Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis

Tuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure-based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X-ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT i.s stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution.

A quantum chemical study on a set of non-imidazole H(3) antihistamine molecules

Molecular orbital calculations were carried out on a set of 28 non-imidazole H(3) antihistamine compounds using the Hartree-Fock method in order to investigate the possible relationships between electronic structural properties and binding affinity for H3 receptors (pK(i)). It was observed that the frontier effective-for-reaction molecular orbital (FERMO) energies were better correlated with pK(i) values than highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy values. Exploratory data analysis through hierarchical cluster (HCA) and principal component analysis (PCA) showed a separation of the compounds in two sets, one grouping the molecules with high pK(i) values, the other gathering low pK(i) value compounds. This separation was obtained with the use of the following descriptors: FERMO energies (epsilon(FERMO)), charges derived from the electrostatic potential on the nitrogen atom (N(1)), electronic density indexes for FERMO on the N(1) atom (Sigma((FERMO))c(i)(2)). and electrophilicity (omega`). These electronic descriptors were used to construct a quantitative structure-activity relationship (QSAR) model through the partial least-squares (PLS) method with three principal components. This model generated Q(2) = 0.88 and R(2) = 0.927 values obtained from a training set and external validation of 23 and 5 molecules, respectively. After the analysis of the PLS regression equation and the values for the selected electronic descriptors, it is suggested that high values of FERMO energies and of Sigma((FERMO))c(i)(2), together with low values of electrophilicity and pronounced negative charges on N(1) appear as desirable properties for the conception of new molecules which might have high binding affinity. 2010 Elsevier Inc. All rights reserved.

Non-durable consumption and real-estate prices in Brazil: panel-data analysis at the state level

Housing is an important component of wealth for a typical household in many countries. The objective of this paper is to investigate the effect of real-estate price variation on welfare, trying to close a gap between the welfare literature in Brazil and that in the U.S., the U.K., and other developed countries. Our first motivation relates to the fact that real estate is probably more important here than elsewhere as a proportion of wealth, which potentially makes the impact of a price change bigger here. Our second motivation relates to the fact that real-estate prices boomed in Brazil in the last five years. Prime real estate in Rio de Janeiro and São Paulo have tripled in value in that period, and a smaller but generalized increase has been observed throughout the country. Third, we have also seen a recent consumption boom in Brazil in the last five years. Indeed, the recent rise of some of the poor to middle-income status is well documented not only for Brazil but for other emerging countries as well. Regarding consumption and real-estate prices in Brazil, one cannot imply causality from correlation, but one can do causal inference with an appropriate structural model and proper inference, or with a proper inference in a reduced-form setup. Our last motivation is related to the complete absence of studies of this kind in Brazil, which makes ours a pioneering study. We assemble a panel-data set for the determinants of non-durable consumption growth by Brazilian states, merging the techniques and ideas in Campbell and Cocco (2007) and in Case, Quigley and Shiller (2005). With appropriate controls, and panel-data methods, we investigate whether house-price variation has a positive effect on non-durable consumption. The results show a non-negligible significant impact of the change in the price of real estate on welfare consumption), although smaller then what Campbell and Cocco have found. Our findings support the view that the channel through which house prices affect consumption is a financial one.

Estudo do genoma do vírus causador da mionecrose infecciosa em camarões e desenvolvimento de métodos para detecção de diferentes variantes

Shrimp farming is one of the activities that contribute most to the growth of global aquaculture. However, this business has undergone significant economic losses due to the onset of viral diseases such as Infectious Myonecrosis (IMN). The IMN is already widespread throughout Northeastern Brazil and affects other countries such as Indonesia, Thailand and China. The main symptom of disease is myonecrosis, which consists of necrosis of striated muscles of the abdomen and cephalothorax of shrimp. The IMN is caused by infectious myonecrosis virus (IMNV), a non-enveloped virus which has protrusions along its capsid. The viral genome consists of a single molecule of double-stranded RNA and has two Open Reading Frames (ORFs). The ORF1 encodes the major capsid protein (MCP) and a potential RNA binding protein (RBP). ORF2 encodes a probable RNA-dependent RNA polymerase (RdRp) and classifies IMNV in Totiviridae family. Thus, the objective of this research was study the IMNV complete genome and encoded proteins in order to develop a system differentiate virus isolates based on polymorphisms presence. The phylogenetic relationship among some totivirus was investigated and showed a new group to IMNV within Totiviridae family. Two new genomes were sequenced, analyzed and compared to two other genomes already deposited in GenBank. The new genomes were more similar to each other than those already described. Conserved and variable regions of the genome were identified through similarity graphs and alignments using the four IMNV sequences. This analyze allowed mapping of polymorphic sites and revealed that the most variable region of the genome is in the first half of ORF1, which coincides with the regions that possibly encode the viral protrusion, while the most stable regions of the genome were found in conserved domains of proteins that interact with RNA. Moreover, secondary structures were predicted for all proteins using various softwares and protein structural models were calculated using threading and ab initio modeling approaches. From these analyses was possible to observe that the IMNV proteins have motifs and shapes similar to proteins of other totiviruses and new possible protein functions have been proposed. The genome and proteins study was essential for development of a PCR-based detection system able to discriminate the four IMNV isolates based on the presence of polymorphic sites

