Structural bioinformatics study of cyclin-dependent kinases complexed with inhibitors

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

Structural Basis for Interaction of Inhibitors with Cyclin-Dependent Kinase 2

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

BaZrO3 Photoluminescence Property: An Ab Initio Analysis of Structural Deformation and Symmetry Changes

This article reports a theoretical study based on experimental results for barium zirconate, BaZrO3 (BZ) thin films, using periodic mechanic quantum calculations to analyze the symmetry change in a structural order-disorder simulation. Four periodic models were simulated using CRYSTAL98 code to represent the ordered and disordered BZ structures. The results were analyzed in terms of the energy level diagrams and atomic orbital distributions to explain and understand the BZ photoluminescence properties (PL) at room temperature for the disordered structure based on structural deformation and symmetry changes. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 111: 694-701, 2011

A cost optimization-based design of precast concrete floors using genetic algorithms

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Effects of biofertilizer rates on the structural, morphogenetic and productive characteristics of Piata grass

The objective of this study was to investigate the influence of different levels of biofertilizers from cattle and swine manure on the structural, morphogenetic and productive characteristics of Brachiaria brizantha cv. Piata. The experiment was arranged in a completely randomized factorial design with split plots. The plots were defined by eight treatments: two biofertilizers (cattle and swine), four levels (0, 100, 200 and 300 kg N.ha(-1)) and subplots by four different cutting periods. The cutting for plant uniformity was performed at 45 days after sowing at 15 cm above the soil surface. The biofertilizeres were applied in a single level, after the cutting of plants, in rates of 0, 0.23 and 0.19, 0.45 and 0.38, 0.68 and 0.57 liters pot(-1) for the biofertilizers from cattle and swine manure, respectively. These rates were also equivalent to levels of 0, 100, 200 and 300 kg N.ha(-1). There was no significant difference between the types of biofertilizers as there was no interaction between them and the different levels, hence both biofertilizers could be applied without any loss of nutrient intake by the plants used in this experiment. There was a significant difference between the production of green and dry matter, the leaf appearance rate, phyllochron, leaf and pseudostem elongation rates, number of green leaves, final leaf length, number and weight of tillers, according to the increase of nitrogen rates, following linear prediction model. Effect of the cutting periods was also observed, once the plants harvested during the summer presented greater performance of structural and morphogenetic characteristics.

Spectroscopic characterization of SnO2 gels - Code: CP11

Excitation and dynamic emission spectra of Eu3+ ions were simultaneously used with FTIR and Raman spectroscopy to study the structural evolution during SnO2 sol → gel → xerogel conversion. Results make evident an increase of the surroundings symmetry for the Eu3+ ions dissolved in SnO2 matrix and a decrease of the amount of hydroxo groups (Sn-OH) during drying. These phenomena were associated to the pursuit of the condensation reaction after gelation. © 1994 Kluwer Academic Publishers.

Design of the main racetrack microtron accelerator end magnets of the Institute of Physics of University of São Paulo

This work deals with the design of the Institute of Physics of the University of São Paulo (IFUSP) main racetrack microtron accelerator end magnets. This is the last stage of acceleration, comprised of an accelerating section (1.04 m) and two end magnets (0.1585 T), in which a 5.10 MeV beam, produced by a racetrack microtron booster has its energy raised up to 31.15 MeV after 28 accelerations. POISSON code was used to give the final configuration that includes auxiliary pole pieces (clamps) and auxiliary homogenizing gaps. The clamps create a reverse fringe field region and avoid the vertical defocusing and the horizontal displacement of the beam produced by extended fringe fields; PTRACE code was used to perform the trajectory calculations in the fringe field region. The auxiliary homogenizing gaps improve the field uniformity as they create a magnetic shower that provides uniformity of ±0.3%, before the introduction of the correcting coils that will be attached to the pole faces. This method of correction, used in the IFUSP racetrack microtron booster magnets, enabled uniformity of ±0.001% in an average field of 0.1 T and will also be employed for these end magnets. © 1999 The American Physical Society.

