Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of quantum chemical calculations. The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the ``high energy'' character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results can aid the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes. (c) 2005 Elsevier B.V. All rights reserved.

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Influence of Geometrical Factors on the Physico-Chemical Properties of Perovskite and Layered Perovskite Oxides

A brief qualitative comparison is made of perovskite ABO sub 3 and layered perovskite ABO sub 3 and layered perovskite A sub 2 BO sub 4 oxides with special emphasis on the influence of geometrical factors on certain physico-chemical properties. The layered perovskite oxides are distinguished from three-dimensional oxides by a looser packing, frustration in three-dimensional interactions, more internal pressure on B--O bonds for small tolerance factors, and by different values of site-percolation thresholds. Their influence on electronic configurations of metal ions, stabilities and syntheses of compounds is discussed. The influence of increased anisotropy in layered oxides on localisation of charge carriers and in suppressing the onset of long-range ferromagnetic ordering is also discussed.

Studies of cryotreatment on the performance of integral diaphragm pressure transducers for space application

The integral diaphragm pressure transducers machined out of precipitation hardened martensite stainless steel (APX4) are widely used for propellant pressure measurements in space applications. These transducers are expected to exhibit dimensional stability and linearity for their entire useful life. These vital factors are very critical for the reliable performance and dependability of the pressure transducers. However, these transducers invariably develop internal stresses during various stages of machining. These stresses have an adverse effect on the performance of the transducers causing deviation from linearity. In order to eliminate these possibilities, it was planned to cryotreat the machined transducers to improve both the long-term linearity and dimensional stability. To study these effects, an experimental cryotreatment unit was designed and developed based on the concept of indirect cooling using the concept of cold nitrogen gas forced closed loop convection currents. The system has the capability of cryotreating large number of samples for varied rates of cooling, soaking and warm-up. After obtaining the initial levels of residual stress and retained austenite using X-ray diffraction techniques, the pressure transducers were cryotreated at 98 K for 36 h. Immediately after cryotreatment, the transducers were tempered at 510 degrees C for 3 h in vacuum furnace. Results after cryo treatment clearly indicated significant reduction in residual stress levels and conversion of retained austenite to martensite. These changes have brought in improvements in long term zero drift and dimensional stability. The cryotreated pressure transducers have been incorporated for actual space applications. (c) 2010 Published by Elsevier Ltd.

Stereochemically constrained peptides. Theoretical and experimental studies on the conformations of peptides containing 1-aminocyclohexane carboxylic acid

Conformational energy calculations on the model system N-acetyl- 1 -aminocyclohexanecarboxylic acid N'methylamide (Ac-Acc6-NHMe), using an average geometry derived from 13 crystallographic observations, establish that the Acc6 residue is constrained to adopt conformations in the helical regions of In contrast, the a,a-dialkylated residue with linear hydrocarbon side chains, a,a-di-n-propylglycine favors fully extended backbone structures (6 1= $ = 180'). The crystal structures of two model peptides, Boc-(Acc6),-OMe (type 111 @-turn at -Acc6(1)-Acc6(2)-) and Boc-Pro-Acc6-Ala-OMe (type I1 P-turn at -Pro-Acc6-), establish that Acc6 residues can occupy either position of type 111 P-turns and the i + 2 position of type I1 @-turns. The stereochemical rigidity of these peptides is demonstrated in solution by NMR studies, which establish the presence of one intramolecular hydrogen bond in each peptide in CDCI, and (CDJ2S0. Nuclear Overhauser effects permit characterization of the @-turn conformations in solution and establish their similarity to the solid-state structures. The implications for the use of Acc6 residues in conformational design are considered.

Computer modelling studies on the mechanism of action of ribonuclease T1

The mechanism of action of ribonuclease (RNase) T1 is still a matter of considerable debate as the results of x-ray, 2-D nmr and site-directed mutagenesis studies disagree regarding the role of the catalytically important residues. Hence computer modelling studies were carried out by energy minimisation of the complexes of RNase T1 and some of its mutants (His40Ala, His40Lys, and Glu58Ala) with the substrate guanyl cytosine (GpC), and of native RNase T1 with the reaction intermediate guanosine 2',3'-cyclic phosphate (G greater than p). The puckering of the guanosine ribose moiety in the minimum energy conformer of the RNase T1-GpC (substrate) complex was found to be O4'-endo and not C3'-endo as in the RNase T1-3'-guanylic acid (inhibitor/product) complex. A possible scheme for the mechanism of action of RNase T1 has been proposed on the basis of the arrangement of the catalytically important amino acid residues His40, Glu58, Arg77, and His92 around the guanosine ribose and the phosphate moiety in the RNase T1-GpC and RNase T1-G greater than p complexes. In this scheme, Glu58 serves as the general base group and His92 as the general acid group in the transphosphorylation step. His40 may be essential for stabilising the negatively charged phosphate moiety in the enzyme-transition state complex.

