Thermodynamic and kinetic modelling of the redox properties of tetrahaem cytochromes C3

Dissertação apresentada para obtenção do grau de Doutor em Bioquímica,especialidade Bioquímica-Física, pela Universidade Nova de Lisboa, Faculdade de Cincias e Tecnologia

31P NMR magnetization transfer study of the control of ATP turnover in Saccharomyces cerevisiae.

31P NMR magnetization transfer measurements have been used to measure the steady state flux between Pi and ATP in yeast cells genetically modified to overexpress an adenine nucleotide translocase isoform. An increase in Pi -> ATP flux and apparent ratio of moles of ATP synthesized/atoms of oxygen consumed (P:O ratio), when these cells were incubated with glucose, demonstrated that the reactions catalyzed by the translocase and F1F0 ATP synthase were readily reversible in vivo. However, when the same cells were incubated with ethanol alone, translocase overexpression had no effect on the measured Pi -> ATP flux or apparent P:O ratio, suggesting that the synthase was now operating irreversibly. This change was accompanied by an increase in the intracellular ADP concentration. These observations are consistent with a model proposed for the kinetic control of mitochondrial ATP synthesis, which was based on isotope exchange measurements with isolated mammalian mitochondria [LaNoue, K. F., Jeffries, F. M. H. & Radda, G. K. (1986) Biochemistry 25, 7667-7675].

Addition stéréosélective de nucléophiles sur un centre acétal : synthèse de nucléosides 1’,2’-cis

Plusieurs analogues de nucléosides thérapeutiques (Ara-C, Clofarabine), utilisés pour le traitement de leucémies, présentent un arrangement 1’,2’-cis entre la nucléobase reliée au centre anomère et le substituant (électroattracteur) en C-2’. Récemment, notre laboratoire a développé une approche synthétique pour former sélectivement des analogues de nucléosides et de thionucléosides 1’,2’-trans et 1’,2’-cis à partir de précurseurs acycliques. Ce mémoire présente une nouvelle méthodologie pour accéder efficacement aux analogues de nucléosides 1’,2’-cis à partir de furanosides. Différents groupements en position anomérique ont été examinés, sous conditions cinétiques en utilisant le bromure de diméthylbore pour générer sélectivement des produits acycliques ou cycliques. Les intermédiaires cinétiques de différents furanosides de méthyle formés en présence de Me2BBr ont été piégés in situ par un thiol pour générer des thioacétals acycliques avec de bonnes voire d’excellentes diastéréosélectivités. Les produits générés sont en accord avec une rétention globale de l’information stéréochimique du centre acétal et deux déplacements SN2 consécutifs ont été suggérés pour rationaliser ces résultats. Toutefois, l’objectif de synthétiser des analogues de nucléosides à partir de furanosides de méthyle a échoué. Tel que démontré par le Dr Michel Prévost, l’activation par Me2BBr des lactols des quatres différents furanosides suivie d’une addition in situ d’une base silylée a permis de former diastéréosélectivement les analogues de nucléosides 1’,2’-cis correspondants avec d’excellents rendements. Nous avons démontré que d’autres substrats peuvent être employés et que l’induction stéréochimique est sous contrôle du substituant électroattracteur en C-2. D’autres acides de Lewis, tel que TMSBr, peuvent également être utilisés. Cette méthodologie a également été étendue à d’autres nucléophiles tels que des Grignards ou des éthers d’énols silylés, conduisant à de bonnes sélectivités.

