The Critical Role of N- and C-Terminal Contact in Protein Stability and Folding of a Family 10 Xylanase under Extreme Conditions

Background: Stabilization strategies adopted by proteins under extreme conditions are very complex and involve various kinds of interactions. Recent studies have shown that a large proportion of proteins have their N- and C-terminal elements in close contact and suggested they play a role in protein folding and stability. However, the biological significance of this contact remains elusive. Methodology: In the present study, we investigate the role of N- and C-terminal residue interaction using a family 10 xylanase (BSX) with a TIM-barrel structure that shows stability under high temperature,alkali pH, and protease and SDS treatment. Based on crystal structure,an aromatic cluster was identified that involves Phe4, Trp6 and Tyr343 holding the Nand C-terminus together; this is a unique and important feature of this protein that might be crucial for folding and stabilityunder poly-extreme conditions. Conclusion: A series of mutants was created to disrupt this aromatic cluster formation and study the loss of stability and function under given conditions. While the deletions of Phe4 resulted in loss of stability, removal of Trp6 and Tyr343 affected in vivo folding and activity. Alanine substitution with Phe4, Trp6 and Tyr343 drastically decreased stability under all parameters studied. Importantly,substitution of Phe4 with Trp increased stability in SDS treatment.Mass spectrometry results of limited proteolysis further demonstrated that the Arg344 residue is highly susceptible to trypsin digestion in sensitive mutants such as DF4, W6A and Y343A, suggesting again that disruption of the Phe4-Trp6-Tyr343 (F-W-Y) cluster destabilizes the N-and C-terminal interaction. Our results underscore the importance of N- and C-terminal contact through aromatic interactions in protein folding and stability under extreme conditions, and these results may be useful to improve the stability of other proteins under suboptimal conditions.

Time Scale Separated Nonlinear Partial Integrated Guidance and Control of Interceptors in the Terminal Phase

The paper proposes a time scale separated partial integrated guidance and control of an interceptor for engaging high speed targets in the terminal phase. In this two loop design, the outer loop is an optimal control formulation based on nonlinear model predictive spread control philosophies. It gives the commanded pitch and yaw rates whereas necessary roll-rate command is generated from a roll-stabilization loop. The inner loop tracks the outer loop commands using the dynamicinversion philosophy. However, unlike conventional designs, in both the loops the Six degree of freedom (Six-DOF) interceptor model is used directly. This intelligent manipulation preserves the inherent time scale separation property between the translational and rotational dynamics, and hence overcomes the deficiency of current IGC designs, while preserving its benefits. Six-DOF simulation studies have been carried out accounting for three dimensional engagement geometry. Different comparison studies were also conducted to measure the performance of the algorithm.

Using Water as a Design Element in Crystal Engineering. Host-Guest Compounds of Hydrated 3,5-Dihydroxybenzoic Acid

Thirteen host guest compounds of 3,5-dihydroxybenzoic acid (DHBA) have been structurally characterized. Water molecules occupy the peripheries of a hexagonal void, created with DHBA molecules, and act as ``hooks'' to connect the guest molecules with the host-framework via hydrogen bonding. The ``water hook'' is an OH group acting as a donor. Consequently, the guest molecules were chosen so that they contain good hydrogen bond acceptor functionalities. A number of multicomponent hydrates were isolated with stoichiometries (DHBA)(x)(H2O). (guest),. Of these, compounds with the following as guests were obtained as crystals that were good enough for single crystal work: ethyl acetate (EtOAc), diethyl oxalate, dimethyl oxalate, di(n-propyl) oxalate, diethyl malonate, diethyl succinate, chloroacetonitrile, N,N-dimethyl formamide (DMF), acetone, dimethyl sulfoxide (DMSO), 1-propanol, and 2-butanol. From 2-butanol, a hemihydrate, (DHBA)(2)(H2O), was also obtained concomitantly. Further to guest stabilization, water acts as a good mediator of effective crystal packing and also determines the topology of the host framework. En the present series of compounds, the role of water is wide ranging, and it is not easy to classify it specifically as a host or as a guest.

