Site-directed mutagenesis and structural modeling of Coq10p indicate the presence of a tunnel for coenzyme Q6 binding

Coq10p is a protein required for coenzyme Q function, but its specific role is still unknown. It is a member of the START domain superfamily that contains a hydrophobic tunnel implicated in the binding of lipophilic molecules. We used site-directed mutagenesis, statistical coupling analysis and molecular modeling to probe structural determinants in the Coq10p putative tunnel. Four point mutations were generated (coq10-K50E, coq10-L96S, coq10-E105K and coq10-K162D) and their biochemical properties analysed, as well as structural consequences. Our results show that all mutations impaired Coq10p function and together with molecular modeling indicate an important role for the Coq10p putative tunnel. (C) 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Structural modeling of high-affinity thyroid receptor-ligand complexes

Understanding the molecular basis of the binding modes of natural and synthetic ligands to nuclear receptors is fundamental to our comprehension of the activation mechanism of this important class of hormone regulated transcription factors and to the development of new ligands. Thyroid hormone receptors (TR) are particularly important targets for pharmaceuticals development because TRs are associated with the regulation of metabolic rates, body weight, and circulating levels of cholesterol and triglycerides in humans. While several high-affinity ligands are known, structural information is only partially available. In this work we obtain structural models of several TR-ligand complexes with unknown structure by docking high affinity ligands to the receptors` ligand binding domain with subsequent relaxation by molecular dynamics simulations. The binding modes of these ligands are discussed providing novel insights into the development of TR ligands. The experimental binding free energies are reasonably well-reproduced from the proposed models using a simple linear interaction energy free-energy calculation scheme.

Improving the Detectability of Sequential Injection Chromatography (SIC): Determination of Triazines by Exploiting Liquid Core Waveguide (LCW) Detection

Coupling a liquid core waveguide cell to a sequential injection chromatograph improved the detection limits for determination of triazine herbicides without compromising peak resolution. Separation of simazine, atrazine, and propazine was achieved in water samples by a 25mm long C18 monolithic column. Detection was made at 238nm using a type II LCW (silica capillary coated with Teflon (R) AF2400) cell with 100cm of optical path length. Detection limits for simazine, atrazine, and propazine were 2.3, 1.9, and 4.5 mu g L-1, respectively. Reduced analysis time and low solvent consumption are other remarkable features of the proposed method.

Asymmetric phase-transfer catalytic sulfanylation of some 2-methylsulfinyl cyclanones. Modeling of the stereochemical course of the aldol reaction of (SS,2S)-2-methylsulfinyl-2-methylsulfanylcyclohexanone

Increased diastereoisomeric excesses are obtained for the sulfanylation reactions of some 2-methylsulfinyl cyclanones under phase-transfer catalysis using the chiral catalyst QUIBEC instead of TEBA. The optically pure (SS,2S)-2-methylsulfinyl-2-methylsulfanylcyclohexanone thus prepared reacts with ethyl acetate lithium enolate affording, after hydrolysis, (R)-2-[(ethoxycarbonyl)methyl]-2-hydroxycyclohexanone in 60% ee. Density functional theory calculations (at the B3LYP/6-311++G(d,p) level) can successfully explain the origin of this result as the kinetically favored axial attack of the nucleophile to the carbonyl group of the most stable conformer of the cyclanone, in which the CH(3)SO and CH(3)S groups are at the equatorial and axial positions, respectively. (C) 2010 Elsevier Ltd. All rights reserved.

Syntheses of Cross-Linking Agents, Molecular Modeling of Oligonucleotides and Polypeptide-Ion Complexes

Each section of this thesis will be subdivided into three parts encompassing all of the research in which I have been involved during the past three years. These will be referred to under the headings "Syntheses:' "Molecular Modeling," and "Cross-linking Efficiencies." Each of these subdivisions may have divisions within them when necessary in order to fully detail the research.

Modeling Of District Metered Areas With Relatively High Leakage Rate. The Case Study Of Kalipoli’s DMA

The article reviews the modelling of District Metered Areas (DMAs) with relatively high leakage rate. As a generally recognised approach in modelling of leakage does not exist, modelling of leakage by enginners and other researchers usually takes place by dividing the whole leakage rate evenly to all available nodes of the model. In this article, a new methodology is proposed to determine the nodal leakage by using a hydraulic model. The proposed methodology takes into consideration the IWA water balance methodology, the Minimum Night Flow (MNF) analysis, the number of connections related to each node and the marerial of pipes. In addition, the model is illustrated by a real case study, as it was applied in Kalipoli’s DMA. Results show that the proposed model gives reliable results.

