Na primeira parte deste trabalho foi estudada a interação da porfirina catiônica meso-tetrakis N-metil-4-piridil (TMPyP) e a porfirina aniônica meso-tetrakis 4-fenilsulfonato (TPPS4) nas formas de base livre com sistemas modelos de membrana biológica (micelas iônicas, micelas mistas e vesículas de fosfolipídios) em soluções aquosas, através das técnicas de absorção ótica, espalhamento de luz ressonante (RLS do inglês \"resonante light scattering), fluorescência e SAXS, do inglês \"Small Angle X-Ray Scattering\". As curvas de SAXS das micelas catiônicas de CTAC (cloreto de cetiltrimetilamônio) foram ajustadas como um elipsóide prolato na ausência e na presença de 2-10 mM de TPPS4. Os dados de SAXS mostraram que a presença da porfirina TPPS4 modifica o centro hidrofóbico micelar, levando a formação de micelas menores. Através das análises dos dados de SAXS das micelas de SDS (dodecilsulfato de sódio) observamos que a forma da micela na ausência e na presença de 2-10 mM TMPyP apresenta a forma de um elipsóide prolato sem mudanças. Entretanto, o coeficiente de ionização, diminuiu com o aumento da concentração de porfirina, sugerindo a \"blindagem\" da carga aniônica do SDS pela porfirina catiônica. A supressão de fluorescência da TPPS4 e TMPyP foi estudada na ausência e na presença de diferentes micelas de surfactantes, tais como as de SDS, CTAC, HPS (N-hexadecil-N,N,dimetil-3-amônio-1-propano sulfato) e TX-100 (t-octil-fenoxi-polietoxi-etanol). O iodeto de potássio (KI) foi utilizado como supressor. Os gráficos de Stern-Volmer dos dados de fluorescência no estado estacionário foram ajustados pela equação quadrática, incluindo a supressão dinâmica (KD) e estática (KS). Os valores de KS são muito menores do que os valores de KD. Os resultados da TMPyP são consistentes com as constantes de ligação reportadas na literatura: uma redução significativa de supressão acontece para a TMPyP na presença de SDS, e uma redução moderada é observada para o sistema TMPyP-HPS e quase nenhuma mudança é vista para a TMPyP na presença de TX-100. Para o sistema CTAC-TPPS4 um aumento na supressão foi observado quando comparada com a TPPS4 em tampão puro. Isto provavelmente é associado ao acúmulo de iodeto na interface da micela catiônica. A atração entre a cabeça polar do CTAC e I-, e a repulsão entre SDS e I-, aumenta e reduz a supressão de fluorescência, respectivamente, das porfirinas que se localizam na interface micelar. A pequena supressão da TPPS4 em TX-100 é coerente com a forte ligação entre a TPPS4-TX-100 reportada na literatura. A TPPS4 e a TMPyP na presença de concentrações baixas dos surfactantes CTAC e SDS, respectivamente, apresentaram formação de agregados pré-micelares. A adição de surfactante neutro, TX-100, reduziu o efeito de agregação, acompanhada pelas várias técnicas espectroscópicas utilizadas neste trabalho. Portanto, sob condições onde temos a máxima formação de agregados (porfirina-surfactante), a titulação da TPPS4 com micelas de 40%CTAC-60%TX-100 e a TMPyP com micelas de 80%SDS-20%TX-100 não foi suficiente para eliminar a agregação, apesar da diminuição significativa do efeito de supressão de fluorescência e da intensidade de luz espalhada. A interação da TMPyP com 1-Palmitoil-2-Oleoil-sn-Glicero-3-fosfocolina (POPC), 1-Palmitoil-2-Oleoil-sn-Glicero-3-[Fosfo-rac-(1-glicero)] (POPG) e a mistura POPC + POPG é predominantemente devido à contribuição de eletrostática. O aumento da carga negativa, devido à adição de POPG, favorece a interação das vesículas com a porfirina catiônica. Na segunda parte deste trabalho foram estudados os efeitos de três surfactantes na estrutura oligomérica da hemoglobina extracelular gigante de Glossoscolex paulistus (HbGp) na sua forma oxi. O estudo com o SDS, CTAC e HPS permitiu diferenciar os efeitos de cargas opostas da cabeça polar dos surfactantes na dissociação da estrutura oligomérica e na autoxidação da hemoglobina. A interação do HPS com HbGp foi claramente menos intensa que a interação desta hemoglobina com os surfactantes catiônico (CTAC) e aniônico (SDS). Provavelmente, esta menor interação da HbGp com HPS, quando comparada com o SDS e o CTAC, é devido a menor atração eletrostática entre o HPS e os sítios iônicos da proteina. Dados espectroscópicos foram discutidos e comparados com os da literatura, afim de compreender a interação hemoglobina-surfactante, e como o ponto isoelétrico ácido (pI) pode influenciar na relação da estrutura-atividade das hemoglobinas gigantes extracelulares. As amostras de HbGp foram estudadas por espalhamento de luz dinâmico (DLS do inglês \"Dynamic light scattering\"). Na faixa de pH 6.0 a 8.0, HbGp é bastante estável e a distribuição de tamanho das partículas é monodispersa com um diâmetro hidrodinâmico médio (Dh) de 27 nm. O aumento dos valores de pH (pH>9.0) induziu um processo de dissociação irreversível, resultando num valor do Dh menor (10 nm). A diminuição do Dh sugere uma dissociação completa da hemoglobina. Em pH>9,0 a cinética de dissociação é lenta, com um mínimo 24 h para ser completada. As constantes cinéticas de dissociação aumentam progressivamente, com o aumento do valor do pH. As curvas de melting point para HbGp apresentaram dissociação oligomérica e desnaturação da proteina em função do pH. Os processos de autoxidação e dissociação estão intimamente relacionados, de modo que a dissociação da proteina oligomérica promove um aumento na velocidade de autoxidação e vice-versa. / In