Cloning and characterization of the cDNA for the Brazilian Cratomorphus distinctus larval firefly luciferase: Similarities with European Lampyris noctiluca and Asiatic Pyrocoelia luciferases

Studies on firefly (Lampyridae) luciferases have focused on nearctic species of Photinus and Photuris and Euroasiatic species of Lampyris, Luciola, Hotaria, and Pyrocoelia. Despite accounting for the greatest diversity of fireflies in the world, no molecular studies have been carried out on the highly diverse genera from the neotropical region. Here we report the luciferase cDNA cloning for the larva of the Brazilian firefly Cratomorphus distinctus. The cDNA has 1978 bp and codes for a 547-residue-long polypeptide. Noteworthy, sequence comparison as well as functional properties show the highest degree of similarity with Lampyris noctiluca (93%) and Pyrocoelia spp. (91%) luciferases, suggesting a close phylogenetic relationship despite the geographical distance separating these species. The bioluminescence emission spectrum peaks at 550 nm and, as expected, is sensitive to pH, shifting to 605 nm at pH 6. The kinetic properties of the recombinant luciferase were similar to those of other firefly luciferases. © 2004 Elsevier Inc. All rights reserved.

The structural origin and biological function of pH-sensitivity in firefly luciferases

Firefly luciferases are called pH-sensitive because their bioluminescence spectra display a typical red-shift at acidic pH, higher temperatures, and in the presence of heavy metal cations, whereas other beetle luciferases (click beetles and railroadworms) do not, and for this reason they are called pH-insensitive. Despite many studies on firefly luciferases, the origin of pH-sensitivity is far from being understood. This subject is revised in view of recent results. Some substitutions of amino-acid residues influencing pH-sensitivity in firefly luciferases have been identified. Sequence comparison, site-directed mutagenesis and modeling studies have shown a set of residues differing between pH-sensitive and pH-insensitive luciferases which affect bioluminescence colors. Some substitutions dramatically affecting bioluminescence colors in both groups of luciferases are clustered in the loop between residues 223-235 (Photinus pyralis sequence). A network of hydrogen bonds and salt bridges involving the residues N229-S284-E311-R337 was found to be important for affecting bioluminescence colors. It is suggested that these structural elements may affect the benzothiazolyl side of the luciferin-binding site affecting bioluminescence colors. Experimental evidence suggest that the residual red light emission in pH-sensitive luciferases could be a vestige that may have biological importance in some firefly species. Furthermore, the potential utility of pH-sensitivity for intracellular biosensing applications is considered. © The Royal Society of Chemistry and Owner Societies.

A preliminary physicochemical, exergetic and economic study of hydrogen production utilizing glycerol