Country factors and the dynamic modeling of capital structure : an empirical study of latin american firms

Desenvolvemos modelos de ajuste parcial e de duration para testar a relevância de fatores específicos de países na determinação da estrutura de capital de empresas listadas nas bolsas de valores brasileira, chilena e mexicana. Utilizamos dados em painel, em um período que se estende do quarto trimestre de 1996 ao segundo trimestre de 2010, abrangendo 4403 observações relacionadas a 139 empresas diferentes. Os resultados obtidos sugerem que a dinâmica da estrutura de capital varia por país e que idiossincrasias locais são determinantes-chave dos níveis de alavancagem das empresas. Não detectamos comportamento explicado pela Teoria de Trade Off entre as empresas brasileiras, chilenas e mexicanas, o que indica que teorias alternativas possam comandar os processos de decisão de financiamento dos gestores latino americanos.

Robust statistical modeling of portfolios

Atypical points in the data may result in meaningless e±cient frontiers. This follows since portfolios constructed using classical estimates may re°ect neither the usual nor the unusual days patterns. On the other hand, portfolios constructed using robust approaches are able to capture just the dynamics of the usual days, which constitute the majority of the business days. In this paper we propose an statistical model and a robust estimation procedure to obtain an e±cient frontier which would take into account the behavior of both the usual and most of the atypical days. We show, using real data and simulations, that portfolios constructed in this way require less frequent rebalancing, and may yield higher expected returns for any risk level.

Analysis an development of a prototype based on media wiki and semantic media wiki integrated with a design modeling that allows modeling of organizations based on demo

In a world where organizations are ever more complex the need for the knowledge of the organizational self is a growing necessity. The DEMO methodology sets a goal in achieving the specification of the organizational self capturing the essence of the organization in way independent of its implementation and also coherent, consistent, complete, modular and objective. But having such organization self notion is of little meaning if this notion is not shared by the organization actors. To achieve this goal in a society that has grown attached to technology and where time is of utmost importance, using a tool such as a semantic Wikipedia may be the perfect way of making the information accessible. However, to establish DEMO methodology in such platform there is a need to create bridges between its modeling components and semantic Wikipedia. It’s in that aspect that our thesis focuses, trying to establish and implement, using a study case, the principles of a way of transforming the DEMO methodology diagrams in comprehensive pages on semantic Wikipedia but keeping them as abstract as possible to allow expansibility and generalization to all diagrams without losing any valuable information so that, if that is the wish, those diagrams may be recreated from the semantic pages and make this process a full cycle.

Compósitos Portland-biopolímeros para cimentação de poços de petróleo

The oil production in mature areas can be improved by advanced recovery techniques. In special, steam injection reduces the viscosity of heavy oils, thus improving its flow to surrounding wells. On the other hand, the usually high temperatures and pressures involved in the process may lead to cement cracking, negatively affecting both the mechanical stability and zonal isolation provided by the cement sheath of the well. The addition of plastic materials to the cement is an alternative to prevent this scenario. Composite slurries consisting of Portland cement and a natural biopolymer were studied. Samples containing different contents of biopolymer dispersed in a Portland cement matrix were prepared and evaluated by mechanical and rheological tests in order to assess their behavior according to API (American Petroleum Institute) guidelines. FEM was also applied to map the stress distribution encountered by the cement at bottom bole. The slurries were prepared according to a factorial experiment plan by varying three parameters, i.e., cement age, contents of biopolymer and water-to-cement ratio. The results revealed that the addition of the biopolymer reduced the volume of free water and the setting time of the slurry. In addition, tensile strength, compressive strength and toughness improved by 30% comparing hardened composites to plain Portland slurries. FEM results suggested that the stresses developed at bottomhole may be 10 to 100 times higher than the strength of the cement as evaluated in the lab by unconfined mechanical testing. An alternative approach is proposed to adapt the testing methodology used to evaluate the mechanical behavior of oilwell cement slurries by simulating the confined conditions encountered at bottornhole

Otimização de vazão de poços injetores em projeto de injeção de água utilizando simulação por linhas de fluxo

Until the early 90s, the simulation of fluid flow in oil reservoir basically used the numerical technique of finite differences. Since then, there was a big development in simulation technology based on streamlines, so that nowadays it is being used in several cases and it can represent the physical mechanisms that influence the fluid flow, such as compressibility, capillarity and gravitational segregation. Streamline-based flow simulation is a tool that can help enough in waterflood project management, because it provides important information not available through traditional simulation of finite differences and shows, in a direct way, the influence between injector well and producer well. This work presents the application of a methodology published in literature for optimizing water injection projects in modeling of a Brazilian Potiguar Basin reservoir that has a large number of wells. This methodology considers changes of injection well rates over time, based on information available through streamline simulation. This methodology reduces injection rates in wells of lower efficiency and increases injection rates in more efficient wells. In the proposed model, the methodology was effective. The optimized alternatives presented higher oil recovery associated with a lower water injection volume. This shows better efficiency and, consequently, reduction in costs. Considering the wide use of the water injection in oil fields, the positive outcome of the modeling is important, because it shows a case study of increasing of oil recovery achieved simply through better distribution of water injection rates

