On the use of open or closed traps in the capture of drosophilids

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

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.

Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases

Spider venom sphingomyelinases D catalyze the hydrolysis of sphingomyelin via an Mg2+ ion-dependent acid-base catalytic mechanism which involves two histidines. In the crystal structure of the sulfate free enzyme determined at 1.85 angstrom resolution, the metal ion is tetrahedrally coordinated instead of the trigonal-bipyramidal coordination observed in the sulfate bound form. The observed hyperpolarized state of His47 requires a revision of the previously suggested catalytic mechanism. Molecular modeling indicates that the fundamental structural features important for catalysis are fully conserved in both classes of SMases D and that the Class II SMases D contain an additional intra-chain disulphide bridge (Cys53-Cys201). Structural analysis suggests that the highly homologous enzyme from Loxosceles bonetti is unable to hydrolyze sphingomyelin due to the 95G1y -> Asn and 134Pro -> Glu mutations that modify the local charge and hydrophobicity of the interfacial face. Structural and sequence comparisons confirm the evolutionary relationship between sphingomyelinases D and the glicerophosphodiester phosphoesterases which utilize a similar catalytic mechanism. (c) 2006 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction analysis of the catalytic subunit of ADP-glucose pyrophosphorylase from potato tuber

ADP-glucose pyrophosphorylase is the key regulatory enzyme in the biosynthesis of starch in plants and glycogen in bacteria. The enzyme from potato tuber is comprised of a regulatory subunit and a catalytic subunit and is present as a heterotetramer (alpha(2)beta(2)) the catalytic subunit from potato tuber (50 kDa) was crystallized in four different forms, two of which are suitable for structural studies. A tetragonal crystal form obtained in the presence of the substrate analog Cr-ATP diffracted to 2.2 Angstrom and belongs to space group P4(1) (or its enantiomorph), with unit-cell parameters a = b = 110.57, c = 190.14 Angstrom. A second crystal form obtained diffracted to 2.8 Angstrom and belongs to space group PZ, with unit-eel parameters a = 80.06, b = 138.84, c = 92.20 Angstrom, beta = 112.40 degrees. As this protein displays no significant homology to any currently known protein structure, a search for heavy-atom derivatives has been initiated.

Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D

Sphingomyelinases D (SMases D) from Loxosceles spider venom are the principal toxins responsible for the manifestation of dermonecrosis, intravascular hemolysis, and acute renal failure, which can result in death. These enzymes catalyze the hydrolysis of sphingomyelin, resulting in the formation of ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidyl choline, generating the lipid mediator lysophosphatidic acid. This report represents the first crystal structure of a member of the sphingomyelinase D family from Loxosceles laeta (SMase I), which has been determined at 1.75-angstrom resolution using the quick cryo-soaking technique and phases obtained from a single iodine derivative and data collected from a conventional rotating anode x-ray source. SMase I folds as an (alpha/beta)(8) barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface. Substrate binding and/or the transition state are stabilized by a Mg2+ ion, which is coordinated by Glu(32), Asp(34), Asp(91), and solvent molecules. In the proposed acid base catalytic mechanism, His(12) and His(47) play key roles and are supported by a network of hydrogen bonds between Asp(34), Asp(52), Trp(230), Asp(233), and Asn(252).

The critical number of atoms in an attractive Bose-Einstein condensate on optical plus harmonic traps

The stability of an attractive Bose-Einstein condensate on a joint one-dimensional optical lattice and an axially symmetrical harmonic trap is studied using the numerical solution of the time-dependent mean-field Gross-Pitaevskii equation and the critical number of atoms for a stable condensate is calculated. We also calculate this critical number of atoms in a double-well potential which is always greater than that in an axially symmetrical harmonic trap. The critical number of atoms in an optical trap can be made smaller or larger than the corresponding number in the absence of the optical trap by moving a node of the optical lattice potential in the axial direction of the harmonic trap. This variation of the critical number of atoms can be observed experimentally and compared with the present calculations.

Bound states of attractive Bose-Einstein condensates in shallow traps in two and three dimensions

Using variational and numerical solutions of the mean-field Gross-Pitaevskii equation for attractive interaction (with cubic or Kerr nonlinearity), we show that a stable bound state can appear in a Bose-Einstein condensate (BEC) in a localized exponentially screened radially symmetric harmonic potential well in two and three dimensions. We also consider an axially symmetric configuration with zero axial trap and a exponentially screened radial trap so that the resulting bound state can freely move along the axial direction like a soliton. The binding of the present states in shallow wells is mostly due to the nonlinear interaction with the trap playing a minor role. Hence, these BEC states are more suitable to study the effect of the nonlinear force on the dynamics. We illustrate the highly nonlinear nature of breathing oscillations of these states. Such bound states could be created in BECs and studied in the laboratory with present knowhow.

