Ionic Liquids (ILs) has been attracting attention, both from academia and industry, given the numerous applications of these systems. ILs are salts, usually composed by an organic ion, and a counterion which could be organic or inorganic, and, interestingly they are found at liquid state at room temperature. Our interest in studying ILs comes from its low toxicity. Some recent studies have shown that the toxicity of the ILs ishigher than believed, in particular for biologically relevant systems. The main goal of this research is to study the influence of the ionic liquid 1-tetradecyl-3-methylimidazolium chloride ([C14MIM][Cl]) with membrane systems. To do so, we made use of different lipids: POPC, Sphingomyelin, Cholesterol, POPG, DPPC, DPPG and DMPC. For each of these systems, the influence of ILs concentration were elucidated by means of a systematic study through different experimental techniques: Small Angle X-ray scattering (SAXS), dynamic light scattering (DLS), fluorescence anisotropy, optical microscopy and z-potential. Since [C14MIM][Cl] has a positive charge on the imidazolium group, the superficial charge of all vesicles increased. For zwitterionic vesicles no significant change in size and melting temperature were noticed. The imidazolium-based ionic liquid diminished the gel-fluid transition temperature for negatively charged lipids. For DPPC:DPPG (1:1), for instance, the transition temperature decreased from 42.50±0.13oC to 25.27±0.33oC and for DPPG from 46.12±0.22 oC to 36.6±0.38 oC. For DPPG, the vesicle hydrodynamic diameter increased from 84±0.1nm to 176±0.1nm, whereas for DPPC:DPPG it increased from 95±0.1nm to 196±0.1nm. The electronic density profile, obtained by SAXS, supported the penetration of the [C14MIM][Cl] into the negative bilayer structure. 15 mol% of [C14MIM][Cl] increased the polar head thickness of DPPC vesicles from 11.1±0.6 Å to 18.0±0.7 Å, without alter significantly the inner region of the membrane.Qualitative results obtained with optical microscopy showed that the IL incorporation destabilize the membrane asymmetry (between the leaflets) leading to the formation of pores (evidenced by optical contrast lost) and the presence of buds. We believe that this work could improve the understanding of the effects of ILs in the presence of biological relevant systems / Os líquidos iônicos (LI) tem atraído grande atenção, tanto da academia quanto da indústria, devido às suas numerosas aplicações. LI são sais, normalmente compostos por um íon orgânico, e um contra-íon que pode ser orgânico ou inorgânico, mas que tem como característica ser encontrado no estado líquido à temperaturas próximas a ambiente. Nosso interesse em estudar LIs vem de sua baixa toxicidade, atribuída a sua baixa volatilidade. Entretanto, alguns estudos recentes mostraram que a toxicidade dos LI é maior do que se acreditava, em particular com sistemas de relevância biológica.O objetivo principal desta dissertação é estudar a influência do líquido iônico 1-tetradecil-3-metilimidazólio cloreto ([C14MIM][Cl]) com sistemas de membrana. Para isso, utilizamos diferentes lipídios, como o POPC, esfingomielina, colesterol, POPG, DPPC,DPPG e o DMPC. Para cada um destes sistemas, a influência da concentração de LI foi elucidada por meio de um estudo sistemático através de diferentes técnicas experimentais, tais como: espalhamento de raio-X a baixos ângulos (SAXS), espalhamento dinâmico de luz (DLS), anisotropia de fluorescência, microscopia óptica e potencial-z. Uma vez que o componente iônico de [C14MIM][Cl] tem uma carga positiva no grupo imidazólio, a carga superficial de todas as vesículas estudadas aqui aumentou. Entretanto, para asvesículas compostas pelos lipídeos zwitteriónicos, não tenha sido observada qualquer alteração significativa no tamanho e na temperatura de transição de fase gel-fluido. O [C14MIM][Cl] altera a organização interna entre as moléculas de lipídio com carga negativa. Consequentemente, à medida que a quantidade de LI aumenta, a temperatura de transição de fase diminui e o tamanho médio das vesículas aumenta. Para o sistema DPPC:DPPG (1:1) a temperatura de transição de fase caiu de 42.50 ± 0.13 oC para 25.27 ± 0.33 oC e para as vesículas de DPPG de 46.12±0.22 oC para 36.6±0.38 oC. Quanto ao diâmetro hidrodinâmico médio, no caso do DPPG este valor aumentou de 84±0.1 nm para 176±0.1 nm, enquanto que para a mistura DPPC:DPPG (1:1) ele passou de 95±0.1nm para 196±0.1nm. Indicando assim que o LI incorpora na bicamada lipídica negativamente carregada. O perfil de densidade eletrônica, obtido por SAXS, confirma a penetração do [C14MIM][Cl] na bicamada lipídica. Diferentemente, para a membrana lipídica zwitteriónica o LI tende a se situar perto da região da cabeça polar sem afetar significativamente a região do interior da bicamada lipídica. Por outro lado, a presença de15 mol% de [C14MIM][Cl] aumenta a espessura da região polar das bicamadas das vesículas de DPPC de ~ 11.1±0.6 Å para ~ 18.0±0.7 Å. Os resultados qualitativos da microscopia óptica mostraram que a incorporação da LI desestabiliza a assimetria da membrana entre as camadas interna e externa, além de sugerir o aparecimento de poros (evidenciado pela perda do contraste ótico das vesículas) e estruturas chamadas de buds. Esperamos que este trabalho melhore a compreensão dos efeitos do LI na presença de organismos biológicos.

