The design and synthesis of redox core-alpha amino acid composites based on thiol-disulfide exchange mechanism and a comparative study of their zinc abstraction potential from [CCXX] boxes in proteins

The design and synthesis of agents that can abstract zinc from their [CCXX] (C=cysteine; X=cysteine/histidine) boxes by thioldisulfide exchange-having as control, the redox parities of the core sulfur ligands of the reagent and the enzyme, has been illustrated, and their efficiency demonstrated by monitoring the inhibition of the transcription of calf thymus DNA by E. coli RNA polymerase, which harbors two zinc atoms in their [CCXX] boxes of which one is exchangeable. Maximum inhibition possible with removal of the exchangeable zinc was seen with redox-sulfanilamide-glutamate composite. In sharp contrast, normal chelating agents (EDTA, phenanthroline) even in a thousand fold excess showed only marginal inhibition, thus supporting an exchange mechanism for the metal removal. (C) 2002 Elsevier Science Ltd. All rights reserved.

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.

Effect of Reagent Addition Rate and Temperature on Synthesis of Gold Nanoparticles in Microemulsion Route

Nanoparticle synthesis in a microemulsion route is typically controlled by changing the water to surfactant ratio, concentration of precursors, and/or concentration of micelles. The experiments carried out in this work with chloroauric acid and hydrazine hydrate as precursors in water/AOT-Brij30/isooctane microemulsions show that the reagent addition rate can also be used to tune the size of stable spherical gold nanoparticles to some extent. The particle size goes through a minimum with variation in feed addition rate. The increase in particle size with an increase in reaction temperature is in agreement with an earlier report. A population balance model is used to interpret the experimental findings. The reduced extent of nucleation at low feed addition rates and suppression of nucleation due to the finite rate of mixing at higher addition rates produce a minimum in particle size. The increase in particle size at higher reaction temperatures is explained through an increase in fusion efficiency of micelles which dissipates supersaturation; increase in solubility is shown to play an insignificant role. The moderate polydispersity of the synthesized particles is due to the continued nucleation and growth of particles. The polydispersity of micelle sizes by itself plays a minor role.

Monodisperse sub-10 nm gold nanoparticles by reversing the order of addition in Turkevich method - The role of chloroauric acid

The Turkevich method for synthesizing gold nanoparticles, using sodium citrate as the reducing agent, is renowned for its ability to produce biocompatible colloids with mean size >10 nm. Here we show that monodisperse gold nanoparticles in the 5-10 nm size range can be synthesized by simply reversing the order of addition of reactants, i.e. adding chloroauric acid to citrate solution. Kinetic studies and electron microscopic characterization revealed that the reactivity of chloroauric acid, initial molar ratio of citrate to chloroauric acid (MR), and reaction mixture pH play an important role in producing monodisperse gold nanoparticles. Reversing the order of addition also enhanced the stabilization of nanoparticles at high MR values. Remarkably, the system exhibits a `memory' of the order of addition, even when the timescale of mixing is much shorter than the timescale of synthesis. (C) 2011 Elsevier Inc. All rights reserved.

Poly(lactic-co-glycolic acid): Carbon nanofiber composites for myocardial tissue engineering applications

