Deuterium Equilibrium Time in Saliva of Newborn Infants

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

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.

Monitoring the positioning of short polycationic peptides in model lipid bilayers by combining hydrogen/deuterium exchange and electrospray ionization mass spectrometry

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

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)

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.

Shikimate Kinase (EC 2.7.1.71) from Mycobacterium tuberculosis: Kinetics and Structural Dynamics of a Potential Molecular Target for Drug Development

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

Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

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

Desempenho e composição corporal de novilhas alimentadas com dois níveis de concentrado e bagaço de cana submetidos a diferentes processos de hidrólise

O objetivo deste trabalho foi testar duas formas de hidrólise do bagaço de cana (com [17kgf/cm²]e sem [4kgf/cm²] rápida descompressão pós-hidrólise) e dois níveis de concentrado (25 e 45% MS) no desempenho e na composição corporal de novilhas em crescimento sob regime confinado durante 112 dias. Vinte e quatro novilhas Nelore e 12 Canchim foram distribuídas em delineamento de blocos casualizados em arranjo fatorial 2x2. Os resultados demonstraram que a omissão da explosão pós-hidrólise e o uso de níveis mais elevados de concentrado aumentaram o ganho de peso e o consumo de alimentos. Os resultados para ganho de peso e consumo de matéria seca, respectivamente, para tratamento sem vs com descompressão e 45 vs 25% de concentrado, foram 0,76 vs 0,67 e 0,76 vs 0,66 kg/d e 6,7 vs 5,8 e 6,8 vs 5,7 kg/dia. Entretanto, não houve diferença entre os tratamentos para conversão alimentar. Não foram observadas diferenças entre os tratamentos quanto à composição corporal determinada por meio do espaço de deutério ao final do período de confinamento, embora a taxa estimada de deposição de lipídios tenha sido maior para o tratamento sem explosão (216 vs 175 g/d) e o tratamento com 45% de concentrado (225 vs 166 g/d). Não foram observadas vantagens na descompressão rápida pós-hidrólise em alta pressão na eficiência de conversão de alimentos. Os resultados demonstram que animais alimentados com bagaço hidrolisado em níveis altos de ingestão (2,9% PV) e proporções baixas de concentrado apresentaram eficiência de utilização da dieta semelhante a dietas com níveis mais altos de concentrado.

Ultraviolet excitation of photoconductivity in thin films of sol-gel SnO2

Tin dioxide (SnO2) thin film photoconductivity spectra were measured for a large temperature range using a deuterium source, the intensity of photocurrent spectra in the range 200-400 nm is temperature dependent, and the photocurrent increases in the ultraviolet even for illumination with photon energies much higher than the bandgap transition. This behavior is related to recombination of photogenerated electron-hole pairs with oxygen adsorbed at grain boundaries, which is consistent with nanoscopic crystallite size of sol-gel deposited films. (c) 2005 Elsevier Ltd. All rights reserved.

Electron scattering and effects of sources of light on photoconductivity of SnO2 coatings prepared by sol-gel

Electro-optical properties of sol-gel derived 2 mol% antimony or niobium doped tin dioxide films have been measured. The electron density has been calculated considering all the relevant scattering mechanisms and experimental conductivity data measured in the range -197 to 25 degrees C. The results support the hypothesis that both ionised impurity scattering and grain boundary scattering have comparable effects in the resistivity of coatings, for free electron density congruent to 5 x 10(18) cm(-3). We have measured variation of photoconductivity excitation with wavelength using xenon and deuterium lamp as light sources. Results show that the main band in the photoconductivity spectrum is dependent on the spectral light source emission, the excitation peak reaching 5 eV (deuterium lamp). This band is due to the recombination process involving oxygen species and photogenerated electron-hole pairs. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Bioavailability of synthetic and biosynthetic deuterated lycopene in humans