A theoretical and experimental analysis of cold-formed steel shapes subjected to bending - Channel and simple lipped channel

Cold-formed steel shapes have been widely employed in steel construction, where they frequently offer a lower cost solution than do traditional laminated shapes. A classic application of cold-formed steel shapes is purlins in the roof panel of industrial buildings, connected to the roof panel by means of screws. The combined effect of these two elements has been the subject of investigations in some countries. Design criteria were included in the AISI Code in 1991 and 1996. This paper presents and discusses the results obtained from bending tests carried out on shapes commonly used in Brazil, i.e., the channel and the simple lipped channel, Tests were carried out on double shapes with 4.5 and 6.0 meter spans, which were subjected to concentrated loads and braced against each other on the supports and at intermediary points in three different load situations. The panel shape was also analyzed experimentally, simulating the action of wind by means of a vacuum box designed specifically for this purpose. The test results were then compared to those obtained through the theoretical analysis, enabling us to extract important information upon which to base proposed design criteria for the new Brazilian code.

Structural basis for inhibition of cyclin-dependent kinase 9 by flavopiridol

Flavopiridol has been shown to potently inhibit CDK1 and 2 (cyclin-dependent kinases 1 and 2) and most recently it has been found that it also inhibits CDK9. The complex CDK9-cyclin T1 controls the elongation phase of transcription by RNA polymerase II. The present work describes a molecular model for the binary complex CDK9-flavopiridol. This structural model indicates that the inhibitor strongly binds to the ATP-binding pocket of CDK9 and the structural comparison of the complex CDK2-flavopiridol correlates the structural differences with differences in inhibition of these CDKs by flavopiridol. This structure opens the possibility of testing new inhibitor families, in addition to new substituents for the already known leading structures such as flavones and adenine derivatives. © 2002 Elsevier Science (USA). All rights reserved.

Brazilian results on structural masonry concrete blocks

The purpose of this paper is to study the mechanical behavior of concrete blocks and prisms when performing axial compression tests within the Brazilian base of knowledge, intending to foment data of this kind for a world-based network. The blocks were built using five different mixtures in which the quantity of cement and the compacting ratio (density) were varied (during the fabrication process). The three-course-high prisms were assembled using 1 cm (0.39 in.) thick full-bedded joints, always trying to leave the mortar's characteristics constant. The axial compression tests were conducted according to Brazilian practice code recommendations, because most of these standards are very similar to international practice codes. The compressive strength, strains, and rupture form of each mixture studied were recorded. Attempts were made to correlate the strength, efficiency ratio (block strength/prism strength) of the prisms, strains, and rupture form; with the quantity of cement and compacting ratio. The data are presented in tables and figures, and the obtained results are discussed throughout the text. Copyright © 2007, American Concrete Institute. All rights reserved.

Chorismate synthase: An attractive target for drug development against orphan diseases

The increase in incidence of infectious diseases worldwide, particularly in developing countries, is worrying. Each year, 14 million people are killed by infectious diseases, mainly HIV/AIDS, respiratory infections, malaria and tuberculosis. Despite the great burden in the poor countries, drug discovery to treat tropical diseases has come to a standstill. There is no interest by the pharmaceutical industry in drug development against the major diseases of the poor countries, since the financial return cannot be guaranteed. This has created an urgent need for new therapeutics to neglected diseases. A possible approach has been the exploitation of the inhibition of unique targets, vital to the pathogen such as the shikimate pathway enzymes, which are present in bacteria, fungi and apicomplexan parasites but are absent in mammals. The chorismate synthase (CS) catalyses the seventh step in this pathway, the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate. The strict requirement for a reduced flavin mononucleotide and the anti 1,4 elimination are both unusual aspects which make CS reaction unique among flavin-dependent enzymes, representing an important target for the chemotherapeutic agents development. In this review we present the main biochemical features of CS from bacterial and fungal sources and their difference from the apicomplexan CS. The CS mechanisms proposed are discussed and compared with structural data. The CS structures of some organisms are compared and their distinct features analyzed. Some known CS inhibitors are presented and the main characteristics are discussed. The structural and kinetics data reviewed here can be useful for the design of inhibitors. © 2007 Bentham Science Publishers Ltd.

