Structural studies of shikimate 5-dehydrogenase from Mycobacterium tuberculosis

Tuberculosis (TB) remains the leading cause of mortality due to a single bacterial pathogen, Mycobacterium tuberculosis. The reemergence of TB as a potential public health threat, the high susceptibility of human immunodeficiency virus-infected persons to the disease, the proliferation of multi-drug-resistant strains (MDR-TB) and, more recently, of extensively drug resistant isolates (XDR-TB) have created a need for the development of new antimycobacterial agents. Amongst the several proteins and/or enzymes to be studied as potential targets to develop novel drugs against M. tuberculosis, the enzymes of the shikimate pathway are attractive targets because they are essential in algae, higher plants, bacteria, and fungi, but absent from mammals. The mycobacterial shikimate pathway leads to the biosynthesis of chorismate, which is a precursor of aromatic amino acids, naphthoquinones, menaquinones, and mycobactins. Here we report the structural studies by homology modeling and circular dichroism spectroscopy of the shikimate dehydrogenase from M. tuberculosis (MtSDH), which catalyses the fourth step of the shikimate pathway. Our structural models show that the MtSDH has similar structure to other shikimate dehydrogenase structures previously reported either in presence or absence of NADP, despite the low amino acid sequence identity. The circular dichroism spectra corroborate the secondary structure content observed in the MtSDH models developed. The enzyme was stable up to 50 degrees C presenting a cooperative unfolding profile with the midpoint of the unfolding temperature value of similar to 63-64 degrees C, as observed in the unfolding experiment followed by circular dichroism. Our MtSDH structural models and circular dichroism data showed small conformational changes induced by NADP binding. We hope that the data presented here will assist the rational design of antitubercular agents.

Effects of cement thickness and bonding on the failure loads of CAD/CAM ceramic crowns: Multi-physics FEA modeling and monotonic testing

Objective. To determine the influence of cement thickness and ceramic/cement bonding on stresses and failure of CAD/CAM crowns, using both multi-physics finite element analysis and monotonic testing.Methods. Axially symmetric FEA models were created for stress analysis of a stylized monolithic crown having resin cement thicknesses from 50 to 500 mu m under occlusal loading. Ceramic-cement interface was modeled as bonded or not-bonded (cement-dentin as bonded). Cement polymerization shrinkage was simulated as a thermal contraction. Loads necessary to reach stresses for radial cracking from the intaglio surface were calculated by FEA. Experimentally, feldspathic CAD/CAM crowns based on the FEA model were machined having different occlusal cementation spaces, etched and cemented to dentin analogs. Non-bonding of etched ceramic was achieved using a thin layer of poly(dimethylsiloxane). Crowns were loaded to failure at 5 N/s, with radial cracks detected acoustically.Results. Failure loads depended on the bonding condition and the cement thickness for both FEA and physical testing. Average fracture loads for bonded crowns were: 673.5 N at 50 mu m cement and 300.6 N at 500 mu m. FEA stresses due to polymerization shrinkage increased with the cement thickness overwhelming the protective effect of bonding, as was also seen experimentally. At 50 mu m cement thickness, bonded crowns withstood at least twice the load before failure than non-bonded crowns.Significance. Occlusal "fit" can have structural implications for CAD/CAM crowns; pre-cementation spaces around 50-100 mu m being recommended from this study. Bonding benefits were lost at thickness approaching 450-500 mu m due to polymerization shrinkage stresses. (C) 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

The rigid-flexible nonlinear robotic manipulator: Modeling and control

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

Purification, sequencing and structural characterization of the phospholipase A(1) from the venom of the social wasp Polybia paulista (Hymenoptera, Vespidae)

The biochemical and functional characterization of wasp venom toxins is an important prerequisite for the development of new tools both for the therapy of the toxic reactions due to envenomation caused by multiple stinging accidents and also for the diagnosis and therapy of allergic reactions caused by this type of venom. PLA(1) was purified from the venom of the neotropical social wasp Polybia paulista by using molecular exclusion and cation exchange chromatographies; its amino acid sequence was determined by using automated Edman degradation and compared to the sequences of other vespid venom PLA(1)'s. The enzyme exists as a 33,961.40 da protein, which was identified as a lipase of the GX class, liprotein lipase superfamily, pancreatic lipases (ab20.3) homologous family and RP2 sub-group of phospholipase. P. paulista PLA(1) is 53-82% identical to the phospholipases from wasp species from Northern Hemisphere. The use restrained-based modeling permitted to describe the 3-D structure of the enzyme, revealing that its molecule presents 23% alpha-helix, 28% beta-sheet and 49% coil. The protein structure has the alpha/beta fold common to many lipases; the core consists of a tightly packed beta-sheet constituted of six-stranded parallel and one anti-parallel beta-strand, surrounded by four alpha-helices. P. paulista PLA(1) exhibits direct hemolytic action against washed red blood cells with activity similar to the Cobra cardiotoxin from Naja naja atra. In addition to this, PLA(1) was immunoreactive to specific IgE from the sera of P. paulista-sensitive patients. (c) 2007 Elsevier Ltd. All rights reserved.

