Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

The effect of locked screw angulation on the biomechanical properties of the S.P.S. Free-Block plate

Objectives: Among the locked internal fixators is one denominated S.P.S. (Synthesis Pengo System) Free-Block, which was designed with a locking ring that allows the screw to be locked and positioned obliquely. Due to the paucity of biomechanical studies on this system, the present work aimed to evaluate the influence of locked screw angulation on the resistance of the S.P.S. Free--Block plate. Methods: Forty synthetic bone cylinders with 10 mm fracture gap were used. Forty seven-hole 3.5 mm stainless steel plates (two AO-like dynamic compression holes and five locked holes) were assembled according to the orientation of the locked screws: mono cortical screws were positioned at 90° to the long axis of the cylinder (Group 1), and monocortical screws were positioned at 70° to its cylinder long axis (Group 2). In both groups, AO-like dynamic compression hole screws were positioned bicortically and neutrally. For each group, six specimens were tested until failure, three in bending and three in compression, to determine the loads for fatigue testing. Subsequently, for each group, 14 specimens were tested for failure --seven by bending and seven in compression. Results: No significant failure differences were observed between Groups 1 and 2 under static-loading or fatigue test. Clinical significance: In a fracture gap model the orientation of the locked monocortical screws did not show any influence on the mechanical performance of the S.P.S. Free-Block to tests of axial compression and four-point bending. © Schattauer 2013.

Photo-Fenton degradation kinetics of low ciprofloxacin concentration using different iron sources and pH

The aim of the present study was to compare the degradation kinetics of low (1 mg L-1) and high (25 mg L-1) concentrations of ciprofloxacin (CIP) aiming to decrease the concentration of additives and evaluate the pH limitation by the use of low iron concentrations and organic ligands. A parameterized kinetic model was satisfactorily fitted to the experimental data in order to study the performance of photo-Fenton process with specific iron sources (iron citrate, iron oxalate, iron nitrate) under different pH medium (2.5, 4.5, 6.5). The process modeling allowed selecting those process conditions (iron source, additives concentrations and pH medium) which maximize the two performance parameters related to the global equilibrium conversion and kinetic rate of the process. For the high CIP concentration, degradation was very influenced by the iron source, resulting in much lower efficiency with iron nitrate. At pH 4.5, highest TOC removal (0.87) was achieved in the presence of iron citrate, while similar CIP conversions were obtained with oxalate and citrate (0.98 after 10 min). For the low CIP concentration, much higher conversion was observed in the presence of citrate or oxalate in relation to iron nitrate up to pH 4.5. This behavior denotes the importance of complexation also at low dosages. Appropriate additives load (320 μM H 2O2; 6 μM Fe) resulted in a CIP conversion of 0.96 after10 min reaction with citrate up to pH 4.5. © 2013 Elsevier B.V. All rights reserved.

The Mode of Action of Recombinant Mycobacterium tuberculosis Shikimate Kinase: Kinetics and Thermodynamics Analyses

Tuberculosis remains as one of the main cause of mortality worldwide due to a single infectious agent, Mycobacterium tuberculosis. The aroK-encoded M. tuberculosis Shikimate Kinase (MtSK), shown to be essential for survival of bacilli, catalyzes the phosphoryl transfer from ATP to the carbon-3 hydroxyl group of shikimate (SKH), yielding shikimate-3-phosphate and ADP. Here we present purification to homogeneity, and oligomeric state determination of recombinant MtSK. Biochemical and biophysical data suggest that the chemical reaction catalyzed by monomeric MtSK follows a rapid-equilibrium random order of substrate binding, and ordered product release. Isothermal titration calorimetry (ITC) for binding of ligands to MtSK provided thermodynamic signatures of non-covalent interactions to each process. A comparison of steady-state kinetics parameters and equilibrium dissociation constant value determined by ITC showed that ATP binding does not increase the affinity of MtSK for SKH. We suggest that MtSK would more appropriately be described as an aroL-encoded type II shikimate kinase. Our manuscript also gives thermodynamic description of SKH binding to MtSK and data for the number of protons exchanged during this bimolecular interaction. The negative value for the change in constant pressure heat capacity (ΔCp) and molecular homology model building suggest a pronounced contribution of desolvation of non-polar groups upon binary complex formation. Thermodynamic parameters were deconvoluted into hydrophobic and vibrational contributions upon MtSK:SKH binary complex formation. Data for the number of protons exchanged during this bimolecular interaction are interpreted in light of a structural model to try to propose the likely amino acid side chains that are the proton donors to bulk solvent following MtSK:SKH complex formation. © 2013 Rosado et al.