Structural Aspects of the Distinct Biochemical Properties of Glutaredoxin 1 and Glutaredoxin 2 from Saccharomyces cerevisiae

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

Structural and Biochemical Characterization of Peroxiredoxin Q beta from Xylella fastidiosa CATALYTIC MECHANISM and HIGH REACTIVITY

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

Structural features of the epididymal region of the domestic duck (Anas plathyrynchos)

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

The position effect of structural Eucalyptus round timber on the flexural modulus of elasticity

A madeira roliça possui grande emprego nas construções civis, desempenhando a função de vigas, colunas, fundações, postes para distribuição de energia elétrica, entre outras, apresentando a vantagem de não ser processada, como é o caso da madeira serrada. O projeto envolvendo elementos roliços requer, além de outras variáveis estruturais, o conhecimento do módulo de elasticidade. No Brasil, os documentos normativos que tratam da determinação das propriedades de rigidez e resistência para peças roliças de madeira estão em vigência há mais de vinte anos sem revisão técnica. A madeira roliça, por geralmente possuir eixo com curvatura não nula, pode apresentar, segundo a posição da peça no ensaio de flexão, valores diferentes do módulo de elasticidade. Este trabalho tem como objetivo analisara influência da posição de peças roliças de madeira de Eucalyptus grandis na determinação do módulo de elasticidade na flexão. O ensaio de flexão utilizado é o de três pontos, sendo cada peça avaliada em duas posições distintas, definidas mediante o giro da seção transversal em torno do eixo. Os resultados encontrados indicam a necessidade do ensaio de flexão em, pelo menos, duas posições distintas da peça.

Fabrication, structural characterization, and applications of Langmuir and Langmuir-Blodgett films of a poly(azo)urethane

The synthesis of a poly(azo)urethane by fixing CO2 in bis-epoxide followed by a polymerization reaction with an azodiamine is presented. Since isocyanate is not used in the process, it is termed clean method and the polymers obtained are named NIPUs (non-isocyanate polyurethanes). Langmuir films were formed at the air-water interface and were characterized by surface pressure vs mean molecular area per met unit (Pi-A) isotherms. The Langmuir monolayers were further studied by running stability tests and cycles of compression/expansion (possible hysteresis) and by varying the compression speed of the monolayer formation, the subphase temperature, and the solvents used to prepare the spreading polymer solutions. The Langmuir-Blodgett (LB) technique was used to fabricate ultrathin films of a particular polymer (PAzoU). It is possible to grow homogeneous LB films of up to 15 layers as monitored using UV-vis absorption spectroscopy. Higher number of layers can be deposited when PAzoU is mixed with stearic acid, producing mixed LB films. Fourier transform infrared (FTIR) absorption spectroscopy and Raman scattering showed that the materials do not interact chemically in the mixed LB films. The atomic force microscopy (AFM) and micro-Raman technique (optical microscopy coupled to Raman spectrograph) revealed that mixed LB films present a phase separation distinguishable at micrometer or nanometer scale. Finally, mixed and neat LB films were successfully characterized using impedance spectroscopy at different temperatures, a property that may lead to future application as temperature sensors. Principal component analysis (PCA) was used to correlate the data.

Synthesis and structural characterization of Eu(III)-doped Zn7Sb2O12

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

Structural modeling and mutational analysis of yeast eukaryotic translation initiation factor 5A reveal new critical residues and reinforce its involvement in protein synthesis

Eukaryotic translation initiation factor 5A (eIF5A) is a protein that is highly conserved and essential for cell viability. This factor is the only protein known to contain the unique and essential amino acid residue hypusine. This work focused on the structural and functional characterization of Saccharomyces cerevisiae eIF5A. The tertiary structure of yeast eIF5A was modeled based on the structure of its Leishmania mexicana homologue and this model was used to predict the structural localization of new site-directed and randomly generated mutations. Most of the 40 new mutants exhibited phenotypes that resulted from eIF-5A protein-folding defects. Our data provided evidence that the C-terminal alpha-helix present in yeast eIF5A is an essential structural element, whereas the eIF5A N-terminal 10 amino acid extension not present in archaeal eIF5A homologs, is not. Moreover, the mutants containing substitutions at or in the vicinity of the hypusine modification site displayed nonviable or temperature-sensitive phenotypes and were defective in hypusine modification. Interestingly, two of the temperature-sensitive strains produced stable mutant eIF5A proteins - eIF5A(K56A) and eIF5A(Q22H,L93F)- and showed defects in protein synthesis at the restrictive temperature. Our data revealed important structural features of eIF5A that are required for its vital role in cell viability and underscored an essential function of eIF5A in the translation step of gene expression.