Molecular modeling and small angle X-ray scattering studies of Hoplosternum littorale cathodic haemoglobin

Considerable interest is currently focused on fish haemoglobins in order to identify the structural basis for their diversity of functional behavior. Hoplosternum littorale is a catfish that presents bimodal gill (water)/gut (air) -breathing, which allows this species to survive in waters with low oxygen content. The hemolysate of this fish showed the presence of two main haemoglobins, cathodic and anodic. This work describes structural features analyzed here by integration of molecular modeling with small angle X-ray scattering. Here is described a molecular model for the cathodic haemoglobin in the unliganded and liganded states. The models were determined by molecular modeling based on the high-resolution crystal structure of fish haemoglobins. The structural models for both forms of H. littorale haemoglobin were compared to human haemoglobin. (C) 2004 Elsevier B.V. All rights reserved.

Modeling and simulation of cephalosporin C production in a fed-batch tower-type bioreactor

Immobilized cell utilization in tower-type bioreactor is one of the main alternatives being studied to improve the industrial bioprocess. Other alternatives for the production of beta -lactam antibiotics, such as a cephalosporin C fed-batch p recess in an aerated stirred-tank bioreactor with free cells of Cepha-losporium acremonium or a tower-type bioreactor with immobilized cells of this fungus, have proven to be more efficient than the batch profess. In the fed-batch process, it is possible to minimize the catabolite repression exerted by the rapidly utilization of carbon sources (such as glucose) in the synthesis of antibiotics by utilizing a suitable flow rate of supplementary medium. In this study, several runs for cephalosporin C production, each lasting 200 h, were conducted in a fed-batch tower-type bioreactor using different hydrolyzed sucrose concentrations, For this study's model, modifications were introduced to take into account the influence of supplementary medium flow rate. The balance equations considered the effect of oxygen limitation inside the bioparticles. In the Monod-type rate equations, eel concentrations, substrate concentrations, and dissolved oxygen were included as reactants affecting the bioreaction rate. The set of differential equations was solved by the numerical method, and the values of the parameters were estimated by the classic nonlinear regression method following Marquardt's procedure with a 95% confidence interval. The simulation results showed that the proposed model fit well with the experimental data,and based on the experimental data and the mathematical model an optimal mass flow rate to maximize the bioprocess productivity could be proposed.

Parmodel: a web server for automated comparative modeling of proteins

Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models ford a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools/parmodel. (C) 2004 Elsevier B.V. All rights reserved.

Structural and functional characterization of myotoxin I, a Lys49 phospholipase A(2) homologue from Bothrops moojeni (Caissaca) snake venom