Microwave activation of the electro-oxidation of glucose in alkaline media

The oxidation of glucose is a complex process usually requiring catalytically active electrode surfaces or enzyme modified electrodes. In this study the effect of high intensity microwave radiation on the oxidation of glucose in alkaline solution at Au, Cu, and Ni electrodes is reported. Calibration experiments with the Fe(CN)(6)(3-/4-) redox system in aqueous 0.1 M NaOH indicate that strong thermal effects occur at both 50 and 500 mu m diameter electrodes with temperatures reaching 380 K. Extreme mass transport effects with mass transport coefficients of k(mt) > 0.01 m s(-1) (or k(mt) > 1.0 cm s(-1)) are observed at 50 mu m diameter electrodes in the presence of microwaves. The electrocatalytic oxidation of glucose at 500 mu m diameter Au, Cu, or Ni electrodes immersed in 0.1 M NaOH and in the presence of microwave radiation is shown to be dominated by kinetic control. The magnitude of glucose oxidation currents at Cu electrodes is shown to depend on the thickness of a pre-formed oxide layer. At 50 mu m diameter Au, Cu, or Ni electrodes microwave enhanced current densities are generally higher, but only at Au electrodes is a significantly increased rate for the electrocatalytic oxidation of glucose to gluconolactone observed. This rate enhancement appears to be independent of temperature but microwave intensity dependent, and therefore non-thermal in nature. Voltammetric currents observed at Ni electrodes in the presence of microwaves show the best correlation with glucose concentration and are therefore analytically most useful.

Microwave activation of the electro-oxidation of glucose in alkaline media

The oxidation of glucose is a complex process usually requiring catalytically active electrode surfaces or enzyme-modified electrodes. In this study the effect of high intensity microwave radiation on the oxidation of glucose in alkaline solution at Au, Cu, and Ni electrodes is reported. Calibration experiments with the Fe(CN)63–/4– redox system in aqueous 0.1 M NaOH indicate that strong thermal effects occur at both 50 and 500 µm diameter electrodes with temperatures reaching 380 K. Extreme mass transport effects with mass transport coefficients of kmt > 0.01 m s–1(or kmt > 1.0 cm s–1) are observed at 50 µm diameter electrodes in the presence of microwaves. The electrocatalytic oxidation of glucose at 500 µm diameter Au, Cu, or Ni electrodes immersed in 0.1 M NaOH and in the presence of microwave radiation is shown to be dominated by kinetic control. The magnitude of glucose oxidation currents at Cu electrodes is shown to depend on the thickness of a pre-formed oxide layer. At 50 µm diameter Au, Cu, or Ni electrodes microwave enhanced current densities are generally higher, but only at Au electrodes is a significantly increased rate for the electrocatalytic oxidation of glucose to gluconolactone observed. This rate enhancement appears to be independent of temperature but microwave intensity dependent, and therefore non-thermal in nature. Voltammetric currents observed at Ni electrodes in the presence of microwaves show the best correlation with glucose concentration and are therefore analytically most useful.

Thermodynamic characterization of the palm tree Roystonea regia peroxidase stability

The structural stability of a peroxidase, a dimeric protein from royal palm tree (Roystonea regia) leaves, has been characterized by high-sensitivity differential scanning calorimetry, circular dichroism, steady-state tryptophan fluorescence and analytical ultracentifugation under different solvent conditions. It is shown that the thermal and chemical (using guanidine hydrochloride (Gdn-HCl)) folding/unfolding of royal palm tree peroxidase (RPTP) at pH 7 is a reversible process involving a highly cooperative transition between the folded dimer and unfolded monomers, with a free stabilization energy of about 23 kcal per mol of monomer at 25 degrees C. The structural stability of RPTP is pH-dependent. At pH 3, where ion pairs have disappeared due to protonation, the thermally induced denaturation of RPTP is irreversible and strongly dependent upon the scan rate, suggesting that this process is under kinetic control. Moreover, thermally induced transitions at this pH value are dependent on the protein concentration, allowing it to be concluded that in solution RPTP behaves as dimer, which undergoes thermal denaturation coupled with dissociation. Analysis of the kinetic parameters of RPTP denaturation at pH 3 was accomplished on the basis of the simple kinetic scheme N ->(k) D, where k is a first-order kinetic constant that changes with temperature, as given by the Arrhenius equation; N is the native state, and D is the denatured state, and thermodynamic information was obtained by extrapolation of the kinetic transition parameters to an infinite heating rate. Obtained in this way, the value of RPTP stability at 25 degrees C is ca. 8 kcal per mole of monomer lower than at pH 7. In all probability, this quantity reflects the contribution of ion pair interactions to the structural stability of RPTP. From a comparison of the stability of RPTP with other plant peroxidases it is proposed that one of the main factors responsible for the unusually high stability of RPTP which enhances its potential use for biotechnological purposes, is its dimerization. (c) 2008 Elsevier Masson SAS. All rights reserved.