the first part of this work interactions of the cationic meso tetrakis (4-N-methilpyridil) porphyrin (TMPyP) and meso-tetrakis (4-sulfonatophenyl) porphyrin (TPPS4) in the free base forms with membrane model systems (ionic micelles, mixed micelles and phospholipids vesicles) in aqueous solutions, have been investigated by optical absorption, resonance light scattering (RLS), fluorescence and SAXS (Small Angle X-Ray Scattering). The best-fit SAXS curves were obtained assuming for cetyltrimethylammonium chloride (CTAC) micelle a prolate ellipsoidal shape in the absence and upon incorporation of 2-10 mM TPPS4. SAXS results show that the presence of TPPS4 impacts on micellar hydrophobic core, leading to a micellar reassembling into smaller micelles. SAXS data analysis demonstrated a prolate ellipsoidal shape for sodium dodecyl sulfate (SDS) micelles; no significant changes in shape and size were observed for SDS-TMPyP co-micelles. Moreover, the ionization coefficient, α, decreases with the increase of the porphyrin concentration, suggesting the \"screening\" of the anionic charge of SDS by the cationic porphyrin. These results are consistent with optical absorption, fluorescence and RLS spectroscopies data, allowing to conclude that neutral surfactants present a smaller interaction with the cationic porphyrin as compared with ionic surfactants. Fluorescence quenching of TPPS4 and TMPyP is studied in aqueous solution and upon addition of micelles of SDS, CTAC, N-hexadecyl-N,N-dimethyl-3-ammonio-1- propanesulfonate (HPS) and t-octylphenoxypolyethoxyethanol (Triton X-100). Potassium iodide (KI) was used as quencher. Steady-state Stern-Volmer plots were best fitted by a quadratic equation, including dynamic (KD) and static (KS) quenching. KS was significantly smaller than KD. For TMPyP quenching results are consistent with reported binding constants: a significant reduction of quenching takes place for SDS, a moderate reduction is observed for HPS and almost no change is seen for Triton X-100. For CTAC-TPPS4 system an enhancement of quenching was observed as compared to pure buffer. This is probably associated to accumulation of iodide at the cationic micellar interface. The attraction between CTAC headgroups and I-, and repulsion between SDS and I-, enhances and reduces the fluorescence quenching, respectively, of porphyrins located at the micellar interface. The small quenching of TPPS4 in Triton X-100 is consistent with strong binding as reported in the literature. Anionic TPPS4 and cationic TMPyP in the presence of low concentrations of the surfactants CTAC and SDS, respectively, showed formation of aggregates, monitored by optical absorption, fluorescence and resonance light scattering intensity (RLS). The addition of nonionic surfactant, Triton X-100, reduced the effect of aggregation monitored by the various techniques used in the present work. Therefore, under conditions for the maximum of aggregate formation (porphyrin-surfactant), apparently, the CTAC: TX-100 ratio equal to 40:60 and SDS:TX-100 ratio equal to 80:20 are not sufficient to eliminate aggregation, despite the significant decrease of the quenching effect of fluorescence and of the light scattering intensity. The interaction of TMPyP with 1-Palmitoyl-2-Oleoyl-sn- Glycero-3-Phosphocholine (POPC), 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-rac-(1- glycerol)] (POPG) and the mixture POPC+POPG is predominantly due to the electrostatic contribution. The increase of the negative charge, due to addition of POPG, favors the interaction of vesicles with the cationic porphyrin. On the second part of this work the effects of three surfactants upon the oligomeric structure of the giant extracellular hemoglobin of Glossoscolex paulistus (HbGp) in the oxy - form was studied. The use of SDS, CTAC and HPS has allowed to differentiate the effects of opposite headgroup charges on the oligomeric structure dissociation and hemoglobin autoxidation. Furthermore, the interaction of HPS with HbGp was clearly less intense than the interaction of this hemoglobin with cationic (CTAC) and anionic (SDS) surfactants. Probably, this lower interaction with HPS is due to the lower electrostatic attraction between the HPS surfactant and the protein surface ionic sites when compared to the electrostatic interaction between HbGp and cationic and anionic surfactants. Spectroscopic data are discussed and compared with the literature in order to improve the understanding of hemoglobin-surfactant interaction as well as the acid isoelectric point (pI) influence of the giant extracellular hemoglobins on its structure-activity relationship. HbGp samples were studied by dynamic light scattering (DLS). In the pH from range 6.0 to 8.0, HbGp is stable and a monodisperse size distribution with a z-average hydrodynamic diameter (Dh) of 27±1 nm is observed. More alkaline pH (pH>9.0) induced an irreversible dissociation process, resulting in smaller Dh of 10±1 nm. Dh decrease suggests a complete hemoglobin dissociation. At pH 9.0 the dissociation kinetics is slow, taking a minimum of 24 h to be completed. Dissociation rate constants progressively increase at higher pH. Melting curves for HbGp showed oligomeric dissociation and protein denaturation as a function of pH. Autoxidation and dissociation processes are intimately related, so that oligomeric protein dissociation promotes the increase of autoxidation rate and vice-versa.

