Ferredoxin and ferredoxin–heme maquettes

A 16-amino acid residue peptide derived from a consensus motif of natural ferredoxins incorporates a tetranuclear iron sulfur cluster under physiological conditions. Successful assembly of the [4Fe–4S]2+/1+ cluster within a monomeric peptide was demonstrated using size exclusion chromatography, UV-visible, visible CD, and cryogenic EPR spectroscopies. The robustness of [4Fe–4S]2+/1+ formation was tested using peptides with either the ligating cysteine exchanged for alanine or with the intervening amino acids replaced by glycine. The small size of the peptide allows for modular incorporation into more complex protein structures. In one larger structure, we describe a tetra-α-helix bundle that self-assembles both iron–sulfur clusters and hemes, thereby demonstrating feasibility for the general synthesis of maquettes containing multiple, juxtaposed redox cofactors. This is a motif common to the catalytic sites of native oxidoreductases.

Copper binding to the prion protein: Structural implications of four identical cooperative binding sites

Evidence is growing to support a functional role for the prion protein (PrP) in copper metabolism. Copper ions appear to bind to the protein in a highly conserved octapeptide repeat region (sequence PHGGGWGQ) near the N terminus. To delineate the site and mode of binding of Cu(II) to the PrP, the copper-binding properties of peptides of varying lengths corresponding to 2-, 3-, and 4-octarepeat sequences have been probed by using various spectroscopic techniques. A two-octarepeat peptide binds a single Cu(II) ion with Kd ≈ 6 μM whereas a four-octarepeat peptide cooperatively binds four Cu(II) ions. Circular dichroism spectra indicate a distinctive structuring of the octarepeat region on Cu(II) binding. Visible absorption, visible circular dichroism, and electron spin resonance spectra suggest that the coordination sphere of the copper is identical for 2, 3, or 4 octarepeats, consisting of a square-planar geometry with three nitrogen ligands and one oxygen ligand. Consistent with the pH dependence of Cu(II) binding, proton NMR spectroscopy indicates that the histidine residues in each octarepeat are coordinated to the Cu(II) ion. Our working model for the structure of the complex shows the histidine residues in successive octarepeats bridged between two copper ions, with both the Nɛ2 and Nδ1 imidazole nitrogen of each histidine residue coordinated and the remaining coordination sites occupied by a backbone amide nitrogen and a water molecule. This arrangement accounts for the cooperative nature of complex formation and for the apparent evolutionary requirement for four octarepeats in the PrP.

Structure and function in rhodopsin: high level expression of a synthetic bovine opsin gene and its mutants in stable mammalian cell lines.

Stable mammalian cell lines harboring a synthetic bovine opsin gene have been derived from the suspension-adapted HEK293 cell line. The opsin gene is under the control of the immediate-early cytomegalovirus promoter/enhancer in an expression vector that also contains a selectable marker (Neo) governed by a relatively weak promoter. The cell lines expressing the opsin gene at high levels are selected by growth in the presence of high concentrations of the antibiotic geneticin. Under the conditions used for cell growth in suspension, opsin is produced at saturated culture levels of more than 2 mg/liter. After reconstitution with 11-cis-retinal, rhodopsin is purified to homogeneity in a single step by immunoaffinity column chromatography. Rhodopsin thus prepared (> 90% recovery at concentrations of up to 15 microM) is indistinguishable from rhodopsin purified from bovine rod outer segments by the following criteria: (i) UV/Vis absorption spectra in the dark and after photobleaching and the rate of metarhodopsin II decay, (ii) initial rates of transducin activation, and (iii) the rate of phosphorylation by rhodopsin kinase. Although mammalian cell opsin migrates slower than rod outer segment opsin on SDS/polyacrylamide gels, presumably due to a different N-glycosylation pattern, their mobilities after deglycosylation are identical. This method has enabled the preparation of several site-specific mutants of bovine opsin in comparable amounts.

Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer.

The green fluorescent protein (GFP) of the jellyfish Aequorea Victoria has attracted widespread interest since the discovery that its chromophore is generated by the autocatalytic, posttranslational cyclization and oxidation of a hexapeptide unit. This permits fusion of the DNA sequence of GFP with that of any protein whose expression or transport can then be readily monitored by sensitive fluorescence methods without the need to add exogenous fluorescent dyes. The excited state dynamics of GFP were studied following photo-excitation of each of its two strong absorption bands in the visible using fluorescence upconversion spectroscopy (about 100 fs time resolution). It is shown that excitation of the higher energy feature leads very rapidly to a form of the lower energy species, and that the excited state interconversion rate can be markedly slowed by replacing exchangeable protons with deuterons. This observation and others lead to a model in which the two visible absorption bands correspond to GFP in two ground-state conformations. These conformations can be slowly interconverted in the ground state, but the process is much faster in the excited state. The observed isotope effect suggests that the initial excited state process involves a proton transfer reaction that is followed by additional structural changes. These observations may help to rationalize and motivate mutations that alter the absorption properties and improve the photo stability of GFP.