Myotoxin-I (MjTX-I) was purified to homogeneity from the venom of Bothrops moojeni by ion-exchange chromatography on CM-Sepharose. Its molecular weight, estimated by SDS-PAGE, was 13,400 (reduced) or 26,000 (unreduced). The extinction coefficient (E-1.0 cm(1.0 mg/ml)) of MjTX-I was 1.145 at lambda = 278 nm, pH 7.0, and its isoelectric point was 8.2 at ionic strength mu = 0.1. When lyophilized and stored at 4 degrees C, dimeric, trimeric, and pentameric forms of the protein were identified by SDS-PAGE. This heterogeneous sample could be separated into three fractions by gel filtration on Sephadex 6-50. The fractions were analyzed by isoelectric focusing, immunoelectrophoresis, and amino acid composition, which indicated that heterogeneity was the result of different levels of self-association. Protein sequencing indicated that MjTX-I is a Lys49 myotoxin and consists of 121 amino acids (M-r = 13,669), containing a high proportion of basic and hydrophobic residues. It shares a high degree of sequence identity with other Lys49 PLA(2)-like myotoxins, but shows a significantly lower identity with catalytically active Asp49 PLA(2)s. The three-dimensional structure of MjTX-I was modeled based on the crystal structures of three highly homologous Lys49 PLA(2)-like myotoxins. This model showed that the amino acid substitutions are conservative, and mainly the beta-wing region, and the C-terminal extended random coil. MjTX-I displays local myotoxic and edema-inducing activities in mice, and is lethal by intraperitoneal injection, with an LD50 value of 8.5 +/- 0.8 mg/kg, In addition, it is cytotoxic to myoblasts/ myotubes in culture, and disrupts negatively charged liposomes. In comparison with the freshly prepared dimeric sample, the more aggregated forms showed significantly reduced myotoxic activity. However, the edema-inducing activity of MjTX-I was independent of molecular association. Phospholipase A(2) activity on egg yolk, as well as anticoagulant activity, were undetectable both in the native and in the more associated forms. His, Tyr, and Trp residues of the toxin were chemically modified by specific reagents. Although the myotoxic and lethal activities of the modified toxins were reduced by these treatments, neither its edema-inducing or Liposome-disrupting activities were significantly altered. Rabbit antibodies to native MjTX-I cross-reacted with the chemically modified forms, and both the native and modified MjTX-I preparations were recognized by antibodies against the C-terminal region 115-129 of myotoxin II from B. asper, a highly Lys49 PLA(2)-homologue with high sequencial similarity. (C) 2000 Academic Press.

Dynamic modeling and simulation of a flexible robotic manipulator

This work focuses on the dynamic modeling of a flexible robotic manipulator with two flexible links and two revolute joints, which rotates in the horizontal plane. The dynamic equations are derived using the Newton-Euler formulation and the finite element method, based on elementary beam theory. Computer simulation results are presented to illustrate this study. The dynamic model becomes necessary for use in future design and control applications.

Functional and structural analysis of two fibrinogen-activating enzymes isolated from the venoms of Crotalus durissus terrificus and Crotalus durissus collilineatus

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

Object oriented modeling of piston engines

This work reports a conception phase of a piston engine global model. The model objective is forecast the motor performance (power, torque and specific consumption as a function of rotation and environmental conditions). Global model or Zero-dimensional is based on flux balance through each engine component. The resulting differential equations represents a compressive unsteady flow, in which, all dimensional variables are areas or volumes. A review is presented first. The ordinary differential equation system is presented and a Runge-Kutta method is proposed to solve it numerically. The model includes the momentum conservation equation to link the gas dynamics with the engine moving parts rigid body mechanics. As an oriented to objects model the documentation follows the UML standard. A discussion about the class diagrams is presented, relating the classes with physical model related. The OOP approach allows evolution from simple models to most complex ones without total code rewrite. Copyright © 2001 Society of Automotive Engineers, Inc.

Modeling metabolizable energy utilization in broiler breeder pullets

The objective of this study was to determine models for ME requirements for broiler breeder pullets using the factorial method. The influence of the temperature on maintenance ME requirements was determined by experiments conducted in three environmental rooms with temperature kept constant at 15, 22, and 30°C, using the comparative slaughter technique. The energy requirements for weight gain were determined based on the body energy content and efficiency of energy utilization for weight gain. Two ME requirement models for each age were developed using the coefficients for maintenance and weight gain. The models for 3 to 8 wk were ME = W 0.75 (186.52 - 1.94T) + 2.47WG, and ME = W 0.75 (174 - 1.88T) + 2.83WG; for 9 to 14 wk, ME = W 0.75 (186.52 - 1.94T) + 2.69WG, and ME = W 0.75 (174 - 1.88T) + 2.50WG; and 15 to 20 wk, ME = W 0.75 (186.52 - 1.94T) + 2.76WG, and ME = W 0.75 (174 - 1.88T) + 3.24WG. In these equations, W is BW (kg), T is temperature (°C), and WG is daily weight gain (g). These models were compared to the breeder's recommendations in a feeding trial from 5 to 20 wk of age. Models 1 and 2 provided energy intakes that promoted BW smaller than the breeder's recommendation. However, all breeder pullets had weights above the standard recommendation. Model 2 gave the smallest ME intake and BW close to the standard recommendation and provided the best prediction of ME requirements.