The role of hydration on the mechanism of allosteric regulation: In situ measurements of the oxygen-linked kinetics of water binding to hemoglobin

We report here the first direct measurements of changes in protein hydration triggered by a functional binding. This task is achieved by weighing hemoglobin (Hb) and myoglobin films exposed to an atmosphere of 98%, relative humidity during oxygenation. The binding of the first oxygen molecules to Hb tetramer triggers a change in protein conformation, which increases binding affinity to the remaining empty sites giving rise to the appearance of cooperative phenomena. Although crystallographic data have evidenced that this structural change increases the protein water-accessible surface area, isobaric osmotic stress experiments in aqueous cosolutions have shown that water binding is linked to Hb oxygenation. Now we show that the differential hydration between fully oxygenated and fully deoxygenated states of these proteins, determined by weighing protein films with a quartz crystal microbalance, agree with the ones determined by osmotic stress in aqueous cosolutions, from the linkage between protein oxygen affinity and water activity. The agreements prove that the changes in water activity brought about by adding osmolytes to the buffer solution shift biochemical equilibrium in proportion to the number of water molecules associated with the reaction. The concomitant kinetics of oxygen and of water binding to Hb have been also determined. The data show that the binding of water molecules to the extra protein surface exposed on the transition from the low-affinity T to the high-affinity R conformations of hemoglobin is the rate-limiting step of Hb cooperative reaction. This evidences that water binding is a crucial step on the allosteric mechanism regulating cooperative interactions, and suggests the possibility that environmental water activity might be engaged in the kinetic control of some important reactions in vivo.

Relações entre as propriedades físicas de combustíveis sólidos e sua reatividade

Pós-graduação em Física - IGCE

Estudo de reações de óxido-redução em vidros fosfato com altas concentrações de óxido de tungstênio

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)

Oxygen reduction reaction catalyzed by epsilon-MnO2: Influence of the crystalline structure on the reaction mechanism

The oxygen reduction reaction (ORR) was studied in KOH electrolyte on carbon supported epsilon-manganese dioxide (epsilon-MnO2/C). The epsilon-MnO2/C catalyst was prepared via thermal decomposition of manganese nitrate and carbon powder (Vulcan XC-72) mixtures. X-ray powder diffraction (XRD) measurements were performed in order to determine the crystalline structure of the resulting composite, while energy dispersive X-ray analysis (EDX) was used to evaluate the chemical composition of the synthesized material. The electrochemical studies were conducted using cyclic voltammetry (CV) and quasi-steady state polarization measurements carried out with an ultra thin layer rotating ring/disk electrode (RRDE) configuration. The electrocatalytic results obtained for 20% (w/w) Pt/C (E-TEK Inc., USA) and alpha-MnO2/C for the ORR, considered as one of the most active manganese oxide based catalyst for the ORR in alkaline media, were included for comparison. The RRDE results revealed that the ORR on the MnO2 catalysts proceeds preferentially through the complete 4e(-) reduction pathway via a 2 plus 2e(-) reduction process involving hydrogen peroxide as an intermediate. A benchmark close to the performance of 20% (w/w) Pt/C (E-TEK Inc., USA) was observed for the epsilon-MnO2/C material in the kinetic control region, superior to the performance of alpha-MnO2/C, but a higher amount of HO2- was obtained when epsilon-MnO2/C was used as catalyst. The higher production of hydrogen peroxide on epsilon-MnO2/C was related to the presence of structural defects, typical of this oxide, while the better catalytic performance in the kinetic control region compared to alpha-MnO2/C was related with the higher electrochemical activity for the proton insertion kinetics, which is a structure sensitive process. (C) 2012 Elsevier Ltd. All rights reserved.