Dexamethasone negatively regulates phenobarbitone-activated transcription but synergistically enhances cytoplasmic levels of cytochrome P-450b/e messenger RNA

Dexamethasone has a potentiating effect on phenobarbitone mediated induction of cytochrome P-450b + e mRNAs in adult rat liver. However, the glucocorticoid inhibits phenobarbitone-activated transcription of cytochrome P-450b + e mRNAs by 60-70%. This inhibitory effect is evident in run-off transcription of the endogenous genes as well as in the transcription of an added cloned gene fragment. Dexamethasone inhibits the phenobarbitone-mediated increase in the binding of a transcription factor(s) to the upstream region of the gene as evidenced by gel retardation and Southwestern blot analysis. The glucocorticoid does not stabilize the phenobarbitone-induced polyribosomal cytochrome P-450b + e mRNAs but appears to stabilize the nuclear transcripts. It is proposed that a negative element may mediate the action of dexamethasone at the level of nuclear transcription and stabilization of the nuclear transcript may account for the potentiating effect of the glucocorticoid on phenobarbitone-mediated increase in cytochrome P-450b + e mRNAs in the cytoplasm of the adult rat liver. However, the cytochrome P-450b protein levels are slightly lower in phenobarbitone + dexamethasone treatment than in phenobarbitone-treated liver microsomes.

Solar pond technology

Solar pond technology has made substantial progress in the last fifteen years. This paper reviews the basic principles of solar ponds and the problems encountered in their operation and maintenance. The factors which influence the technical and economic viability of solar ponds for thermal applications and power generation have been discussed.

Identification of Critical Residues of the Mycobacterial Dephosphocoenzyme A Kinase by Site-Directed Mutagenesis

Dephosphocoenzyme A kinase performs the transfer of the c-phosphate of ATP to dephosphocoenzyme A, catalyzing the last step of coenzyme A biosynthesis. This enzyme belongs to the P-loop-containing NTP hydrolase superfamily, all members of which posses a three domain topology consisting of a CoA domain that binds the acceptor substrate, the nucleotide binding domain and the lid domain. Differences in the enzymatic organization and regulation between the human and mycobacterial counterparts, have pointed out the tubercular CoaE as a high confidence drug target (HAMAP database). Unfortunately the absence of a three-dimensional crystal structure of the enzyme, either alone or complexed with either of its substrates/regulators, leaves both the reaction mechanism unidentified and the chief players involved in substrate binding, stabilization and catalysis unknown. Based on homology modeling and sequence analysis, we chose residues in the three functional domains of the enzyme to assess their contributions to ligand binding and catalysis using site-directed mutagenesis. Systematically mutating the residues from the P-loop and the nucleotide-binding site identified Lys14 and Arg140 in ATP binding and the stabilization of the phosphoryl intermediate during the phosphotransfer reaction. Mutagenesis of Asp32 and Arg140 showed catalytic efficiencies less than 5-10% of the wild type, indicating the pivotal roles played by these residues in catalysis. Non-conservative substitution of the Leu114 residue identifies this leucine as the critical residue from the hydrophobic cleft involved in leading substrate, DCoA binding. We show that the mycobacterial enzyme requires the Mg2+ for its catalytic activity. The binding energetics of the interactions of the mutant enzymes with the substrates were characterized in terms of their enthalpic and entropic contributions by ITC, providing a complete picture of the effects of the mutations on activity. The properties of mutants defective in substrate recognition were consistent with the ordered sequential mechanism of substrate addition for CoaE.

Ab initio molecular orbital calculations on ion pair-water complexes of metal halides and oxides

Ab initio MO calculations are performed on a series of ion-molecular and ion pair-molecular complexes of H2O + MX (MX = LiF, LiCl, NaCl, BeO and MgO) systems. BSSE-corrected stabilization energies, optimized geometrical parameters, internal force constants and harmonic vibrational frequencies have been evaluated for all the structures of interest. The trends observed in the geometrical parameters and other properties calculated for the mono-hydrated contact ion pair complexes parallel those computed for the complexes of the individual ions. The bifurcated structures are found to be saddle points with an imaginary frequency corresponding to the rocking mode of water molecules. The solvent-shared ion pair complexes have high interaction energies. Trends in the internal force constant and harmonic frequency values are discussed in terms of ion-molecular and ion-pair molecular interactions.

