Structure of chorismate synthase from Mycobacterium tuberculosis

In bacteria, fungi, plants, and apicomplexan parasites, the aromatics compounds, such as aromatics amino acids, are synthesized through seven enzymes from the shikimate pathway, which are absent in mammals. The absence of this pathway in mammals make them potential targets for development of new therapy against infectious diseases, such as tuberculosis, which is the world's second commonest cause of death from infectious disease. The last enzyme of shikimate pathway is the chorismate synthase (CS), which is responsible for conversion of the 5-enolpyruvylshikimate-3-phosphate to chorismate. Here, we report the crystallographic structure of CS from Mycobacterium tuberculosis (MtCS) at 2.65 angstrom resolution. The MtCS structure is similar to other CS structures, presenting beta-alpha-beta sandwich structural topology, in which each monomer of MtCS consists of a central helical core. The MtCS can be described as a tetramer formed by a dimer of dimers. However, analytical ultracentrifugation studies suggest the MtCS is a dimer with a more asymmetric shape than observed on the crystallographic dimer and the existence of a low equilibrium between dimer and tetramer. Our results suggest that the MtCS oligomerization is concentration dependent and some conformational changes must be involved on that event. (c) 2005 Elsevier B.V. All rights reserved.

Dynamics of glyphosate-induced conformational changes of Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) determined by hydrogen-deuterium exchange and electrospray mass spectrometry

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the reaction between shikimate 3-phosphate and phosphoenolpyruvate to form 5-enolpyruvylshikimate 3-phosphate, an intermediate in the shikimate pathway, which leads to the biosynthesis of aromatic amino acids. EPSPS exists in an open conformation in the absence of substrates and/or inhibitors and in a closed conformation when bound to the substrate and/or inhibitor. In the present report, the H/D exchange properties of EPSPS from Mycobacterium tuberculosis (Mt) were investigated for both enzyme conformations using ESI mass spectrometry and circular dichroism (CD). When the conformational changes identified by H/D exchanges were mapped on the 3-D structure, it was observed that the apoenzyme underwent extensive conformational changes due to glyphosate complexation, characterized by an increase in the content of alpha-helices from 40% to 57%, while the beta-sheet content decreased from 30% to 23%. These results indicate that the enzyme underwent a series of rearrangements of its secondary structure that were accompanied by a large decrease in solvent access to many different regions of the protein. This was attributed to the compaction of 71% of alpha-helices and 57% of beta-sheets as a consequence of glyphosate binding to the enzyme. Apparently, MtEPSPS undergoes a series of inhibitor-induced conformational changes, which seem to have caused synergistic effects in preventing solvent access to the core of molecule, especially in the cleft region. This may be part of the mechanism of inhibition of the enzyme, which is required to prevent the hydration of the substrate binding site and also to induce the cleft closure to avoid entrance of the substrates.

Hydrogen/deuterium exchange mass spectrometry for characterizing phosphoenolpyruvate-induced structural transitions in Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.1)

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

Phosphate closes the solution structure of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Mycobacterium tuberculosis

The 5-enolpyruvylshikimate-3-phosphate synthase catalyses the sixth step of the shikimate pathway that is responsible for synthesizing aromatic compounds and is absent in mammals, which makes it a potential target for drugs development against microbial diseases. Here, we report the phosphate binding effects at the structure of the 5-enolpyruvyl shikimate-3-phosphate synthase from Mycobacterium tuberculosis. This enzyme is formed by two similar domains that close on each other induced by ligand binding, showing the occurrence of a large conformation change. We have monitored the phosphate binding effects using analytical ultracentrifugation, small angle X-ray scattering and, circular dichroism techniques. The low resolution results showed that the enzyme in the presence of phosphate clearly presented a more compact structure. Thermal-induced unfolding experiments followed by circular dichroism suggested that phosphate rigidified the enzyme. Summarizing, these data suggested that the phosphate itself is able to induce conformational change resulting in the closure movement in the M. tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase. (c) 2006 Elsevier B.V. All rights reserved.