Latexpartikel als Trägermaterialien in der durch Postmetallocene katalysierten Ethenpolymerisation

Die vorliegende Arbeit beschäftigte sich mit der Immobilisierung von Postmetallocenen auf einem organischen Trägermaterial für die heterogene Ethenpolymerisation. Dabei konnte gezeigt werden, dass sich mit nukleophilen Gruppen funktionalisierte Latexpartikel als Trägermaterial für empfindliche Bis(phenoxyimin)titankatalysatoren eignen. Durch geschickte Kombination aus Trägermaterial, Katalysator und Cokatalysator wurde ein Katalysatorsysteme erhalten, das ultrahochmolekulares Polyethylen mit einem Molekulargewicht Mw von bis zu 7.000.000 g/mol (GPC, PS-Standard) bei einer enger Molekulargewichtsverteilung von weniger als 3 erzeugt. Die erhaltenen Produktivitäten erreichten dabei die Anforderungen an industriellen Katalysatorsystemen. Erstaunlich war, dass nukleophile Gruppen auf den Latexpartikeln, die dafür bekannt sind, dass sie den Katalysator deaktivieren können, ein wichtige Schutzfunktion für den Titankatalysator bilden. So konnte gezeigt werden, dass Pyridingruppen auf der Oberfläche der Latexpartikel als Scavenger gegen Trimethylaluminium wirken, welches ansonsten den aktiven Titankomplex zersetzen würde. An ausgewählten Systemen auf der Basis unterschiedlicher Postmetallocene und einem Metallocen für die Ethenpolymerisation wurde durch Anwendung verschiedener Methoden das Polymerisationsverhalten der Latex-geträgerten Katalysatorsysteme untersucht. Eine Methode war die so genannte Videomikroskopie, bei der in Gasphase Ethen polymerisiert wird und so das Wachstumsverhalten der Katalysatorpartikel analysiert werden kann. In Kombination mit einer kinetischen Kontrolle des Monomerumsatzes in Suspensionspolymerisation, konnte gezeigt werden, dass die auf Latexpartikel geträgerten Katalysatorsysteme ein anderes Polymerisationsverhalten besitzen wie in der Literatur beschriebene Silica-geträgerte Katalysatoren. Dies kann auf die unterschiedliche Beschaffenheit des Trägermaterials zurückgeführt werden. Während das harte Silica-Material Monomer nur in den Poren aufnimmt und so rasch nach Beginn der Polymerisation in eine diffusionskontrollierte Polymerisation übergeht, quillt das organische Trägermaterial mit dem Monomeren an und kann den aktiven Katalysator damit bedienen bis weiteres Monomer von außen in das Katalysatorpartikel nach diffundiert ist. Durch die weiche Beschaffenheit der organischen Latexpartikel kann das entstehende Polymer das Katalysatorpartikel außerdem leicht auseinandertreiben werden. Die Polymerisation kann so im ganzen Katalysatorpartikel beginnen, während das Silica-Trägermaterial nur langsam von außen nach innen fragmentieren kann.

