Estudos computacionais de esfingomielinases D: docking, dinâmica molecular e métodos híbridos QM/MM

Pós-graduação em Biofísica Molecular - IBILCE

Enhanced Polymer Grafting from Multiwalled Carbon Nanotubes through Living Anionic Surface-Initiated Polymerization

Anionic surface-initiated polymerization of ethylene oxide and styrene has been performed using multiwalled carbon nanotubes (MWNTs) functionalized with anionic initiators. The surface of MWNTs was modified via covalent attachment of precursor anions such as 4-hydroxyethyl benzocyclobutene (BCBEO) and 1-benzocyclobutene-1′-phenylethylene (BCB-PE) through Diels-Alder cycloaddition at 235 °C. Surface-functionalized MWNTs-g-(BCB-EO) n and MWNTs-g-(BCB-PE) n with 23 and 54 wt % precursor initiators, respectively, were used for the polymerizations. Alkoxide anion on the surface of MWNTs-g-(BCB-EO) n was generated through reaction with potassium triphenylmethane for the polymerization of ethylene oxide in tetrahydrofuran and phenyl substituted alkyllithium was generated from the surface of MWNTs-g-(BCB-PE) n using sec-butyllithium for the polymerization of styrene in benzene. In both cases, the initiation was found to be very slow because of the heterogeneous reaction medium. However, the MWNTs gradually dispersed in the reaction medium during the polymerization. A pale green color was noticed in the case of ethylene oxide polymerization and the color of initiator as well as the propagating anions was not discernible visually in styrene polymerization. Polymer grafted nanocomposites, MWNTs-g-(BCB-PEO) n and MWNTs-g-(BCB-PS) n containing a very high percentage of hairy polymer with a small fraction of MWNTs (<1 wt %) were obtained. The conversion of ethylene oxide and the weight percent of PEO on the surface of the MWNTs increased with increasing reaction time indicating a controlled polymerization. The polymer-grafted MWNTs were characterized using FTIR, 1H NMR, Raman spectroscopy, differential scanning calorimetry, thermogravimetric analysis, and transmission electron microscopy (TEM). Size exclusion chromatography of the polymer grafted MWNTs revealed broad molecular weight distributions (1.3 < Mw/Mn < 1.8) indicating the presence of different sizes of polymer nanocomposites. The TEM images showed the presence of thick layers of polymer up to 30 nm around the MWNTs. The living nature of the growing polystyryllithium was used to produce diblock copolymer grafts using sequential polymerization of isoprene on the surface of MWNTs.

Holocarboxylase Synthetase-dependent Biotinylation of Histone H4

Holocarboxylase synthetase (HCS) catalyzes the binding of biotin to lysine (K) residues in histones H3 and H4. Histone biotinylation marks play important roles in the repression of genes and retrotransposons. Preliminary studies suggested that K16 in histone H4 is a target for biotinylation by HCS. Here we demonstrated that H4K16bio is overrepresented in repeat regions {pericentromeric alpha satellite repeats; long terminal repeats (LTR)} compared with euchromatin promoters. H4K16bio was also enriched in the repressed interleukin-2 gene promoter. The enrichment at LTR22 and promoter 1 of the sodium-dependent multivitamin transporter (SMVT) depended on biotin supply; and was significantly lower in fibroblasts from an HCS-deficient patient compared with an HCS wild-type control. We conclude that H4K16bio is a real phenomenon and plays a role in the transcriptional repression of repeats and genes. HCS catalyzes the covalent binding of biotin to carboxylases, in addition to its role as a histone biotinyl ligase. HCS null individuals are not viable whereas HCS deficiency is linked to developmental delays and phenotypes such as short life span and low stress resistance. Here, we developed a 96-well plate assay for high-throughput analysis of HCS based on the detection of biotinylated p67 using IRDye-streptavidin and infrared spectroscopy. We demonstrated that the catalytic activity of rHCS depends on temperature and time, and proposed optimal substrate and enzyme concentrations to ensure ideal measurement of rHCS activity and its kinetics. Additionally, we demonstrated that this assay is sensitive enough to detect biotinylation of p67 by endogenous HCS from Jurkat lymphoid cells.

