La calmoduline (CaM) est une protéine modulatrice de la réponse cellulaire chez les eucaryotes composée de quatre domaines de liaison au calcium et d'une hélice centrale flexible. Elle peut interagir avec d'autres protéines en présence de calcium, entraînant l'activation et l'inhibition d'enzymes, l'ouverture de canaux membranaires et modulant le trafic intracellulaire. L'identification de protéines parternaires de la CaM requière la mise au point de techniques permettant de mesurer les paramètres de la liaison pour un grand nombre de protéines dans des conditions variables mimant l'environnement cellulaire (par exemple en présence de ligands ou d'autres protéines). Le premier objectif de cette thèse a été de développer une technique de mesure des interactions CaM-parternaire reposant sur des mesures d'anisotropie de fluorescence. Les tests ont été ensuite utilisés pour caractériser de manière quantitative l'interaction préalablement mise en évidence de deux protéines chloroplastiques (NADK2 et Tic32) avec la CaM. Afin d'identifier d'autres cibles chloroplastiques de la CaM nous avons alors effectué une analyse à haut-débit en couplant une purification par affinité à des analyses protéomiques. La validation des interactions a été réalisée grâce à l'utilisation de méthodes biochimiques complémentaires. Nous avons ensuite focalisé notre attention sur la protéine ceQORH dont la très forte affinité pour la CaM a pu être confirmée. Nos résultats fournissent par ailleurs de nouveaux éléments pour la compréhension de ces interactions. Afin de vérifier la présence de CaM ou de CaM-like (CML) dans le chloroplaste nous avons utilisé une approche biochimique et protéomique. Nous avons d'autre part étudié la localisation de CMLs potentiellement chloroplastiques fusionnées à la GFP dans des protoplastes d'Arabidopsis. A ce jour ces deux approches ne nous ont pas permis d'identifier ce type de protéines dans le chloroplaste. / Calmodulin (CaM) is an important modulator of cell responses of eukaryotes. This protein is composed of four calcium (Ca2+)-binding sites and a flexible central helix. CaM can interact with other proteins in a Ca2+-dependent way. This leads to a wide variety of effects, such as activation/inhibition of enzymes, opening of membrane channels and regulation of protein trafficking. The identification of high-affinity CaM targets requires techniques allowing the study of the CaM-binding parameters of a large number of protein, and in several conditions mimicking the cell environment (e.g. presence of ligands or other proteins). The first objective of this PhD was to develop flexible and quantitative assays of CaM-partners interactions based on measurements of fluorescence anisotropy. these tests were used to perform a quantitative characterization of the interaction between CaM and two previously identified targets located in Arabidopsis chloroplast (NADK2 and Tic32). We then performed a high-throughput analysis (CaM-affinity chromatography coupled with mass spectrometry) in order to detect new potential plastidial CaM targets. We validated our approach with several biochemical techniques. We finally focused our attention on the ceQORH protein, whose high CaM affinity was confirmed by several tests. Our results confirm the Ca2+-dependent CaM affinity of NADK2, Tic32 and ceQORH and provide new elements for understanding the effects of these interactions. In addition, in order to verify the presence of CaMs or CaM-like proteins in the chloroplast, we used a biochemical and proteomic approach. We also studied the intracellular localization of some putative plastidial CMLs tagged with GFP in Arabidopsis protoplasts. For the moment, these approaches did not allow identifying such proteins in the chloroplast.

Le suivi des interactions entre protéines, localisées à la membrane plasmique ou à l’intérieur de cellules, a été réalisé au cours de cette thèse par imagerie de fluorescence et par l’analyse de processus dits de FRET (Forster Resonance Energy Transfer). Pour quantifier le FRET entre nos protéines d’intérêt, nous avons choisi le contraste de durée de vie de fluorescence car cette méthode est indépendante de la concentration et de l’intensité de fluorescence. Afin d’obtenir une résolution suffisante pour des problématiques neurobiologiques, un microscope TIRFLIM (Total Internal Reflection Fluorescence Lifetime Imaging Microscopy) avait préalablement été développé. Celui-ci nous permet de faire de l’imagerie en plein champ avec une résolution axiale sub-longueur d’onde. Ce dispositif a été calibré et optimisé au cours de cette thèse pour répondre au mieux à des problématiques biologiques. Différentes approches ont ainsi été testées dans le but de calibrer la profondeur de pénétration de l’onde évanescente. Des surfaces plasmoniques ont entre autres été utilisées pour augmenter la sélectivité axiale du montage. Notre microscope a été dédié à l’étude de l’effet du cholestérol sur l’interaction entre la protéine précurseur de l’amyloïde APP, protéine transmembranaire impliquée