Role of lattice defects and crystallite morphology in the UV and visible-light-induced photo-catalytic properties of combustion-prepared TiO2

The physico-chemical, photo-physical and micro-structural properties responsible for the strikingly different photocatalytic behavior of combustion-prepared TiO2 (c.TiO2) and Degussa P25 (d.TiO2) samples are elucidated in this study. Electron microscopy and selected area electron diffraction micrographs revealed that the two samples exhibited different morphologies. The grains of c.TiO2 were spherical and comprised of 5-6 nm size primary particle. On the other hand, d.TiO2 consisted of large (0.5-3.0 mu m) size and irregular shape aggregates having primary particles of 15-40 nm cross-sectional diameter. The ESR study revealed that the presence of certain defect states in c.TiO2 helped in stabilization of O-. and Ti3+-OH type species during room-temperature UV-irradiation. No such paramagnetic species were however formed over d.TiO2 under similar conditions. C1s and Ti 2p XPS spectra provide evidence for the presence of some lattice vacancies in c.TiO2 and also for the bulk Ti4+ -> Ti3+ conversion during its UV-irradiation. Compared to d.TiO2, c.TiO2 displayed considerably higher activity for discoloration of methyl orange but very poor activity for splitting of water, both under UV and visible light radiations. This is attributed to enhanced surface adsorption of dye molecules over c.TiO2, because of its textural features and also the presence of photo-active ion-radicals. On the other hand, the poor activity of c.TiO2 for water splitting is related to certain defect-induced inter-band charge trapping states in the close vicinity of valence and conduction bands of c.TiO2, as revealed by thermoluminescence spectroscopy. Further, the dispersion of nanosize gold particles gave rise to augmented activity of both the catalysts, particularly for water splitting. This is explained by the promotional role of Au-0 or Au-0/TiO2 interfacial sites in the adsorption and charge-adsorbate interaction processes. (C) 2011 Elsevier B.V. All rights reserved.

Propensity of formation of zipper architecture vs. Lincoln log arrangement in solvated molecular complexes of melamine with hydroxybenzoic acids

Molecular complexes of melamine with hydroxy and dihydroxybenzoic acids have been analyzed to assess the collective role of the hydroxyl (OH) and carboxyl (COOH) functionalities in the recognition process. In most cases, solvents of crystallization do play a major role in self-assembly and structure stabilization. Hydrated compounds generate linear chains of melamine molecules with acid molecules pendant resulting in a zipper architecture. However, anhydrous and solvated compounds generate tetrameric units consisting of melamine dimers together with acid molecules. These tetramers in turn interweave to form a Lincoln log arrangement in the crystal. The salt/co-crystal formation in these complexes cannot be predicted apriori on the basis of Delta pK(a) values as there exists a salt-to-co-crystal continuum.

Calcium ruthenates: Determination of Gibbs energies of formation using electrochemical cells

Metallic Ru has been found to coexist separately with CaO, RuO2, and the interoxide phases, Ca2RuO4, Ca3Ru2O7, and CaRuO3, present along the pseudobinary system CaO-RuO2. The standard Gibbs energies of formation (Df((ox))G(o)) of the three calcium ruthenates from their component oxides have been measured in the temperature range 925-1350 K using solid-state cells with yttria-stabilized zirconia as the electrolyte and Ru+RuO2 as the reference electrode. The standard Gibbs energies of formation (Deltaf((ox))G(o)) of the compounds can be represented by Ca2RuO4:Deltaf((ox))G(o)/J mol(-1)=-38,340-6.611 T (+/-120), Ca3Ru2O7 : Df((ox))G(o)/J mol(-1)=-75,910-11.26 T (+/-180), and CaRuO3 : Deltaf((ox))G(o)/J mol(-1)=-35,480-3.844 T(+/-70). The data for Ca2RuO4 corresponds to the stoichiometric composition, which has an orthorhombic structure, space group Pbca, with short c axis ("S'' form). The structural features of the ternary oxides responsible for their mild entropy stabilization are discussed. A three-dimensional oxygen potential diagram for the system Ca-Ru-O is developed as a function of composition and temperature from the results obtained. Using the Neumann-Kopp rule to estimate the heat capacity of the ternary oxides relative to their constituent binary oxides, the standard enthalpies of formation of the three calcium ruthenates from the elements and their standard entropies at 298.15 K are evaluated. (C) 2003 The Electrochemical Society.

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.

Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase

Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug an application that has been actively pursued for a variety of therapeutic strategies. The catalytic mechanism of this enzyme is governed by a conserved histidine that coordinates a magnesium ion at the active site. Despite substantial structural and biochemical information on NDK, the mechanistic feature of the phospho-transfer that leads to auto-phosphorylation remains unclear. While the role of the histidine residue is well documented, the other active site residues, in particular the conserved serine remains poorly characterized. Studies on some homologues suggest no role for the serine residue at the active site, while others suggest a crucial role for this serine in the regulation and quaternary association of this enzyme in some species. Here we report the biochemical features of the Staphylococcus aureus NDK and the mutant enzymes. We also describe the crystal structures of the apo-NDK, as a transition state mimic with vanadate and in complex with different nucleotide substrates. These structures formed the basis for molecular dynamics simulations to understand the broad substrate specificity of this enzyme and the role of active site residues in the phospho-transfer mechanism and oligomerization. Put together, these data suggest that concerted changes in the conformation of specific residues facilitate the stabilization of nucleotide complexes thereby enabling the steps involved in the ping-pong reaction mechanism without large changes to the overall structure of this enzyme. (C) 2011 Elsevier B.V. All rights reserved.

