Adsorption of immunoglobulin Y in supermacroporous continuous cryogel with immobilized Cu2+ ions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Materiais derivados de hidróxidos duplos lamelares: síntese, caracterização e aplicação em adsorção e processos avançados de oxidação

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

Purificação parcial e caracterização bioquímica de uma isoforma de β-glicosidase do fungo termofílico Myceliophthora thermophila M.7.7

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

On the stability of the extracellular hemoglobin of Glossoscolex paulistus, in two iron oxidation states, in the presence of urea

The stability of the Glossoscolex paulistus hemoglobin (HbGp), in two iron oxidation states (and three forms), as monitored by optical absorption, fluorescence emission and circular dichroism (CD) spectroscopies, in the presence of the chaotropic agent urea, is studied. HbGp oligomeric dissociation, denaturation and iron oxidation are observed. CD data show that the cyanomet-HbGp is more stable than the oxy-form. Oxy- and cyanomet-HbGp show good fits on the basis of a two state model with critical urea concentrations at 220-222 nm of 5.1 +/- 0.2 and 6.1 +/- 0.1 mol/L, respectively. The three-state model was able to reveal a subtle second transition at lower urea concentration (1.0-2.0 mol/L) associated to partial oligomeric dissociation. The intermediate state for oxy- and cyanomet-HbGp is very similar to the native state. For met-HbGp, a different equilibrium, in the presence of urea, is observed. A sharp transition at 1.95 +/- 0.05 mol/L of denaturant is observed, associated to oligomeric dissociation and hemichrome formation. In this case, analysis by a three-state model reveals the great similarity between the intermediate and the unfolded states. Analysis of spectroscopic data, by two-state and three-state models, reveals consistency of obtained thermodynamic parameters for HbGp urea denaturation. (C) 2012 Elsevier Inc. All rights reserved.

Determinação dos parâmetros cinéticos e termodinâmicos da adsorção de L-cisteína em ouro por meio da técnica de microbalança a cristal de quartzo

This article discusses the adsorption kinetics of a L-cysteine monolayer onto a gold surface by means of information obtained through the QCM technique. The results indicate that the adsorption process is rapid and follows the Langmuir isotherm, in which adsorption and desorption are considered. From these measurements the following parameter values were obtained: k d = (4.2 ± 0.4) x 10-3 s-1, k a = 75 ± 6 M-1 s-1, Keq=(1.8 ± 0.3) x 10(4) M-1 and ΔGads = - (5.8 ± 0.2) kcal mol-1.

Molecular interactions: metal ions and protein chaperones in the urease system from Helicobacter pylori

Although nickel is a toxic metal for living organisms in its soluble form, its importance in many biological processes recently emerged. In this view, the investigation of the nickel-dependent enzymes urease and [NiFe]-hydrogenase, especially the mechanism of nickel insertion into their active sites, represent two intriguing case studies to understand other analogous systems and therefore to lead to a comprehension of the nickel trafficking inside the cell. Moreover, these two enzymes have been demonstrated to ensure survival and colonization of the human pathogen H. pylori, the only known microorganism able to proliferate in the gastric niche. The right nickel delivering into the urease active site requires the presence of at least four accessory proteins, UreD, UreE, UreF and UreG. Similarly, analogous process is principally mediated by HypA and HypB proteins in the [NiFe]-hydrogenase system. Indeed, HpHypA and HpHypB also have been proposed to act in the activation of the urease enzyme from H. pylori, probably mobilizing nickel ions from HpHypA to the HpUreE-HpUreG complex. A complete comprehension of the interaction mechanism between the accessory proteins and the crosstalk between urease and hydrogenase accessory systems requires the determination of the role of each protein chaperone that strictly depends on their structural and biochemical properties. The availability of HpUreE, HpUreG and HpHypA proteins in a pure form is a pre-requisite to perform all the subsequent protein characterizations, thus their purification was the first aim of this work. Subsequently, the structural and biochemical properties of HpUreE were investigated using multi-angle and quasi-elastic light scattering, as well as NMR and circular dichroism spectroscopy. The thermodynamic parameters of Ni2+ and Zn2+ binding to HpUreE were principally established using isothermal titration calorimetry and the importance of key histidine residues in the process of binding metal ions was studied using site-directed mutagenesis. The molecular details of the HpUreE-HpUreG and HpUreE-HpHypA protein-protein assemblies were also elucidated. The interaction between HpUreE and HpUreG was investigated using ITC and NMR spectroscopy, and the influence of Ni2+ and Zn2+ metal ions on the stabilization of this association was established using native gel electrophoresis, light scattering and thermal denaturation scanning followed by CD spectroscopy. Preliminary HpUreE-HpHypA interaction studies were conducted using ITC. Finally, the possible structural architectures of the two protein-protein assemblies were rationalized using homology modeling and docking computational approaches. All the obtained data were interpreted in order to achieve a more exhaustive picture of the urease activation process, and the correlation with the accessory system of the hydrogenase enzyme, considering the specific role and activity of the involved protein players. A possible function for Zn2+ in the chaperone network involved in Ni2+ trafficking and urease activation is also envisaged.