dans la maladie d’Alzheimer et une de ses enzymes de clivage BACE1. Nous avons ainsi effectué un suivi dynamique de l’effet du cholestérol sur l’interaction entre APP et BACE1 dans des cellules HEK-293 et dans des cultures primaires de neurones d’hippocampe d’embryons de rat, de la membrane plasmique à l’intérieur des cellules grâce à notre dispositif TIRFLIM. La mesure d’anisotropie de fluorescence résolue en temps a également été implémentée sur notre montage. Ces mesures résolues en temps et en polarisation ont permis de mesurer le temps de corrélation rotationnelle de fluorophores et de mettre en évidence de manière qualitative différents niveaux d’homodimérisation de protéines impliquées dans la maladie d’Alzheimer. / In the framework of this thesis, we have used FRET (Forster Resonance Energy Transfer) as a mechanism to follow the interaction of proteins from the plasma membrane to the cytoplasm of cells. To quantify FRET, we have chosen Fluorescence Lifetime Imaging Microscopy (FLIM) since this method is independent of the concentration and intensity of the fluorophores. To have a good axial resolution, a TIRFLIM set-up (Total Internal Reflection Fluorescence Lifetime Imaging Microscopy) was developed and this allowed us to perform wide-field imaging with sub-wavelength axial resolution. This set-up was calibrated and optimized in order to answer biological questions. Different approaches were tested in order to measure the penetration depth of the evanescent field and especially plasmonic surfaces were used to further enhance the axial resolution. Our set-up was dedicated to the study of the effect of cholesterol on the interaction between the Amyloid Precursor Protein (APP), a transmembrane protein involved in Alzheimer Disease, and one of its cleaving enzyme (BACE1). We performed a dynamic tracking of APP and BACE1 proximity under the effect of cholesterol, in HEK-293 cells and primary cultures of embryonic rat hippocampal neurons, thanks to our TIRFLIM set-up.Time-resolved fluorescence anisotropy has been implemented on our set-up. This has enabled us to measure the rotational correlation time of fluorophores and to investigate quantitatively different states of homodimerization of proteins involved in Alzheimer’s disease.

Apresentamos os resultados de estudos sobre a utilização de técnicas baseadas no fenômeno de fluorescência para a investigação de processos relacionados a membranas modelo. Nessa investigação, estão envolvidas medidas de propriedades espectrais de absorção e emissão de luz por cromóforos adequados, determinação xperimental de perfis de decaimento temporal da fluorescência e correlação temporal de emissão fluorescente, bem como a utilização apropriada de metodologias para análise e interpretação dos dados experimentais. Foram utilizados diversos compostos que apresentam absorção e emissão na região ultravioleta/visível, como as sondas lipofílicas 2-Amino-N-hexadecil-benzamida (Ahba), 6-lauryl-2-dimethylaminonaphthalene (Laurdan), N-(7-nitrobenz-2-oxa-1,3- diazol-4-yl) (NBD), em diferentes condições: meio aquoso homogêneo, suspensões de micelas de Sodium Dodecyl Sulfate (SDS), Cetyl-trimethyl-ammonium-bromide (CTAB) e 3-(Dodecyl-Dimethyl-Ammonio)-propane-sulfonate (DPS) e vesículas de fosfolipídios, como o 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), o 1,2-Dimyristoyl-sn-Glycero-3-[Phospho-rac-(1-glycerol)](Sodium Salt) (DMPG) e o 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphocholine (POPC). Supressores alquilpiridínios de diferentes comprimentos da cadeia alquila e, portanto, diferentes afinidades por agregados anfifílicos, foram utilizados em experimentos de supressão da fluorescência da sonda Ahba. Usando o formalismo que descreve fenômenos de supressão dependente de colisões entre fluoróforo e supressor, observamos que as taxas de supressão são maiores em presença de agregados anfifílicos carregados negativamente: micelas de SDS e vesículas de DMPG; em micelas zwiteriônicas o processo é mais eficiente quando a hidrofobicidade do supressor é grande, o que ocorre quando a cadeia alquila é mais longa. Realizamos experimentos de transferência de energia por ressonância de Förster (FRET) onde o grupo fluorescente da sonda lipofílica Ahba atuou como doador. Como aceitadores utilizamos os compostos Acridina Laranja, -(2,4,dinitrofenil)-etilenodiamina (Eddnp) e o NBD ligado a fosfolipídios. Fizemos uso do programa CONTIN para análise de dados experimentais de perfis de decaimento da fluorescência em sistemas em que ocorre transferência de energia e obtivemos distribuições de distâncias para os pares Ahba/Eddnp e Ahba/NBD-fosfolipídios na presença de vesículas de fosfolipídios. Para este último par, verificou-se que a distribuição de distâncias depende da temperatura do sistema, ou seja, da fase da bicamada, da concentração de aceitador e da posição onde o NBD está ligado ao fosfolipídio. Analisamos a utilização da sonda Laurdan em presença de vesículas de DMPC e POPC, em experimentos de espectroscopia de correlação de fluorescência. Embora