Photo-induced inactivation of viruses: adsorption of methylene blue, thionine, and thiopyronine on Qbeta bacteriophage.

The adsorption of cationic organic dyes (methylene blue, thionine, and thiopyronine) on Qbeta bacteriophage was studied by UV-visible and fluorescence spectroscopy. The dyes have shown a strong affinity to the virus and some have been used as sensitizers for photo-induced inactivation of virus. In the methylene blue concentration range of 0.1-5 microM and at high ratios of dye to virus (greater than 1000 dye molecules per virion), the dyes bind as aggregates on the virus. Aggregation lowers the efficiency of photoinactivation because of self-quenching of the dye. At lower ratios of dye to virus (lower than 500 dye molecules per virion), the dye binds to the virus as a monomer. Fluorescence polarization and time-resolved studies of the fluorescence support the conclusions based on fluorescence quenching. Increasing the ionic strength (adding NaCl) dissociates bound dye aggregates on the virus and releases monomeric dye into the bulk solution.

Synthesis and Characterisation of Functional Magnetic and Plasmonic Nanomaterials

The main aim of this thesis is the controlled and reproducible synthesis of functional materials at the nanoscale. In the first chapter, a tuning of morphology and magnetic properties of magnetite nanoparticles is presented. It was achieved by an innovative approach, which involves the use of an organic macrocycle (calixarene) to induce the oriented aggregation of NPs during the synthesis. This method is potentially applicable to the preparation of other metal oxide NPs by thermal decomposition of the respective precursors. Products obtained, in particular the multi-core nanoparticles, show remarkable magnetic and colloidal properties, making them very interesting for biomedical applications. The synthesis and functionalisation of plasmonic Au and Ag nanoparticles is presented in the second chapter. Here, a supramolecular approach was exploited to achieve a controlled and potentially reversible aggregation between Au and Ag NPs. This aggregation phenomena was followed by UV - visible spectroscopy and dynamic light scattering. In the final chapters, the conjugation of plasmonic and magnetic functionalities was tackled through the preparation of dimeric nanostructures. Au - Fe oxide heterodimeric nanoparticles were prepared and their magnetic properties thoroughly characterised. The results demonstrate the formation of FeO (wustite), together with magnetite, during the thermal decomposition of the iron precursor. By an oxidation process that preserves Au in the dimeric structures, wustite completely disappeared, with the formation of either magnetite and / or maghemite, much better from the magnetic point of view. The plasmon resonance of Au results damped by the presence of the iron oxide, a material with high refractive index, but it is still present if the Au domain of the nanoparticles is exposed towards the bulk. Finally, remarkable hyperthermia, also in vitro, was found for these structures.

Propriedades de soluções filmogênicas e de filmes de gelatina ou colágeno com extrato de boldo-do-Chile

