Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1

The crystal structures of five new non-electrophilic β-strand-templated thrombin active-site inhibitors have been determined bound to the enzyme. Four co-crystallize with hirugen and inhibitor isomorphously to produce thrombin-hirugen crystals (monoclinic, space group C2), while one co-crystallizes in the hexagonal system, space group P65. A 1,4-substituted cyclohexyl moiety is conserved at the P1 position of all the inhibitors, along with a fused hetero-bicyclic five- and six-membered ring that occupies the P2 site. Amino, amidino and aminoimidazole groups are attached to the cyclohexyl ring for recognition at the S1 specificity site, while benzylsulfonyl and diphenyl groups enhance the binding at the S3 subsite. The cyclohexyl groups at the P1 positions of three of the inhibitors appear to be in the energetically favored chair conformation, while the imidazole-substituted cyclohexyl rings are in a boat conformation. Somewhat unexpectedly, the two cyclohexyl-aminoimidazole groups bind differently in the specificity site; the unique binding of one is heretofore unreported. The other inhibitors generally mimic arginyl binding at S1. This group of inhibitors combines the nonelectrophilicity and selectivity of DAPA-like compounds and the more optimal binding features of the S1-S3 sites of thrombin for peptidic molecules, which results in highly potent (binding constants 12 nM-16 pM, one being 1.1 μM) and selective (ranging from 140 to 20 000 times more selective compared with trypsin) inhibitors of thrombin. The binding modes of these novel inhibitors are correlated with their binding constants, as is their selectivity, in order to provide further insight for the design of therapeutic antithrombotic agents that inhibit thrombin directly at the active site.

Biophysical Characterization of Interactions Involving Importin-α during Nuclear Import

Proteins containing the classical nuclear localization sequences (NLSs) are imported into the nucleus by the importin-α/β heterodimer. Importin-α contains the NLS binding site, whereas importin-β mediates the translocation through the nuclear pore. We characterized the interactions involving importin-α during nuclear import using a combination of biophysical techniques (biosensor, crystallography, sedimentation equilibrium, electrophoresis, and circular dichroism). Importin-α is shown to exist in a monomeric autoinhibited state (association with NLSs undetectable by biosensor). Association with importin-β (stoichiometry, 1:1; K D = 1.1 × 10 -8 M) increases the affinity for NLSs; the importin-α/β complex binds representative monopartite NLS (simian virus 40 large T-antigen) and bipartite NLS (nucleoplasmin) with affinities (K D = 3.5 × 10 -8 M and 4.8 × 10 -8 M, respectively) comparable with those of a truncated importin-α lacking the autoinhibitory domain (T-antigen NLS, K D = 1.7 × 10 -8 M; nucleoplasmin NLS, K D = 1.4 × 10 -8 M). The autoinhibitory domain (as a separate peptide) binds the truncated importin-α, and the crystal structure of the complex resembles the structure of full-length importin-α. Our results support the model of regulation of nuclear import mediated by the intrasteric autoregulatory sequence of importin-α and provide a quantitative description of the binding and regulatory steps during nuclear import.

Crystallographic, dielectric and optical properties of SrBi 2Ta2O9 thin films prepared by the polymeric precursor method

Strontium bismuth tantalate thin films were prepared on several substrates (platinized silicon (Pt/Ti/SiO 2 /Si), n -type (100)-oriented and p -type (111)-oriented silicon wafers, and fused silica) by the solution deposition method. The resin was obtained by the polymeric precursor method, based on the Pechini process, using strontium carbonate, bismuth oxide, and tantalum ethoxide as starting reagents. Characterizations by XRD and SEM were performed for structural and microstructural evaluations. The electrical measurements, carried on the MFM configuration, showed P r values of 6.24 μC/cm 2 and 31.5 kV/cm for the film annealed at 800 C. The film deposited onto fused silica and treated at 700 C presented around 80% of transmittance. © 2002 Taylor & Francis.

Spectroscopic characteristics of Er3+ in the two crystallographic sites of Gd2SiO5

Gd2SiO5 is among the interesting and suitable hosts for Er3+ which find extensive applications in the infrared, visible and ultraviolet spectral regions. In order to investigate its potentialities, a prior study of the spectroscopic behaviour of Er3+ substituting for Gd3+ ions in the two crystallographic sites of the host was performed. Absorption, excitation, site-selective emission and time-resolved spectroscopies were employed in the visible spectral region to study transitions between excited 4S3/2 and ground 4I15/2 states. These levels multiplets were attributed to each site separately, and their corresponding 4S3/2 lifetimes (1.8 ± 0.1 μs for site 1 and 3.2 ± 0.1 μs for site 2) were determined.