The inhibition of 5-enolpyruvylshikimate-3-phosphate synthase as a model for development of novel antimicrobials

EPSP synthase (EPSPS) is an essential enzyme in the shikimate pathway, transferring the enolpyruvyl group of phosphoenolpyruvate to shikimate-3-phosphate to form 5-enolpyruvyl-3-shikimate phosphate and inorganic phosphate. This enzyme is composed of two domains, which are formed by three copies of βαβαββ-folding units; in between there are two crossover chain segments hinging the nearly topologically symmetrical domains together and allowing conformational changes necessary for substrate conversion. The reaction is ordered with shikimate-3-phosphate binding first, followed by phosphoenolpyruvate, and then by the subsequent release of phosphate and EPSP. N-[phosphomethyl]glycine (glyphosate) is the commercial inhibitor of this enzyme. Apparently, the binding of shikimate-3-phosphate is necessary for glyphosate binding, since it induces the closure of the two domains to form the active site in the interdomain cleft. However, it is somehow controversial whether binding of shikimate-3-phosphate alone is enough to induce the complete conversion to the closed state. The phosphoenolpyruvate binding site seems to be located mainly on the C-terminal domain, while the binding site of shikimate-3-phosphate is located primarily in the N-terminal domain residues. However, recent results demonstrate that the active site of the enzyme undergoes structural changes upon inhibitor binding on a scale that cannot be predicted by conventional computational methods. Studies of molecular docking based on the interaction of known EPSPS structures with (R)- phosphonate TI analogue reveal that more experimental data on the structure and dynamics of various EPSPS-ligand complexes are needed to more effectively apply structure-based drug design of this enzyme in the future. © 2007 Bentham Science Publishers Ltd.

Generating VHDL-AMS models of digital-to-analogue converters from MATLAB®/SIMULINK®

Today, the trend within the electronics industry is for the use of rapid and advanced simulation methodologies in association with synthesis toolsets. This paper presents an approach developed to support mixed-signal circuit design and analysis. The methodology proposed shows a novel approach to the problem of developing behvioural model descriptions of mixed-signal circuit topologies, by construction of a set of subsystems, that supports the automated mapping of MATLAB®/SIMULINK® models to structural VHDL-AMS descriptions. The tool developed, named MS 2SV, reads a SIMULINK® model file and translates it to a structural VHDL-AMS code. It also creates the file structure required to simulate the translated model in the System Vision™. To validate the methodology and the developed program, the DAC08, AD7524 and AD5450 data converters were studied and initially modelled in MATLAB®/ SIMULINK®. The VHDL-AMS code generated automatically by MS 2SV, (MATLAB®/SIMULINK® to System Vision™), was then simulated in the System Vision™. The simulation results show that the proposed approach, which is based on VHDL-AMS descriptions of the original model library elements, allows for the behavioural level simulation of complex mixed-signal circuits.

Blade design and forming for fans using finite elements

The necessity of adapting the standardized fan models to conditions of higher temperature has emerged due to the growth of concerning referring to the consequences of the gas expelling after the Mont Blanc tunnel accident in Italy and France, where even though, with 100 fans in operation, 41 people died. However, since then, the defied solutions have pointed to aerodynamic disadvantages or have seemed nonappropriate in these conditions. The objective of this work is to present an alternative to the market standard fans considering a new technology in constructing blades. This new technology introduces the use of the stainless steel AISI 409 due to its good adaptation to temperatures higher than 400°C, particularly exposed to temperatures of gas exhaust from tunnels in fire situation. Furthermore, it presents a very good resistance to corrosion and posterior welding and pressing, due to its alloyed elements. The innovation is centered in the process of a deep drawing of metallic shells and posterior welding, in order to keep the ideal aerodynamic superficies for the fan ideal performance. On the other hand, the finite element method, through the elasto-plastic software COSMOS permitted the verification of the thickness and structural stability of the blade in relation to the aerodynamic efforts established in the project. In addition, it is not advisable the fabrication of blades with variable localized thickness not even, non-uniform ones, due to the verified concentration of tensions and the difficulties observed in the forming. In this way, this study recommends the construction of blades with uniform variations of thickness. © 2007 Springer.

A methodology and a tool to design of mixed-signal technology

This paper presents a tool box developed to read files describing a SIMULINK® model and translates it into a structural VHDL-AMS description. In translation process, all files and directory structures to simulate the translated model on SystemVision™ environment is generate. The tool box named MS2SV was tested by three models of commercially available digital-to-analogue converters. All models use the R2R ladder network to conversion, but the functionality of these three components is different. The methodology of conversion of the model is presents together with sort theory about R-2R ladder network. In the evaluation of the translated models, we used a sine waveform input signal and the waveform generated by D/A conversion process was compared by FFT analysis. The results show the viability of this type of approach. This work considers some of challenges set by the electronic industry for the further development of simulation methodologies and tools in the field of mixed-signal technology. © 2007 IEEE.