Bamboo overabundance alters forest structure and dynamics in the Atlantic Forest hotspot

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

Genetic structure in a tropical lek-breeding bird, the blue manakin (Chiroxiphia caudata) in the Brazilian Atlantic Forest

Determining the genetic structure of tropical bird populations is important for assessing potential genetic effects of future habitat fragmentation and for testing hypotheses about evolutionary mechanisms promoting diversification. Here we used 10 microsatellite DNA loci to describe levels of genetic differentiation for five populations of the lek-mating blue manakin (Chiroxiphia caudata), sampled along a 414-km transect within the largest remaining continuous tract of the highly endangered Atlantic Forest habitat in southeast Brazil. We found small but significant levels of differentiation between most populations. F-ST values varied from 0.0 to 0.023 (overall F-ST = 0.012) that conformed to a strong isolation by distance relationship, suggesting that observed levels of differentiation are a result of migration-drift equilibrium. N(e)m values estimated using a coalescent-based method were small (<= 2 migrants per generation) and close to the minimum level required to maintain genetic similarity between populations. An implication of these results is that if future habitat fragmentation reduces dispersal between populations to even a small extent, then individual populations may undergo a loss of genetic diversity due to an increase in the relative importance of drift, since inbreeding effective population sizes are relatively small (N-e similar to 1000). Our findings also demonstrate that population structuring can occur in a tropical bird in continuous habitat in the absence of geographical barriers possibly due to behavioural features of the species.

High fat-induced obesity associated with insulin-resistance increases FGF-2 content and causes stromal hyperplasia in rat ventral prostate

Obesity affects sex hormone secretion, which can negatively influence prostatic structure, homeostasis, and disease. This investigation aimed to evaluate the repercussions of obesity induced by a high-fat diet on the rat prostate, with or without treatment with the aromatase inhibitor, Letrozole. Adult Wistar rats were fed a high-fat diet (20% saturated fat, O) for 15 weeks to induce obesity or received a balanced diet (4% fat, C). Then, a group of C and O rats were daily treated with Letrozole (1 mg/kg b.w. per day) for 2 weeks (CL and OL, respectively). Subsequently, ventral prostate was processed for analysis by transmission electron microscopy, immunohistochemistry, and Western blotting. Obesity decreased 70% of the testosterone plasma level. The prostate showed epithelial atrophy and dilated acini in the intermediate portion and epithelial wrinkling in the distal tips. The relative frequency of smooth muscle alpha-actin in the O group increased by 67%. Ultrastructurally, epithelial cells in obese animals presented altered secretory organelles, lipid droplets, and thicker subjacent fibromuscular layer. Letrozole treatment caused a partial restoration of the prostatic changes caused by obesity. Obesity increased the prostatic content of fibroblast growth factor-2 (FGF-2) by 150%, and Letrozole treatment increased this protein even more in the control and obese groups. This investigation shows that obesity provokes structural and ultrastructural changes in the epithelium of rat prostate; these changes might affect gland homeostasis and physiology. The epithelial and smooth muscle cell hyperplasia and increased FGF-2 expression observed in this experimental model of obesity/insulin-resistance might explain the high frequency of benign prostatic hyperplasia in insulin-resistant men.

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1)

The 1.7 angstrom resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved P-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Dynamically induced spontaneous symmetry breaking in 3-3-1 models

We show that in SU(3)(C) circle times SU(3)(L) circle times U(1)(N) (3-3-1) models embedded with a singlet scalar playing the role of the axion, after imposing scale invariance, the breaking of Peccei-Quinn symmetry occurs through the one-loop effective potential for the singlet field. We, then, analyze the structure of spontaneous symmetry breaking by studying the new scalar potential for the model, and verify that electroweak symmetry breaking is tightly connected to the 3-3-1 breaking by the strong constraints among their vacuum expectation values. This offers a valuable guide to write down the correct pattern of symmetry breaking for multi-scalar theories. We also obtained that the accompanying massive pseudo-scalar, instead of acquiring mass of order of Peccei-Quinn scale as we would expect, develops a mass at a much lower scale, a consequence solely of the breaking via Coleman-Weinberg mechanism. (c) 2005 Published by Elsevier B.V.