Relation between Local Structure and Glass Forming Ability of Liquid Alloys

An attempt has been made to describe the glass forming ability (GFA) of liquid alloys, using the concepts of the short range order (SRO) and middle range order (MRO) characterizing the liquid structure.A new approach to obtain good GFA of liquid alloys is based on the following four main factors: (1) formation of new SRO and competitive correlation with two or more kinds of SROs for crystallization, (2) stabilization of dense random packing by interaction between different types of SRO, (3) formation of stable cluster (SC) or middle range order (MRO) by harmonious coupling of SROs, and (4) difference between SRO characterizing the liquid structure and the near-neighbor environment in the corresponding equilibrium crystalline phases. The atomic volume mismatch estimated from the cube of the atomic radius was found to be a close relation with the minimum solute concentration for glass formation. This empirical guideline enables us to provide the optimum solute concentration for good GFA in some ternary alloys. Model structures, denoted by Bernal type and the Chemical Order type, were again tested in the novel description for the glass structure as a function of solute concentration. We illustrated the related energetics of the completion between crystal embryo and different types of SRO. Recent systematic measurements also provide that thermal diffusivity of alloys in the liquid state may be a good indicator of their GFA.

Structure of the Pyridine-Chloranil Complex in Solution: A Surprise from Depolarized Hyper-Rayleigh Scattering Measurements

In this article, we report the structure of a 1:1 charge transfer complex between pyridine (PYR) and chloranil (CHL) in solution (CHCl(3)) from the measurement of hyperpolarizability (beta(HRS)) and linear and circular depolarization ratios, D and D', respectively, by the hyper-Rayleigh scattering technique and state-of-the-art quantum chemical calculations. Using linearly (electric field vector along X) and circularly polarized incident light, respectively, we have measured two macroscopic depolarization ratios D = I(X,X)(2 omega)/I(X,Z)(2 omega) and D' = I(X,C)(2 omega)/I(Z,C)(2 omega) in the laboratory fixed XYZ frame by detecting the second harmonic (SH) scattered light in a polarization resolved fashion. The stabilization energy and the optical gap calculated through the MP2/cc-pVDZ method using Gaussian09 were not significantly different to distinguish between the cofacial and T-shape structures. Only when the experimentally obtained beta(HRS) and the depolarization ratios, D and D', were matched with the theoretically computed values from single and double configuration interaction (SDCI) calculations performed using the ZINDO-SCRF technique, we concluded that the room temperature equilibrium structure of the complex is cofacial. This is in sharp contrast to an earlier theoretical prediction of the T-shape structure of the complex.

Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands

The enzyme telomerase synthesizes the G-rich DNA strands of the telomere and its activity is often associated with cancer. The telomerase may be therefore responsible for the ability of a cancer cell-to escape apoptosis. The G-rich DNA sequences often adopt tetra-stranded structure, known as the G-quadruplex DNA (G4-DNA). The stabilization of the telomeric DNA into the G4-DNA structures by small molecules has been the focus of many researchers for the design and development of new anticancer agents. The compounds which stabilize the G-quadruplex in the telomere inhibit the telomerase activity. Besides telomeres, the G4-DNA forming sequences are present in the genomic regions of biological significance including the transcriptional regulatory and promoter regions of several oncogenes. Inducing a G-quadruplex structure within the G-rich promoter sequences is a potential way of achieving selective gene regulation. Several G-quadruplex stabilizing ligands are known. Minor groove binding ligands (MGBLs) interact with the double-helical DNA through the minor grooves sequence-specifically and interfere with several DNA associated processes. These MGBLs when suitably modified switch their preference sometimes from the duplex DNA to G4-DNA and stabilize the G4-DNA as well. Herein, we focus on the recent advances in understanding the G-quadruplex structures, particularly made by the human telomeric ends, and review the results of various investigations of the interaction of designed organic ligands with the G-quadruplex DNA while highlighting the importance of MGBL-G-quadruplex interactions.