Filmes à base de biopolímeros podem ser utilizados para produção de embalagens ativas, que além de proteger os alimentos, podem interagir com o produto. No caso de embalagens ativas com atividade antioxidante, tem-se privilegiado o uso de agentes antioxidantes naturais, considerando-se que o uso de antioxidantes sintéticos tem sido questionado, sobretudo em relação à sua inocuidade. Existem muitos extratos de plantas já conhecidos por sua atividade antioxidante, que têm sido utilizados com frequência em estudos de filmes à base de biopolímeros, não somente por serem ricos em polifenóis, mas principalmente por sua boa interação com a matriz polimérica. O extrato de boldo-do-Chile (Peumus boldus) possui atividade antioxidante comprovada, entretanto, não existem relatos sobre sua adição em filmes. Dessa forma, o objetivo geral desta tese foi o desenvolvimento de filmes à base de colágeno ou gelatina adicionados de extrato de boldo-do-Chile, com propriedades físicas e funcionais para seu emprego como embalagens bioativas. Foram realizadas as caracterizações (fenólicos totais, ABTS, DPPH, cor, °Brix e pH) do extrato aquoso de boldo-do-Chile, preparado em quatro diferentes temperaturas. Além disso, foram avaliadas as propriedades reológicas e térmicas da solução de gelatina, e também foram elaborados filmes com as soluções de gelatina e colágeno a partir de soluções filmogênicas com diferentes concentrações de macromoléculas e extrato de boldo. Esses filmes foram caracterizados para conhecimento de suas propriedades mecânicas (tração e perfuração), propriedades óticas (cor e opacidade), espessura, umidade e solubilidade em água. Uma concentração de macromoléculas foi escolhida para a realização de análises complementares, a saber: análises térmicas (DSC), cristalinidade por difração de raio X (DRX), permeabilidade ao vapor de água (PVA), microscopia eletrônica de varredura (MEV), brilho, espectroscopia de infravermelho com transformada de Fourier (FTIR), ângulo de contato, propriedades de barreira UV/Visível e atividade antioxidante. A adição do extrato de boldo-do-Chile nos filmes de gelatina e colágeno produziu filmes com atividade antioxidante, sem prejuízo às demais propriedades estudadas. Observou-se que o extrato aquoso de boldo-do-Chile apresentou propriedades antioxidantes, mas que foram dependentes da temperatura de extração. O extrato de boldo-do-Chile foi capaz de modificar as propriedades térmicas das soluções filmogênicas de gelatina, não sendo observado efeito nas análises reológicas. Por outro lado, o extrato aquoso de boldo-do-Chile não influenciou as propriedades mecânicas, solubilidade, umidade, cristalinidade e a permeabilidade ao vapor de água dos filmes de gelatina ou colágeno. Algumas propriedades térmicas sofreram efeito dos extratos, mas as análises de FTIR não mostraram a formação de novas interações. As propriedades óticas e de barreira UV/Visível foram influenciadas pelo extrato de boldo-do-Chile, sendo que os filmes se apresentaram mais amarelados com o aumento da concentração do extrato de boldo-do-Chile. As micrografias mostraram filmes de gelatina bastante homogêneos e filmes de colágeno com superfícies mais rugosas. Os resultados de brilho e ângulo de contato corroboraram com estas respostas. Em conclusão, os filmes de ambas macromoléculas apresentaram atividade antioxidante, podendo dessa forma, serem considerados como filmes ativos.

Spectroscopic, calorimetric, and catalytic evidences of hydrophobicity on Ti-MCM-41 silylated materials for olefin epoxidations

Hydrophobic Ti-MCM-41 samples prepared by post-synthesis silylation treatment demonstrate to be highly active and selective catalysts in olefins epoxidation by using organic hydroperoxides as oxidizing agents in liquid phase reaction systems. Epoxide yields show important enhancements with increased silylation degrees of the Ti-mesoporous samples. Catalytic studies are combined and correlated with spectroscopic techniques (e.g. XRD, XANES, UV-Visible, 29Si MAS-NMR) and calorimetric measurements to better understand the changes in the surface chemistry of Ti-MCM-41 samples due to the post-synthesis silylation treatment and to ascertain the role of these trimethylsilyl groups incorporated in olefin epoxidation. In such manner, the effect of the organic moieties on solids, and both water and glycol molecules contents on the catalytic activity and selectivity are analyzed in detail. Results show that the hydrophobicity level of the samples is responsible for the decrease in water adsorption and, consequently, the negligible formation of the non-desired glycol during the catalytic process. Thus, catalyst deactivation by glycol poisoning of Ti active sites is greatly diminished, this increasing catalyst stability and leading to practically quantitative production of the corresponding epoxide. The extended use of these hydrophobic Ti-MCM-41 catalysts together with organic hydroperoxides for the highly efficient and selective epoxidation of natural terpenes is also exemplified.

Desarrollo de sistemas nano/micro-particulados con aplicación en la fotodegradación selectiva de contaminantes orgánicos en solución