Deterministic Solutions for a Step-growth Polymerization

Chain topology, including branch node, chain link and cross-link dynamics that contribute to the number of elastically active strands and junctions, are calculated using purely deterministic derivations. Solutions are not coupled to population density distributions. An eigenzeit transformation assists in the conversion of expressions derived by chemical reaction principles from time to conversion space, yielding transport phenomena type expressions where the rate of change in the molar concentrations of branch nodes with respect to conversion is expressed as functions of the fraction of reactive sites on precursors and reactants. Analogies are hypothesized to exist in cross-linking space that effectively distribute branch nodes with i reacted moieties between cross-links having j bonds extending to the gel. To obtain solutions, reacted sites on nodes or links with finite chain extensions are examined in terms of stoichiometry associated with covalent bonding. Solutions replicate published results based on Miller and Macosko’s recursive procedure and results obtained from truncated weighted sums of population density distributions as suggested by Flory.

Estudos computacionais de esfingomielinases D: docking, dinâmica molecular e métodos híbridos QM/MM

Pós-graduação em Biofísica Molecular - IBILCE

Influence of the use of Aliquat 336 in the immobilization procedure in sol-gel of lipase from Bacillus sp ITP-001

Aliquat 336, a liquid hydrophobic material, was used at different concentrations (0.5-3.0%, w/v) as an additive in the preparation of encapsulated lipase from Bacillus sp. ITP-001 on sol-gel silica matrices using tetraethoxysilane (TEOS) as the precursor. The resulting hydrophobic matrices and immobilized lipases were characterized with regard to specific surface area (BET method), adsorption-desorption isotherms, pore volume (Vp) and size (dp) by nitrogen adsorption (BJH method) and scanning electron microscopy (SEM). The catalytic activities and the corresponding coupling yields were assayed in the hydrolysis of olive oil. In comparison with pure silica matrices, the immobilization process in the presence of Aliquat 336 decreased the values for specific surface area and increased the values for pore specific volume (Vp) and mean pore diameter (dp). This behavior may be related to the partial adsorption of the enzyme on the external surface of the hydrophobic matrix as indicated by scanning electron microscopy. Aliquat 336 concentrations in the range from 0.5 to 1.5% (w/v) provided immobilized derivatives with higher coupling yields and better substrate affinity. The highest coupling yield (Y-A = 71%) was obtained for the immobilized enzyme prepared in the presence of 1.5% Aliquat which gave the following morphological properties: specific surface area = 183 m(2)/g, pore specific volume (Vp) = 0.36 cc/g and mean pore diameter (dp)= 91 angstrom. (c) 2012 Elsevier B.V. All rights reserved.

Structural and Luminescence Properties of Silica-Based Hybrids Containing New Silylated-Diketonato Europium(III) Complex

A new betadiketonate ligand displaying a trimethoxysilyl group as grafting function and a diketone moiety as complexing site (TTA-Si = 4,4,4-trifluoro-2-(3-trimethoxysilyl)propyl)-1-3-butanedione (C4H3S)COCH[(CH2)(3)Si(OCH3)(3)]COCF3) and its highly luminescent europium(III) complex [Eu(TTA-Si)(3)] have been synthesized and fully characterized. Luminescent silica-based hybrids have been prepared as well with this new complex grafted on the surface of dense silica nanoparticles (28 +/- 3 nm) or on mesoporous silica particles. The covalent bonding of Eu(TTA-Si)(3) inside the core of uniform silica nanoparticles (40 +/- 5 nm) was also achieved. Luminescence properties are discussed in relation to the europium chemical environment involved in each of the three hybrids. The general methodology proposed allowed high grafting ratios and overcame chelate release and tendency to agglomeration, and it could be applied to any silica matrix (in the core or at the surface, nanosized or not, dense or mesoporous) and therefore numerous applications such as luminescent markers and luminophors could be foreseen.

Spermatophoric reaction reappraised: Novel insights into the functioning of the loliginid spermatophore based on Doryteuthis plei (Mollusca: Cephalopoda)

During copulation, spermatophores produced by male coleoid cephalopods undergo the spermatophoric reaction, a complex process of evagination that culminates in the attachment of the spermatangium (everted spermatophore containing the sperm mass) on the female's body. To better understand this complicated phenomenon, the present study investigated the functional morphology of the spermatophore of the squid Doryteuthis plei applying in vitro analysis of the reaction, as well as light and electron microscopy investigation of spermatangia obtained either in vitro, or naturally attached on females. Hitherto unnoticed functional features of the loliginid spermatophore require a reappraisal of some important processes involved in the spermatophoric reaction. The most striking findings concern the attachment mechanism, which is not carried out solely by cement adhesive material, as previously believed, but rather by an autonomous, complex process performed by multiple structures during the spermatophoric reaction. During evagination, the ejaculatory apparatus provides anchorage on the targeted tissue, presumably due to the minute stellate particles present in the exposed spiral filament. Consequently, the ejaculatory apparatus maintains the attachment of the tip of the evaginating spermatophore until the cement body is extruded. Subsequently, the cement body passes through a complex structural rearrangement, which leads to the injection of both its viscid contents and pointed oral region onto the targeted tissue. The inner membrane at the oral region of the cement body contains numerous stellate particles attached at its inner side; eversion of this membrane exposes these sharp structures, which presumably adhere to the tissue and augment attachment. Several naturally attached spermatangia were found with their bases implanted at the deposition sites, and the possible mechanisms of perforation are discussed based on present evidence. The function of the complex squid spermatophore and its spermatophoric reaction is revisited in light of these findings. J. Morphol. 2012. (C) 2011 Wiley Periodicals, Inc.