tenha apresentado sinal elevado de fluorescência, a sonda é fotodegradável. Os mesmos experimentos de correlação de fluorescência foram realizados com o Ahba que, apesar de ter se mostrado bastante fotoestável, revelou não ser uma sonda adequada para uso em tal técnica. O espectro de excitação a dois fótons foi obtido para esta sonda, com máximo de absorção em 695 nm. Em experimentos de microscopia de fluorescência, o Ahba mostrou ser um bom marcador fluorescente para membranas lipídicas, ao possibilitar a aquisição de imagens de fluorescência de vesículas gigantes marcadas. / In this work we showed results from studies about the use of fluorescence spectroscopy techniques as a tool to investigate amphiphilic aggregates, used as a model of the cell membrane. We performed measurements on the spectral properties of light absorption and emission of adequate chromophors, registered the experimental timeresolved decay of fluorescence and time correlated fluorescence emission of the probes and used also adequate methodologies for the analysis and interpretation of experimental data. Several compounds presenting absorption and emission in the UV/visible spectral range were employed: the lipophilic probes 2-Amino-N-hexadecil-benzamida (Ahba), 6-lauryl-2-dimethylaminonaphthalene (Laurdan), N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) (NBD), in different environment:homogeneous aqueous medium, micelles of surfactants like Sodium Dodecyl Sulfate (SDS), Cetyl-trimethyl-ammonium-bromide (CTAB) and 3- (Dodecyl-Dimethyl-Ammonio)-propane-sulfonate (DPS) and phospholipid vesicles of 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 1,2-Dimyristoyl-sn-Glycero-3- [Phospho-rac-(1-glycerol)](Sodium Salt) (DMPG) and 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphocholine (POPC). Alkyilpyridinium halides with different alkyl chain length were employed fluorescence quenchers of the Ahba probe. Using the Stern-Volmer model to describe the quenching phenomena dependent on fluorophor/quencher collision, we observed that higher quenching rates were obtained in the presence of negatively charged amphiphilic agreggates: SDS micelles and DMPG vesicles; in the presence of zwitterionic vesicles the quenching efficiency was more efficient when the quencher hydrophobicity was high (long alkyl chain). We performed Förster resonance energy transfer (FRET) experiments where the fluorescent moiety of the probe Ahba was the energy donor. As acceptors molecules we used Acridine Orange, Ethylene-diamine-dinitrophenyl (Eddnp) and NBD-labeled phospholipids. The computational package CONTIN was adapted to analyze the experimentally obtained fluorescence decay profiles of the donor in the presence of the acceptor, in order to determine the distance distribution between the Ahba/Eddnp and Ahba/NBD-phospholipids pairs in the presence of lipid vesicles. For the Ahba/NBD pair, the distances were dependent on the emperature of the system (or the phase bilayer behavior), the acceptor concentration and the NBD position in the phospholipid. We observed that the Laurdan probe can be used in studies about DMPC vesicles diffusion using fluorescence correlation spectroscopy techniques. Investigation about the use of the probe Ahba with this technique had shown that its maximum absorption for two photon excitation occurs near to 695 nm, but it is not an appropriated probe to FCS experiments due to its very low brightness. On the other hand, Ahba can be used as a membrane fluorescent label in membrane fluorescence microscopy, as we can see in the fluorescence imaging experiments with giant vesicles labeled with Ahba.

A proteína tirosina fosfatase eta de rato (rPTPeta), é uma RPTP transmembranar do tipo classe I. A rPTP eta e seu homólogo DEP-1 provenientes, respectivamente, de ratos e de humanos, estão inibidas em células neoplásicas. Este fenótipo maligno é revertido após reconstituição exógena, o que sugere que a capacidade restauradora da rPTP eta pode ser uma ferramenta importante na terapia de alguns tipos de câncer. Portanto, o objetivo deste projeto incluiu o estudo molecular, biofísico e estrutural do domínio catalítico da rPTPeta (rPTPetaDC). Para isso, sub-clonamos no vetor pET-28a(+) o inserto que codifica para a região C-terminal da rPTPeta . Em seguida, bactérias E. coli da linhagem BL21 (DE3) foram transformadas com o plasmídeo e a proteína recombinante expressada e purificada. A His6-rPTPetaDC purificada teve a cauda de histidina subseqüentemente removida por digestão com trombina. O ponto isoelétrico de 7,3 da proteína de 41kDa foi medido experimentalmente e a sua funcionalidade acessada pelo ensaio de hidrólise do pNPP. A enzima apresentou uma atividade específica de 9nmol/min/microg a qual é compatível com as atividades específicas descritas para as RPTPu, RPTPalfa, PTPB1 e SHP2. A estrutura secundária e a estabilidade da rPTPetaDC recombinante foi analisada por dicroísmo circular e espectroscopia de fluorescência. A rPTPetaDC mostrou-se estável a 18 graus Celsius e propriamente enovelada (Santos, et al., Prot. Expr. Purif., 2005. Anexo A). A proteína foi, em seguida, submetida a diferentes condições de cristalização e a estudos estruturais em solução. Nas condições de 0,1M de MES, pH 6,5 e 20% PEG 10000 cresceram cristais que difrataram na resolução de 1,87Å. Os cristais pertencem ao grupo espacial P2(1)2(1)2(1) com parâmetros de célula unitária: a=46,46; b=63,07; c=111,64 Å, e com uma única molécula por unidade assimétrica (Matozo, et al., Acta crystallogr. F, 2006. Anexo B). A estrutura da rPTPetaDC, em solução, foi analisada usando-se a técnica de SAXS e medidas de anisotropia de fluorescência. Os dados de SAXS mostraram que a proteína, forma dímeros alongados, com Rg de 2,65nm e Dmax de 8,5nm. A conformação da rPTPetaDC analisada por modelos de homologia sugere que seu dímero está mais próxima da estrutura cristalográfica dimérica da RPTPalfa-D1. Alem disso, a caracterização da rPTPetaDC por anisotropia de fluorescência demonstrou que o Kd do dímero da rPTPetaDC é de 21,6 + 2,0uM e a variação da energia livre de Gibbs dímero-monômero é de 7,2kcal/mol (Mtozo, et al., Biophys. J., 2007. Anexo C ). / The rat protein tyrosine phosphatase eta, rPTPeta, is a transmembrane RPTP, with an intracellular portion composed of a unique catalytic region. The rPTPeta and the human homolog DEP-1 are down-regulated in rat and human neoplastic cells, respectively. However, the malignant phenotype is reverted after exogenous reconstitution of rPTPeta, suggesting that its function restoration could be an important tool for gene therapy of several types of cancer. Therefore, the objective of our project aimed on the molecular, biophysical and structural study of the catalytic domain of rPTPeta, rPTPetaDC. We began our study cloning the rPTPetaDC into PET28a(+) vector, followed by its expression in Escherichia coli, and purification. The His6-tag from the rPTPetaDC purified was subsequently removed by thrombin digestion. PhastGel IEF electrophoresis demonstrated that the isoelectric point of the 41kDa was 7.3. To assess the functionality of the rPTPetaDC we used the pNPP hydrolysis assay and observed that the enzyme has a specific activity of 9nmol/min/ug. The experimentally determined rPTPetaDC specific activity showed to be in the same range as the previously reported activities for RPTPu, RPTPalfa, PTPB1 and SHP2. The secondary structure and stability of the recombinant protein was analyzed by circular dichroism and fluorescence spectroscopy. The results demonstrated that rPTPetaDC was stable at 18 Celsius and properly folded (Santos, et al., Prot. Expr. Purif., 2005. In attachment A). Then, the purified protein was submitted to different crystallization conditions and structural studies in solution. Crystals appeared at 0.1M MES, pH 6.5 and 20% PEG 10,000 and diffracted with resolution of 1.87Å. The crystals belong to spatial group P2(1)2(1)2(1) with unit cell parameters of a=46.46, b=63.07, c=111.64Å and contained one molecule for asymmetric unit (Matozo, et al., Acta crystallog. F, 2006. In attachment B). Also, the structural of rPTPetaDC, in solution, was analyzed by SAXS and fluorescence anisotropy. SAXS data showed that the protein forms elongated dimers in solution with an Rg of 2.65nm and a Dmax of 8.5nm. The rPTPetaDC conformation in solution, studied by homology models, suggested that the rPTPetaDC dimer architecture is more closely related to the crystal structure of RPTPalfa-D1. The characterization of rPTPetaDC by fluorescence anisotropy measurements demonstrated that the Kd of the dimer is 21.6 + 2.0uM and the energy Gibbs dimer-monomer is equal to 7.2kcal/mol (Matozo, et al., Bioph. J., 2007. In attachment C).

Apresentamos os resultados de estudos sobre a utilização de técnicas baseadas no fenômeno de fluorescência para a investigação de processos relacionados a membranas modelo. Nessa investigação, estão envolvidas medidas de propriedades espectrais de absorção e emissão de luz por cromóforos adequados, determinação xperimental de perfis de decaimento temporal da fluorescência e correlação temporal de emissão fluorescente, bem como a utilização apropriada de metodologias para análise e interpretação dos dados experimentais. Foram utilizados diversos compostos que apresentam absorção e emissão na região ultravioleta/visível, como as sondas lipofílicas 2-Amino-N-hexadecil-benzamida (Ahba), 6-lauryl-2-dimethylaminonaphthalene (Laurdan), N-(7-nitrobenz-2-oxa-1,3- diazol-4-yl) (NBD), em diferentes condições: meio aquoso homogêneo, suspensões de micelas de Sodium Dodecyl Sulfate (SDS), Cetyl-trimethyl-ammonium-bromide (CTAB) e 3-(Dodecyl-Dimethyl-Ammonio)-propane-sulfonate (DPS) e vesículas de fosfolipídios, como o 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), o 1,2-Dimyristoyl-sn-Glycero-3-[Phospho-rac-(1-glycerol)](Sodium Salt) (DMPG) e o 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphocholine (POPC). Supressores alquilpiridínios de diferentes comprimentos da cadeia alquila e, portanto, diferentes afinidades por agregados anfifílicos, foram utilizados