Movimentos coletivos prestam um papel fundamental na dinâmica e energética de biomoléculas em solução. Estes movimentos permitem o acoplamento de regiões significativamente distantes, apresentando considerável influência, por exemplo, no alosterismo para a formação de complexos macromoleculares e no funcionamento integrado de proteínas multidomínios como \"máquinas moleculares\". Neste trabalho de doutoramento, serão apresentados os resultados referentes à aplicação conjunta de técnicas experimentais biofísicas, de modelagem estrutural e de dinâmica molecular no estudo de dois sistemas para os quais estes movimentos coletivos demonstram considerável importância funcional. Para a interação do receptor nuclear do ácido 9-cis-retinóico com seu elemento responsivo específico no DNA (HRE), a comparação de estudos de dinâmica molecular com ensaios de afinidade por anisotropia de fluorescência sugere que a resistência inicial para a associação do monômero, seguida da acentuada colaboratividade na associação do dímero é regida por um impedimento da associação do domínio de ligação ao DNA (DBD) para o primeiro à sequência responsiva devido, em última análise, a uma não complementaridade dos modos coletivos mútuos. Este impedimento para a associação monomérica inicial é mais acentuado para o monômero 5\' (para o qual a menor especificidade de ligação à seqüência específica já é bem documentada), devido aos efeitos conjuntos de um \"defeito\" natural no empacotamento de bases da seqüência responsiva, que se manifesta mais significativamente na interface entre o meio-sítio 5\' e a seqüência espaçadora, e dos modos vibracionais entre os dois sítios decorrentes de seu faseamento relativo na topologia do DNA na seqüência responsiva, caracterizando um mecanismo \"chave e fechadura\" para a interação obrigatoriamente simultânea dos dois monômeros ao DNA. No segundo caso, um estudo integrado utilizando a técnica experimental de espalhamento de raios X a baixos ângulos e uma abordagem de modelagem estrutural baseada em dinâmica molecular foi realizado para a celobiohidrolase I de Trichoderma harziannum. Este estudo permitiu tanto a elaboração de um modelo estrutural de maior resolução para esta enzima de alto potencial biotecnológico como a constatação dos possíveis mecanismos moleculares a partir dos quais as glicosilações no peptídeo conector impõem restrições à orientação e modos vibracionais entre seus dois domínios de forma condizente com sua ação concertada na interação e no deslize da enzima sobre a superfície celulósica, ambos de fundamental importância para a processividade da enzima na hidrólise do substrato microcristalino. / Collective motions play a fundamental role in solution biomolecule dynamics and energetics. These movements can couple very distant regions in the protein structures affection, for instance, allosteric mechanisms, the establishment of macromolecular complexes, and on the integrated function of multidomain proteins as molecullar machines. In this thesis, we present results concerning to the joint use of experimental biophysical techniques, structural modeling and molecular dynamics simulations on the study of two systems for which these collective motions have substantial importance. First, we study the interaction of the nuclear retinoid X receptor with its specific DNA hormone response element (HRE) using a combination of molecular dynamics simulations and affinity assays performed by using fluorescence anisotropy. We find out that collective motions mediate the low binding affinity of monomers and the high cooperative binding of HRE dimers. The lower binding affinity of the monomer is more prominent for 5´ monomers. This occur due to an natural ineffective stacking of the last base pair step at the 5´-half-site and to the phasing of the two binding half-sites in the DNA topology, that impose a collective motions that tends to occlude the 5´ binding site. This behavior, in turn, is concurrent with the well known 3´ polarity and the decreased binding specificity to the 5´ half site for the hRXRα monomer. This same pattern impose a lock-and-key mechanisms dependent on the binding of the full dimer. Second, an integrated Small angle X ray scattering and molecular dynamics based structural modeling was used to comprehend the interdomain motions of cellobiohydrolase I of Trichoderma harziannum. We manage to build a refined model for this enzime, with important biotechnological potential. We also provide insights into molecular mechanisms of linker and glycosylation imposed restraints on the orientation and vibrational modes of the full-length enzyme, supporting a mechanism of sliding of on the cellulose surface. This mechanism is fundamental for the high processivity on the hydrolysis of microcrystalline cellulose.

