Structural basis for the functional and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Plasmodium falciparum

The beta-hydroxyacyl-acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) catalyzes the third and important reaction of the fatty acid elongation cycle. The crystal structure of PfFabZ is available in hexameric (active) and dimeric (inactive) forms. However, PfFabZ has not been crystallized with any bound inhibitors until now. We have designed a new condition to crystallize PfFabZ with its inhibitors bound in the active site, and determined the crystal structures of four of these complexes. This is the first report on any FabZ enzyme with active site inhibitors that interact directly with the catalytic residues. Inhibitor binding not only stabilized the substrate binding loop but also revealed that the substrate binding tunnel has an overall shape of ``U''. In the crystal structures, residue Phe169 located in the middle of the tunnel was found to be in two different conformations, open and closed. Thus, Phe169, merely by changing its side chain conformation, appears to be controlling the length of the tunnel to make it suitable for accommodating longer substrates. The volume of the substrate binding tunnel is determined by the sequence as well as by the conformation of the substrate binding loop region and varies between organisms for accommodating fatty acids of different chain lengths. This report on the crystal structures of the complexes of PfFabZ provides the structural basis of the inhibitory mechanism of the enzyme that could be used to improve the potency of inhibitors against an important component of fatty acid synthesis common to many infectious organisms. (C) 2011 Elsevier Inc. All rights reserved.

Atomic layer deposition of ZrO2 thin films: Study of growth kinetics and dielectric behaviour

Thin films of ZrO2 have been deposited by ALD on Si(100) and SIMOX using two different metalorganic complexes of Zr as precursors. These films are characterized by X-ray diffraction, transmission and scanning electron microscopies, infrared spectroscopy, and electrical measurements. These show that amorphous ZrO2 films of high dielectric quality may be grown on Si(100) starting about 400degreesC. As the growth temperature is raised, the films become crystalline, the phase formed and the microstructure depending on precursor molecular structure. The phase of ZrO2 formed depends also on the relative duration of the precursor and oxygen pulses. XPS and IR spectroscopy show that films grown at low temperatures contain chemically unbound carbon, its extent depending on the precursor. C-V measurements show that films grown on Si(100) have low interface state density, low leakage current, a hysteresis width of only 10-250 mV and a dielectric constant of similar to16-25.

A Rare Phenoxido/Acetato/Azido Bridged Trinuclear and an Unprecedented Phenoxido/Azido Bridged One-Dimensional Polynuclear Nickel(II) Complexes: Synthesis, Crystal Structure, and Magnetic Properties with Theoretical Investigations on the Exchange Mechanism

The reaction of a tridentate Schiff base ligand HL (2-(3-dimethylaminopropylimino)-methyl]-phenol) with Ni(II) acetate or perchlorate salts in the presence of azide as coligand has led to two new Ni(II) complexes of formulas Ni3L2(OAc)(2)(mu(1,1)-N-3)(2)(H2O)(2)]center dot 2H(2)O (1) and Ni2L2(mu(1,1)-N-3) (mu(1,3)-N-3)](n)(2). Single crystal X-ray structures show that complex 1 is a linear trinuclear Ni(II) compound containing a mu(2)-phenwddo, an end-on (EO) azido and a syn-syn acetato bridge between the terminal and the central Ni(II) ions. Complex 2 can be viewed as a one-dimensional (1D) chain in which the triply bridged (di-mu(2)-phenoxido and EO azido) dimeric Ni-2 units are linked to each other in a zigzag pattern by a single end-to-end (EE) azido bridge. Variable-temperature magnetic susceptibility studies indicate the presence of moderate ferromagnetic exchange coupling in complex 1 with J value of 16.51(6) cm(-1). The magnetic behavior of 2 can be fitted in an alternating ferro- and antiferromagnetic model J(FM) = +34.2(2.8) cm(-1) and J(AF) = -21.6(1.1) cm(-1)] corresponding to the triple bridged dinuclear core and EE azido bridge respectively. Density functional theory (DFT) calculations were performed to corroborate the magnetic results of 1 and 2. The contributions of the different bridges toward magnetic interactions in both compounds have also been calculated.