em experimentos de supressão da fluorescência da sonda Ahba. Usando o formalismo que descreve fenômenos de supressão dependente de colisões entre fluoróforo e supressor, observamos que as taxas de supressão são maiores em presença de agregados anfifílicos carregados negativamente: micelas de SDS e vesículas de DMPG; em micelas zwiteriônicas o processo é mais eficiente quando a hidrofobicidade do supressor é grande, o que ocorre quando a cadeia alquila é mais longa. Realizamos experimentos de transferência de energia por ressonância de Förster (FRET) onde o grupo fluorescente da sonda lipofílica Ahba atuou como doador. Como aceitadores utilizamos os compostos Acridina Laranja, -(2,4,dinitrofenil)-etilenodiamina (Eddnp) e o NBD ligado a fosfolipídios. Fizemos uso do programa CONTIN para análise de dados experimentais de perfis de decaimento da fluorescência em sistemas em que ocorre transferência de energia e obtivemos distribuições de distâncias para os pares Ahba/Eddnp e Ahba/NBD-fosfolipídios na presença de vesículas de fosfolipídios. Para este último par, verificou-se que a distribuição de distâncias depende da temperatura do sistema, ou seja, da fase da bicamada, da concentração de aceitador e da posição onde o NBD está ligado ao fosfolipídio. Analisamos a utilização da sonda Laurdan em presença de vesículas de DMPC e POPC, em experimentos de espectroscopia de correlação de fluorescência. Embora tenha apresentado sinal elevado de fluorescência, a sonda é fotodegradável. Os mesmos experimentos de correlação de fluorescência foram realizados com o Ahba que, apesar de ter se mostrado bastante fotoestável, revelou não ser uma sonda adequada para uso em tal técnica. O espectro de excitação a dois fótons foi obtido para esta sonda, com máximo de absorção em 695 nm. Em experimentos de microscopia de fluorescência, o Ahba mostrou ser um bom marcador fluorescente para membranas lipídicas, ao possibilitar a aquisição de imagens de fluorescência de vesículas gigantes marcadas. / In this work we showed results from studies about the use of fluorescence spectroscopy techniques as a tool to investigate amphiphilic aggregates, used as a model of the cell membrane. We performed measurements on the spectral properties of light absorption and emission of adequate chromophors, registered the experimental timeresolved decay of fluorescence and time correlated fluorescence emission of the probes and used also adequate methodologies for the analysis and interpretation of experimental data. Several compounds presenting absorption and emission in the UV/visible spectral range were employed: the lipophilic probes 2-Amino-N-hexadecil-benzamida (Ahba), 6-lauryl-2-dimethylaminonaphthalene (Laurdan), N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) (NBD), in different environment:homogeneous aqueous medium, micelles of surfactants like Sodium Dodecyl Sulfate (SDS), Cetyl-trimethyl-ammonium-bromide (CTAB) and 3- (Dodecyl-Dimethyl-Ammonio)-propane-sulfonate (DPS) and phospholipid vesicles of 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 1,2-Dimyristoyl-sn-Glycero-3- [Phospho-rac-(1-glycerol)](Sodium Salt) (DMPG) and 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphocholine (POPC). Alkyilpyridinium halides with different alkyl chain length were employed fluorescence quenchers of the Ahba probe. Using the Stern-Volmer model to describe the quenching phenomena dependent on fluorophor/quencher collision, we observed that higher quenching rates were obtained in the presence of negatively charged amphiphilic agreggates: SDS micelles and DMPG vesicles; in the presence of zwitterionic vesicles the quenching efficiency was more efficient when the quencher hydrophobicity was high (long alkyl chain). We performed Förster resonance energy transfer (FRET) experiments where the fluorescent moiety of the probe Ahba was the energy donor. As acceptors molecules we used Acridine Orange, Ethylene-diamine-dinitrophenyl (Eddnp) and NBD-labeled phospholipids. The computational package CONTIN was adapted to analyze the experimentally obtained fluorescence decay profiles of the donor in the presence of the acceptor, in order to determine the distance distribution between the Ahba/Eddnp and Ahba/NBD-phospholipids pairs in the presence of lipid vesicles. For the Ahba/NBD pair, the distances were dependent on the emperature of the system (or the phase bilayer behavior), the acceptor concentration and the NBD position in the phospholipid. We observed that the Laurdan probe can be used in studies about DMPC vesicles diffusion using fluorescence correlation spectroscopy techniques. Investigation about the use of the probe Ahba with this technique had shown that its maximum absorption for two photon excitation occurs near to 695 nm, but it is not an appropriated probe to FCS experiments due to its very low brightness. On the other hand, Ahba can be used as a membrane fluorescent label in membrane fluorescence microscopy, as we can see in the fluorescence imaging experiments with giant vesicles labeled with Ahba.