Structural study of aged saturated silica gels obtained from tetramethoxysilane sonohydrolysis with different water/tetramethoxysilane molar ratio

The structural characteristics of saturated silica sonogels were studied by means of small-angle x-ray scattering (SAXS) and thermogravimetric analysis (TG), after a long time of aging in saturated conditions. The sonogels were obtained by a sol-gel routine from ultrasound stimulated tetramethoxysilane (TMOS) hydrolysis carried out with the initial water/TMOS molar ratio (r) ranging from 2 to 10. The saturated sonogel structure can be described as composed by mass fractal-like aggregates (clusters) of primary silica particles, all imbibed in a liquid phase. The values of the mass fractal dimension (D) of the clusters was found all around 2.5, while the characteristic size of the clusters (ξ) was found generally increasing with r, going from approximately 2.3 nm (r = 2) to 4.5 nm (r = 10). The volume fraction of the clusters was estimated from the SAXS data. The results were compared to the values of weight loss fraction at the inflection point that has been found in the derivative of the TG curve, which should accounts for the instant in which the meniscus of the liquid phase penetrates into the clusters under a rapid evaporation process as in a TG test.

An ellipsometric study of manganese oxide films: In situ characterization of the deposition and electroreduction of MnO2

The electrodeposition of manganese oxide films onto a platinum substrate was investigated by means of in situ ellipsometry. In the thickness range from 0 to 150 nm, the anodic oxide behaves as an Isotropic single layer with optical constants that are independent of thickness. Deviations at higher thickness are explained in terms of anisotropic properties of the film. The electroreduction of thin films (up to ca. 150 nm) in an alkaline electrolyte leads to a decrease in both the refractive index and the extinction coefficient and is accompanied by a thickness increase of ca. 10%. The Mn(IV) to Mn(III) conversion takes place from the oxide/electrolyte interface inwards. © 2004 The Electrochemical Society. All rights reserved.

Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of nucleosides and deoxynucleosides, generating ribose 1-phosphate and the purine base, which is an important step of purine catabolism pathway. The lack of such an activity in humans, owing to a genetic disorder, causes T-cell impairment, and drugs that inhibit this enzyme may have the potential of being utilized as modulators of the immunological system to treat leukemia, autoimmune diseases, and rejection in organ transplantation. Here, we describe kinetics and crystal structure of human PNP in complex with 7-methyl-6-thio-guanosine, a synthetic substrate, which is largely used in activity assays. Analysis of the structure identifies different protein conformational changes upon ligand binding, and comparison of kinetic and structural data permits an understanding of the effects of atomic substitution on key positions of the synthetic substrate and their consequences to enzyme binding and catalysis. Such knowledge may be helpful in designing new PNP inhibitors. © 2005 Elsevier Inc. All rights reserved.

Structure of myotoxin II, a catalytically inactive Lys49 phospholipase A2 homologue from Atropoides nummifer venom

Lys49 snake-venom phospholipase A2 (PLA2) homologues are highly myotoxic proteins which, although lacking catalytic activity, possess the ability to disrupt biological membranes, inducing significant muscle-tissue loss and permanent disability in severely envenomed patients. Since the structural basis for their toxic activity is still only partially understood, the structure of myotoxin II, a monomeric Lys49 PLA2 homologue from Atropoides nummifer, has been determined at 2.08 Å resolution and the anion-binding site has been characterized. © 2006 International Union of Crystallography. All rights reserved.

cDNA cloning and 1.75 Å crystal structure determination of PPL2, an endochitinase and N-acetylglucosamine-binding hemagglutinin from Parkia platycephala seeds

Parkia platycephala lectin 2 was purified from Parkia platycephala (Leguminosae, Mimosoideae) seeds by affinity chromatography and RP-HPLC. Equilibrium sedimentation and MS showed that Parkia platycephala lectin 2 is a nonglycosylated monomeric protein of molecular mass 29 407 ± 15 Da, which contains six cysteine residues engaged in the formation of three intramolecular disulfide bonds. Parkia platycephala lectin 2 agglutinated rabbit erythrocytes, and this activity was specifically inhibited by N-acetylglucosamine. In addition, Parkia platycephala lectin 2 hydrolyzed β(1-4) glycosidic bonds linking 2-acetoamido-2-deoxy-β-d-glucopyranose units in chitin. The full-length amino acid sequence of Parkia platycephala lectin 2, determined by N-terminal sequencing and cDNA cloning, and its three-dimensional structure, established by X-ray crystallography at 1.75 Å resolution, showed that Parkia platycephala lectin 2 is homologous to endochitinases of the glycosyl hydrolase family 18, which share the (βα) 8 barrel topology harboring the catalytic residues Asp125, Glu127, and Tyr182. © 2006 The Authors.