Photocatalytic degradation with combustion synthesized WO3 and WO3-TiO2 mixed oxides under UV and visible light

The photocatalytic activity of commercial titanium dioxide under UV and visible radiation was improved by composites of tungsten trioxide (WO3) with TiO2. WO3 was prepared by solution combustion synthesis and the mixed oxides/composites of WO3-TiO2 were prepared in different weight ratios (0, 0.10, 0.15, 0.20, 0.25, 0.50, 0.75, and 1) by physical mixing. These catalysts were characterized by XRD, DRS, BET, SEM, TEM, pH drift method, TGA and photoluminescence. The photocatalytic activity varies with the WO3 loading in the composites. The optimum loading of WO3 in the composites was found to be 15 wt% for both UV and visible radiation. This loading showed faster dye degradation rate than commercial TiO2 (TiO2-C) and WO3 (WO3-C). The effect of initial concentrations of methylene blue (MB) and orange G (OG) and the effect of the functional group on dye degradation was studied with both anionic and cationic dyes with 15 wt% WO3-TiO2. (C) 2012 Elsevier B.V. All rights reserved.

High-temperature, high-pressure granulites (retrogressed eclogites) in the central region of the Lewisian, NW Scotland: Crustal-scale subduction in the Neoarchaean

Eclogites and associated high-pressure (HP) rocks in collisional and accretionary orogenic belts preserve a record of subduction and exhumation, and provide a key constraint on the tectonic evolution of the continents. Most eclogites that formed at high pressures but low temperatures at > 10-11 kbar and 450-650 degrees C can be interpreted as a result of subduction of cold oceanic lithosphere. A new class of high-temperature (HT) eclogites that formed above 900 degrees C and at 14 to 30 kbar occurs in the deep continental crust, but their geodynamic significance and processes of formation are poorly understood. Here we show that Neoarchaean mafic-ultramafic complexes in the central granulite facies region of the Lewisian in NW Scotland contain HP/HT garnet-bearing granulites (retrogressed eclogites), gabbros, Iherzolites, and websterites, and that the HP granulites have garnets that contain inclusions of omphacite. From thermodynamic modeling and compositional isopleths we calculate that peak eclogite-facies metamorphism took place at 24-22 kbar and 1060-1040 degrees C. The geochemical signature of one (G-21) of the samples shows a strong depletion of Eu indicating magma fractionation at a crustal level. The Sm-Nd isochron ages of HP phases record different cooling ages of ca. 2480 and 2330 Ma. We suggest that the layered mafic-ultramafic complexes, which may have formed in an oceanic environment, were subducted to eclogite depths, and exhumed as HP garnet-bearing orogenic peridotites. The layered complexes were engulfed by widespread orthogneisses of tonalite-trondhjemite-granodiorite (TTG) composition with granulite facies assemblages. We propose two possible tectonic models: (1) the fact that the relicts of eclogitic complexes are so widespread in the Scourian can be taken as evidence that a >90 km x 40 km-size slab of continental crust containing mafic-ultramafic complexes was subducted to at least 70 km depth in the late Archaean. During exhumation the gneiss protoliths were retrogressed to granulite facies assemblages, but the mafic-ultramafic rocks resisted retrogression. (2) The layered complexes of mafic and ultramafic rocks were subducted to eclogite-facies depths and during exhumation under crustal conditions they were intruded by the orthogneiss protoliths (TTG) that were metamorphosed in the granulite facies. Apart from poorly defined UHP metamorphic rocks in Norway, the retrogressed eclogites in the central granulite/retrogressed eclogite facies Lewisian region, NW Scotland have the highest crustal pressures so far reported for Archaean rocks, and demonstrate that lithospheric subduction was transporting crustal rocks to HP depths in the Neoarchaean. (C) 2012 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Carbohydrate-Appended Tumor Targeting Iron(III) Complexes Showing Photocytotoxicity in Red Light