Multicomponent nanodevices based on molecular and nanocrystal moieties

Nanoscience is an emerging and fast-growing field of science with the aim of manipulating nanometric objects with dimension below 100 nm. Top down approach is currently used to build these type of architectures (e.g microchips). The miniaturization process cannot proceed indefinitely due to physical and technical limitations. Those limits are focusing the interest on the bottom-up approach and construction of nano-objects starting from “nano-bricks” like atoms, molecules or nanocrystals. Unlike atoms, molecules can be “fully programmable” and represent the best choice to build up nanostructures. In the past twenty years many examples of functional nano-devices able to perform simple actions have been reported. Nanocrystals which are often considered simply nanostructured materials, can be active part in the development of those nano-devices, in combination with functional molecules. The object of this dissertation is the photophysical and photochemical investigation of nano-objects bearing molecules and semiconductor nanocrystals (QDs) as components. The first part focuses on the characterization of a bistable rotaxane. This study, in collaboration with the group of Prof. J.F. Stoddart (Northwestern University, Evanston, Illinois, USA) who made the synthesis of the compounds, shows the ability of this artificial machine to operate as bistable molecular-level memory under kinetic control. The second part concerns the study of the surface properties of luminescent semiconductor nanocrystals (QDs) and in particular the effect of acid and base on the spectroscopical properties of those nanoparticles. In this section is also reported the work carried out in the laboratory of Prof H. Mattoussi (Florida State University, Tallahassee, Florida, USA), where I developed a novel method for the surface decoration of QDs with lipoic acid-based ligands involving the photoreduction of the di-thiolane moiety.

(Table 1) Age determination of stalagmites of the Marcello Arévalo Cave in Chile

Stalagmites are important palaeo-climatic archives since their chemical and isotopic signatures have the potential to record high-resolution changes in temperature and precipitation over thousands of years. We present three U/Th-dated records of stalagmites (MA1-MA3) in the superhumid southern Andes, Chile (53°S). They grew simultaneously during the last five thousand years (ka BP) in a cave that developed in schist and granodiorite. Major and trace elements as well as the C and O isotope compositions of the stalagmites were analysed at high spatial and temporal resolution as proxies for palaeo-temperature and palaeo-precipitation. Calibrations are based on data from five years of monitoring the climate and hydrology inside and outside the cave and on data from 100 years of regional weather station records. Water-insoluble elements such as Y and HREE in the stalagmites indicate the amount of incorporated siliciclastic detritus. Monitoring shows that the quantity of detritus is controlled by the drip water rate once a threshold level has been exceeded. In general, drip rate variations of the stalagmites depend on the amount of rainfall. However, different drip-water pathways above each drip location gave rise to individual drip rate levels. Only one of the three stalagmites (MA1) had sufficiently high drip rates to record detrital proxies over its complete length. Carbonate-compatible element contents (e.g. U, Sr, Mg), which were measured up to sub-annual resolution, document changes in meteoric precipitation and related drip-water dilution. In addition, these soluble elements are controlled by leaching during weathering of the host rock and soils depending on the pH of acidic pore waters in the peaty soils of the cave's catchment area. In general, higher rainfall resulted in a lower concentration of these elements and vice versa. The Mg/Ca record of stalagmite MA1 was calibrated against meteoric precipitation records for the last 100 years from two regional weather stations. Carbonate-compatible soluble elements show similar patterns in the three stalagmites with generally high values when drip rates and detrital tracers were low and vice versa. d13C and d18O values are highly correlated in each stalagmite suggesting a predominantly drip rate dependent kinetic control by evaporation and/or outgassing. Only C and O isotopes from stalagmite MA1 that received the highest drip rates show a good correlation between detrital proxy elements and carbonate-compatible elements. A temperature-related change in rainwater isotope values modified the MA1 record during the Little Ice Age (~0.7-0.1 ka BP) that was ~1.5 °C colder than today. The isotopic composition of the stalagmites MA2 and MA3 that formed at lower drip rates shows a poor correlation with stalagmite MA1 and all other chemical proxies of MA1. 'Hendy tests' indicate that the degassing-controlled isotope fractionation of MA2 and MA3 had already started at the cave roof, especially when drip rates were low. Changing pathways and residence times of the seepage water caused a non-climatically controlled isotope fractionation, which may be generally important in ventilated caves during phases of low drip rates. Our proxies indicate that the Neoglacial cold phases from ~3.5 to 2.5 and from ~0.7 to 0.1 ka BP were characterised by 30% lower precipitation compared with the Medieval Warm Period from 1.2 to 0.8 ka BP, which was extremely humid in this region.