Low-temperature photoluminescence emission was found to be dominated by basal stacking faults along with near-band emission. Raman spectroscopy shows that the a-GaN film is of reasonably good quality and compressively strained. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Primary Sequence That Determines the Functional Overlap between Mitochondrial Heat Shock Protein 70 Ssc1 and Ssc3 of Saccharomyces cerevisiae

The evolutionary diversity of the HSP70 gene family at the genetic level has generated complex structural variations leading to altered functional specificity and mode of regulation in different cellular compartments. By utilizing Saccharomyces cerevisiae as a model system for better understanding the global functional cooperativity between Hsp70 paralogs, we have dissected the differences in functional properties at the biochemical level between mitochondrial heat shock protein 70 (mtHsp70) Ssc1 and an uncharacterized Ssc3 paralog. Based on the evolutionary origin of Ssc3 and a high degree of sequence homology with Ssc1, it has been proposed that both have a close functional overlap in the mitochondrial matrix. Surprisingly, our results demonstrate that there is no functional cross-talk between Ssc1 and Ssc3 paralogs. The lack of in vivo functional overlap is due to altered conformation and significant lower stability associated with Ssc3. The substrate-binding domain of Ssc3 showed poor affinity toward mitochondrial client proteins and Tim44 due to the open conformation in ADP-bound state. In addition to that, the nucleotide-binding domain of Ssc3 showed an altered regulation by the Mge1 co-chaperone due to a high degree of conformational plasticity, which strongly promotes aggregation. Besides, Ssc3 possesses a dysfunctional inter-domain interface thus rendering it unable to perform functions similar to generic Hsp70s. Moreover, we have identified the critical amino acid sequence of Ssc1 and Ssc3 that can ``make or break'' mtHsp70 chaperone function. Together, our analysis provides the first evidence to show that the nucleotide-binding domain of mtHsp70s plays a critical role in determining the functional specificity among paralogs and orthologs across kingdoms.

Ultrasonic wave characteristics of a monolayer graphene on silicon substrate

The present work deals with an ultrasonic type of wave propagation characteristics of monolayer graphene on silicon (Si) substrate. An atomistic model of a hybrid lattice involving a hexagonal lattice of graphene and surface atoms of diamond lattice of Si is developed to identify the carbon-silicon bond stiffness. Properties of this hybrid lattice model is then mapped into a nonlocal continuum framework. Equivalent force constant due to Si substrate is obtained by minimizing the total potential energy of the system. For this equilibrium configuration, the nonlocal governing equations are derived to analyze the ultrasonic wave dispersion based on spectral analysis. From the present analysis we show that the silicon substrate affects only the flexural wave mode. The frequency band gap of flexural mode is also significantly affected by this substrate. The results also show that, the silicon substrate adds cushioning effect to the graphene and it makes the graphene more stable. The analysis also show that the frequency bang gap relations of in-plane (longitudinal and lateral) and out-of-plane (flexural) wave modes depends not only on the y-direction wavenumber but also on nonlocal scaling parameter. In the nonlocal analysis, at higher values of the y-directional wavenumber, a decrease in the frequency band gap is observed for all the three fundamental wave modes in the graphene-silicon system. The atoms movement in the graphene due to the wave propagation are also captured for all the tree fundamental wave modes. The results presented in this work are qualitatively different from those obtained based on the local analysis and thus, are important for the development of graphene based nanodevices such as strain sensor, mass and pressure sensors, atomic dust detectors and enhancer of surface image resolution that make use of the ultrasonic wave dispersion properties of graphene. (C) 2011 Elsevier Ltd. All rights reserved.

A Procedure for the 3D Reconstruction of Biological Organs from 2D Image Sequences

In this work, a procedure is presented for the reconstruction of biological organs from image sequences obtained through CT-scan. Although commercial software, which can accomplish this task, are readily available, the procedure presented here needs only free software. The procedure has been applied to reconstruct a liver from the scan data available in literature. 3D biological organs obtained this way can be used for the finite element analysis of biological organs and this has been demonstrated by carrying out an FE analysis on the reconstructed liver.