Glucose-appended photocytotoxic iron(III) complexes of a tridentate Schiff base phenolate ligand Fe(bpyag) (L)] (NO3) (1-3), where bpyag is N,N-bis(2- pyridylmethyl)-2-aminoethyl-beta-D-glucopyranoside and H2L is 3-(2-hydroxyphenylimino)-1-phenylbutan-1-one (H(2)phap) in 1, 3-(2-hydroxyphenylimino)-9-anthrylbutan-1-one (H(2)anap) 2, and 3- (2-hydroxyphenylimino)-1-pyrenylbutan-1-one (H(2)pyap) in 3, were synthesized and characterized. The complex Fe(dpma)(anapn(NO3) (4), having bis-(2-pyridylmethyl)benzylamine (dpma), in which the glucose moiety of bpyag is substituted by a phenyl group, was used as a control, and the complex Fe(dpma)(anap)](PF6) (4a) was structurally characterized by X-ray crystallography. The structure shows a FeN4O2 core in a distorted octahedral geometry. The high-spin iron(III) complexes with magnetic moment value of similar to 5.9 mu(B) showed a low-energy phenolate-to-Fe(III) charge-transfer (CT) absorption band as a shoulder near 500 nm with a tail extending to 700 nm and an irreversible Fe(III)-Fe(II) redox couple near -0.6 V versus saturated calomel electrode. The complexes are avid binders to calf thymus DNA and showed photocleavage of supercoiled pUC19 DNA in red (647 nm) and green (532 nm) light. Complexes 2 and 3 displayed significant photocytotoxicity in red light, with an IC50 value of similar to 20 mu M in HeLa and HaCaT cells, and no significant toxicity in dark. The cell death is via an apoptotic pathway, by generation of reactive oxygen species. Preferential internalization of the carbohydrate-appended complexes 2 and 3 was evidenced in HeLa cells as compared to the control complex 4. A 5-fold increase in the cellular uptake was observed for the active complexes in HeLa cells. The photophysical properties of the complexes are rationalized from the density functional theory calculations.

TSpred: a web server for the rational design of temperature-sensitive mutants

Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.

Contrasting reactivity behaviour of the RuHCl(CO)(PNP)] complex with electrophilic reagents XOTf (X = H, CH3, Me3Si)

A new ruthenium pincer complex RuHCl(CO)(PNP)] (PNP = PhCH2N(CH2CH2PPh2)(2)) (1) was synthesized and characterized. The reactivity of complex 1 with electrophilic reagents XOTf (X = H, CH3, and Me3Si; OTf = CF3SO3) was studied by variable temperature NMR spectroscopy with an aim to observe and characterize sigma complexes of type Ru(eta(2)-HX)Cl(CO)(PNP)]OTf] (X = H (2), CH3 (3), Me3Si (4)). Reaction of complex 1 with HOTf resulted in the formation of the dihydrogen complex, Ru(eta(2)-H-2)Cl(CO)(PNP)OTf] (2). On the other hand, the reaction between complex 1 and MeOTf and Me3SiOTf resulted in the direct elimination of MeCl and Me3SiCl via a S(N)2 type of reaction without the intermediacy of the respective sigma complexes 3 and 4. This contrasting reactivity behaviour has been rationalized taking into consideration the approach of the relatively bulky electrophites CH3+ and Me3Si+ onto the hydride moiety of the ruthenium fragment, which is sterically hindered.