Chemical Profile and Biological Potential of Non-Polar Fractions from Centroceras clavulatum (C. Agardh) Montagne (Ceramiales, Rhodophyta)

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

Presence of autoantibodies against HeLa small nuclear ribonucleoproteins in chagasic and non-chagasic cardiac patients

We detected anti-human small nuclear ribonucleoprotein (snRNP) autoantibodies in chagasic patients by different immunological methods using HeLa snRNPs. ELISA with Trypanosoma cruzi total lysate antigen or HeLa human U small nuclear ribonucleoproteins (UsnRNPs) followed by incubation with sera from chronic chagasic and non-chagasic cardiac patients was used to screen and compare serum reactivity. Western blot analysis using a T. cruzi total cell extract was also performed in order to select some sera for Western blot and immunoprecipitation assays with HeLa nuclear extract. ELISA showed that 73 and 95% of chronic chagasic sera reacted with HeLa UsnRNPs and T. cruzi antigens, respectively. The Western blot assay demonstrated that non-chagasic cardiac sera reacted with high molecular weight proteins present in T. cruzi total extract, probably explaining the 31% reactivity found by ELISA. However, these sera reacted weakly with HeLa UsnRNPs, in contrast to the chagasic sera, which showed autoantibodies with human Sm (from Stefanie Smith, the first patient in whom this activity was identified) proteins (B/B', D1, D2, D3, E, F, and G UsnRNP). Immunoprecipitation reactions using HeLa nuclear extracts confirmed the reactivity of chagasic sera and human UsnRNA/RNPs, while the other sera reacted weakly only with U1snRNP. These findings agree with previously reported data, thus supporting the idea of the presence of autoimmune antibodies in chagasic patients. Interestingly, non-chagasic cardiac sera also showed reactivity with T. cruzi antigen and HeLa UsnRNPs, which suggests that individuals with heart disease of unknown etiology may develop autoimmune antibodies at any time. The detection of UsnRNP autoantibodies in chagasic patients might contribute to our understanding of how they develop upon initial T. cruzi infection.

Effect of the microwave oven on structural, morphological and electrical properties of SrBi4Ti4O15 thin films grown on Pt/Ti/SiO2/Si substrates by a soft chemical method

Thin films of SrBi4Ti4O15 (SBTi), a prototype of the Bi-layered-ferroelectric oxide family, were obtained by a soft chemical method and crystallized in a domestic microwave oven. For comparison, films were also crystallized in a conventional method at 700 degrees C for 2 h. Structural and morphological characterization of the SBTi thin films were investigated by Xray diffraction (XRD) and atomic force microscopy (AFM), respectively. Using platinum coated silicon substrates, the ferroelectric properties of the films were determined. Remanent polarization P-r and a coercive field E-c values of 5.1 mu C/cm(2) and 135 kV/cm for the film thermally treated in the microwave oven and 5.4 mu C/cm(2) and 85 kv/cm for the film thermally treated in conventional furnace were found. The films thermally treated in the conventional furnace exhibited excellent fatigue-free characteristics up to 10(10) switching cycles indicating that SBTi thin films are a promising material for use in non-volatile memories. (C) 2007 Elsevier B.V. All rights reserved.

Carbon fiber non-crimp multi-axial reinforcement and epoxy mono-component system composite: fatigue behavior

Fiber reinforced polymer composites have been widely applied in the aeronautical field. However, composite processing, which uses unlocked molds, should be avoided in view of the tight requirements and also due to possible environmental contamination. To produce high performance structural frames meeting aeronautical reproducibility and low cost criteria, the Brazilian industry has shown interest to investigate the resin transfer molding process (RTM) considering being a closed-mold pressure injection system which allows faster gel and cure times. Due to the fibrous composite anisotropic and non homogeneity characteristics, the fatigue behavior is a complex phenomenon quite different from to metals materials crucial to be investigated considering the aeronautical application. Fatigue sub-scale specimens of intermediate modulus carbon fiber non-crimp multi-axial reinforcement and epoxy mono-component system composite were produced according to the ASTM 3039 D. Axial fatigue tests were carried out according to ASTM D 3479. A sinusoidal load of 10 Hz frequency and load ratio R = 0.1. It was observed a high fatigue interval obtained for NCF/RTM6 composites. Weibull statistical analysis was applied to describe the failure probability of materials under cyclic loads and fractures pattern was observed by scanning electron microscopy. (C) 2010 Published by Elsevier Ltd.