Microarray based real-time analysis of nucleic acid hybridization kinetics and thermodynamics

Ziel dieser Dissertation ist die experimentelle Charakterisierung und quantitative Beschreibung der Hybridisierung von komplementären Nukleinsäuresträngen mit oberflächengebundenen Fängermolekülen für die Entwicklung von integrierten Biosensoren. Im Gegensatz zu lösungsbasierten Verfahren ist mit Microarray Substraten die Untersuchung vieler Nukleinsäurekombinationen parallel möglich. Als biologisch relevantes Evaluierungssystem wurde das in Eukaryoten universell exprimierte Actin Gen aus unterschiedlichen Pflanzenspezies verwendet. Dieses Testsystem ermöglicht es, nahe verwandte Pflanzenarten auf Grund von geringen Unterschieden in der Gen-Sequenz (SNPs) zu charakterisieren. Aufbauend auf dieses gut studierte Modell eines House-Keeping Genes wurde ein umfassendes Microarray System, bestehend aus kurzen und langen Oligonukleotiden (mit eingebauten LNA-Molekülen), cDNAs sowie DNA und RNA Targets realisiert. Damit konnte ein für online Messung optimiertes Testsystem mit hohen Signalstärken entwickelt werden. Basierend auf den Ergebnissen wurde der gesamte Signalpfad von Nukleinsärekonzentration bis zum digitalen Wert modelliert. Die aus der Entwicklung und den Experimenten gewonnen Erkenntnisse über die Kinetik und Thermodynamik von Hybridisierung sind in drei Publikationen zusammengefasst die das Rückgrat dieser Dissertation bilden. Die erste Publikation beschreibt die Verbesserung der Reproduzierbarkeit und Spezifizität von Microarray Ergebnissen durch online Messung von Kinetik und Thermodynamik gegenüber endpunktbasierten Messungen mit Standard Microarrays. Für die Auswertung der riesigen Datenmengen wurden zwei Algorithmen entwickelt, eine reaktionskinetische Modellierung der Isothermen und ein auf der Fermi-Dirac Statistik beruhende Beschreibung des Schmelzüberganges. Diese Algorithmen werden in der zweiten Publikation beschrieben. Durch die Realisierung von gleichen Sequenzen in den chemisch unterschiedlichen Nukleinsäuren (DNA, RNA und LNA) ist es möglich, definierte Unterschiede in der Konformation des Riboserings und der C5-Methylgruppe der Pyrimidine zu untersuchen. Die kompetitive Wechselwirkung dieser unterschiedlichen Nukleinsäuren gleicher Sequenz und die Auswirkungen auf Kinetik und Thermodynamik ist das Thema der dritten Publikation. Neben der molekularbiologischen und technologischen Entwicklung im Bereich der Sensorik von Hybridisierungsreaktionen oberflächengebundener Nukleinsäuremolekülen, der automatisierten Auswertung und Modellierung der anfallenden Datenmengen und der damit verbundenen besseren quantitativen Beschreibung von Kinetik und Thermodynamik dieser Reaktionen tragen die Ergebnisse zum besseren Verständnis der physikalisch-chemischen Struktur des elementarsten biologischen Moleküls und seiner nach wie vor nicht vollständig verstandenen Spezifizität bei.