Seleno-Nucleobases and Their Water-Soluble Ruthenium-Arene Half-Sandwich Complexes: Chemistry and Biological Activity

Half-sandwich organometallic ruthenium complexes of seleno-nucleobases, 3 and 4, were synthesized and characterized. The structures of both complexes were determined by X-ray crystallography and are the first crystal structures of ruthenium complexes with seleno-nucleobases. Interestingly, 3 self-assembles aided by adventitious water in DMF to give a tetranuclear square 3a center dot 6H(2)O. Complex 4 is active against Jurkat and Molt-4 cell lines but inactive against the K562 cell line, whereas 3 is completely inactive against all three cell lines. The free ligand 6-selenopurine (1) and 6-selenoguanine (2) are highly active against these cell lines. Compound 2, like its thio analogue, is unstable under UVA light, whereas 4 is stable under similar conditions, which suggests that the ruthenium complex could reduce problems associated with the instability of the free ligand, 2, under irradiation.

Effect of metal oxidation state on FRET: a Cu(I) silent but selectively Cu(II) responsive fluorescent reporter and its bioimaging applications

Copper(II) and copper(I) complexes of a newly designed and crystallographically characterized Schiff base (HL) derived from rhodamine hydrazide and cinnamaldehyde were isolated in pure form formulated as Cu(L)(NO3)] (L-Cu) (1) and Cu(HL)(CH3CN)(H2O)]ClO4 (HL-Cu) (2), and characterized by physicochemical and spectroscopic tools. Interestingly, complex 1 but not 2 offers red fluorescence in solution state, and eventually HL behaves as a Cu(II) ions selective FRET based fluorosensor in HEPES buffer (1 mM, acetonitrile-water: 1/5, v/v) at 25 degrees C at biological pH with almost no interference of other competitive ions. The dependency of the FRET process on the +2 oxidation state of copper has been nicely supported by exhaustive experimental studies comprising electronic, fluorimetric, NMR titration, and theoretical calculations. The sensing ability of HL has been evaluated by the LOD value towards Cu(II) ions (83.7 nM) and short responsive time (5-10 s). Even the discrimination of copper(I) and copper(II) has also been done using only UV-Vis spectroscopic study. The efficacy of this bio-friendly probe has been determined by employing HL to detect the intercellular distribution of Cu(II) ions in HeLa cells by developing image under fluorescence microscope.

Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity

Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of beta-galactosides for jacalin compared with beta-galactosides is caused by steric interactions of the substituents in the former with the protein. This issue has been explored energetically and structurally using different appropriate carbohydrate complexes of jacalin. It turns out that the earlier postulation is not correct. The interactions of the substituent with the binding site remain essentially the same irrespective of the anomeric nature of the substitution. This is achieved through a distortion of the sugar ring in beta-galactosides. The difference in energy, and therefore in affinity, is caused by a distortion of the sugar ring in beta-galactosides. The elucidation of this unprecedented distortion of the ligand as a strategy for modulating affinity is of general interest. The crystal structures also provide a rationale for the relative affinities of the different carbohydrate ligands for jacalin.

Remarkable Selectivity and Photo-Cytotoxicity of an Oxidovanadium(IV) Complex of Curcumin in Visible Light

Oxidovanadium(IV) complexes of 2-(2'-pyridyl)-1,10-phenanthroline (pyphen), viz. VO(pyphen)(acac)](ClO4) (1), VO(pyphen)(anacac)](ClO4) (2) and VO(pyphen)(cur)](ClO4) (3), where acac is acetylacetonate (in 1), anacac is anthracenylacetylacetonate (in 2) and cur is curcumin monoanion (in 3) were synthesized, characterized and their photo-induced DNA cleavage activities and photo-cytotoxicities studied. The complexes are 1: 1 electrolytes in DMF. The one-electron paramagnetic complexes show a d-d band near 760 nm in DMF. Complexes 2 and 3 are blue and green emissive, respectively, in DMSO. The complexes exhibit irreversible V-IV/V-III reductive responses near -1.1 V and V-V/V-IV oxidative responses near 0.85 V vs. SCE in DMF-0.1 M TBAP. Complexes 2 and 3 display significant and selective photo-cytotoxicity upon irradiation with visible light giving an IC50 value of about 5 mu M against HeLa and MCF-7 cancer cells; they are significantly less-toxic against normal 3T3 control cells and in the absence of light. Complex 1 was used as a control. Both cytosolic and nuclear localization of the complexes were observed on the basis of fluorescence imaging. The complexes, avid binders to calf thymus (ct) DNA, were found to photocleave supercoiled pUC19 DNA upon irradiation with near-IR light (785 nm) by generating hydroxyl radical (OH) as the reactive oxygen species (ROS). Cell death events noted with HeLa and MCF-7 cell lines likely are attributable to apoptotic pathways involving light-assisted generation of intracellular ROS.