The objective of the present in vitro research was to investigate cardiac tissue cell functions (specifically cardiomyocytes and neurons) on poly(lactic-co-glycolic acid) (PLGA) (50:50 wt.%)-carbon nanofiber (CNF) composites to ascertain their potential for myocardial tissue engineering applications. CNF were added to biodegradable PLGA to increase the conductivity and cytocompatibility of pure PLGA. For this reason, different PLGA:CNF ratios (100:0, 75:25, 50:50,25:75, and 0:100 wt.%) were used and the conductivity as well as cytocompatibility of cardiomyocytes and neurons were assessed. Scanning electron microscopy, X-ray diffraction and Raman spectroscopy analysis characterized the microstructure, chemistry, and crystallinity of the materials of interest to this study. The results show that PLGA:CNF materials are conductive and that the conductivity increases as greater amounts of CNF are added to PLGA, from OS m(-1) for pure PLGA (100:0 wt.%) to 5.5 x 10(-3) S m(-1) for pure CNF (0:100 wt.%). The results also indicate that cardiomyocyte density increases with greater amounts of CNF in PLGA (up to 25:75 wt.% PLGA:CNF) for up to 5 days. For neurons a similar trend to cardiomyocytes was observed, indicating that these conductive materials promoted the adhesion and proliferation of two cell types important for myocardial tissue engineering applications. This study thus provides, for the first time, an alternative conductive scaffold using nanotechnology which should be further explored for cardiovascular applications. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Synthesis of electrically conducting copolymers of o-/m-toluidines and o-/m-amino benzoic acid in an organic peroxide system and their characterization

Copolymers of o-lm-toluidine with o-lm-amino benzoic acid have been synthesized by chemical polymerization using inverse emulsion pathway and characterized by a number of techniques including UV-Vis, FT-IR, FT Raman, EPR and NMR spectroscopies, thermal analysis and conductivity. The solubility of the copolymers in organic solvents increases with increase in the amount of amino benzoic acid in the feed. The copolymers synthesized at room temperature show relatively higher conductivity and are obtained in higher yield compared to those synthesized at 0 and 60 degreesC. The spectral studies have revealed restricted conjugation along the polymer chain. The effect of -COOH substituent on the copolymer structure is discussed. (C) 2003 Elsevier Science B.V All rights reserved.

Ternary copper(II) complexes of thiosemicarbazones and heterocyclic bases showing N3OS coordination as models for the type-2 centers of copper monooxygenases

Six ternary copper(II) complexes of general formulation [CuLB] (1-6), where L is dianionic ONS-donor thiosemicarbazones derived from the condensation of salicylaldehyde with thiosemicarbazides and B is NN-donor heterocyclic bases like 2,2'-bipyridine, 1,10-phenanthroline and 2,9-dimethyl-1,10-phenanthroline, are prepared from a reaction of copper(II) acetate hydrate with the heterocyclic base (B) and the thiosemicarbazone (H2L) in MeOH, and structurally characterized by X-ray diffraction technique. Crystal structures of the complexes display a distorted square-pyramidal (4 + 1) coordination geometry having the ONS-donor thiosemicarbazone bonded at the basal plane. The chelating heterocyclic bases exhibit axial-equatorial mode of bonding. The complexes are one-electron paramagnetic and they show axial X-band EPR spectra in DMF-toluene glass at 77 K giving g(parallel to)(A(parallel to)) and g(perpendicular to) values of similar to2.2 (175 x 10(-4) cm(-1)) and similar to2.0 indicating a {d(x2-y2)}(1) ground state. The complexes show a d-d band near 570 nm and a charge transfer band near 400 nm in DMF. The complexes are redox active and exhibit a quasireversible Cu(II)-Cu(I) couple in DMF-0.1 M tetrabutylammonium perchlorate near 0.1 V vs. SCE. They are catalytically active in the oxidation of ascorbic acid in presence of dioxygen. The complexes with a CuN3OS coordination model the ascorbate oxidation property of dopamine beta-hydroxylase and peptidylglycine a-hydroxylating monooxygeanase. (C) 2003 Elsevier Science B.V. All rights reserved.

Understanding the building-up process of three dimensional open-framework metal phosphates: Acid degradation of the 3D structures to lower dimensional structures

Acid degradation of 3D zinc phosphates primarily yields a one-dimensional ladder compound, an observation that is significant considering that the latter forms 3D structures on heating in water.