PHYSICO-CHEMICAL, SPECTROSCOPICAL AND THERMAL CHARACTERIZATION OF BIODIESEL OBTAINED BY ENZYMATIC ROUTE AS A TOOL TO SELECT THE MOST EFFICIENT IMMOBILIZED LIPASE

Two microbial lipases from Burkholderia cepacia and Pseudomonas fluorescens were evaluated as catalysts for the enzymatic transesterification of beef tallow with ethanol and the most efficient lipase source was selected by taking into account the properties of the product to be used as fuel. Both lipases were immobilized on an epoxy silica-polyvinyl alcohol composite by covalent immobilization and used to perform the reactions under the following operational conditions: beef tallow-to-ethanol molar ratio of 1:9, 45 degrees C and 400 units of enzymatic activity per gram of fat. Products, characterized using Fourier Transform Infrared spectroscopy (FTIR), viscosimetry, thermogravimetry and H-1 NMR spectroscopy, suggested that the biodiesel sample obtained in the reaction catalyzed by Burkholderia cepacia lipase has the best set of properties for fuel usage.

Iron(III) Porphyrin Covalently Supported onto Magnetic Amino-Functionalized Nanospheres as Catalyst for Hydrocarbon and Herbicide Oxidations

This work describes the covalent immobilization of an ironporphyrin, 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin iron(III) chloride (FeTFPP), onto maghemite/silica magnetic nanospheres covered with aminofunctionalized silica. The resulting material (gamma-Fe2O3/SiO2-NHFeP) was characterized by diffuse reflectance infrared spectroscopy (DRIFTS) and UV-Vis absorption spectroscopy. The catalytic activity of this magnetic ironporphyrin was investigated in the oxidation of hydrocarbons (styrene, (Z)-cyclooctene and R-(+)-limonene) and an herbicide (simazine) by hydrogen peroxide or 3-chloroperoxybenzoic acid. Hydrocarbon and simazine oxidation reaction products were analyzed by gas chromatography (GC) and high performance liquid chromatography (HPLC), respectively. This catalytic system proved to be efficient and selective for hydrocarbon oxidation, leading to high product yields from styrene (89%), cyclooctene (71%) and R-(+) -limonene (86%). Simazine oxidation was attained with 100% selectivity for a dechlorinated product (OEAT), while several oxidation products were obtained for the same catalyst in homogeneous media. The catalyst can be easily recovered through application of an external magnetic field and washed after reaction. Catalyst reuse experiments for R-(+)-limonene oxidation have shown that the catalytic activity is kept at 90% after 10 consecutive reactions.

Metal binding selectivity of oxa-aza macrocyclic ligand: a DFT study of first- and second-row transition metal for four coordination systems

A detailed theoretical study of the 1,7,1l,17-tetraoxa-2,6,12,16-tetraaza-cycloeicosane ligand ([20]AneN(4)O(4)) coordinated to Fe2+, Co2+, Ni2+, Ru2+, Rh2+, and Pd2+ transition metal ions was carried out with the B3LYP method. Two different cases were performed: when nitrogen is the donor atom (1a (q) ) and also with the oxygen as the donor atom (1b (q) ). For all the cases performed in this study 1a (q) structures were always more stable than the 1b (q) ones. Considering each row is possible to see that the energy increases with the increase of the atomic number. The M2+ cation binding energies for the 1a (q) complexes increase with the following order: Fe2+ < Ru2+ < Co2+ < Ni2+ < Rh2+ < Pd2+.