IDENTIFICACIÓN DEL PROBLEMA DE ESTUDIO. Las sustancias orgánicas solubles en agua no biodegradables tales como ciertos herbicidas, colorantes industriales y metabolitos de fármacos de uso masivo son una de las principales fuentes de contaminación en aguas subterráneas de zonas agrícolas y en efluentes industriales y domésticos. Las reacciones fotocatalizadas por irradiación UV-visible y sensitizadores orgánicos e inorgánicos son uno de los métodos más económicos y convenientes para la descomposición de contaminantes en subproductos inocuos y/o biodegradables. En muchas aplicaciones es deseable un alto grado de especificidad, efectividad y velocidad de degradación de un dado agente contaminante que se encuentra presente en una mezcla compleja de sustancias orgánicas en solución. En particular son altamente deseables sistemas nano/micro -particulados que formen suspensiones acuosas estables debido a que estas permiten una fácil aplicación y una eficaz acción descontaminante en grandes volúmenes de fluidos. HIPÓTESIS Y PLANTEO DE LOS OBJETIVOS. El objetivo general de este proyecto es desarrollar sistemas nano/micro particulados formados por polímeros de impresión molecular (PIMs) y foto-sensibilizadores (FS). Un PIMs es un polímero especialmente sintetizado para que sea capaz de reconocer específicamente un analito (molécula plantilla) determinado. La actividad de unión específica de los PIMs en conjunto con la capacidad fotocatalizadora de los sensibilizadores pueden ser usadas para lograr la fotodescomposición específica de moléculas “plantilla” (en este caso un dado contaminante) en soluciones conteniendo mezclas complejas de sustancias orgánicas. MATERIALES Y MÉTODOS A UTILIZAR. Se utilizaran técnicas de polimerización en mini-emulsión para sintetizar los sistemas nano/micro PIM-FS para buscar la degradación de ciertos compuestos de interés. Para caracterizar eficiencias, mecanismos y especificidad de foto-degradación en dichos sistemas se utilizan diversas técnicas espectroscópicas (estacionarias y resueltas en el tiempo) y de cromatografía (HPLC y GC). Así mismo, para medir directamente distribuciones de afinidades de unión y eficiencia de foto-degradación se utilizaran técnicas de fluorescencia de molécula/partícula individual. Estas determinaciones permitirán obtener resultados importantes al momento de analizar los factores que afectan la eficiencia de foto-degradación (nano/micro escala), tales como cantidad y ubicación de foto- sensibilizadores en las matrices poliméricas y eficiencia de unión de la plantilla y los productos de degradación al PIM. RESULTADOS ESPERADOS. Los estudios propuestos apuntan a un mejor entendimiento de procesos foto-iniciados en entornos nano/micro-particulados para aplicar dichos conocimientos al diseño de sistemas optimizados para la foto-destrucción selectiva de contaminantes acuosos de relevancia social; tales como herbicidas, residuos industriales, metabolitos de fármacos de uso masivo, etc. IMPORTANCIA DEL PROYECTO. Los sistemas nano/micro-particulados PIM-FS que se propone desarrollar en este proyecto se presentan como candidatos ideales para tratamientos específicos de efluentes industriales y domésticos en los cuales se desea lograr la degradación selectiva de compuestos orgánicos. Los conocimientos adquiridos serán indispensables para construir una plataforma versátil de sistemas foto-catalíticos específicos para la degradación de diversos contaminantes orgánicos de interés social. En lo referente a la formación de recursos humanos, el proyecto propuesto contribuirá en forma directa a la formación de 3 estudiantes de postgrado y 2 estudiantes de grado. En las capacidades institucionales se contribuirá al acondicionamiento del Laboratorio para Microscopía Óptica Avanzada (LMOA) en el Dpto. de Química de la UNRC y al montaje de un sistema de microscopio de fluorescencia que permitirá la aplicación de técnicas avanzadas de espectroscopia de fluorescencia de molecula individual.

(Bio)funcionalização de superfícies nanoestruturadas para eletrocatálise e desenvolvimento de biossensores eletroquímicos e óticos

Tese de doutoramento, Química (Química Física), Universidade de Lisboa, Faculdade de Ciências, 2016

Size exclusion chromatogram of the Tannermoor 2009 sample after saltout experiments

Samples from a pristine raised peat bog runoff in Austria, the Tannermoor creek, were analysed for their iron linked to natural organic matter (NOM) content. Dissolved organic carbon < 0.45 µm (DOC) was 41 to 64 mg/L, iron 4.4 to 5.5 mg/L. Samples were analysed applying asymmetric field flow fractionation (AsFlFFF) coupled to UV-Vis absorption, fluorescence and inductively coupled plasma mass spectrometry (ICP-MS). The samples showed an iron peak associated with the NOM peak, one sample exhibiting a second peak of iron independent from the NOM peak. As highland peat bogs with similar climatic conditions and vegetation to the Tanner Moor are found throughout the world, including areas adjacent to the sea, we examined the behaviour of NOM and iron in samples brought to euhaline (35 per mil) conditions with artificial sea salt. The enhanced ionic strength reduced NOM by 53% and iron by 82%. Size exclusion chromatography (SEC) of the samples at sea-like salinity revealed two major fractions of NOM associated with different iron concentrations. The larger one, eluting sharply after the upper exclusion limits of 4000-5000 g/mol, seems to be most important for iron chelating. The results outline the global importance of sub-mountainous and mountainous raised peat bogs as a source of iron chelators to the marine environment at sites where such peat bogs release their run-offs into the sea.