Orientador: Ricardo Aparicio / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-24T05:53:06Z (GMT). No. of bitstreams: 1 Reis_MarceloAugustodos_D.pdf: 42698206 bytes, checksum: fa5cd41ff5c44a71b42dd07db4a8fd79 (MD5) Previous issue date: 2013 / Resumo: Neste trabalho de tese, o problema da caracterização estrutural de proteínas foi abordado de maneira contextualizada e com um viés em modelagem computacional utilizando vínculos experimentais obtidos com a técnica de espalhamento de raios X a baixos ângulos (SAXS, Small-Angle X-ray Scattering). Parte das pesquisas foram concentradas na caracterização estrutural da proteína SurE de Xylella fastidiosa (XfSurE) por técnicas experimentais e computacionais. Estudos estruturais da XfSurE realizados com a técnica de SAXS apontaram para um arranjo tetramérico da enzima apo e, do nosso conhecimento, foi a primeira estrutura em solução descrita na literatura para esta família de proteínas. Quando associada às técnicas computacionais ¿ como, por exemplo, análise de modos normais de vibração¿a interpretação das análises por SAXS foi realçada. Neste caso, o vínculo experimental imposto pela curva I(q) possibilitou que uma estrutura em solução fosse modelada apenas com o uso de um único modo normal, cujo efeito estaria relacionado com as possíveis transições alostéricas de XfSurE. Em outra frente de trabalho, um novo programa denominado SAXSTER foi desenvolvido. SAXSTER tem a habilidade de gerar modelos estruturais mais prováveis para uma proteína-alvo a partir de alinhamentos ótimos obtidos por threading e de estruturas similares identificadas em um banco de dados, com o auxílio de SAXS. A partir dos dados de entrada, é realizada uma busca no Protein Data Bank para que a estrutura da proteína-alvo possa ser predita. O programa foi testado para 553 proteínas não redundantes. Foi demonstrado que SAXSTER pode melhorar consistentemente o resultado global da classificação dos alinhamentos, com p-valores que variam de 10 a 10. De acordo com TM-score médio, conclui-se que SAXSTER tende a melhorar o desempenho preditivo conforme a estrutura da proteína-alvo se afasta da forma globular / Abstract: In this work, the protein structure problem was approached from two different perspectives: from the computational modeling to the experimental data mainly collected by Small-Angle X-ray Scattering technique (SAXS) whose data were also used as constraint for modelling. Part of the research was focused on the structural characterization of the protein SurE of Xylella fastidiosa (XfSurE) by experimental and computational techniques. Structural studies of XfSurE performed by SAXS technique indicated a tetrameric arrangement of the apo enzyme and to our knowledge, this was the first solution structure of a SurE protein described in the literature. When combined with computational techniques ¿ for instance, normal mode analysis ¿ the interpretation of SAXS analysis was enhanced. In that case, the experimental constraints imposed by the I(q) curve allowed to reach a new structure model that fits the SAXS profile using only a single normal mode. This effect would be associated with the possible allosteric transitions of the XfSurE. It was also developed a new program called SAXSTER (SAXS-assisted multi-source ThreadER). SAXSTER has the ability to generate more likely structural models for the target protein from optimal alignments obtained by threading and similar structures identified in the Protein Data Bank aided by SAXS. The program was tested on 553 nonredundant proteins. It was shown that SAXSTER can consistently improve the overall classification of the alignments, with p-values ranging from 10 to 10. According to average TM-score, a more promising use of the SAXSTER algorithm would be to improve the template recognition results for protein whose structure is more rod-like than globular-like ones / Doutorado / Físico-Química / Doutor em Ciências

Les anticorps sont des molécules de reconnaissance du non-soi permettant de distinguer spécifiquement des marqueurs antigéniques appelés épitopes. Deux types d’anticorps ont été découverts jusqu’à présents : les anticorps « classiques » et les anticorps de camélidés, également appelés nanobody. Cette thèse porte sur des études structurales de fragments d’anticorps d’intérêt thérapeutique et biotechnologique. Au cours d’un premier volet, j’ai résolu la structure par cristallographie aux rayons X du fragment d’un anticorps d’intérêt thérapeutique, MIC12, à une résolution de 1,5 Å. Dans le but de résoudre la structure des complexes de MIC12 avec des protéines homologues du CMH de classe I, j’ai obtenu des cristaux diffractant à une résolution allant jusqu’à 7 Å. En parallèle, des analyses par diffusion de rayons X aux petits angles (SAXS) combinées à des prédictions d’interaction par docking ont été conduites afin d’obtenir une première description de la région globale d’interaction de MIC12 sur l’une de ses cibles. Concernant le second volet, 4 nanobody ont été obtenus contre la protéine périplasmique PorM (pPorM) du système de sécrétion de type 9 de Porphyromonas gingivalis. J’ai résolu la structure par cristallographie du nanobody nb02, à une résolution de 1,5 Å. Leur utilisation comme chaperonne de cristallisation m’a permis de résoudre la structure de la partie N-terminale de pPorM. J’ai également mené une étude par SAXS de la protéine pPorM entière. L’ensemble des résultats que j’ai obtenu par cristallographie et par SAXS, combinés aux résolutions des structures des autres domaines de pPorM, ont permis de proposer un modèle structural de la protéine pPorM entière. / Antibodies are non-self recognition molecules wich help to specifically distinguish antigenic markers called epitopes. Two types of antibody were discovered so far: “classic” antibodies and camelid antibodies, also called nanobodies. This PhD deals with structural studies of antibodies fragments of therapeutic and biotechnological interest. During the first part, I solved the structure of the therapeutic antibody targeting homologous proteins of the MHC class I, MIC12, using X-ray crystallography at a resolution of 1.5 Å. In order to solve the structure of the complexes of MIC12 with its MIC antigens, I obtained crystals of the complexes diffracting at a resolution of up to 7 Å. In parallel, analyses by Small Angles X-ray Scattering (SAXS) combined with in silico docking predictions were led to obtain a first description of the global binding region of MIC12 on one of its targets. Concerning the second part, 4 nanobodies were obtained against the periplasmic protein PorM (pPorM) of the secretion system type 9 from Porphyromonas gingivalis. I solve the structure of the nanobody nb02, at a resolution of 1.5 Å. Their use as chaperones of crystallization helped me to solve the structure of the N-terminal part of pPorM. I also conducted a study by SAXS of the whole pPorM protein. All these results, obtained by crystallography and SAXS studies, combined with the solving of the structures of the other domains of pPorM, made it possible to propose a structural model of the entire pPorM protein.