Effect of amino acid substitutions at the subunit interface on the stabiity and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the dimer interface of thymidylate synthase

The significance of two interface arginine residues on the structural integrity of an obligatory dimeric enzyme thymidylate synthase (TS) from Lactobacillus casei was investigated by thermal and chemical denaturation. While the R178F mutant showed apparent stability to thermal denaturation by its decreased tendency to aggregate, the Tm of the R218K mutant was lowered by 5 degrees C. Equilibrium denaturation studies in guanidinium chloride (GdmCl) and urea indicate that in both the mutants, replacement of Arg residues results in more labile quaternary and tertiary interactions. Circular dichroism studies in aqueous buffer suggest that the protein interior in R218K may be less well-packed as compared to the wild type protein. The results emphasize that quaternary interactions may influence the stability of the tertiary fold of TS. The amino acid replacements also lead to notable alteration in the ability of the unfolding intermediate of TS to aggregate. The aggregated state of partially unfolded intermediate in the R178F mutant is stable over a narrower range of denaturant concentrations. In contrast, there is an exaggerated tendency on the part of R218K to aggregate in intermediate concentrations of the denaturant. The 3 A crystal structure of the R178F mutant reveals no major structural change as a consequence of amino acid substitution. The results may be rationalized in terms of mutational effects on both the folded and unfolded state of the protein. Site specific amino acid substitutions are useful in identifying specific regions of TS involved in association of non-native protein structures.

Effects of Zr and Ti doping on the dielectric response of CeO2: A comparative first-principles study

Zr doping in ceria (CeO2) results in enhanced static dielectric response compared to pure ceria. On the other hand, Ti doping in ceria keeps its dielectric constant unchanged. We use first-principles density functional theory calculations based on pseudopotentials and a plane wave basis to determine electronic properties and dielectric response of Zr/Ti-doped and oxygen-vacancy-introduced ceria. Softening of phonon modes is responsible for the enhancement in dielectric response of Zr-doped ceria compared to that of pure ceria. The ceria-zirconia mixed oxides should have potential use as high-k materials in the semiconductor industry. (c) 2010 Elsevier Ltd. All rights reserved.

Kinetic studies on the interaction of gold(III) with nucleic acids. I. Native DNA-Au(III) system-spectrophotometric studies

Kinetics of the interaction of Au(III) with native calf thymus DNA has been studied spectrophotometrically to determine the kinetic parameters and to examine their dependency on the concentrations of DNA and Au(III), temperature, ionic strength and pH. The reaction is of the first order with respect to both the nucleotide unit of DNA and Au(III) in the stoichiometry of 2∶1 respectively. The rate constants vary with the initial ratio of DNA to Au(III) and is attributed to the effect of free chloride ions and the existence of a number of reaction sites with slight difference in the rate constants. The activation energies of this interaction have been found to be 14–16 kcal/mol. From the effect of ionic strength the reaction is found to occur between a positive and a negative ion in the rate-limiting step. The logarithm of rate constants are the linear function of pH and the slopes are dependent on ther-values. A plausible mechanism has been proposed which involves a primary dissociation of the major existing species (AuCl2(OH)2)−, to give (AuCl2)+ which then reacts with a site in the nucleotide unit of DNA in the rate-liminting step followed by a rapid binding to another site on the complementary strand of the DNA double helix. There exist a number of binding sites with slight difference in reactivity.

Phenyl-Ring-Bearing Cationic Surfactants: Effect of Ring Location on the Micellar Structure

A series of isomeric cationic surfactants (S1-S5) bearing a long alkyl chain that carries a 1,4-phenylene unit and a trimethyl ammonium headgroup was synthesized; the location of the phenyl ring within the alkyl tail was varied in an effort to understand its influence on the amphiphilic properties of the surfactants. The cmc's of the surfactants were estimated using ionic conductivity measurements and isothermal calorimetric titrations (ITC); the values obtained by the two methods were found to be in excellent agreement. The ITC measurements provided additional insight into the various thermodynamic parameters associated with the micellization process. Although all five surfactants have exactly the same molecular formula, their micellar properties were seen to vary dramatically depending on the location of the phenyl ring; the cmc was seen to decrease by almost an order of magnitude when the phenyl ring was moved from the tail end (cmc of S1 is 23 mM) to the headgroup region (cmc of S5 is 3 mM). In all cases, the enthalpy of micellization was negative but the entropy of micellization was positive, suggesting that in all of these systems the formation of micelles is both enthalpically and entropically favored. As expected, the decrease in cmc values upon moving the phenyl ring from the tail end to he headgroup region is accompanied by an increase in the thermodynamic driving force (Delta G) for micellization. To understand further the differences in the micellar structure of these surfactants, small-angle neutron scattering (SANS) measurements were carried out; these measurements reveal that the aggregation number of the micelles increases as the cmc decreases. This increase in the aggregation number is also accompanied by an increase in the asphericity of the micellar aggregate and a decrease in the fractional charge. Geometric packing arguments are presented to account for these changes in aggregation behavior as a function of phenyl ring location.