Ce travail présente la synthèse, la caractérisation et l’utilisation (transfert électronique photo-induit) de foldamères de taille nanométriques constitués d’unité quinolines. Grâce a une stratégie de synthèse de doublement de segment une grande variété d’oligomères (jusqu’à 96 unités) ont pu être préparé à partir du synthon 8 aminoquinoline-2-carboxylate.Leurs propriétés dynamiques de ces objets ont été étudiées en solution et en phase gazeuse. La spectrométrie de masse de mobilité ionique a permis de déterminer leur conformation en phase gazeuse. Les expériences de RMN DOSY et d’anisotropie de Fluorescence ont permis de déterminer leurs propriétés de diffusion (transrationnelle et rotationnelle). Ces résultats ont révélés qui ces foldamères sont rigides et que leur architecture hélicoïdale est conservée.Le transport électronique photo-induit à travers ces foldamères de taille nanométrique ont été étudié et le mécanisme de transfert ainsi que son efficacité ont été déterminé pour une série de composés de tailles variables. / Herein, synthesis, characterization and application (photoinduced electron transport) of nanosized quinoline-based foldamers have been explored. With double segment strategy, a variety of helical nanosized foldamers (up to 96 quinoline units) were successfully prepared based on 8-aminoquinoline-2-carboxylic acid monomer.The dynamic properties in gas phase and solution were investigated. Ion mobility mass spectrometry afforded access to the conformation state of foldamers ingas phase; DOSY and fluorescence anisotropy assessed the diffusion (translational and rotational, respectively) of foldamers in solution. All of these techniques revealed that quinoline-based foldamers are rigid and that helical conformation is conserved. Photoinduced electron transport through nanosized foldamer was also studied and the mechanism and the transport ratios were revealed.

The presented diploma thesis is focused on the preparation, characterization and study of membrane properties of liposomal systems which were composed of the neutral phosphatidylcholine (DPPC), cholesterol, negatively charged phosphatidylglycerol (DPPG), polyethylenglycol bounded to phosphatidylethanolamine (PEG5000–PE) and polycation N,N,N-trimethylchitosan (TMC). The influence of individual components and their concentrations on the average particle size, zeta potential and changes in the outer and inner part of the bilayer was investigated. In this matter, methods of dynamic and electrophoretic light scattering and fluorescence spectroscopy with the application of laurdan and DPH probes were used. Based on the above-mentioned parameters, concentrations of components that most suitably influence properties of liposomes in terms of the intended application were selected for the definite complex. It was managed to prepare a liposomal complex stealth liposome–N,N,N-trimethylchitosan, which, due to the optimized composition, could have suitable attributes as a drug delivery system for inhalation administration of biologically active substances.