Um Prozesse in biologischen Systemen auf molekularer Ebene zu untersuchen, haben sich vor allem fluoreszenzspektroskopische Methoden bewährt. Die Möglichkeit, einzelne Moleküle zu beobachten, hat zu einem deutlichen Fortschritt im Verständnis von elementaren biochemischen Prozessen geführt. Zu einer der bekanntesten Methoden der Einzelmolekülspektroskopie zählt die Fluoreszenz-Korrelations-Spektroskopie (FCS), mit deren Hilfe intramolekulare und diffusionsgesteuerte Prozesse in einem Zeitbereich von µs bis ms untersucht werden können. Durch die Verwendung von sog. Fluoreszenzsonden können Informationen über deren molekulare Mikroumgebung erhalten werden. Insbesondere für die konfokale Mikroskopie und die Einzelmolekülspektroskopie werden Fluoreszenzfarbstoffe mit einer hohen Photostabilität und hohen Fluoreszenzquantenausbeute benötigt. Aufgrund ihrer hohen Fluoreszenzquantenausbeute und der Möglichkeit, maßgeschneiderte“ Farbstoffe in einem breiten Spektralbereich für die Absorption und Fluoreszenz zu entwickeln, sind Cyaninfarbstoffe von besonderem Interesse für bioanalytische Anwendungen. Als Fluoreszenzmarker finden diese Farbstoffe insbesondere in der klinischen Diagnostik und den Lebenswissenschaften Verwendung. Die in dieser Arbeit verwendeten Farbstoffe DY-635 und DY-647 sind zwei typische Vertreter dieser Farbstoffklasse. Durch Modifizierung können die Farbstoffe kovalent an biologisch relevante Moleküle gebunden werden. Aufgrund ihres Absorptionsmaximums oberhalb von 630nm werden sie insbesondere in der Bioanalytik eingesetzt. In der vorliegenden Arbeit wurden die spektroskopischen Eigenschaften der Cyaninfarbstoffe DY-635 und DY-647 in biomimetischen und biologischen Modellsystemen untersucht. Zur Charakterisierung wurden dabei neben der Absorptionsspektroskopie insbesondere fluoreszenzspektroskopische Methoden verwendet. Dazu zählen die zeitkorrelierte Einzelphotonenzählung zur Ermittlung des Fluoreszenzabklingverhaltens, Fluoreszenz-Korrelations-Spektroskopie (FCS) zur Beobachtung von Diffusions- und photophysikalischen Desaktivierungsprozessen und die zeitaufgelöste Fluoreszenzanisotropie zur Untersuchung der Rotationsdynamik und Beweglichkeit der Farbstoffe im jeweiligen Modellsystem. Das Biotin-Streptavidin-System wurde als Modellsystem für die Untersuchung von Protein-Ligand-Wechselwirkungen verwendet, da der Bindungsmechanismus weitgehend aufgeklärt ist. Nach Bindung der Farbstoffe an Streptavidin wurde eine erhebliche Veränderung in den Absorptions- und Fluoreszenzeigenschaften beobachtet. Es wird angenommen, dass diese spektralen Veränderungen durch Wechselwirkung von benachbarten, an ein Streptavidintetramer gebundenen Farbstoffmolekülen und Bildung von H-Dimeren verursacht wird. Für das System Biotin-Streptavidin ist bekannt, dass während der Bindung des Liganden (Biotin) an das Protein eine Konformationsänderung auftritt. Anhand von zeitaufgelösten Fluoreszenzanisotropieuntersuchungen konnte in dieser Arbeit gezeigt werden, dass diese strukturellen Veränderungen zu einer starken Einschränkung der Beweglichkeit des Farbstoffes DY-635B führen. Liegt eine Mischung von ungebundenem und Streptavidin-gebundenem Farbstoff vor, können die Anisotropieabklingkurven nicht nach einem exponentiellen Verlauf angepasst werden. Es konnte im Rahmen dieser Arbeit gezeigt werden, dass in diesem Fall die Auswertung mit Hilfe des Assoziativen Anisotropiemodells möglich ist, welches eine Unterscheidung der Beiträge aus den zwei verschiedenen Mikroumgebungen ermöglicht. Als zweites Modellsystem dieser Arbeit wurden Mizellen des nichtionischen Tensids Tween-20 eingesetzt. Mizellen bilden eines der einfachsten Systeme, um die Mikroumgebung einer biologischen Membran nachzuahmen. Sind die Farbstoffe in den Mizellen eingelagert, so kommt es zu keiner Veränderung der Mizellgröße. Die ermittelten Werte des Diffusionskoeffizienten der mizellar eingelagerten Farbstoffe spiegeln demzufolge die Translationsbewegung der Tween-20-Mizellen wider. Die Beweglichkeit der Farbstoffe innerhalb der Tween-20-Mizellen wurde durch zeitaufgelöste Fluoreszenzanisotropiemessungen untersucht. Neben der „Wackelbewegung“, entsprechend dem wobble-in-a-cone-Modell, wird zusätzlich noch die laterale Diffusion der Farbstoffe entlang der Mizelloberfläche beschrieben. / To investigate processes in biological systems on a molecular level, particularly fluorescence spectroscopic methods have proven. The possibility to observe single molecules led to significant progress in the understanding of basic biochemical processes. Fluorescence correlation spectroscopy (FCS) is one of the most popular methods of single molecule spectroscopy and is a powerful technique for the investigation of intramolecular and diffusion-controlled processes on a µs to ms time scale. The photophysical characteristics of fluorescent probes are often strongly influenced by their microenvironment. For confocal microscopy and single molecule detection applications fluorescent dyes with properties, such as high photostability and high fluorescence efficiency are highly needed. Due to the high fluorescence efficiency and the high potential to design tailor-made fluorescence probes covering a wide spectral range in absorption and fluorescence, cyanine