Dynamics of Bose-Einstein condensates in cigar-shaped traps

The Gross-Pitaevskii equation for a Bose-Einstein condensate confined in an elongated cigar-shaped trap is reduced to an effective system of nonlinear equations depending on only one space coordinate along the trap axis. The radial distribution of the condensate density and its radial velocity are approximated by Gaussian functions with real and imaginary exponents, respectively, with parameters depending on the axial coordinate and time. The effective one-dimensional system is applied to a description of the ground state of the condensate, to dark and bright solitons, to the sound and radial compression waves propagating in a dense condensate, and to weakly nonlinear waves in repulsive condensate. In the low-density limit our results reproduce the known formulas. In the high-density case our description of solitons goes beyond the standard approach based on the nonlinear Schrodinger equation. The dispersion relations for the sound and radial compression waves are obtained in a wide region of values of the condensate density. The Korteweg-de Vries equation for weakly nonlinear waves is derived and the existence of bright solitons on a constant background is predicted for a dense enough condensate with a repulsive interaction between the atoms.

Influence of support on catalytic behavior of nickel catalysts in the steam reforming of ethanol for hydrogen production

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Influence of rare earth doping on the structural and catalytic properties of nanostructured tin oxide

Nanoparticles of tin oxide, doped with Ce and Y, were prepared using the polymeric precursor method. The structural variations of the tin oxide nanoparticles were characterized by means of nitrogen physisorption, carbon dioxide chemisorption, X-ray diffraction, and X-ray photoelectron spectroscopy. The synthesized samples, undoped and doped with the rare earths, were used to promote the ethanol steam reforming reaction. The SnO2-based nanoparticles were shown to be active catalysts for the ethanol steam reforming. The surface properties, such as surface area, basicity/base strength distribution, and catalytic activity/selectivity, were influenced by the rare earth doping of SnO2 and also by the annealing temperatures. Doping led to chemical and micro-structural variations at the surface of the SnO2 particles. Changes in the catalytic properties of the samples, such as selectivity toward ethylene, may be ascribed to different dopings and annealing temperatures.

Surface structure and electronic properties of Pt-Fe/C nanocatalysts and their relation with catalytic activity for oxygen reduction

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

Platinum-coated nanostructured oxides for active catalytic electrodes

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Strontium zirconate heterogeneous catalyst for biodiesel production: Synthesis, characterization and catalytic activity evaluation

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Anuran captured in pitfall traps in three agrossystem in Northwestern São Paulo State, Brazil

Embora seja geralmente assumido que a agricultura influencia negativamente populações de anfíbios, existem poucos estudos sobre os efeitos dos cultivos agrícolas em anuros neotropicais. Visando contribuir para diminuir essa lacuna de conhecimento, no presente estudo buscamos verificar quais espécies de anuros estão presentes nos agrossistemas. Para isso, usamos dados de anuros capturados em armadilhas de queda, inicialmente proposto para o levantamento da fauna de opiliões em três agrossistemas (milho, soja e seringal). Nós registramos quatro espécies de anuros nas armadilhas de queda: Leptodactulus fuscus, L. mystacinus (Leptodactylidae), Eupemphix nattereri e Physalaemus cuvieri (Leiuperidae). Na plantação de milho foram registradas quatro espécies e 30 indivíduos, no seringal quatro espécies e 11 indivíduos e na plantação de soja três espécies e oito indivíduos. Nossos resultados mostram que os anuros estão presentes nos agrossistemas, principalmente espécies de anuros generalistas.

Composition and diversity of bees (Hymenoptera) attracted by Moericke traps in an agricultural area in Rio Claro, state of São Paulo, Brasil

Foram estudadas a composição e diversidade de abelhas em uma área agrícola no município de Rio Claro, Estado de São Paulo, de maio de 2003 a junho de 2004, utilizando armadilha de Moericke. O local de coleta, uma área com 58,08 hectares, caracteriza-se pela produção de grãos e a prática de plantio direto, sendo que 70% da área de entorno é utilizada para o plantio de cana-de-açúcar. Foram coletadas 456 abelhas distribuídas em 20 gêneros, pertencentes às famílias Andrenidae (4,8%), Apidae (40,8%) e Halictidae (54,4%). Espécimes dos gêneros Dialictus (38%) e Diadasia (30%) foram predominantes nesta área. A diversidade de espécies avaliadas pelos índices de Shannon e Simpson foram H =1,88 e 1/D= 4.15, respectivamente, e o índice de Equitatibilidade de 0,61.