Small-angle x-ray scattering study of the structural evolution of the drying of sonogels with the liquid phase exchanged by acetone

The structural evolution on the drying of wet sonogels of silica with the liquid phase exchanged by acetone, obtained from tetraethoxisilane sonohydrolysis, was studied in situ by small-angle x-ray scattering (SAXS). The periods associated to the structural evolution as determined by SAXS are in agreement with those classical ones established on basis of the features of the evaporation rate of the liquid phase in the obtaining of xerogels. The wet gel can be described as formed by primary particles (microclusters), with characteristic length a ∼ 0.67 nm and surface which is fractal, linking together to form mass fractal structures with mass fractal dimension D=2.24 in a length scale ξ∼6.7 nm. As the network collapses while the liquid/vapor meniscus is kept out of the gel volume, the mass fractal structure becomes more compacted by increasing D and decreasing ξ, with smoothing of the fractal surface of the microclusters. The time evolution of the density of the wet gels was evaluated exclusively from the SAXS parameters ξ, D, and a. The final dried acetone-exchanged gel presents Porod's inhomogeneity length of about 2.8 nm and apparently exhibits an interesting singularity D →3, as determined by the mass fractal modeling used to fit the SAXS intensity data for the obtaining of the parameters ξ and D.

Modeling energy utilization and growth parameter description for broiler chickens

Two experiments were conducted to develop and evaluate a model to estimate ME requirements and determine Gompertz growth parameters for broilers. The first experiment was conducted to determine maintenance energy requirements and the efficiencies of energy utilization for fat and protein deposition. Maintenance ME (ME m) requirements were estimated to be 157.8, 112.1, and 127.2 kcal of ME/kg 0.75 per day for broilers at 13, 23, and 32°C, respectively. Environmental temperature (T) had a quadratic effect on maintenance requirements (ME m = 307.87 - 15.63T + 0.3105T 2; r 2= 0.93). Energy requirements for fat and protein deposition were estimated to be 13.52 and 12.59 kcal of ME/g, respectively. Based on these coefficients, a model was developed to calculate daily ME requirements: ME = BW 0.75 (307.87 - 15.63T + 0.3105 T 2) + 13.52 G f + 12.59 G p. This model considers live BW, the effects of environmental temperature, and fractional fat (G f) and protein (G p) deposition. The second experiment was carried out to estimate the growth parameters of Ross broilers and to collect data to evaluate the ME requirement model proposed. Live BW, empty feather-free carcass, weight of the feathers, and carcass chemical compositions were analyzed until 16 wk of age. Parameters of Gompertz curves for each component were estimated. Males had higher growth potential and higher capacity to deposit nutrients than females, except for fat deposition. Data of BW and body composition collected in this experiment were fitted into the energy model proposed herein and the equations described by Emmans (1989) and Chwalibog (1991). The daily ME requirements estimated by the model determined in this study were closer to the ME intake observed in this trial compared with other models. ©2005 Poultry Science Association, Inc.

Identification of structural damage in flexible structures using system norm and neural networks

Nowadays there is great interest in damage identification using non destructive tests. Predictive maintenance is one of the most important techniques that are based on analysis of vibrations and it consists basically of monitoring the condition of structures or machines. A complete procedure should be able to detect the damage, to foresee the probable time of occurrence and to diagnosis the type of fault in order to plan the maintenance operation in a convenient form and occasion. In practical problems, it is frequent the necessity of getting the solution of non linear equations. These processes have been studied for a long time due to its great utility. Among the methods, there are different approaches, as for instance numerical methods (classic), intelligent methods (artificial neural networks), evolutions methods (genetic algorithms), and others. The characterization of damages, for better agreement, can be classified by levels. A new one uses seven levels of classification: detect the existence of the damage; detect and locate the damage; detect, locate and quantify the damages; predict the equipment's working life; auto-diagnoses; control for auto structural repair; and system of simultaneous control and monitoring. The neural networks are computational models or systems for information processing that, in a general way, can be thought as a device black box that accepts an input and produces an output. Artificial neural nets (ANN) are based on the biological neural nets and possess habilities for identification of functions and classification of standards. In this paper a methodology for structural damages location is presented. This procedure can be divided on two phases. The first one uses norms of systems to localize the damage positions. The second one uses ANN to quantify the severity of the damage. The paper concludes with a numerical application in a beam like structure with five cases of structural damages with different levels of severities. The results show the applicability of the presented methodology. A great advantage is the possibility of to apply this approach for identification of simultaneous damages.