The Cysteine-Rich Protein Thimet Oligopeptidase as a Model of the Structural Requirements for S-glutathiolation and Oxidative Oligomerization

Thimet oligopeptidase (EP24.15) is a cysteine-rich metallopeptidase containing fifteen Cys residues and no intra-protein disulfide bonds. Previous work on this enzyme revealed that the oxidative oligomerization of EP24.15 is triggered by S-glutathiolation at physiological GSSG levels (10-50 mu M) via a mechanism based on thiol-disulfide exchange. In the present work, our aim was to identify EP24.15 Cys residues that are prone to S-glutathiolation and to determine which structural features in the cysteinyl bulk are responsible for the formation of mixed disulfides through the reaction with GSSG and, in this particular case, the Cys residues within EP24.15 that favor either S-glutathiolation or inter-protein thiol-disulfide exchange. These studies were conducted by in silico structural analyses and simulations as well as site-specific mutation. S-glutathiolation was determined by mass spectrometric analyses and western blotting with anti-glutathione antibody. The results indicated that the stabilization of a thiolate sulfhydryl and the solvent accessibility of the cysteines are necessary for S-thiolation. The Solvent Access Surface analysis of the Cys residues prone to glutathione modification showed that the S-glutathiolated Cys residues are located inside pockets where the sulfur atom comes into contact with the solvent and that the positively charged amino acids are directed toward these Cys residues. The simulation of a covalent glutathione docking onto the same Cys residues allowed for perfect glutathione posing. A mutation of the Arg residue 263 that forms a saline bridge to the Cys residue 175 significantly decreased the overall S-glutathiolation and oligomerization of EP24.15. The present results show for the first time the structural requirements for protein S-glutathiolation by GSSG and are consistent with our previous hypothesis that EP24.15 oligomerization is dependent on the electron transfer from specific protonated Cys residues of one molecule to previously S-glutathionylated Cys residues of another one.

A model to explain spermatophore implantation in cephalopods (Mollusca: Cephalopoda) and a discussion on its evolutionary origins and significance

Male coleoid cephalopods produce spermatophores that can attach autonomously on the female's body during a complex process of evagination called the spermatophoric reaction, during which the ejaculatory apparatus and spiral filament of the spermatophore are everted and exposed to the external milieu. In some deepwater cephalopods, the reaction leads to the intradermal implantation of the spermatophore, a hitherto enigmatic phenomenon. The present study builds upon several lines of evidence to propose that spermatophore implantation is probably achieved through the combination of (1) an evaginating-tube mechanism performed by the everting ejaculatory apparatus and (2) the anchorage provided by the spiral filament's stellate particles. The proposed theoretical model assumes that, as it is exposed to the external milieu, each whorl of the spiral filament anchors to the surrounding tissue by means of its sharp stellate particles. As the ejaculatory apparatus tip continues evaginating, it grows in diameter and stretches lengthwise, enlarging the diameter of the whorl and propelling it, consequently tearing and pushing the anchored tissue outward and backward, and opening space for the next whorl to attach. After the ejaculatory apparatus has been everted and has perforated tissue, the cement body is extruded, possibly aiding in final attachment, and the sperm mass comes to lie inside the female tissue, encompassed by the everted ejaculatory apparatus tube. It is proposed that this unique, efficient spermatophore attachment mechanism possibly evolved in intimate relationship with the adoption of an active mode of life by coleoids. The possible roles of predation pressure and sperm competition in the evolution of this mechanism are also discussed. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 711726.

Hydrogen bond and the resonance effect on the formamide-water complexes

The interaction of formamide and the two transition states of its amide group rotation with one, two, or three water molecules was studied in vacuum. Great differences between the electronic structure of formamide in its most stable form and the electronic structure of the transition states were noticed. Intermolecular interactions were intense, especially in the cases where the solvent interacted with the amide and the carbonyl groups simultaneously. In the transition states, the interaction between the lone pair of nitrogen and the water molecule becomes important. With the aid of the natural bond orbitals, natural resonance theory, and electron localization function (ELF) analyses an increase in the resonance of planar formamide with the addition of successive water molecules was observed. Such observation suggests that the hydrogen bonds in the formamidewater complexes may have some covalent character. These results are also supported by the quantitative ELF analyses. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Th2NiC2: a low density of states superconductor

The metallic carbides exhibit many novel prototypes of crystalline structure. Among these compounds Th2NiC2 was reported in 1991 as a new carbide which crystallizes in the U2IrC2 prototype structure. In this work we report a reinvestigation of the synthesis of this compound. We find that Th2NiC2 is a new superconductor. Our results suggest that this phase is stable only at high temperatures in the system Th-Ni-C. The substitution of Th by Sc stabilizes the phase and improves the superconducting properties. The highest superconducting critical temperature occurs at 11.2 K with nominal composition Th1.8Sc0.2NiC2. The electronic coefficient determined by specific heat measurements is close to zero. This unusual result can be explained by covalent bonding in the compound.