Microwave-induced fast decalcification of rat bone for electron microscopic analysis: An ultrastructural and cytochemical study

Bone decalcification is a time-consuming process. It takes weeks and preservation of the tissue structure depends on the quality and velocity of the demineralization process. In the present study, a decalcification methodology was adapted using microwaving to accelerate the decalcification of rat bone for electron microscopic analysis. The ultrastructure of the bone decalcified by microwave energy was observed. Wistar rats were perfused with paraformaldehyde and maxillary segments were removed and fixed in glutaraldehyde. Half of specimens were decalcified by conventional treatment with immersion in Warshawsky solution at 4oC during 45 days, and the other half of specimens were placed into the beaker with 20 mL of the Warshawsky solution in ice bath and thereafter submitted to irradiation in a domestic microwave oven (700 maximum power) during 20 s/350 W/±37°C. In the first day, the specimens were irradiated 9 times and stored at 40°C overnight. In the second day, the specimens were irradiated 20 times changing the solution and the ice after each bath. After decalcification, some specimens were postfixed in osmium tetroxide and others in osmium tetroxide and potassium pyroantimonate. The specimens were observed under transmission electron microscopy. The results showed an increase in the decalcification rate in the specimens activated by microwaving and a reduction of total experiment time from 45 days in the conventional method to 48 hours in the microwave-aided method.

Observation of piezoelectric response on tungsten doped barium zirconium titanate ceramics

This study describes observation of piezoelectric response of Ba(Zr 0.10Ti 0.90.O3 ceramics modified with tungsten (BZT:2W) by the mixed oxide method. According to X ray diffraction analysis, the ceramics are free of secondary phases. Transmission electron microscopy (TEM) analyses reveals the absence of segregates in the grain boundaries indicates the high solubility of WO3 in the BZT matrix. The dielectric permittivity measured at a frequency of 10 KHz was equal to 6500 with dieletric loss of 0.15. A typical hysteresis loop was observed at room temperature. Electron Paramagnetic Resonance (EPR) analyses reveals that substitution of W6+ by Ti4+ causes distortion in the crystal structure changing lattice parameter. Polarization reversal was investigated by applying dc voltage through a conductive tip during the area scanning. Piezoelectric force microscopy images reveals that in-plane response may not change its sign upon polarization switching, while the out-of-plane response does. Copyright © 2010 American Scientific Publishers.

Template-based fluoropolymer ferroelectrets with multiple layers of tubular channels

Significant efforts are devoted to developing new ferroelectrets with well-controlled void distributions or uniform voids and with good long-term and thermal stability of the piezoelectricity. Here, we describe the concept, the fabrication, and the most relevant properties of fluoropolymer ferroelectret systems with three separate films of fluoroethylenepropylene (FEP), alternating with two polytetrafluoroethylene (PTFE) templates. The FEP films are selectively fused by means of a lamination process. Two practically identical PTFE templates are used, which have parallel rectangular openings (1.5×30 mm 2) separated by PTFE ridges of 1.5 mm width. After removing the PTFE templates, a three-layer FEP-film sandwich with tubular channels is obtained. We demonstrate that such FEP-film systems exhibit significant and stable piezoelectricity after charging under a high DC voltage. The resulting piezoelectric effect may be further improved by carefully assembling and arranging the PTFE templates during preparation. ©2010 IEEE.

Microscopic and dielectric analyses of vanadium and tungsten modified barium zirconium titanate ceramics

Dielectric spectroscopy was used in this study to examine polycrystalline vanadium and tungstendoped BaZr 0.1Ti 0.90O 3 (BZT10:2V and BZT10:2W) ceramics obtained by the mixed oxide method. According to X-ray diffraction analyses, addition of vanadium and tungsten lead to ceramics free of secondary phases. SEM analyses reveal that both dopants result in slower oxygen ion motion and consequently lower grain growth rate. Temperature dependence dielectric study showed normal ferroelectric to paraelectric transition well above the room temperature for the BZT10 and BZT10:2V ceramics. However, BZT10:2W ceramic showed a relaxor-like behavior near phase transition characterized by the empirical parameter γ. Piezoelectric force microscopy images reveals that the piezoelectric coefficient is strongly influenced by type of donor dopant suggesting promising applications for dynamic random access memories and data-storage media. Copyright © 2010 American Scientific Publishers All rights reserved.

Structure of a novel class II phospholipase D: Catalytic cleft is modified by a disulphide bridge

Phospholipases D (PLDs) are principally responsible for the local and systemic effects of Loxosceles envenomation including dermonecrosis and hemolysis. Despite their clinical relevance in loxoscelism, to date, only the SMase I from Loxosceles laeta, a class I member, has been structurally characterized. The crystal structure of a class II member from Loxosceles intermedia venom has been determined at 1.7. Å resolution. Structural comparison to the class I member showed that the presence of an additional disulphide bridge which links the catalytic loop to the flexible loop significantly changes the volume and shape of the catalytic cleft. An examination of the crystal structures of PLD homologues in the presence of low molecular weight compounds at their active sites suggests the existence of a ligand-dependent rotamer conformation of the highly conserved residue Trp230 (equivalent to Trp192 in the glycerophosphodiester phosphodiesterase from Thermus thermophofilus, PDB code: 1VD6) indicating its role in substrate binding in both enzymes. Sequence and structural analyses suggest that the reduced sphingomyelinase activity observed in some class IIb PLDs is probably due to point mutations which lead to a different substrate preference. © 2011 Elsevier Inc.