Remarkable enhancement in photocytotoxicity and hydrolytic stability of curcumin on binding to an oxovanadium(IV) moiety

Oxovanadium(IV) complexes of polypyridyl and curcumin-based ligands, viz. VO(cur)(L)Cl] (1, 2) and VO(scur)(L)Cl] (3, 4), where L is 1,10-phenanthroline (phen in 1 and 3), dipyrido3,2-a:2',3'-c]phenazine (dppz in 2 and 4), Hcur is curcumin and Hscur is diglucosylcurcumin, were synthesized and characterized and their cellular uptake, photocytotoxicity, intracellular localization, DNA binding, and DNA photo-cleavage activity studied. Complex VO(cur)(phen)Cl] (1) has (VN2O3Cl)-N-IV distorted octahedral geometry as evidenced from its crystal structure. The sugar appended complexes show significantly higher uptake into the cancer cells compared to their normal analogues. The complexes are remarkably photocytotoxic in visible light (400-700 nm) giving an IC50 value of <5 mu M in HeLa, HaCaT and MCF-7 cells with no significant dark toxicity. The green emission of the complexes was used for cellular imaging. Predominant cytosolic localization of the complexes 1-4 to a lesser extent into the nucleus was evidenced from confocal imaging. The complexes as strong binders of calf thymus DNA displayed photocleavage of supercoiled pUC19 DNA in red light by generating (OH)-O-center dot radicals as the ROS. The cell death is via an apoptotic pathway involving the ROS. Binding to the VO2+ moiety has resulted in stability against any hydrolytic degradation of curcumin along with an enhancement of its photocytotoxicity.

Unusually Short Chalcogen Bonds Involving Organoselenium: Insights into the Se-N Bond Cleavage Mechanism of the Antioxidant Ebselen and Analogues

Structural studies on the polymorphs of the organoselenium antioxidant ebselen and its derivative show the potential of organic selenium to form unusually short Se center dot center dot center dot O chalcogen bonds that lead to conserved supramolecular recognition units. Se center dot center dot center dot O interactions observed in these polymorphs are the shortest such chalcogen bonds known for organoselenium compounds. The FTIR spectral evolution characteristics of this interaction from solution state to solid crystalline state further validates the robustness of this class of supramolecular recognition units. The strength and electronic nature of the Se center dot center dot center dot O chalcogen bonds were explored using high-resolution X-ray charge density analysis and atons-in-molecules (AIM) theoretical analysis. A charge density study unravels the strong electrostatic nature of Se center dot center dot center dot O chalcogen bonding and soft-metal-like behavior of organoselenium. An analysis of the charge density around Se-N and Se-C covalent bonds in conjunction with the Se center dot center dot center dot O chalcogen bonding modes in ebselen and its analogues provides insights into the mechanism of drug action in this class of organoselenium antioxidants. The potential role of the intermolecular Se center dot center dot center dot O chalcogen bonding in forming the intermediate supramolecular assembly that leads to the bond cleavage mechanism has been proposed in terms of electron density topological parameters in a series of molecular complexes of ebselen with reactive oxygen species (ROS).