This work has as objective to demonstrate technical and economic viability of hydrogen production utilizing glycerol. The volume of this substance, which was initially produced by synthetic ways (from oil-derived products), has increased dramatically due mainly to biodiesel production through transesterification process which has glycerol as main residue. The surplus amount of glycerol has been generally utilized to feed poultry or as fuel in boilers, beyond other applications such as production of soaps, chemical products for food industry, explosives, and others. The difficulty to allocate this additional amount of glycerol has become it in an enormous environment problem, in contrary to the objective of biodiesel chain, which is to diminish environmental impact substituting oil and its derivatives, which release more emissions than biofuels, do not contribute to CO2-cycle and are not renewable sources. Beyond to utilize glycerol in combustion processes, this material could be utilized for hydrogen production. However, a small quantity of works (theoretical and experimental) and reports concerning this theme could be encountered. Firstly, the produced glycerol must be purified since non-reacted amounts of materials, inclusively catalysts, contribute to deactivate catalysts utilized in hydrogen production processes. The volume of non-reacted reactants and non-utilized catalysts during transesterification process could be reutilized. Various technologies of thermochemical generation of hydrogen that utilizes glycerol (and other fuels) were evaluated and the greatest performances and their conditions are encountered as soon as the most efficient technology of hydrogen production. Firstly, a physicochemical analysis must be performed. This step has as objective to evaluate the necessary amount of reactants to produce a determined volume of hydrogen and determine thermodynamic conditions (such as temperature and pressure) where the major performances of hydrogen production could be encountered. The calculations are based on the process where advance degrees are found and hence, fractions of products (especially hydrogen, however, CO2, CO, CH4 and solid carbon could be also encountered) are calculated. To produce 1 Nm3/h of gaseous hydrogen (necessary for a PEMFC - Proton Exchange Membrane Fuel Cell - containing an electric efficiency of about 40%, to generate 1 kWh), 0,558 kg/h of glycerol is necessary in global steam reforming, 0,978 kg/h of glycerol in partial oxidation and cracking processes, and 0,782 kg/h of glycerol in autothermal reforming process. The dry reforming process could not be performed to produce hydrogen utilizing glycerol, in contrary to the utilization of methane, ethanol, and other hydrocarbons. In this study, steam reforming process was preferred due mainly to higher efficiencies of production and the need of minor amount of glycerol as cited above. In the global steam reforming of glycerine, for one mole of glycerol, three moles of water are necessary to produce three moles of CO2 and seven moles of H2. The response reactions process was utilized to predict steam reforming process more accurately. In this mean, the production of solid carbon, CO, and CH4, beyond CO2 and hydrogen was predicted. However, traces of acetaldehyde (C2H2), ethylene (C2H4), ethylene glycol, acetone, and others were encountered in some experimental studies. The rates of determined products obviously depend on the adopted catalysts (and its physical and chemical properties) and thermodynamic conditions of hydrogen production. Eight reactions of steam reforming and cracking were predicted considering only the determined products. In the case of steam reforming at 600°C, the advance degree of this reactor could attain its maximum value, i.e., overall volume of reactants could be obtained whether this reaction is maintained at 1 atm. As soon as temperature of this reaction increases the advance degree also increase, in contrary to the pressure, where advance degree decrease as soon as pressure increase. The fact of temperature of reforming is relatively small, lower costs of installation could be attained, especially cheaper thermocouples and smaller amount of thermo insulators and materials for its assembling. Utilizing the response reactions process in steam reforming, the predicted volumes of products, for the production of 1 Nm3/h of H2 and thermodynamic conditions as cited previously, were 0,264 kg/h of CO (13% of molar fraction of reaction products), 0,038 kg/h of CH4 (3% of molar fraction), 0,028 kg/h of C (3% of molar fraction), and 0,623 kg/h of CO2 (20% of molar fraction). Through process of water-gas shift reactions (WGSR) an additional amount of hydrogen could be produced utilizing mainly the volumes of produced CO and CH4. The overall results (steam reforming plus WGSR) could be similar to global steam reforming. An attention must to be taking into account due to the possibility to produce an additional amount of CH4 (through methanation process) and solid carbon (through Boudouard process). The production of solid carbon must to be avoided because this reactant diminishes (filling the pores) and even deactivate active area of catalysts. To avoid solid carbon production, an additional amount of water is suggested. This method could be also utilized to diminish the volume of CO (through WGSR process) since this product is prejudicial for the activity of low temperature fuel cells (such as PEMFC). In some works, more three or even six moles of water are suggested. A net energy balance of studied hydrogen production processes (at 1 atm only) was developed. In this balance, low heat value of reactant and products and utilized energy for the process (heat supply) were cited. In the case of steam reforming utilizing response reactions, global steam reforming, and cracking processes, the maximum net energy was detected at 700°C. Partial oxidation and autothermal reforming obtained negative net energy in all cited temperatures despite to be exothermic reactions. For global steam reforming, the major value was 114 kJ/h. In the case of steam reforming, the highest value of net energy was detected in this temperature (-170 kJ/h). The major values were detected in the cracking process (up to 2586 kJ/h). The exergetic analysis has as objective, associated with physicochemical analysis, to determine conditions where reactions could be performed at higher efficiencies with lower losses. This study was performed through calculations of exergetic and rational efficiencies, and irreversibilities. In this analysis, as in the previously performed physicochemical analysis, conditions such as temperature of 600°C and pressure of 1 atm for global steam reforming process were suggested due to lower irreversibility and higher efficiencies. Subsequently, higher irreversibilities and lower efficiencies were detected in autothermal reforming, partial oxidation and cracking process. Comparing global reaction of steam reforming with more-accurate steam reforming, it was verified that efficiencies were diminished and irreversibilities were increased. These results could be altered with introduction of WGSR process. An economic analysis could be performed to evaluate the cost of generated hydrogen and determine means to diminish the costs. This analysis suggests an annual period of operation between 5000-7000 hours, interest rates of up to 20% per annum (considering Brazilian conditions), and pay-back of up to 20 years. Another considerations must to be take into account such as tariffs of utilized glycerol and electricity (to be utilized as heat source and (or) for own process as pumps, lamps, valves, and other devices), installation (estimated as US$ 15.000 for a plant of 1 Nm3/h) and maintenance cost. The adoption of emission trading schemes such as carbon credits could be performed since this is a process with potential of mitigates environment impact. Not considering credit carbons, the minor cost of calculated H2 was 0,16288 US$/kWh if glycerol is also utilized as heat sources and 0,17677 US$/kWh if electricity is utilized as heat sources. The range of considered tariff of glycerol was 0-0,1 US$/kWh (taking as basis LHV of H2) and the tariff of electricity is US$ 0,0867 US$/kWh, with demand cost of 12,49 US$/kW. The costs of electricity were obtained by Companhia Bandeirante, localized in São Paulo State. The differences among costs of hydrogen production utilizing glycerol and electricity as heat source was in a range between 0,3-5,8%. This technology in this moment is not mature. However, it allows the employment generation with the additional utilization of glycerol, especially with plants associated with biodiesel plants. The produced hydrogen and electricity could be utilized in own process, increasing its final performance.