Adsorption of macromolecules on interfaces studied by isothermal titration calorimetry

The mixing of nanoparticles with polymers to form composite materials has been applied for decades. They combine the advantages of polymers (e.g., elasticity, transparency, or dielectric properties) and inorganic nanoparticles (e.g., specific absorption of light, magneto resistance effects, chemical activity, and catalysis etc.). Nanocomposites exhibit several new characters that single-phase materials do not have. Filling the polymeric matrix with an inorganic material requires its homogeneous distribution in order to achieve the highest possible synergetic effect. To fulfill this requirement, the incompatibility between the filler and the matrix, originating from their opposite polarity, has to be resolved. A very important parameter here is the strength and irreversibility of the adsorption of the surface active compound on the inorganic material. In this work the Isothermal titration calorimetry (ITC) was applied as a method to quantify and investigate the adsorption process and binding efficiencies in organic-inorganic–hybrid-systems by determining the thermodynamic parameters (ΔH, ΔS, ΔG, KB as well as the stoichiometry n). These values provide quantification and detailed understanding of the adsorption process of surface active molecules onto inorganic particles. In this way, a direct correlation between the adsorption strength and structure of the surface active compounds can be achieved. Above all, knowledge of the adsorption mechanism in combination with the structure should facilitate a more rational design into the mainly empirically based production and optimization of nanocomposites.

Estimation of the risks of thermal stress due to the microclimate for manual fruit and vegetable harvesters in central Italy

Agricultural workers are exposed to various risks, including chemical agents, noise, and many other factors. One of the most characteristic and least known risk factors is constituted by the microclimatic conditions in the different phases of work (in field, in greenhouse, etc). A typical condition is thermal stress due to high temperatures during harvesting operations in open fields or in greenhouses. In Italy, harvesting is carried out for many hours during the day, mainly in the summer, with temperatures often higher than 30 degrees C. According to ISO 7243, these conditions can be considered dangerous for workers' health. The aim of this study is to assess the risks of exposure to microclimatic conditions (heat) for fruit and vegetable harvesters in central Italy by applying methods established by international standards. In order to estimate the risk for workers, the air temperature, radiative temperature, and air speed were measured using instruments in conformity with ISO 7726. Thermodynamic parameters and two more subjective parameters, clothing and the metabolic heat production rate related to the worker's physical activity, were used to calculate the predicted heat strain (PHS) for the exposed workers in conformity with ISO 7933. Environmental and subjective parameters were also measured for greenhouse workers, according to ISO 7243, in order to calculate the wet-bulb globe temperature (WBGT). The results show a slight risk for workers during manual harvesting in the field. On the other hand, the data collected in the greenhouses show that the risk for workers must not be underestimated. The results of the study show that, for manual harvesting work in climates similar to central Italy, it is essential to provide plenty of drinking water and acclimatization for the workers in order to reduce health risks. Moreover, the study emphasizes that the possible health risks for greenhouse workers increase from the month of April through July.

Use of alternative fuels obtained from renewable sources in brayton cycles

Analysis and simulation of the behaviour of gas turbines for power generation using different nonconventional fuels obtained from different renewable sources are presented. Three biomass-tobiofuel processes are considered: anaerobic digestion of biomass (biogas), biomass gasification (synthesis gas) and alcoholic fermentation of biomass and dehydration (bioethanol), each of them with two different biomass substrates (energy crops and municipal solid waste) as input. The gas turbine behaviour in a Brayton cycle is simulated both in an isolated operation and in combined cycle. The differences in gas turbine performance when fired with the considered biofuels compared to natural gas are studied from different points of view related with the current complex energetic context: energetic and exergetic efficiency of the simple/combined cycle and CO2 emissions. Two different tools have been used for the simulations, each one with a different approach: while PATITUG (own software) analyses the behaviour of a generic gas turbine allowing a total variability of parameters, GT-PRO (commercial software) is more rigid, albeit more precise in the prediction of real gas turbine behaviour. Different potentially interesting configurations and its thermodynamic parameters have been simulated in order to obtain the optimal range for all of them and its variation for each fuel.