Les bactériocines de classe IIa présentent une activité antimicrobienne résultant d'un mécanisme d'action ciblant les membranes des bactéries à Gram positif. Cette activité est modulée par différentes caractéristiques des surfaces bactériennes. Les propriétés physico-chimiques de surface de dix-huit souches bactériennes ont été déterminées afin d'étudier le lien entre ces propriétés et les phénotypes de résistance/sensibilité à Cbn BM1. Les résultats obtenus indiquent une grande diversité des propriétés physico-chimiques des surfaces analysées, sans cependant permettre d’établir un lien entre celles-ci et le phénotype de sensibilité/résistance à CbnBM1. Les mécanismes d'action de Cbn BM1 ont ensuite été étudiés sur Carnobacterium maltaromaticum DSM20730 et Listeria monocytogenes EGDe. L'atteinte de l'intégrité physique des membranes plasmiques par l'action de Cbn BM1 montre une hétérogénéité de réponse des populations bactériennes. Ce résultat a été confirmé par microscopie de force atomique in vivo à haute résolution. L'interaction de Cbn BM1 avec les membranes a été mise en évidence par mesure de l'anisotropie de fluorescence. Cette approche a révélé que Cbn BM1 présente des degrés de pénétration différents dans la membrane de C. maltaromaticum DSM20730 par rapport à L. monocytogenes EGDe. L'action de Cbn BM1 conduit cependant, pour les deux souches, à la modification de la force protomotrice membranaire. Ces différentes approches retenues pour l'étude des mécanismes d'action ont révélé que C. maltaromaticum DSM20730 et L. monocytogenes EGDe présentent une sensibilité à Cbn BM1 uniquement lorsque les cellules sont en phase exponentielle de croissance. / The antimicrobial activity of class IIa bacteriocins toward Gram positive bacteria relies on their membrane targeting mechanisms of action. These mechanisms are modulated by the bacterial surface properties. The physico-chemical surface properties of eighteen bacterial strains were determined to link these properties to the resistance/sensitivity to Cbn BM1 of the bacterial strains. In this way, two approaches were undertaken : the microbial adhesion to solvents and electrophoretic mobility measurements. The results show a large diversity of the determined properties among the strains but without establishing a direct link between the surface properties and the resistance/sensitivity phenotypes. Mechanisms of action of the bacteriocin Cbn BM1 on Carnobacterium maltaromaticum DSM20730 and Listeria monocytogenes EGDe were determined. Syto9® and propidium iodide allowed to show the heterogeneity of the bacterial populations toward the alteration of the membrane integrity. The interaction of Cbn BM1 with the bacterial membrane was studied by monitoring the fluorescence anisotropy of DPH and TMA-DPH. The results highlight a difference between the mechanism of action of Cbn BM1 on C. maltaromaticum DSM20730 and on L. monocytogenes EGDe. However, a treatment by Cbn BM1 leads to a perturbation of the component of the proton-motive force of the membrane for both strains. These approaches revealed that these bacterial strains exhibit a sensitivity to Cbn BM1 only when treated in log growth phase. Modification of nano-mechanical properties of C. maltaromaticum DSM20730 after a treatment by Cbn BM1 were assessed by an atomic force microscopy approach.

The homo and hetero dimerisation of two spectroscopically different chromophores were studied, namely: 4,4-difluoro-4-bora-3a,4a-diazas-indacene (g-BODIPY) and its 5-styryl-derivative (r-BODIPY). Various spectroscopic properties of the r-BODIPY in different common solvents were determined. It was shown that g- and r-BODIPY in the ground state can form homo- as well as hetero dimers. We demonstrate that the ganglioside GM1 in lipid bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) exhibits a non-uniform lateral distribution, which is an argument in favour of self-aggregation of GM1 being an intrinsic property of the GM1. This was concluded from energy transfer/migration studies of BODIPY-labelled gangliosides. An algorithm is presented that quantitatively accounts for donor–donor energy migration (DDEM) among fluorophore-labelled proteins forming regular non-covalent polymers. The DDEM algorithm is based on Monte Carlo (MC) and Brownian dynamics (BD) simulations and applies to the calculation of fluorescence depolarisation data, such as the fluorescence anisotropy. Thereby local orientations, as well as reorienting motions of the fluorescent groups are considered in the absence and presence of DDEM among them. A new method, in which a genetic algorithm (GA) was combined with BD and MC simulations, was developed to analyse fluorescence depolarisation data collected by the time-correlated single photon counting technique. It was applied to study g-BODIPY-labelled filamentous actin (F-actin). The technique registered the local order and reorienting motions of the fluorophores, which were covalently coupled to cysteine 374 (C374) in actin and interacted by means of electronic energy migration within the polymer. Analyses of F-actin samples composed of different fractions of labelled actin molecules revealed the known helical organiszation of F-actin, and demonstrated the usefulness of this technique for structure determination of complex protein polymers. The distance from the filament axis to the fluorophore was found to be considerably less than expected from the proposed position of C374 at a high filament radius. In addition, polymerisation experiments with BODIPY-actin suggest a 25-fold more efficient signal for filament formation than pyrene-actin.

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