La maturation des ARNt en 5' est réalisée par RNase P. C'est un ribozyme chez les bactéries, les fungi et les nuclei des mammifères et un enzyme protéique dans les plantes ou des organelles des mammifères qui s’appelle PRORP. Il y a trois PRORP dans A. thaliana. PRORP contiennent deux domaines : un domaine PPR qui reconnaît spécifiquement des séquences d'ARN et un domaine nucléase qui assure la coupure endonucléolytique 5' des précurseurs d’ARNt. Pendant ma thèse j'ai pu montré par des méthodes biophysiques et structurales comme SRCD et SAXS que PRORP1 et 2 sont composées en majorité des hélices alpha Elles ont un rayon de giration de 33 Å et contiennent deux domaines distincts avec et une dimension maximale de 110 Å. Pour le complex entre un substrat d'ARNt et PRORP une constante de dissociation de 1 uM a pu être confirmé par la microcalorimétrie, la thermophorèse et l'ultracentrifugation analytique. Ces analyses nous ont permis de construire un modèle PRORP et un substrat d'ARNt. / RNase P cleaves 5’ leaders of precursor tRNAs. RNase P is a ribozyme in bacteria, fungi and animal nuclei and a protein in animal organelles, plants and many other organism. There are three PRORPs in A. thaliana. MALS, SRCD and SAXS provided first structural information: 1) PRORPs are monomers in solution. 2) PRORP 1-2 have a high alpha-helical content. 3) PRORPs are composed of two distinct domains with a radius of gyration of 33 A. These results together with homology modelling enabled us to build a first model of PRORPs in complex with tRNA. Using three different methods, isothermal titration calorimetry, microscale thermophoresis and analytical ultracentrifugation, a binding constant of about 1 µM could be determined for the system PRORP2mDD and L5T0 tRNA. This helped us conducting a SAXS experiment taking into account the low resolution affinity and designed to provide the direct structural data of a complex of proteinaceous RNase P with a substrate tRNA.

Le carbure de silicium (SiC) est un matériau léger possédant de nombreuses propriétés avantageuses : forte résistance mécanique, bonne conductivité et faible expansion thermiques, ainsi que chimiquement inerte sur une large gamme de températures. Ces caractéristiques font de lui un matériau de choix pour de nombreuses applications dans des conditions extrêmes, allant de la catalyse au gainage de combustible nucléaire de génération IV. Pour satisfaire aux spécificités de ces applications, le SiC se doit de posséder une surface spécifique élevée, et une porosité contrôlée.Nous avons étudié la faisabilité de la synthèse de SiC mésoporeux par une voie dite de « soft templating » utilisant des semifluoroalcanes (SFA) linéaires pour structurer un précurseur moléculaire du SiC, le 1,3,5-trisilacyclohexane (TSCH). En effet, la polymérisation du TSCH en polycarbosilane autour d’assemblages de SFA permet de structurer la matrice, puis de créer de la porosité lors du retrait du template. Le polycarbosilane est ensuite converti en SiC par un processus de calcination au cours duquel la porosité doit être conservée.Dans un premier temps, nous avons temps étudié les capacités d’auto assemblage des SFA dans le cyclohexane comme solvant modèle, puis dans le TSCH, par des techniques de diffusion des rayons X et des simulations des diagrammes de diffusion. Nous en avons appréhendé le comportement et déterminé les paramètres contrôlant la taille des objets. Nous avons ensuite réalisé la synthèse de SiC à partir du TSCH en présence de SFA.Les matériaux obtenus ne présentant pas les caractéristiques de surface spécifique et de porosité visées, nous avons élargi nos recherches à d’autres templates, dont un copolymère tribloc styrène-butadiène-styrène, qui a permis d’obtenir des SiC mésoporeux, amorphes ou cristallins, par une voie impliquant le greffage des précurseurs de SiC sur le copolymère. / Silicon carbide (SiC) is a light material with numerous interesting properties: strong mechanical resistance, weak thermal expansion, good heat conductivity and chemically inert on a large range of temperatures. These characteristics make SiC an appropriate material for various applications in extreme conditions, from catalyst to generation IV nuclear fuel cladding material. Nevertheless, to fulfill these application specificities, SiC has to show high specific surface area, and a controlled porosity.We have studied the possibility to synthetize mesoporous SiC by a soft templating approach using semifluorinated alkanes (SFA) to structure a SiC molecular precursor, the 1,3,5-trisilacyclohexane (TSCH). The TSCH polymerization into polycarbosilane around SFA aggregates can structure the matrix, that will create porosity after the template removal. Then polycarbosilane is converted into a SiC by a calcination process conserving the porosity.In a first time, we studied the self-aggregation capacities of SFA in cyclohexane as model solvent, and then in TSCH, by X-ray scattering techniques and simulations of scattering patterns. We discussed the behavior of SFA and determined the parameters controlling the size of the aggregates. Then, we proceeded to SiC synthesis from TSCH in presence of SFA.As resulting materials didn’t show the expected specific surface area and porosity characteristics, we enlarged our studies to other templates such as a triblock copolymer styrene-butadiene-styrene, which finally allowed us to obtain mesoporous SiC, amorphous or crystalline, by an approach involving the grafting of the SiC precursor onto the copolymer.