Effect of HCl on the adsorption of oxygen on Cu(110) surface: An eels study

Oxygen is shown to adsorb molecularly on a clean Cu(110) surface at 80 K and dissociate around 150 K forming atomic oxygen. Adsorption of oxygen on an HCl covered surface at low temperatures results in the formation of adsorbed hydroxyl groups and water in addition to adsorbed molecular oxygen. The molecular oxygen species is stable up to 190 K on the HCl covered surface.

Effect of morphology and particle size on the ionic conductivities of composite solid electrolytes

A model incorporating the surface conductivity and morphology of the composite solid electrolytes is envisaged to explain their conduction behaviour. The conductivity data on LinX−50 m/o Al2O3 (X = F−, Cl−, Br−, CO32−, SO42−, PO43−) composites prepared by thermal decomposition of LinX·2nAl(OH)3·mH2O salts and Li2SO4−A (A=Al2O3, CeO2, Y2O3, Yb2O3, Zr2O3, ZrO2 and BaTiO3) composites prepared by mechanical mixing of the components are examined in the light of this model. It is surmised that the particle size of both the dispersoids and the hosts not only influence the ionic conductivity of the host matrix but also affect its bulk properties.

CD and NMR studies on the aggregation of amphotericin-B in solution

We report in this paper the aggregation properties of amphotericin-B (amp-B) in solution using CD and 1H-NMR techniques. Our results indicate that the preferred structure of amp-B in dimethylsulfoxide is a monomer at low concentrations (10−4M and below) and a stable dimer at higher concentrations (range 5 · 103 M to 10−2M). In a DMSO/ethanol mixture (1:1 (v/v)), the antibiotic is monomeric, irrespective of the concentration within the range studied. We propose a head-to-tail model based on NMR data. An understanding of the head-to-tail dimer, is, we believe important, particularly in view of the recent report wherein it is proposed that the drug inserts into bilayers as head-to-tail oligomers.

Comparison of the effect of processing parameters and degradation on the DC and microwave properties of thin films and polycrystalline bulk high-Tc superconducting materials

The sharp increase in microwave power loss (the reverse of what has previously been reported) at the transition temperature in high-Tc superconducting systems such as YBaCu oxide (polycrystalline bulk and thin films obtained by the laser ablation technique) and BiPbSrCaCu oxide is reported. The differences between DC resistivity ( rho ) and the microwave power loss (related to microwave surface resistance) are analysed from the data obtained by a simultaneous measurement set-up. The influence of various parameters, such as preparation conditions, thickness and aging of the sample and the probing frequency (6-18 GHz), on the variation of microwave power loss with temperature is outlined.

Influence of Starch Polysaccharide on the Remolded Properties of 2 Indian clay Samples

The reported presence in marine clays and the recognized role of polysaccharide as a bonding agent provided the motivation to examine the role of starch polysaccharide in the remoulded properties of nonswelling (kaolinite) and swelling (bentonite) groups of clays. The starch polysaccharide belongs to a group of naturally occurring, large-sized organic molecules (termed polymers) and is built up by extensive repetition of simple chemical units called repeat units. The results of the study indicate that the impact of the starch polysaccharide on the remoulded properties of clays is dependent on the mineralogy of the clays. On addition to bentonite clay, the immensely large number of segments (repeat units) of the starch polysaccharide create several polymer segment - clay surface bonds that cause extensive aggregation of the bentonite units layers. The aggregation of the bentonite unit layers greatly curtails the available surface area of the clay mineral for diffuse ion layer formation. The reduction in diffuse ion layer thickness markedly lowers the consistency limits and vane shear strength of the bentonite clay. On addition to kaolinite, the numerous polymer segment - clay surface bonds enhance the tendency of the kaolinite particles to flocculate. The enhanced particle flocculation is responsible apparently for a small to moderate increase in the liquid limit and remoulded undrained strength of the nonswelling clay.