Current knowledge of the bioavailability of lycopene in humans is limited due to the inability to distinguish newly administered lycopene from the body reserves of lycopene. A quantitative method to assess the absorption and relative bioavailability of newly absorbed synthetic or natural lycopene was developed using two deuterated lycopene sources, in conjunction with an advanced LC/APCI-MS (liquid chromatography/atmospheric pressure chemical ionization-mass spectrometry) to analyze newly absorbed lycopene in blood samples of study subjects. Two subjects (1 male and 1 female) consumed hydroponically grown tomatoes containing deuterium-enriched lycopene (8084 g wet weight tomato containing 16.3 and 17.4 mu mol lycopene, respectively) and two subjects (1 male, and 1 female) consumed 11 mu mol synthetic H-2(10) lycopene in 6 g of corn oil. Tomatoes were steamed and pureed. The doses were given together with a liquid formulated drink with 25% energy from fat. Our results showed that up to 34 days after taking an oral 2 1110 lycopene dose (synthetic or from tomato) with a liquid formula drink, the area under the curve of the average serum percent enrichment response of synthetic lycopene reached 33.9 (+/- 1.7) nmol-day/mu mol lycopene in the dose, whereas that of lycopene from the tomato dose was 11.8 (+/- 0.3) nmol-day/mu mol lycopene in the dose. Our study provides evidence that the absorption of physiological levels of lycopene in intrinsically labeled tomatoes can be studied in humans. From these preliminary investigations, we find that the bioavailability of synthetic lycopene in oil appears to be about three times higher than that of lycopene from steamed and pureed tomatoes. (c) 2005 Elsevier B.V. All rights reserved.

Oxygen related defects excitation and photoconductivity dependence of SnO2 sol-gel films with several light sources

Since oxygen vacancies act as donors in SnO2, the electrical properties are related to deviation from stoichiometric composition. Depending on stoichiometry SnO2 can be highly insulating or may exhibit fairly high n-type conductivity. Since bandgap transitions are in the ultraviolet range, its photoconductivity is strongly dependent on the excitation source. We have measured variation of photoconductivity excitation with wavelength for tin dioxide grown by dip-coating sol-gel technique using several light sources: tungsten lamp, xenon, mercury and deuterium, and present selected results. The main band is obtained in the range 3-4eV according to light source spectrum in the ultraviolet range. The presence of oxygen in the cryostat also affects the spectrum since electron-hole pairs react with adsorbed oxygen specimens. © 1999 OPA (Overseas Publishers Association) N.V. Published by license under the Gordon and Breach Science Publishers imprint.

Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface

The orphan receptor nerve growth factor-induced B (NGFI-B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI-B was shown to be capable of binding both as a monomer to an extended half-site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo- and/or heterodimers. To unveil the structural organization of NGFI-B in solution, we determined the quaternary structure of the NGFI-B LBD by a combination of ab initio procedures from small-angle X-ray scattering (SAXS) data and hydrogen-deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI-B LBD dimer is V-shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI-B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C-terminal fraction of the helix 3. Remarkably, the NGFI-B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI-B and to antagonism of NGFI-B-dependent transcription exercised by GR in cells. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society.

The Mycobacterium tuberculosis Rv2540c DNA sequence encodes a bifunctional chorismate synthase

Background. The emergence of multi- and extensively-drug resistant Mycobacterium tuberculosis strains has created an urgent need for new agents to treat tuberculosis (TB). The enzymes of shikimate pathway are attractive targets to the development of antitubercular agents because it is essential for M. tuberculosis and is absent from humans. Chorismate synthase (CS) is the seventh enzyme of this route and catalyzes the NADH- and FMN-dependent synthesis of chorismate, a precursor of aromatic amino acids, naphthoquinones, menaquinones, and mycobactins. Although the M. tuberculosis Rv2540c (aroF) sequence has been annotated to encode a chorismate synthase, there has been no report on its correct assignment and functional characterization of its protein product. Results. In the present work, we describe DNA amplification of aroF-encoded CS from M. tuberculosis (MtCS), molecular cloning, protein expression, and purification to homogeneity. N-terminal amino acid sequencing, mass spectrometry and gel filtration chromatography were employed to determine identity, subunit molecular weight and oligomeric state in solution of homogeneous recombinant MtCS. The bifunctionality of MtCS was determined by measurements of both chorismate synthase and NADH:FMN oxidoreductase activities. The flavin reductase activity was characterized, showing the existence of a complex between FMN ox and MtCS. FMNox and NADH equilibrium binding was measured. Primary deuterium, solvent and multiple kinetic isotope effects are described and suggest distinct steps for hydride and proton transfers, with the former being more rate-limiting. Conclusion. This is the first report showing that a bacterial CS is bifunctional. Primary deuterium kinetic isotope effects show that C4-proS hydrogen is being transferred during the reduction of FMNox by NADH and that hydride transfer contributes significantly to the rate-limiting step of FMN reduction reaction. Solvent kinetic isotope effects and proton inventory results indicate that proton transfer from solvent partially limits the rate of FMN reduction and that a single proton transfer gives rise to the observed solvent isotope effect. Multiple isotope effects suggest a stepwise mechanism for the reduction of FMNox. The results on enzyme kinetics described here provide evidence for the mode of action of MtCS and should thus pave the way for the rational design of antitubercular agents. © 2008 Ely et al; licensee BioMed Central Ltd.