Estudo de sistemas multicomponentes no processo de injeção cíclica de vapor

In Brazilian Northeast there are reservoirs with heavy oil, which use steam flooding as a recovery method. This process allows to reduce oil viscosity, increasing its mobility and consequently its oil recovery. Steam injection is a thermal method and can occurs in continues or cyclic form. Cyclic steam stimulation (CSS) can be repeated several times. Each cycle consisting of three stages: steam injection, soaking time and production phase. CSS becomes less efficient with an increase of number of cycles. Thus, this work aims to study the influence of compositional models in cyclic steam injection and the effects of some parameters, such like: flow injection, steam quality and temperature of steam injected, analyzing the influence of pseudocomponents numbers on oil rate, cumulative oil, oil recovery and simulation time. In the situations analyzed was compared the model of fluid of three phases and three components known as Blackoil . Simulations were done using commercial software (CMG), it was analyzed a homogeneous reservoir with characteristics similar to those found in Brazilian Northeast. It was observed that an increase of components number, increase the time spent in simulation. As for analyzed parameters, it appears that the steam rate, and steam quality has influence on cumulative oil and oil recovery. The number of components did not a lot influenced on oil recovery, however it has influenced on gas production

Semiparametric modeling of the spatial distribution of occupational accident risk in the casual labor market, Piracicaba, southeast Brazil

The objective of this study was to estimate the spatial distribution of work accident risk in the informal work market in the urban zone of an industrialized city in southeast Brazil and to examine concomitant effects of age, gender, and type of occupation after controlling for spatial risk variation. The basic methodology adopted was that of a population-based case-control study with particular interest focused on the spatial location of work. Cases were all casual workers in the city suffering work accidents during a one-year period; controls were selected from the source population of casual laborers by systematic random sampling of urban homes. The spatial distribution of work accidents was estimated via a semiparametric generalized additive model with a nonparametric bidimensional spline of the geographical coordinates of cases and controls as the nonlinear spatial component, and including age, gender, and occupation as linear predictive variables in the parametric component. We analyzed 1,918 cases and 2,245 controls between 1/11/2003 and 31/10/2004 in Piracicaba, Brazil. Areas of significantly high and low accident risk were identified in relation to mean risk in the study region (p < 0.01). Work accident risk for informal workers varied significantly in the study area. Significant age, gender, and occupational group effects on accident risk were identified after correcting for this spatial variation. A good understanding of high-risk groups and high-risk regions underpins the formulation of hypotheses concerning accident causality and the development of effective public accident prevention policies.

Purification, characterization, crystallization and theoretical molecular modeling of gyroxin fraction from Crotalus durissus terrificus venom (Laurenti, 1768)

The venom of Crotalus durissus terrificus snakes presents various substances, including a serine protease with thrombin-like activity, called gyroxin, that clots plasmatic fibrinogen and promote the fibrin formation. The aim of this study was to purify and structurally characterize the gyroxin enzyme from Crotalus durissus terrificus venom. For isolation and purification, the following methods were employed: gel filtration on Sephadex G75 column and affinity chromatography on benzamidine Sepharose 6B; 12% SDS-PAGE under reducing conditions; N-terminal sequence analysis; cDNA cloning and expression through RT-PCR and crystallization tests. Theoretical molecular modeling was performed using bioinformatics tools based on comparative analysis of other serine proteases deposited in the NCBI (National Center for Biotechnology Information) database. Protein N-terminal sequencing produced a single chain with a molecular mass of similar to 30 kDa while its full-length cDNA had 714 bp which encoded a mature protein containing 238 amino acids. Crystals were obtained from the solutions 2 and 5 of the Crystal Screen Kit (R), two and one respectively, that reveal the protein constitution of the sample. For multiple sequence alignments of gyroxin-like B2.1 with six other serine proteases obtained from snake venoms (SVSPs), the preservation of cysteine residues and their main structural elements (alpha-helices, beta-barrel and loops) was indicated. The localization of the catalytic triad in His57, Asp102 and Ser198 as well as S1 and S2 specific activity sites in Thr193 and Gli215 amino acids was pointed. The area of recognition and cleavage of fibrinogen in SVSPs for modeling gyroxin B2.1 sequence was located at Arg60, Arg72, Gln75, Arg81, Arg82, Lis85, Glu86 and Lis87 residues. Theoretical modeling of gyroxin fraction generated a classical structure consisting of two alpha-helices, two beta-barrel structures, five disulfide bridges and loops in positions 37, 60, 70, 99, 148, 174 and 218. These results provided information about the functional structure of gyroxin allowing its application in the design of new drugs.