Molecular models of protein targets from Mycobacterium tuberculosis

Structural characterization of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design since some of these proteins may be present in the bacterial genome, but absent in humans. Thus, metabolic pathways became potential targets for drug design. The motivation of this work is the fact that Mycobacterium tuberculosis is the cause of the deaths of millions of people in the world, so that the structural characterization of protein targets to propose new drugs has become essential. DBMODELING is a relational database, created to highlight the importance of methods of molecular modeling applied to the Mycobacterium tuberculosis genome with the aim of proposing protein-ligand docking analysis. There are currently more than 300 models for proteins from Mycobacterium tuberculosis genome in the database. The database contains a detailed description of the reaction catalyzed by each enzyme and their atomic coordinates. Information about structures, a tool for animated gif image, a table with a specification of the metabolic pathway, modeled protein, inputs used in modeling, and analysis methods used in this project are available in the database for download. The search tool can be used for reseachers to find specific pathways or enzymes.

Investigation about the efficiency of the bioaugmentation technique when applied to diesel oil contaminated soils

Este trabalho investigou a eficiência da técnica do bioaumento quando aplicada a solos contaminados com óleo diesel coletados em três postos de combustíveis. Experimentos de biodegradação foram realizados em frascos de Bartha (250 mL), usados para medir a produção microbiana de CO2. A eficiência de biodegradação também foi quantificada pela concentração de hidrocarbonetos. Conjuntamente aos experimentos de biodegradação, a capacidade das culturas estudadas e dos microrganismos nativos em biodegradar óleo diesel comprado de um posto de combustíveis local, foi verificada utilizando-se a técnica baseada no indicador redox 2,6 - diclorofenol indofenol (DCPIP). Resultados obtidos com esse teste mostraram que os inóculos empregados nos experimentos de biodegradação foram capazes de biodegradar óleo diesel e os testes com os microrganismos nativos indicaram que estes solos previamente apresentavam uma microbiota adaptada para degradar hidrocarbonetos. em suma, nenhum ganho foi obtido com a adição dos microrganismos ou mesmo efeitos negativos foram observados nos experimentos de biodegradação.

Thrombomodulin-independent activation of protein C and specificity of hemostatically active snake venom serine proteinases - Crystal structures of native and inhibited Agkistrodon contortrix contortrix protein C activator

Protein C activation initiated by the thrombin-thrombomodulin complex forms the major physiological anticoagulant pathway. Agkistrodon contortrix contortrix protein C activator, a glycosylated single-chain serine proteinase, activates protein C without relying on thrombomodulin. The crystal structures of native and inhibited Agkistrodon contortrix contortrix protein C activator determined at 1.65 and 1.54 angstrom resolutions, respectively, indicate the pivotal roles played by the positively charged belt and the strategic positioning of the three carbohydrate moieties surrounding the catalytic site in protein C recognition, binding, and activation. Structural changes in the benzamidine-inhibited enzyme suggest a probable function in allosteric regulation for the anion-binding site located in the C-terminal extension, which is fully conserved in snake venom serine proteinases, that preferentially binds Cl1- instead of SO42-.

Efficiency of extrinsic and intrinsic charge-carrier photogeneration processes obtained from the steady-state photocurrent action spectra of poly(p-phenylene vinylene) derivatives

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The Origin of Nonmonotonic Complex Behavior and the Effects of Nonnative Interactions on the Diffusive Properties of Protein Folding

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

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

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

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.

Efficiency of ethanol conversion induced by controlled modification of pore structure and acidic properties of alumina catalysts

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Impedance Spectroscopy Analysis of the Effect of TiO2 Blocking Layers on the Efficiency of Dye Sensitized Solar Cells

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

Optimization of incubation time of protein Tc85 in the construction of biosensor: Is the EIS a good tool?