Pion structure in the instanton liquid model

The covariant quark model of the pion based on the effective nonlocal quark-hadron Lagrangian involving nonlocality induced by instanton fluctuations of the QCD vacuum is reviewed. Explicit gauge invariant formalism allows us to construct the conserved vector and axial currents and to demonstrate their consistency with the Ward-Takahashi identities and low-energy theorems. The spontaneous breaking of chiral symmetry results in the dynamic quark mass and the vertex of the quark-pion interaction, both momentum-dependent. The parameters of the instanton vacuum, the average size of the instantons, and the effective quark mass are expressed in terms of the vacuum expectation values of the lowest dimension quark-gluon operators and low-energy pion observables. The transition pion form factor for the processes gamma*gamma --> pi (0) and gamma*gamma* --> pi (0) is analyzed in detail. The kinematic dependence of the transition form factor at high momentum transfers allows one to determine the relationship between the light-cone amplitude of the quark distribution in the pion and the quark-pion vertex function. Its dynamic dependence implies that the transition form factor gamma*gamma --> pi (0) at high momentum transfers is acutely sensitive to the size of the nonlocality of nonperturbative fluctuations in the QCD vacuum. In the leading twist, the distribution amplitude and the distribution function of the valence quarks in the pion are calculated at a low normalization point of the order of the inverse average instanton size rho (-1)(c). The QCD results are evolved to higher momentum transfers and are in reasonable agreement with available experimental data on the pion structure.

Miscibility in a degenerate fermionic mixture induced by linear coupling

We consider a one-dimensional mean-field-hydrodynamic model of a two-component degenerate Fermi gas in an external trap, each component representing a spin state of the same atom. We demonstrate that the interconversion between them (linear coupling), imposed by a resonant electromagnetic wave, transforms the immiscible binary gas into a miscible state, if the coupling constant, kappa, exceeds a critical value, kappa(cr). The effect is predicted in a variational approximation, and confirmed by numerical solutions. Unlike the recently studied model of a binary Bose-Einsten condensate with the linear coupling, the components in the immiscible phase of the binary fermion mixture never fill two separated domains with a wall between them, but rather form antilocked (pi-phase-shifted) density waves. Another difference from the bosonic mixture is spontaneous breaking of symmetry between the two components in terms of the numbers of atoms in them, N(1) and N(2). The latter effect is characterized by the parameter nu equivalent to(N(1)-N(2))/(N(1)+N(2)) (only N(1)+N(2) is a conserved quantity), the onset of miscibility at kappa >=kappa(cr) meaning a transition to nu equivalent to 0. At kappa

Structural modifications in stretch-induced crystallization in PVDF films as measured by small-angle X-ray scattering

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

Advancements in the knowledge of induced tooth movement: idiopathic osteosclerosis, cortical bone and orthodontic movement

Movimentar ortodonticamente os dentes por áreas densas do trabeculado ósseo e pelas corticais pode requerer uma redução na intensidade e/ou na concentração das forças aplicadas. em parte, as forças ortodônticas aplicadas são dissipadas e reduzidas pela deflexão óssea que ocorre pelo discreto grau de elasticidade do tecido ósseo em condições de normalidade. Nas áreas de trabeculado denso e nas corticais, essa deflexão deve ser irrisória ou inexistente. Se não houver uma redução na intensidade das forças nessas regiões citadas, toda a força incidirá sobre a estrutura do ligamento periodontal, aumentando o risco de morte dos cementoblastos, hialinização e reabsorções radiculares. Novos trabalhos poderiam avaliar a prevalência dessas consequências em casuísticas selecionadas para essa finalidade, que, assim, deixariam de ser observações aleatórias.

Structure and genetic relationships between Brazilian naturalized and exotic purebred goat domestic goat (Capra hircus) breeds based on microsatellites

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

Stress induced ordering due interstitials in Nb-4.7 at.%Ta

The presence of interstitial elements in metals cause strong changes in their physical, chemical or mechanical properties. These interstitial impurities interact with the metallic matrix atoms by a relaxation process known as stress induced ordering. Relaxation processes give rise to a peak in the internal friction spectrum, known as Snock effect. The presence of substitutional solutes has a strong influence on Snoek effect, particularly if the substitutional solute element is the one, which interacts with the interstitial element. Anelastic spectroscopy measurements provide information of the behavior of these impurities in the metallic matrix. In this paper, polycrystalline samples of Nb-4.7 at.%Ta alloy have been analyzed in the as-received condition. Measurements of anelastic spectroscopy were carried out using an inverted torsion pendulum, operating with frequency of 2.0-30.0 Hz and in a temperature range between 300 and 700 K. It was observed the presence of a relaxation structure that have been attributed to stress induced ordering due to interstitial atoms around atoms of the metallic matrix. The relaxation structure have been decomposed in its constituent peaks, what it allowed to identify the following relaxation processes: Ta-O, Nb-O and Nb-N. (c) 2005 Elsevier B.V. All rights reserved.