Pyrene appended bile acid conjugates: Synthesis and a structure-gelation property study

A wide variety of novel compounds obtained by combining two types of known organogelators, viz., bile acid alkyl amides and pyrene alkanoic acids, were synthesized and screened for their gelation ability. The 3 alpha esters of 1-pyrene butyric acid (PBA) of alkylamides of deoxycholic acid (DCA) turned out to be effective in the gel formation with many organic solvents although the gelation has to be triggered by the addition of a charge transfer (CT) agent 2,4,7-trinitrofluorenone (TNF). The special feature of these molecules is that the organogelation is achieved only after derivatizing the acid moiety of the 1-pyrenealkanoic acids. Additionally, the gelation properties can be fine-tuned by inserting different functional groups at the bile acid side chain. The gels obtained are deep red in colour and optically transparent up to 2% w/v. The SEM studies of the obtained xerogels revealed bundled rod-like morphology without specialized branching.

Volume Change Behaviour of Soil Influenced with Sulfuric Acid

The paper brings out the role of calcium carbonate (CaCO3) on the volume change behaviour of natural black cotton soil with 1N sulfuric acid (H2SO4) as pore fluid. Natural black cotton soil contained predominantly montmorillonite [Ca0.2(Al,Mg)2Si4 O10 (OH)2 .4H2O] along with other minerals such as amesite [(Mg Fe)2 Al (Si Al)2 O5 (OH)4], kalsilite [KAlSiO4] and quartz [SiO2]. The calcitic soil, reacted with H2SO4 during consolidation testing, showed the presence of the new mineral yavapaiite [K Fe(SO4)2]. Consequently, the carbonate soil treated with 1N H2SO4 led to higher swell at seating load and more compression upon loading than the soil with no carbonate. The swelling increased with increase in the amount of carbonate present in the soil.

Volume Change behaviour in Calcitic Soil influenced with Sulphuric Acid using Artificial Neural Networks

This paper elucidates the methodology of applying artificial neural network model (ANNM) to predict the percent swell of calcitic soil in sulphuric acid solutions, a complex phenomenon involving many parameters. Swell data required for modelling is experimentally obtained using conventional oedometer tests under nominal surcharge. The phases in ANN include optimal design of architecture, operation and training of architecture. The designed optimal neural model (3-5-1) is a fully connected three layer feed forward network with symmetric sigmoid activation function and trained by the back propagation algorithm to minimize a quadratic error criterion.The used model requires parameters such as duration of interaction, calcite mineral content and acid concentration for prediction of swell. The observed strong correlation coefficient (R2 = 0.9979) between the values determined by the experiment and predicted using the developed model demonstrates that the network can provide answers to complex problems in geotechnical engineering.

Revisiting the Mechanism of the Triosephosphate Isomerase Reaction: The Role of the Fully Conserved Glutamic Acid 97 Residue

An analysis of 503 available triosephosphate isomerase sequences revealed nine fully conserved residues. Of these, four residues-K12, H95, E97 and E165-are capable of proton transfer and are all arrayed around the dihydroxyacetone phosphate substrate in the three-dimensional structure. Specific roles have been assigned to the residues K12, H95 and E165, but the nature of the involvement of E97 has not been established. Kinetic and structural characterization is reported for the E97Q and E97D mutants of Plasmodium falciparum triosephosphate isomerase (Pf TIM). A 4000-fold reduction in k(cat) is observed for E97Q, whereas the E97D mutant shows a 100-fold reduction. The control mutant, E165A, which lacks the key catalytic base, shows an approximately 9000-fold drop in activity. The integrity of the overall fold and stability of the dimeric structure have been demonstrated by biophysical studies. Crystal structures of E97Q and E97D mutants have been determined at 2.0 angstrom resolution. In the case of the isosteric replacement of glutamic acid by glutamine in the E97Q mutant a large conformational change for the critical K12 side chain is observed, corresponding to a trans-to-gauche transition about the C gamma-C delta (chi(3)) bond. In the E97D mutant, the K12 side chain maintains the wild-type orientation, but the hydrogen bond between K12 and D97 is lost. The results are interpreted as a direct role for E97 in the catalytic proton transfer cycle. The proposed mechanism eliminates the need to invoke the formation of the energetically unfavourable imidazolate anion at H95, a key feature of the classical mechanism.