dyes are highly attractive as fluorescence probes for bioanalytical applications, such as clinical diagnostics and life sciences. The dyes DY-635 and DY-647 are two typical representatives of this class of dyes and can be covalently attached to biologically relevant molecules. Because of their excitation wavelength above 630nm these dyes are especially suited for bioanalytical applications. In this work the spectroscopic properties of DY-635 and DY-647 in biomimetic and biological model systems were studied by absorption and fluorescence spectroscopy techniques: time-correlated single photon counting to determine fluorescence decay behavior, fluorescence correlation spectroscopy (FCS) to observe diffusion and photophysical deactivation processes, and fluorescence anisotropy to study the mobility and rotational behavior of the dyes in the respective model system. The well characterized system biotin-streptavidin was used as a model system for protein-ligand interactions. Binding to streptavidin resulted in significant changes in the steady-state photophysical characteristics of DY-635B and DY-647. These spectral changes are attributed to dye-dye interactions and the formation of H-dimers. Previous studies have demonstrated, that binding of biotin alters the conformation of streptavidin. Based on the evaluation of time-resolved anisotropy data in this study it was shown that these structural changes result in strong hindrance of the rotational freedom of DY-635B. For mixtures of unbound and streptavidin-bound dyes the fluorescence anisotropy decay curves are found to be nonexponential. In this case the concept of an associated anisotropy were applied which allowed discrimination between contributions from different microenvironments. As a second model system, micelles of the nonionic surfactant Tween-20 were used. Micelles are one of the simplest systems to mimic the microenvironment of a biological membrane. Incorporation of the dyes had no effect on the micelle size. The diffusion coefficient of the dyes, obtained by fluorescence correlation spectroscopy (FCS), reflects the translational behavior of Tween-20 micelles. The mobility of the dyes in the Tween-20 micelles was studied by time-resolved fluorescence anisotropy. In addition to a „wobbling“ motion ccording to the wobble-in-a-cone model, a lateral diffusion of the dyes along the micelle surface is described.

An extended Förster theory (EFT), previously derived (L. B.-Å. Johansson et al. J. Chem. Phys., 1996,105) has theoretically been adapted and used in simulations of donor-acceptor energy transfer (DAET), which is a process often referred to as FRET. It was shown that the classical Förster theory is only valid in the initial part of the fluorescence decay. In this thesis an EFT is derived and outlined for electronic energy transport between two fluorescent molecules which are chemically identical, but photophysically non-identical. The energy migration within such asymmetric pairs is partially reversible and therefore referred to as partial donor-donor energy migration (PDDEM). The previously derived model of PDDEM (S. V. Kalinin et al. Spectrochim Acta Part A, 2002,58) is an approximation of the EFT. In particular, the EFT accounts for the time-dependent reorientations as well as the distance that influence the rate of electronic energy migration. The reorientation of the fluorophores transition dipole moments has been simulated using Brownian dynamics. As a result, the related “k2-problem” has been solved. The EFT of PDDEM has also been studied regarding the effect of PDDEM on experimental observables e.g. quantum yield of fluorescence and steady-state anisotropies

No description available.

A proteína tirosina fosfatase eta de rato (rPTPeta), é uma RPTP transmembranar do tipo classe I. A rPTP eta e seu homólogo DEP-1 provenientes, respectivamente, de ratos e de humanos, estão inibidas em células neoplásicas. Este fenótipo maligno é revertido após reconstituição exógena, o que sugere que a capacidade restauradora da rPTP eta pode ser uma ferramenta importante na terapia de alguns tipos de câncer. Portanto, o objetivo deste projeto incluiu o estudo molecular, biofísico e estrutural do domínio catalítico da rPTPeta (rPTPetaDC). Para isso, sub-clonamos no vetor pET-28a(+) o inserto que codifica para a região C-terminal da rPTPeta . Em seguida, bactérias E. coli da linhagem BL21 (DE3) foram transformadas com o plasmídeo e a proteína recombinante expressada e purificada. A His6-rPTPetaDC purificada teve a cauda de histidina subseqüentemente removida por digestão com trombina. O ponto isoelétrico de 7,3 da proteína de 41kDa foi medido experimentalmente e a sua funcionalidade acessada pelo ensaio de hidrólise do pNPP. A enzima apresentou uma atividade específica de 9nmol/min/microg a qual é compatível com as atividades específicas descritas para as RPTPu, RPTPalfa, PTPB1 e SHP2. A estrutura secundária e a estabilidade da rPTPetaDC recombinante foi analisada por dicroísmo circular e espectroscopia de fluorescência. A rPTPetaDC mostrou-se estável a 18 graus Celsius e propriamente enovelada (Santos, et al., Prot. Expr. Purif., 2005. Anexo A). A proteína foi, em seguida, submetida a diferentes condições de cristalização e a