L’expression "Nanoparticules Janus" est utilisée pour se référer aux nanoparticules colloïdales faites de deux moitiés qui présent deux propriétés physiques et/ou chimiques différentes. Au cours des dernières années, plusieurs études théoriques ont été publiées sur les possibilités d’auto-assemblage offertes par ces particules (en particulier par Sciortino, F. et al.), mais peu de travail expérimental a été fait sur ce sujet. Les études théoriques suggèrent que beaucoup de comportements intéressants apparaissent quand la taille des particules s’approche de la portée d’interaction des forces en jeu (des dizaines de nanomètres dans le cas des forces de Van der Waals et des forces hydrophobes). Dans ce manuscrit, nous montrons la formation d’agrégats des hétérodimères de Au–SiO₂ d’une taille inférieure à 100nm. L’auto-assemblage a été déclenché par un échange du ligand hydrophile sur la surface de l’or par un ligand hydrophobe induisant une interaction attractive. L’assemblage a été suivi par spectroscopie d’absorption résolue dans le temps et diffusion des rayons X aux petits angles. Nous avons constaté que les thiols les plus courts ont une période d’induction plus longue et forcent les particules à se rapprocher davantage, comparé à des thiols avec des chaînes plus longues. Nous étudions également un second système : des nanoplaquettes de CdSe. Celles-ci sont des objets quasi-2D en matériau semiconducteur avec des propriétés optiques uniques. Ces propriétés résultant de leur taille réduite dans une dimension. Du fait de leur nouveauté et de leur particularité, leur nucléation et le remarquable mécanisme de croissance de ces particules sont toujours étudiés. Ainsi nous avons suivi leur synthèse par SAXS et WAXS in situ, afin d’obtenir des informations en ce qui concerne ces deux étapes, et notamment d’étudier la déformation de certains de ces systèmes sous forme de feuillets enroulés de CdSe. Les nanoplaquettes de CdSe ont été aussi utilisés pour créer des structures hybrides CdSe–Au. La combinaison de ces deux matériaux a déjà montré des effets uniques, comme une meilleure efficacité catalytique et, combiné avec la dimension réduite et le contrôle des plaquettes, pourrait aboutir à des caractéristiques encore plus intéressantes. Nous proposons une méthode de synthèse qui aboutit à la formation de petites sphères d’or sur les coins des plaquettes. Nous montrons que la taille des sphères dépend de la quantité de précurseur utilisée, et des images de microscopie électronique à haute résolution mettent en évidence la structure cristalline des deux matériaux. / "Janus nanoparticles" is the term used to refer to colloidal nanoparticles made of two halves with different physical and chemical properties. Over the last years, several theoretical studies have been published on the self-assembly possibilities offered by these particles (in particular by Sciortino, F. et al.), but little experimental work has been done on them. The theoretical studies suggest that many interesting behaviors appear when the size of the particles approaches the interaction range of the forces at play (tens of nanometers in the case of van der Waals and hydrophobic forces). In this manuscript, we show the formation of clusters of Au–SiO₂ heterodimers with sizes of less than 100nm. The self-assembly was induced by exchanging the hydrophilic ligand on the Au surface with a hydrophobic one, which provided the attractive interaction. The assembly was followed by time-resolved absorption spectroscopy and small-angle X-ray scattering. We found that shorter thiols have a longer induction period, and cause the particles to come closer together, compared to thiols with longer tails. We also study a second system: CdSe nanoplatelets. These are semiconducting quasi-2D structures with unique optical properties. These properties result from their reduced size in one of the dimensions. Because of their novelty and particularity, the nucleation and growth mechanism of these particles is still being studied. We followed the synthesis using in-situ SAXS and WAXS, to obtain information with regards to this mechanism and to study the deformation which occurs in some of these systems which leads to rolled up sheets of CdSe. The CdSe nanoplatelets were also used to create hybrid CdSe–Au structures. The combination of these two materials has already proven to produce unique effects such as enhanced catalysis and, combined with the reduced dimensionality and control of the platelets, could result in even more interesting characteristics. We propose a synthesis method which results in the formation of small gold spheres on the corners of the platelets. We show that the size of the spheres depends on the amount of precursor used, and show high resolution electron microscopy images which highlight the crystalline structure of both materials.