Analysis of agonist and antagonist effects on thyroid hormone receptor conformation by hydrogen/deuterium exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T 3) or antagonist (NH3). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/ deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, Cterminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T 3, but not NH3, increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T 3 but not NH3.Wepresent data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011). Copyright © 2011 by The Endocrine Society.

The use of molecular spectra simulation for diagnostics of reactive flows

The C 2 * radical is used as a system probe tool to the reactive flow diagnostic, and it was chosen due to its large occurrence in plasma and combustion in aeronautics and aerospace applications. The rotational temperatures of C 2 * species were determined by the comparison between experimental and theoretical data. The simulation code was developed by the authors, using C++ language and the object oriented paradigm, and it includes a set of new tools that increase the efficacy of the C 2 * probe to determine the rotational temperature of the system. A brute force approach for the determination of spectral parameters was adopted in this version of the computer code. The statistical parameter c 2 was used as an objective criterion to determine the better match of experimental and synthesized spectra. The results showed that the program works even with low-quality experimental data, typically collected from in situ airborne compact apparatus. The technique was applied to flames of a Bunsen burner, and the rotational temperature of ca. 2100 K was calculated.

Hydrogen bonding donation of N-methylformamide with dimethylsulfoxide and water

20% N-methylformamide (NMF) mixtures with water and with dimethylsulfoxide (DMSO) have been studied. A comparison between the hydrogen bonding (H-bond) donation of N-methylformamide with both solvents in the mixtures is presented. Results of radial distribution functions, pair distribution energies, molecular dipole moment correlation, and geometry of the H-bonded species in each case are shown. The results indicate that the NMF-solvent H-bond is significantly stronger with DMSO than with water. The solvation shell is best organized in the DMSO mixture than in the aqueous one. © 2013 Elsevier B.V. All rights reserved.

Estudo por dinâmica molecular da estabilidade conformacional de dímeros do peptídeo Eumenine mastoparan-AF em água e mistura TFE-água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Interação do peptídeo MP-I com micela de SDS em solução aquosa: um estudo por dinâmica molecular

Pós-graduação em Biofísica Molecular - IBILCE

Tunelamento quântico molecular: efeito de acoplamentos no malonaldeído

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Desenvolvimento de estruturas porosas de polietileno de ultra alto peso molecular (PEUAPM) recobertas com apatitas para substituição e regeneração óssea

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo das propriedades ópticas e vibracionais de filmes de GaN dopados com Mn elaborados por RF Magnetron Sputtering Reativo

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A simple and fast method for assessment of the nitrogen-phosphorus-potassium rating of fertilizers using high-resolution continuum source atomic and molecular absorption spectrometry

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Stretching of BDT-gold molecular junctions: thiol or thiolate termination?

It is often assumed that the hydrogen atoms in the thiol groups of a benzene-1,4-dithiol dissociate when Au-benzene-1,4-dithiol-Au junctions are formed. We demonstrate, by stability and transport property calculations, that this assumption cannot be made. We show that the dissociative adsorption of methanethiol and benzene-1,4-dithiol molecules on a flat Au(111) surface is energetically unfavorable and that the activation barrier for this reaction is as high as 1 eV. For the molecule in the junction, our results show, for all electrode geometries studied, that the thiol junctions are energetically more stable than their thiolate counterparts. Due to the fact that density functional theory (DFT) within the local density approximation (LDA) underestimates the energy difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital by several electron-volts, and that it does not capture the renormalization of the energy levels due to the image charge effect, the conductance of the Au-benzene-1,4-dithiol-Au junctions is overestimated. After taking into account corrections due to image charge effects by means of constrained-DFT calculations and electrostatic classical models, we apply a scissor operator to correct the DFT energy level positions, and calculate the transport properties of the thiol and thiolate molecular junctions as a function of the electrode separation. For the thiol junctions, we show that the conductance decreases as the electrode separation increases, whereas the opposite trend is found for the thiolate junctions. Both behaviors have been observed in experiments, therefore pointing to the possible coexistence of both thiol and thiolate junctions. Moreover, the corrected conductance values, for both thiol and thiolate, are up to two orders of magnitude smaller than those calculated with DFT-LDA. This brings the theoretical results in quantitatively good agreement with experimental data.

Estudo das interações de peptídeos antimicrobianos e sistemas miméticos de membrana por dinâmica molecular

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Quantum chemical topological analysis of hydrogen bonding in HX…HX and CH3X…HX dimers (X = Br, Cl, F)

We present a systematic investigation of the nature and strength of the hydrogen bonding in HX···HX and CH3X…HX (X = Br, Cl and F) dimers using ab initio MP2/aug-cc-pVTZ calculations in the framework of the quantum theory of atoms in molecules (QTAIM) and electron localisation functions (ELFs) methods. The electron density of the complexes has been characterised, and the hydrogen bonding energy, as well as the QTAIM and ELF parameters, is consistent, providing deep insight into the origin of the hydrogen bonding in these complexes. It was found that in both linear and angular HX…HX and CH3X…HX dimers, F atoms form stronger HB than Br and Cl, but they need short (∼2 Å) X…HX contacts.