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

Comparison of oxidation efficiency of disperse dyes by chemical and photoelectrocatalytic chlorination and removal of mutagenic activity

Degradation of Disperse Orange 1, Disperse Red 1 and Disperse Red 13 dyes has been performed using electrochemical oxidation on Pt electrode, chemical chlorination and photoelectrochemical oxidation on Ti/TiO(2) thin film electrodes in NaCl or Na(2)SO(4) medium. 100% discoloration was obtained for all tested methods after 1 h of treatment. Faster color removal was obtained by photoelectrocatalytic oxidation in 0.1 mol L(-1) NaCl pH 4.0 under UV light and an applied potential of +1.0V (vs SCE reference electrode), which indicates also values around 60% of TOC removal. The conventional chlorination method and electrochemical oxidation on Pt electrode resulted in negligible reduction of TOC removal. All dyes showed positive mutagenic activity in the Salmonella/microsome assay with the strain TA98 in the absence and presence of S9 (exogenous metabolic activation). Nevertheless, there is complete reduction of the mutagenic activity after 1 h of photoelectrocatalytic oxidation, suggesting that this process would be good option to remove disperse azo dyes from aqueous media. (C) 2008 Elsevier Ltd. All rights reserved.

Modelling energy utilization for laying type Pullets

Three trials were carried out to determine energy metabolized (EM) requirement model for starting and growing pullets from different strains, at five ambient temperatures and different percentage feather coverage. In Trial I, metabolizable energy requirements for maintenance (MEm) and efficiency of energy utilization were estimated using 64 birds of two different strains, Hy-Line W36 (HLW36) and Hy-Line Semi-heavy (HLSH), from 9 to 13 weeks of age. The effects of ambient temperature (12, 18, 24, 30 and 36ºC) and percentage feather coverage (0, 50 and 100%) on MEm were assessed in the second trial, using 48 birds per temperature per strain (HLSH and HLW36) from 9 to 13 weeks of age. Trial III evaluated ME requirements for weight gain (MEg) using 1,200 birds from two light strains (HLW36 and Hisex Light, HL) and two semi-heavy strains (HLSH and Hisex Semi-heavy, HSH) reared until 18 weeks of age. According to the prediction models, MEm changed as a function of temperature and feather coverage, whereas MEg changed as a function of age and bird strain. Thus, two models were developed for birds aged 1 to 6 weeks, one model for the light strain and one for the semi-heavy strain. Energy requirements (ER) were different among strains from 7 to 12 weeks, and therefore 4 models were elaborated. From 13 to 18 weeks, one single model was produced for semi-heavy birds, since ER between semi-heavy strains were not different, whereas two different models were elaborated for the light layers. MEg of light birds was higher than MEg of semi-heavy birds, independent of age.

Efficiency of bioaugmentation in the removal of organic matter in aquaculture systems

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

Efficiency of aquatic macrophytes to treat Nile tilapia pond effluents

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

Composição corporal e puberdade de leitoas alimentadas com níveis alto e baixo de proteína na dieta

Com o objetivo de verificar alterarações na composição corporal, diferentes níveis protéicos (12 e 18% PB) foram utilizados na dieta de leitoas de reposição, dos 100 aos 221 dias de idade. Durante esse período foram avaliados o peso corporal, espessura de toucinho (ET), manifestação de estro, características do trato reprodutivo e o balanço nitrogenado. Para a determinação do balanço nitrogenado, as leitoas foram submetidas a dois ensaios de digestibilidade (aos 136 e aos 201 dias de idade). em ambos os ensaios, as leitoas alimentadas com 18% PB apresentaram maior ingestão, retenção e excreção de nitrogênio e maiores níveis de uréia plasmática e urinária (P<0,001). A eficiência da utilização de nitrogênio não foi influenciada pelo nível protéico da dieta (P>0,05). Houve redução de 48% na excreção de nitrogênio com a dieta menos protéica. Leitoas alimentadas com 12% PB apresentaram maior ganho de ET (7,4 mm) em comparação às alimentadas com 18% PB (4,5 mm), dos 100 aos 207 dias de idade (P<0,02). O peso corporal, peso do útero, comprimento dos cornos uterinos e número de corpos lúteos não foram afetados pelo nível de proteína na dieta. A taxa de detecção de estro, até 25 dias após a exposição das leitoas ao cachaço, foi semelhante para as fêmeas recebendo 12% (71%) e 18% PB (75%). Os níveis de proteína da dieta afetaram a composição corporal das fêmeas sem que o peso final, o desencadeamento da puberdade e características do trato reprodutivo fossem afetados, indicando que dietas de baixa proteína podem ser utilizadas como estratégia para aumentar a espessura de toucinho de leitoas de reposição.