Les bactériophages neutralisent les systèmes de défense et détournent les fonctions vitales de leur hôte pour favoriser leur multiplication. Les gènes de phages qui gouvernent cette prise de contrôle de l’hôte restent mal connus, pourtant leur caractérisation présente un intérêt majeur pour mettre à jour des fonctions bactériennes spécifiquement ciblées par les phages et pour concevoir de nouveaux agents antibactériens.Le phage T5 injecte son ADN dans la bactérie Escherichia coli en deux étapes. Seuls les gènes précoces codés par 8% du génome entrent dans la cellule et le transfert s’arrête. Leur expression induit la dégradation du chromosome de l’hôte et l’inactivation de ses systèmes de restriction et de réparation de l’ADN. Après quelques minutes, le reste de la molécule d’ADN est injecté, ce qui permet la production de nouveaux phages. Deux gènes précoces A1 et A2 ont été identifiés comme essentiels pour la reprise du transfert de l’ADN et A1 est également nécessaire pour induire la dégradation de l’ADN de l’hôte. A1 et A2 sont les deux seuls gènes connus pour être impliqués dans la régulation de ce système original d’infection, mais leur fonction n’a jamais été identifiée.Ma thèse porte sur la caractérisation fonctionnelle et structurale des protéines A1 et A2. J’ai purifié A1 et démontré in vitro qu’elle avait une activité DNase dépendante du manganèse. Sa structure atomique a été résolue par cryomicroscopie électronique à 3.01 Å de résolution, montrant une organisation octamérique de symétrie D4 inédite pour une DNase. Chaque monomère (61kDa) contient un domaine exonuclease dont le site actif lie deux ions Mn2+ et qui s’apparente au site catalytique des domaines exonucléases de la DNA polymerase II et des DNAses associées aux systèmes de recombinaison homologue et de réparation de l’ADN comme Mre11. En construisant différents mutants de A1, j’ai identifié certains acides aminés essentiels pour l’activité catalytique et, par des expériences de complémentation fonctionnelle, j’ai montré que cette activité était indispensable pour l’infection. L’ensemble de ces résultats suggèrent que A1 est la DNase, jusqu’ici inconnue, responsable de la dégradation massive du génome de l’hôte au tout début de l’infection. Enfin, j’ai observé que la production de A1 pendant l’infection induit une forte activité recombinase. De nombreux autres bactériophages qui n’appartiennent pas à la famille des T5virus produisent également une protéine similaire à A1 dont la fonction n’a jamais été identifiée. Ce travail est un premier pas vers la compréhension de son rôle dans le mécanisme général d‘infection par les phages. Une deuxième partie de cette thèse porte sur la caractérisation structurale de A2. Des recherches de similarité indiquent la présence d’un domaine Helix-Turn-Helix typique des régulateurs transcriptionnels. J’ai purifié A2 et montré que cette protéine de 14 kDa est un dimère en solution. La caractérisation des propriétés biochimiques de A2 a permis de débuter l’étude de sa structure par RMN.Les résultats de ma thèse ont révélé la structure originale d’une DNase de bactériophage qui contrôle la dégradation du génome bactérien et la régulation du transport de l’ADN viral au début du cycle infectieux. Ces résultats soulèvent des questions intrigantes : comment l’ADN de T5 est-il protégé de l’activité DNase de A1 ? Comment A1 et A2 interagissent-elles lors des étapes de prise de contrôle de l’hôte ? / Bacteriophages defeat bacterial defences and hijack host cell machineries to establish a favourable environment for their multiplication. Early-expressed viral genes that govern host takeover are highly diverse from one phage to another and most of them have no assigned function. They thus represent a pool of novel genes whose products potentially subvert bacterial cell vital functions and could help in designing new antibacterial strategies.T5 phage uses a unique 2-step mechanism to deliver its DNA into its host Escherichia coli. At the onset of the infection, only 8 % of the genome enter the cell before the transfer temporarily stops. Expression of the genes encoded by this DNA portion leads to host chromosome degradation and inactivation of host restriction and DNA mending systems. After a few minutes, T5 DNA transfer resumes, allowing further phage multiplication. A1 and A2 are early genes required for DNA transfer completion and A1 is also necessary to trigger host DNA degradation. A1 and A2 are the only two genes known to be involved in the regulation of this original infection system, but their function yet remains to be characterized.The objectives of this work were to characterize the function and structure of A1 and A2 proteins. I have purified the A1 protein and shown that it has a manganese-dependent DNase activity in vitro. Cryo Electron Microscopy at 3.01 Å resolution unravelled its structure, showing an octameric organization with a D4 symmetry, which is unprecedented for a DNase. Each monomer (61 kDa) carries an exonuclease domain harbouring an active site with two Mn2+ ions. This site is similar to those from the exonuclease domain of the DNA polymerase II and from DNases involved in DNA mending and recombination events like Mre11. I identified essential catalytic residues for the DNase activity and demonstrated that this activity is crucial for infection by engineering A1 mutant proteins and by doing functional complementation assays. Taken together, my results suggest that A1 could then be the elusive DNase responsible for the massive host genome degradation observed during T5 phage infection. Eventually, I uncovered a recombinase activity associated to A1 production during infection. Similar proteins to A1 with unknown functions are produced in several other bacteriophages outside of the T5virus family. This work is a first step towards understanding the role of this protein in the general mechanism of infection by bacteriophages. In a second part, I worked on the structural characterisation of A2 protein. Similarity searches revealed a helix-turn-helix domain typically found in transcriptional regulators. I purified and demonstrated the dimeric organisation of this 14-kDa protein in solution. This initial characterization of A2 has opened avenues for further NMR studies.During my Ph.D., I uncovered the structure of an original bacteriophage DNase that controls bacterial genome degradation and that regulates viral DNA transport at the beginning of the infectious cycle. These results open the intriguing question about the mechanism for T5 DNA protection from A1 DNase activity as well as about the interplay between A1 and A2 during the host takeover.