Use of alternative fuels obtained from renowable sources in Brayton cycles

Analysis and simulation of the behaviour of gas turbines for power generation using different nonconventional fuels obtained from different renewable sources are presented. Three biomass-tobiofuel processes are considered: anaerobic digestion of biomass (biogas), biomass gasification (synthesis gas) and alcoholic fermentation of biomass and dehydration (bioethanol), each of them with two different biomass substrates (energy crops and municipal solid waste) as input. The gas turbine behaviour in a Brayton cycle is simulated both in an isolated operation and in combined cycle. The differences in gas turbine performance when fired with the considered biofuels compared to natural gas are studied from different points of view related with the current complex energetic context: energetic and exergetic efficiency of the simple/combined cycle and CO2 emissions. Two different tools have been used for the simulations, each one with a different approach: while PATITUG (own software) analyses the behaviour of a generic gas turbine allowing a total variability of parameters, GT-PRO (commercial software) is more rigid, albeit more precise in the prediction of real gas turbine behaviour. Different potentially interesting configurations and its thermodynamic parameters have been simulated in order to obtain the optimal range for all of them and its variation for each fuel.

Determinación de la higroscopicidad y comportamiento termodinámico de la madera juvenil y madura a través de sus isotermas de sorción

La respuesta higroscópica de la madera varía a lo largo de la dirección radial del árbol. El aumento de corta de ejemplares jóvenes y el uso de troncos de pequeños diámetros en la industria de los productos forestales, hacen preciso estudiar el comportamiento higroscópico tanto de la madera juvenil como de la madura. Su determinación proporciona información para comprender los mecanismos de sorción. Asimismo, la obtención de las propiedades termodinámicas de ambos tipos de madera facilita la modelización de procesos industriales como el secado o el encolado. En el presente trabajo, se ha comparado el comportamiento higroscópico y las propiedades termodinámicas de la madera juvenil y madura de Abies pinsapo Boissier, Abies alba Mill., Pinus canariensis C. Sm. ex DC., Pinus nigra Arnold, Pinus uncinata Mill. ex Mirb. y Pinus pinea L. Para este propósito se han utilizado las isotermas de sorción obtenidas mediante el método tradicional de sales saturadas descrito por COST Action E8 a 15, 35 y 50ºC en Abies pinsapo, Abies alba, Pinus nigra, Pinus uncinata y Pinus pinea, y a 35 y 50ºC en Pinus canariensis. Igualmente, se ha empleado el equipo dynamic vapor sorption (DVS) en la obtención de las isotermas de Pinus pinea a 35 y 50ºC. El ajuste de las curvas se ha realizado mediante el modelo Guggenheim, Anderson y de Boer-Dent (GAB), cumpliendo todas las muestras los criterios de aceptación establecidos. En el estudio de las isotermas se ha calculado el coeficiente y área de histéresis entre el proceso de adsorción y desorción para cada una de las muestras. Con el fin de comprender el comportamiento higroscópico experimentado por cada madera se ha determinado la composición química, espectros de infrarrojos (FTIR) y difractogramas de rayos X de cada una. Los parámetros termodinámicos - calor isostérico neto y total heat of wetting - se han obtenido a partir de las isotermas de sorción mediante el método de integración de la ecuación de Clausius-Clapeyron. Finalmente, se han comparado los datos obtenidos con el método tradicional de sales saturadas y con dynamic vapor sorption con el propósito de conocer la existencia de similitudes entre ambas metodologías. Los resultados mostraron que los puntos de equilibrio son, en la mayor parte de los casos, superiores en la madera madura frente a la juvenil, y por tanto las isotermas de la madera madura se encuentran siempre por encima de las de la juvenil, debido principalmente a la composición química. Respecto a las propiedades termodinámicas, se ha determinado que la energía involucrada en los procesos de sorción es superior en la madera madura que en la madera juvenil, siendo mayor en el proceso de desorción frente al de adsorción. En la comparación de las metodologías de sales saturadas y dynamic vapor sorption no se han detectado casi diferencias significativas en el proceso de adsorción, mientras que sí se han obtenido en el de desorción. ABSTRACT The hygroscopic response of wood varies throughout the radial direction of the tree. The longer cut of young trees and the use of small-diameter trunks in the forest product industry make it necessary to study the hygroscopic behaviour of both juvenile and mature wood. Determining this behaviour in both types of wood provides information for understanding the sorption mechanisms. Similarly, obtaining the thermodynamic properties of juvenile and mature wood facilitates modelling of industrial processes such as drying and bonding. In this study a comparison was made of the hygroscopic behaviour and thermodynamic properties of juvenile and mature wood of Abies pinsapo Boissier, Abies alba Mill., Pinus canariensis C. Sm. ex DC., Pinus nigra Arnold, Pinus uncinata Mill. ex Mirb. and Pinus pinea L. This was done by obtaining the sorption isotherms using the traditional saturated salt method described by COST Action E8 at 15, 35 and 50ºC in Abies pinsapo, Abies alba, Pinus nigra, Pinus uncinata and Pinus pinea, and at 35 and 50ºC in Pinus canariensis. In addition, dynamic vapour sorption (DVS) was used to obtain the isotherms of Pinus pinea at 35 and 50ºC. The curves were fitted using the Guggenheim, Anderson and de Boer- Dent (GAB) model and all samples met the established acceptance criteria. In the study of the isotherms, the hysteresis coefficient and area of the hysteresis loop between adsorption and desorption were calculated for each sample. To understand the hygroscopic behaviour of juvenile and mature wood, the chemical composition, infrared spectra (FTIR) and X-ray diffractograms of each type of wood were determined. The thermodynamic parameters - net isosteric heat and total heat of wetting - were obtained from the sorption isotherms by applying the integration method of the Clausius-Clapeyron equation. The data obtained using the traditional saturated salt method and with dynamic vapour sorption were compared to determine the similarities between the two methods. The results showed that the equilibrium points are greater in the mature wood than in the juvenile wood in most cases, and therefore the mature wood isotherms are always above the juvenile wood isotherms, mainly because of the chemical composition. As regards the thermodynamic properties, it was determined that the energy involved in the sorption processes is greater in the mature wood than in the juvenile wood, and is greater in the desorption process than in the adsorption process. On comparing the saturated salt and dynamic vapour sorption methods, almost no significant differences were detected in the adsorption process, but significant differences were obtained in the desorption process.

Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure

We have synthesized and characterized a family of structured oligo-N-substituted-glycines (peptoids) up to 36 residues in length by using an efficient solid-phase protocol to incorporate chemically diverse side chains in a sequence-specific fashion. We investigated polypeptoids containing side chains with a chiral center adjacent to the main chain nitrogen. Some of these sequences have stable secondary structure, despite the achirality of the polymer backbone and its lack of hydrogen bond donors. In both aqueous and organic solvents, peptoid oligomers as short as five residues give rise to CD spectra that strongly resemble those of peptide α-helices. Differential scanning calorimetry and CD measurements show that polypeptoid secondary structure is highly stable and that unfolding is reversible and cooperative. Thermodynamic parameters obtained for unfolding are similar to those obtained for the α-helix to coil transitions of peptides. This class of biomimetic polymers may enable the design of self-assembling macromolecules with novel structures and functions.

Multiple four-stranded conformations of human telomere sequence d(CCCTAA) in solution

By detailed NMR analysis of a human telomere repeating unit, d(CCCTAA), we have found that three distinct tetramers, each of which consists of four symmetric single-strands, slowly exchange in a slightly acidic solution. Our new finding is a novel i-motif topology (T-form) where T4 is intercalated between C1 and C2 of the other duplex. The other two tetramers have a topology where C1 is intercalated between C2 and C3 of the other parallel duplex, resulting in the non-stacking T4 residues (R-form), and a topology where C1 is stacked between C3 and T4 of the other duplex (S-form). From the NMR denaturation profile, the R-form is the most stable of the three structures in the temperature range of 15–50°C, the S-form the second and the T-form the least stable. The thermodynamic parameters indicate that the T-form is the most enthalpically driven and entropically opposed, and its population is increased with decreasing temperature. The T-form structure determined by restrained molecular dynamics calculation suggests that inter-strand van der Waals contacts in the narrow grooves should contribute to the enthalpic stabilization of the T-form.

Non-Arrhenius kinetics for the loop closure of a DNA hairpin

Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model and are consistent with steady-state fluorescence measurements. The kinetics of closing the loop show non-Arrhenius behavior, in agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependence (β = 0.83) on the solution viscosity. A much slower intrachain diffusion coefficient in comparison to that of polypeptides was derived based on the first passage time theory of SSS [Szabo, A., Schulten, K. & Schulten, Z. (1980) J. Chem. Phys. 72, 4350–4357], suggesting that intrachain interactions, especially stacking interaction in the loop, might increase the roughness of the free energy surface of the DNA hairpin-loop.