Elucidation of carbohydrate molecular interaction mechanism of recombinant and native ArtinM

The quartz crystal microbalance (QCM) technique has been applied for monitoring the biorecognition of ArtinM lectins at low horseradish peroxidase glycoprotein (HRP) concentrations, using a simple kinetic model based on Langmuir isotherm in previous work.18 The latter approach was consistent with the data at dilute conditions but it fails to explain the small differences existing in the jArtinM and rArtinM due to ligand binding concentration limit. Here we extend this analysis to differentiate sugar-binding event of recombinant (rArtinM) and native (jArtinM) ArtinM lectins beyond dilute conditions. Equivalently, functionalized quartz crystal microbalance with dissipation monitoring (QCM-D) was used as real-time label-free technique but structural-dependent kinetic features of the interaction were detailed by using combined analysis of mass and dissipation factor variation. The stated kinetic model not only was able to predict the diluted conditions but also allowed to differentiate ArtinM avidities. For instance, it was found that rArtinM avidity is higher than jArtinM avidity whereas their conformational flexibility is lower. Additionally, it was possible to monitor the hydration shell of the binding complex with ArtinM lectins under dynamic conditions. Such information is key in understanding and differentiating protein binding avidity, biological functionality, and kinetics. © 2013 American Chemical Society.

Analyzing the effect of homogeneous frustration in protein folding

The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy landscape of protein folding is funneled toward the native state, a conformational state that is consistent with the principle of minimal frustration. It has been accepted that real proteins are selected through natural evolution, satisfying the minimum frustration criterion. However, there is evidence that a low degree of frustration accelerates folding. We examined the interplay between topological and energetic protein frustration. We employed a Cα structure-based model for simulations with a controlled nonspecific energetic frustration added to the potential energy function. Thermodynamics and kinetics of a group of 19 proteins are completely characterized as a function of increasing level of energetic frustration. We observed two well-separated groups of proteins: one group where a little frustration enhances folding rates to an optimal value and another where any energetic frustration slows down folding. Protein energetic frustration regimes and their mechanisms are explained by the role of non-native contact interactions in different folding scenarios. These findings strongly correlate with the protein free-energy folding barrier and the absolute contact order parameters. These computational results are corroborated by principal component analysis and partial least square techniques. One simple theoretical model is proposed as a useful tool for experimentalists to predict the limits of improvements in real proteins. © 2013 Wiley Periodicals, Inc.

Estudo do efeito da adição de frustração no enovelamento de proteínas utilizando modelos baseados em estruturas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Regimes de frustração ótima em enovelamento de proteínas com modelos baseado em estrutura

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

O efeito da orientação do parafuso bloqueado nas propriedades biomecânicas da placa S.P.S. Free-Block em corpos de prova nao osteoporóticos

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Aplicações de secagem para o aproveitamento de resíduos da banana, visando sua aplicação na indústria

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Resíduo de laranja: estudo da cinética de secagem das sementes e influência da temperatura na qualidade do óleo

Pós-graduação em Engenharia e Ciência de Alimentos - IBILCE

Síntese e caracterização de silsesquioxanos organofuncionalizados: aplicações em adsorção, pré-concentração e catálise

Pós-graduação em Ciência dos Materiais - FEIS

A mass transfer model applied to the supercritical extraction with CO2 of curcumins from turmeric rhizomes (Curcuma longa L)

ABSTRACT: Increasing restrictions on the use of artificial pigments in the food industry, imposed by the international market, have increased the importance of raw materials containing natural pigments. Of those natural substances with potential applications turmeric rhizomes (Curcuma longa L), are one of the most important natural sources of yellow coloring. Three different pigments (curcumin, desmetoxycurcumin, and bis-desmetoxycurcumin) constitute the curcuminoids. These pigments are largely used in the food industry as substitutes for synthetic dyes like tartrazin. Extraction of curcuminoids from tumeric rhizomes with supercritical CO2 can be applied as an alternative method to obtain curcuminoids, as natural pigments are in general unstable, and hence degrade when submitted to extraction with organic solvents at high temperatures. Extraction experiments were carried out in a supercritical extraction pilot plant at pressures between 25 and 30 MPa and a temperature of 318 K. The influence of drying pretreatment on extraction yield was evaluated by analyzing the mass transfer kinetics and the content of curcuminoids in the extracts during the course of extraction. The chemical identification of curcuminoids in both the extract and the residual solid was performed by spectrophotometry. Mass transfer within the solid matrix was described by a linear first-order desorption model, while that in the gas phase was described by a convective mass transfer model. Experimental results showed that the concentration profile for curcuminoids during the supercritical extraction process was higher when the turmeric rhizomes were submitted to a drying pretreatment at 343 K.