La chimie douce est attrayante par sa simplicité de mise en œuvre. Cet attrait s’accompagne d’une mauvaise connaissance des phénomènes mis en jeu. Traditionnellement, les théories classiques de nucléation sont invoquées pour décrire la taille des cristaux et leur vitesse d’apparition à partir des ions en solution. Elles négligent cependant par construction (i) tout état réactionnel intermédiaire (ii) toute considération de microstructure. Les vitesses mesurées ont au moins 1010 d’écart avec les prédictions actuelles. Prendre en compte les états intermédiaires et étudier l’impact de ceux-ci sur la structure (pas seulement la taille) devrait permettre de faire progresser la connaissance des phénomènes de cristallisation.Caractériser ces intermédiaires réactionnels reste un défi : ils sont labiles, de taille nanométrique, et se forment en moins d’une seconde. Pour aborder cette problématique, le vanadate d’yttrium dopé europium (YVO4:Eu) est un excellent candidat : il est microstructuré, et sa cristallisation - polycristalline ou monocristalline selon le pH – passe par un état intermédiaire amorphe.Nos travaux précisent les différentes microstructures observées. Ensuite, nous mesurons trois vitesses de germination par diffusion X in situ, avec différents degrés de polycristallinité associés. Nous proposons un modèle simple permettant de prédire la poly/monocristallinité à partir des compétitions germination/croissance cristalline et de l’idée, nouvelle, suivante : le précipité amorphe confine la réaction. En plus de ce rôle, il sert à la fois de réacteur (contient 80% des réactifs) et de moule (fixe la taille finale des particules). Tous les amorphes sont similaires, sa présence seule n’explique donc pas les différences de cinétiques structurales observées. Nous étudions donc ensuite les cinétiques chimiques mises en jeu. Nos mesures montrent que la cinétique de réaction chimique dépend principalement de la quantité d’ions hydroxyles engagés dans l’amorphe.Les méthodes et concepts que nous avons développés sont indépendants du système d’étude, et il est fortement probable que ceux-ci seront valides pour d’autres systèmes : nanoparticules d’oxydes ou cristaux en général. / Soft chemistry is attractive thanks to its easy implementation. However, the related phenomena are poorly understood to this day. Usually, crystal size and their nucleation rate are described using classical nucleation theories. By construction, they neglect (i) any potential intermediate state (ii) any consideration of microstructure. In addition, the nucleation rates measured are in disagreement with the prediction, by a factor of at least 1010. Taking into account the intermediate states and investigate their impact on the structure (not only the size) should be a good way to improve crystallisation theories.The characterisation of those intermediate states remains challenging : they are labile, nanometer-sized, and are formed in less than a second. To address our problem, europium-doped yttrium vanadate (YVO4:Eu) is an excellent candidate : it is microstructured and its crystallisation - polycrystalline or monocrystalline depending on the pH – occurs via an amorphous intermediate state.Our work precises the different microstructures observed. We then measure three different nucleation rates in situ X-ray scattering, with different degrees of polycristallinity associated. We propose a simple model predicting the poly/monocrystallinity from the competition between nucleation and crystal growth and the following new idea : the amorphous precipitate confines the reaction. In addition to this role, it also serves as reactor (contains 80% of the reactants) and as template (as it sets the particles’ final size). All three amorphous are structurally similar, its structure alone cannot explain the differences in structural kinetics we observe. We thus focus on chemical processes in play. In particular, we demonstrate that the reaction kinetics depends mainly on the number of hydroxyl ions engaged in the amorphous network.The methods and concepts developed here are independant on the chemical system used, and it is highly probable that they will prove valid for other compounds : other oxide nanoparticles, or crystals in general.