estudos estruturais em solução. Nas condições de 0,1M de MES, pH 6,5 e 20% PEG 10000 cresceram cristais que difrataram na resolução de 1,87Å. Os cristais pertencem ao grupo espacial P2(1)2(1)2(1) com parâmetros de célula unitária: a=46,46; b=63,07; c=111,64 Å, e com uma única molécula por unidade assimétrica (Matozo, et al., Acta crystallogr. F, 2006. Anexo B). A estrutura da rPTPetaDC, em solução, foi analisada usando-se a técnica de SAXS e medidas de anisotropia de fluorescência. Os dados de SAXS mostraram que a proteína, forma dímeros alongados, com Rg de 2,65nm e Dmax de 8,5nm. A conformação da rPTPetaDC analisada por modelos de homologia sugere que seu dímero está mais próxima da estrutura cristalográfica dimérica da RPTPalfa-D1. Alem disso, a caracterização da rPTPetaDC por anisotropia de fluorescência demonstrou que o Kd do dímero da rPTPetaDC é de 21,6 + 2,0uM e a variação da energia livre de Gibbs dímero-monômero é de 7,2kcal/mol (Mtozo, et al., Biophys. J., 2007. Anexo C ). / The rat protein tyrosine phosphatase eta, rPTPeta, is a transmembrane RPTP, with an intracellular portion composed of a unique catalytic region. The rPTPeta and the human homolog DEP-1 are down-regulated in rat and human neoplastic cells, respectively. However, the malignant phenotype is reverted after exogenous reconstitution of rPTPeta, suggesting that its function restoration could be an important tool for gene therapy of several types of cancer. Therefore, the objective of our project aimed on the molecular, biophysical and structural study of the catalytic domain of rPTPeta, rPTPetaDC. We began our study cloning the rPTPetaDC into PET28a(+) vector, followed by its expression in Escherichia coli, and purification. The His6-tag from the rPTPetaDC purified was subsequently removed by thrombin digestion. PhastGel IEF electrophoresis demonstrated that the isoelectric point of the 41kDa was 7.3. To assess the functionality of the rPTPetaDC we used the pNPP hydrolysis assay and observed that the enzyme has a specific activity of 9nmol/min/ug. The experimentally determined rPTPetaDC specific activity showed to be in the same range as the previously reported activities for RPTPu, RPTPalfa, PTPB1 and SHP2. The secondary structure and stability of the recombinant protein was analyzed by circular dichroism and fluorescence spectroscopy. The results demonstrated that rPTPetaDC was stable at 18 Celsius and properly folded (Santos, et al., Prot. Expr. Purif., 2005. In attachment A). Then, the purified protein was submitted to different crystallization conditions and structural studies in solution. Crystals appeared at 0.1M MES, pH 6.5 and 20% PEG 10,000 and diffracted with resolution of 1.87Å. The crystals belong to spatial group P2(1)2(1)2(1) with unit cell parameters of a=46.46, b=63.07, c=111.64Å and contained one molecule for asymmetric unit (Matozo, et al., Acta crystallog. F, 2006. In attachment B). Also, the structural of rPTPetaDC, in solution, was analyzed by SAXS and fluorescence anisotropy. SAXS data showed that the protein forms elongated dimers in solution with an Rg of 2.65nm and a Dmax of 8.5nm. The rPTPetaDC conformation in solution, studied by homology models, suggested that the rPTPetaDC dimer architecture is more closely related to the crystal structure of RPTPalfa-D1. The characterization of rPTPetaDC by fluorescence anisotropy measurements demonstrated that the Kd of the dimer is 21.6 + 2.0uM and the energy Gibbs dimer-monomer is equal to 7.2kcal/mol (Matozo, et al., Bioph. J., 2007. In attachment C).

Cette étude a consisté en le développement et l’évaluation de nouvelles molécules pour la radiochimiothérapie concomitante. Ce travail a abouti à la conception de nouveaux agents chimiothérapeutiques duaux basés sur la combinaison covalente de deux radiosensibilisateurs: un inhibiteur de la PARP d’une part, et un alkylant de l’ADN (complexe de platine ou témozolomide) d’autre part. Les évaluations biologiques ont permis de mettre en évidence l’intérêt d’une molécule duale inhibiteur de la PARP/platine. Parallèlement à ce projet, le développement d’outils moléculaires pour l’étude d’inhibiteurs de la PARP a été entrepris. Ainsi, plusieurs sondes d’affinité ont été conçues pour une étude d’inhibiteurs de la PARP par protéomique chimique. Ce travail a permis de valider la spécificité d’une sonde d’affinité pour la PARP1 et la PARP2. Finalement, des molécules fluorescentes inhibitrices de la PARP ont été développées dans l’objectif d’un criblage d’inhibiteurs de PARP3 par anisotropie de fluorescence. / The main topic of this work was the development and biological evaluation of dual molecules for concomitant chemoradiotherapy. To this end, new dual chemotherapeutic agents were designed by linking covalently two radiosensitizers: a PARP inhibitor and an alkylating agent (platinum complex or temozolomide). This study led to an efficient PARP inhibitor/platinum dual molecule. A complementary approach was to develop affinity probes to study PARP inhibitors by a chemical proteomic method. This study permitted to validate the selectivity of an affinity probe for PARP1 and PARP2. Finally, fluorescent PARP inhibitor probes were synthesised and evaluated for a PARP3 screening by fluorescence anisotropy.