Obtenção e caracterização de hidrogéis de poliacrilamida-co-metilcelulose como sistemas carreadores de cloridrato de propranolol

Matrizes poliméricas como os hidrogéis são sistemas de liberação controlada que estão sendo largamente utilizados na indústria farmacêutica. Neste trabalho os hidrogéis de PAAm-co-MC foram obtidos e caracterizados afim de carrear o propranolol, fármaco anti-hipertensivo. Os hidrogéis compostos pelos monômeros AAm e MC foram sintetizados por polimerização via radical livre, sendo investigada quatro concentrações de AAm (3,6%; 7,2%; 14,7% e 21,7% m/v). A caracterização dos hidrogéis foi realizada com os estudos de grau de intumescimento, potencial zeta, IR-FT, MEV e análises térmicas (TG, DTA, DTG e DSC). O hidrogel 3,6% apresentou maior grau de intumescimento em todos os meios de análise. O potencial zeta revelou que todos os hidrogéis permanecem próximo do ponto isoelétrico. O espectro de absorção do infravermelho permitiu identificar bandas características, tanto do hidrogel como do propranolol. As curvas de TG dos hidrogéis evidenciaram a degradação dos mesmos em dois estágios, sendo observado na curva DTG a maior perda de massa em torno de 400ºC e as curvas DTA e DSC confirmaram os três eventos endotérmicos. Já o propranolol apresentou um único estágio de degradação e seu pico de fusão foi em 163,4ºC. As microfotografias relevaram a disposição da rede tridimensional dos hidrogéis. A relação da adsorção propranolol/hidrogel foi de 573 mg/g, seguindo o modelo da isoterma de Langmuir. No estudo da cinética de liberação in vitro a liberação do propranolol a partir da matriz do hidrogel foi de aproximadamente 80% do fármaco em 424 horas, apresentando um modelo bimodal. A realização deste trabalho demonstrou que o hidrogel de PAAm-co-MC é um grande promissor para aplicação em sistemas carreadores de fármacos.

Evaluation of Renal Protection From High Doses of Melatonin in an Experimental Model of Renal Ischemia and Reperfusion in Hyperglycemic Rats

Background. Melatonin is a free radical scavenger with important actions in the study of renal ischemia and reperfusion (I/R). This study evaluated possible renal protection of high doses of melatonin in an experimental model of I/R in which rats were submitted to acute hyperglycemia under anesthesia with isoflurane.Method. Forty-four male Wistar rats, weighing more than 300 g, were randomly divided into 5 groups: G1, sham (n = 10); G2, melatonin (n = 10; 50 mg.kg(-1)); G3, hyperglycemia (n = 9; glucose 2.5 g.kg(-1)); G4, hyperglycemia/melatonin (n = 10; 2.5 g.kg(-1) glucose + melatonin 50 mg.kg(-1)); and G5, I/R (n = 5). In all groups, anesthesia was induced with 4% isoflurane and maintained with 1.5% to 2.0% isoflurane. Intraperitoneal injection of melatonin (G1, G4), glucose (G3, G4), or saline (G1, G5) was performed 40 minutes before left renal ischemia. Serum plasma values for creatinine and glucose were determined at baseline (M1), immediately following reperfusion (M2), and 24 hours after completion of the experiment (M3). Histological analysis was performed to evaluate tubular necrosis (0-5).Results. Serum glucose was higher at M2 in the groups supplemented with glucose, hyperglycemia (356.00 +/- 107.83), and hyperglycemia/melatonin (445.3 +/- 148.32). Creatinine values were higher at T3 (P = .0001) for I/R (3.6 +/- 0.37), hyperglycemia/melatonin (3.9 +/- 0.46), and hyperglycemia (3.71 +/- 0.69) and lower in the sham (0.79 +/- 0.16) and melatonin (2.01 +/- 1.01) groups, P < .05. Histology showed no necrosis injury in the G1, lesion grade 2 in the G2, and severe acute tubular necrosis in the G3: (grade 4), G4: (grade 5) and G5: (grade 4) groups (P < .0001).Discussion. Melatonin protected the kidneys submitted to I/R in rats without hyperglycemia; however, this did not occur when the I/R lesion was associated with hyperglycemia.Conclusions. Due to its antioxidant and antiapoptotic action, melatonin was able to mitigate, but not prevent acute tubular necrosis in rats with hyperglycemia under anesthesia by isoflurane.