[pt] A interação entre polímeros e surfactantes de cargas opostas frequentemente resulta na formação de coacervados e pode ser utilizada para promover a deposição de produtos capilares. A compreensão dos efeitos da estrutura molecular, concentração de surfactantes e polímeros, e força iônica é essencial para controlar esse fenômeno. Este estudo utilizou polímeros e surfactantes de cargas opostas que já são aplicados na indústria cosmética: Lauril Éter Sulfato de Sódio (SLES), Lauril Éter Sulfosuccinato Dissódico (SS), Lauroil Sarcosinato de Sódio (LS), Poli(dialildimetilamônio) (PDADMAC) e Hidroxietilcelulose Cationizada (cat-HEC). Para compreender como a estrutura molecular afeta a coloidal na coacervação induzida por diluição, foi usada uma faixa de concentração típica de produtos, o que é raro de se encontrar na literatura. Caracterizamos as amostras pelas técnicas de potencial zeta, espalhamento de raios X a baixos ângulos e microscopia óptica. A deposição sobre fios de cabelo foi avaliada por microscopia óptica e de força atômica. Os sistemas concentrados de SS e LS+PDADMAC foram uma solução micelar que, quando diluídos, se separaram em uma mesofase cúbica Pm3n. O sistema SLES+PDADMAC demonstrou separação de fases mesmo em concentrações elevadas e o planejamento de misturas revelou que pequenas variações na quantidade de PDADMAC têm impacto significativo. O estudo com cat-HEC mostrou que o recobrimento do fio de cabelo pode ocorrer mesmo sem a coacervação, sendo mais dependente da natureza do polímero. Assim, o trabalho correlacionou estruturas coloidais de diferentes sistemas com propriedades macroscópicas possibilitando um controle estratégico de formulações capilares. / [en] The interaction between oppositely charged polymers and surfactants often leads to the formation of coacervates and can be employed to facilitate the deposition of hair care products. Understanding the e ffects of molecular structure, surfactant and polymer concentrations, and ionic strength is essential for controlling this phenomenon. This study utilized polymers and surfactants with opposing charges that are already employed in the cosmetic industry: So dium Laureth Sulfate (SLES), Disodium Laureth Sulfosuccinate (SS), Sodium Lauroyl Sarcosinate (LS), Poly(diallyldimethylammonium chloride) (PDADMAC), and Cationized Hydroxyethylcellulose (cat HEC). To understand how molecular structure affects colloidal st ructure in dilution induced coacervation, a typical concentration range of products was used, which is rare to find in the literature. We employed zeta potential analysis, low angle X ray scattering, and optical microscopy to characterize the materials. De position on hair strands was assessed through optical and atomic force microscopy . The concentrated SS and LS+PDADMAC systems formed micellar solutions that phase separated into a Pm3n cubic mesophase upon dilution. The SLES+PDADMAC system exhibited phase separation even at high concentrations, with mixture design revealing that small variations in the PDADMAC amount had a significant impact. The study with cat HEC demonstrated that hair strand coating could occur even without coacervation, being more depen dent on the nature of the polymer . As a result, this work established a correlation between colloidal structures in different systems and macroscopic properties, enabling strategic control of hair care formulations.

Les métallacarboranes sont des clusters anioniques constitués d'atomes de bore, de carbone et d'hydrogène avec un cation métallique pris en « sandwich » au cœur de ce cluster (Co3+ en général) et hautement stable thermiquement que chimiquement. Ces entités sont représentées trivialement par la lettre grecque « thêta » où leurs pôles sont considérés comme hydrophobes et possèdent une charge négative délocalisée qui peut être contre balancée par un proton acide. Cette forte stabilité ainsi que ces diverses propriétés leur procurent un intérêt particulier dans des applications telles que la co-extraction du Cs et Sr dans les effluents nucléaires ou bien en médecine pour leur aptitude à inhiber la protéase du VIH de par ses liaisons hydrogènes. La chimie du bore étant relativement riche, une synthèse de quelques dérivés a été réalisée en laboratoire. Il est ainsi possible de substituer spécifiquement des atomes d'hydrogène par des atomes d'iode ou de chlore ou bien de changer le métal central par un cation Fe3+ formant respectivement les anions diiodo-COSAN (I2COSAN), dichloro-COSAN (Cl2COSAN) et ferrabisdicarbollide (FESAN). Ces métallacarboranes sont aussi considérés comme une nouvelle classe de tensioactif pour lesquels une première étude de leur auto-assemblage a été réalisée. Les résultats obtenus sur l'un d'entre eux, le cobaltabisdicarbollide ou COSAN, ont montré un effet sur la tension de surface ainsi qu'une structuration spontanée de ces clusters en forme de vésicule (à partir de 0,5 mmol/L) et par interaction Coulombienne, tendent à former des micelles à plus forte concentration (après 15 mmolL). Mais ces derniers offrent davantage de surprise de par la formation de phases lyotropes en solution aqueuse. En effet, ces phases, clairement identifiées par des techniques de diffusion au rayon-X et microscopie, montrent une dépendance en température mais aussi en concentration dont un diagramme de phase a pu être établi pour le I2COSAN en particulier. Cette thèse fait ainsi l'objet de la compréhension des phénomènes contrôlant cette agrégation de ces curieux composés. / Metallacarboranes are anionic clusters composed of boron, carbon and hydrogen with a metallic cation sandwiched at the heart of this cluster (Co3+ in general) and highly stable in thermic and chemical point of view. These entities are trivially represented by the Greek letter "theta" where the poles are considered hydrophobic and have a negative charge delocalized and counter-balanced by an acidic proton. This high stability as well as the various properties gives a particular interest in applications such as the co-extraction of Cs and Sr in nuclear waste or in medicine for their ability to inhibit HIV protease by its hydrogen bonds. The chemistry of boron is relatively rich; a synthesis of some derivatives was performed in laboratory. It is possible to substitute specifically hydrogen by iodine or chlorine atoms or change the metallic heart by other atom as Fe3+, respectively forming diiodo- COSAN (I2COSAN), dichloro-COSAN (Cl2COSAN) and ferrabisdicarbollide (FESAN) anions. Metallacarboranes are also considered as a new class of surfactant where a first study of their self-assembly has been performed. The results of one of them, cobaltabisdicarbollide or COSAN, have shown an effect at the surface tension and theses clusters formed spontaneously vesicles in dilute regime (from 0.5 mmol/L) and by Coulomb interactions, they form micelles at higher concentration (after 15 mmol/L). But they offer more surprise by the formation of lyotropic phases in aqueous solution. Indeed, these phases, clearly identified by X-ray scattering techniques and microscopy, showed temperature and concentration dependence where a phase diagram was established for the I2COSAN in particular. Therefore, the thesis is focused on the understanding of the phenomena controlling the aggregation of these curious compounds.