Studies of the interaction of Potassium(I), Calcium(II), Magnesium(II), and Copper(II) with Cyclosporin A

Metal ion binding properties of the immunosuppressant drug cyclosporin A have been investigated. Complexation studies in acetonitrile solution using H-1 NMR and CD spectroscopy yielded 1:1 metal-peptide binding constants (log(10)K) for potassium(l), < 1, magnesium(II), 4.8 +/- 0.2. and calcium(II), 5.0 +/- 1.0. The interaction of copper(II) with cyclosporin A in methanol was investigated with UV/visible and electron paramagnetic resonance (EPR) spectroscopy. No complexation of copper(II) was observed in neutral solution. In the presence of base, monomeric copper(II) complexes were detected. These results support the possibility that cyclosporin A has ionophoric properties for biologically important essential metal ions. (C) 2003 Elsevier Inc. All rights reserved.

The critical role of tryptophan-116 in the catalytic cycle of dimethylsulfoxide reductase from Rhodobacter capsulatus

In dimethylsulfoxide reductase of Rhodobacter capsulatus tryptophan-116 forms a hydrogen bond with a single oxo ligand bound to the molybdenum ion. Mutation of this residue to phenylalanine affected the UV/visible spectrum of the purified Mo-VI form of dimethylsulfoxide reductase resulting in the loss of the characteristic transition at 720 nm. Results of steady-state kinetic analysis and electrochemical studies suggest that tryptophan 116 plays a critical role in stabilizing the hexacoordinate monooxo Mo-VI form of the enzyme and prevents the formation of a dioxo pentacoordinate Mo-VI species, generated as a consequence of the dissociation of one of the dithiolene ligands of the molybdopterin cofactor from the Mo ion. (C) 2004 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

Transition metal complexes as mediator-titrants in protein redox potentiometry

A selection of nine macrocyclic Fe-III/II and Co-III/II transition metal complexes has been chosen to serve as a universal set of mediator-titrants in redox potentiometry of protein samples. The potential range spanned by these mediators is approximately from +300 to -700 mV vs the normal hydrogen electrode, which covers the range of most protein redox potentials accessible in aqueous solution. The complexes employed exhibit stability in both their oxidized and their reduced forms as well as pH-independent redox potentials within the range 6 < pH < 9. The mediators were also chosen on the basis of their very weak visible absorption maxima in both oxidation states, which will enable (for the first time) optical redox potentiometric titrations of proteins with relatively low extinction coefficients. This has previously been impractical with organic mediators, such as indoles, viologens and quinones, whose optical spectra interfere strongly with those of the protein.

Block co-polymerization by transformation reactions

The aim of this study was to use the transformation of anionic to metathesis polymerization to produce block co-polymers of styrene-b-pentenylene using WC16 /PStLi and WC16/PStLi/ AlEtC12 catalyst systems. Analysis of the products using SEC and 1H and 13C NMR spectroscopy enabled mechanisms for metathesis initiation reactions to be proposed. The initial work involved preparation of the constituent homo-polymers. Solutions of polystyryllithium in cyclohexane were prepared and diluted so that the [PStLi]o<2x10-3M. The dilution produced initial rapid decay of the active species, followed by slower spontaneous decay within a period of days. This was investigated using UV / visible spectrophotometry and the wavelength of maximum absorbance of the PStLi was found to change with the decay from an initial value of 328mn. to λmax of approximately 340nm. after 4-7 days. SEC analysis of solutions of polystyrene, using RI and UV / visible (set at 254nm.) detectors; showed the UV:RI peak area was constant for a range of polystyrene samples of different moleculor weight. Samples of polypentenylene were prepared and analysed using SEC. Unexpectedly the solutions showed an absorbance at 254nm. which had to be considered when this technique was used subsequently to analyse polymer samples to determine their styrene/ pentenylene co-polymer composition. Cyclohexane was found to be a poor solvent for these ring-opening metathesis polymerizations of cyclopentene. Attempts to produce styrene-b-pentenylene block co-polymers, using a range of co-catalyst systems, were generally unsuccessful as the products were shown to be mainly homopolymers. The character of the polymers did suggest that several catalytic species are present in these systems and mechanisms have been suggested for the formation of initiating carbenes. Evidence of some low molecular weight product with co-polymer character has been obtained. Further investigation indicated that this is most likely to be ABA block copolymer, which led to a mechanism being proposed for the termination of the polymerization.