Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-07-13T14:09:49Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Zenaide S Monte - Tese Doutorado - Defesa 15-jul-2016.pdf: 10509605 bytes, checksum: 9a625f96607c0ccae6d58b896ba38772 (MD5) / Made available in DSpace on 2017-07-13T14:09:49Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Zenaide S Monte - Tese Doutorado - Defesa 15-jul-2016.pdf: 10509605 bytes, checksum: 9a625f96607c0ccae6d58b896ba38772 (MD5) Previous issue date: 2016-07-15 / CAPES / Compostos heterocíclicos do tipo pirimidina são conhecidos pela enorme riqueza de seus potenciais biológicos e farmacológicos. Numerosas reações de heterociclização que permitem a obtenção dessa classe de compostos são igualmente reconhecidas, devido à diversidade de atividades e do conhecimento prévio de inúmeras viabilidades sintéticas. As modificações estruturais obtidas na busca da otimização das rotas sintéticas conferem às novas moléculas diferentes propriedades físicas e alteram a reatividade das moléculas, acarretando em mudanças na distribuição nas células e nos tecidos. Essas discretas modificações estruturais podem revelar efeitos biológicos que haviam estado latentes ou eclipsados pelos efeitos colaterais do composto protótipo. Sendo assim, o presente trabalho apresenta a síntese por método convencional dos derivados da pirimidina 3a-q e 5o-q. Estes compostos foram avaliados quanto às propriedades duais: Antimicrobiana e Fotoluminescência, estas apresentaram resultados promissores, podem atuar como boas sondas fluorescentes. Foram realizados também estudos Espectrofotométricos em diferentes solventes além de determinarmos o Cálculo do Orbital Molecular de Fronteira nesta série. Realizou-se também a nanoencapsulação em lipossomas para o composto 3o. Obtivemos também p-arilamidinas 3a-j por método convencional e avaliamos as propriedades Antimicrobiana e Citotóxica, as quais apresentaram resultados significativos. Realizamos a síntese dos derivados pirimidínicos 3a-f e 6a-f pelo método em Irradiação em micro-ondas, em fase sólida e em solução, respectivamente. Estudamos também para estes as propriedades Antimicrobiana e Antioxidante, cujos os resultados foram satisfatórios. Foram obtidos bons rendimentos para todos os compostos obtidos. Um estudo inédito de RMN bidimensional, COSY, HSQC e HMBC foram aplicados às pirimidinas foi realizado, proporcionando a caracterização estrutural destes compostos. Os resultados obtidos apresentaram significativa potencialidades biológicas, farmacológicas e fotofísicas. / Heterocyclic compounds of pyrimidine are known for rich biological and pharmacological potential. A number of heterociclic reactions that enable the obtention of this class of compounds are also recognized, due to the diversity of activities and prior knowledge of their various synthetic viabilities. The structural modifications obtained in search for the best synthetic routes confered different physical properties on the new molecules and altered the reactivity of the molecules, resulting in changes in the distribution in cells and tissues. These discrete structural changes may reveal biological effects that may have been latent or eclipsed by the side effects of the compound prototype. This work presents the synthesis by conventional method of derivatives from pyrimidine 3a-q and 5o-q. These compounds were evaluated for dual properties: antimicrobial and photoluminescence. They showed promising results can act as fluorescent probes. Spectroscopic studies were carried out with different solvents and the Frontier Molecular Orbital calculation for this series was determined. Nanoencapsulation of liposomes for the compound 3o was prepared. The conventional method was used to obtain 3a-j p-arilamidinas. Results were significant for the antimicrobial and cytotoxic properties. Finally, the synthesis of pyrimidines derivatives 3a-f and 6a-f by a new method, solid phase micro-wave and in solution, respectively was carried out. We have studied both the Antimicrobial and Antioxidant properties with satisfactory results. Good yields were obtained for all compounds obtained. New studies of two-dimensional NMR, COSY, HSQC and HMBC were performed besides the characterization of the compounds by standard methods. The results show that the compounds obtained have great biological, pharmacological potential and Photophysical.

Novas abordagens terapêuticas vêm sendo introduzidas para doenças musculares genéticas como distrofias musculares e miopatias congênitas, distúrbios que permanecem sem cura até o momento. Estes recentes avanços motivaram um interesse renovado e crescente por métodos não invasivos para a caracterização e monitoramento do músculo afetado, particularmente durante e após intervenções terapêuticas. Neste contexto, modelos animais são essenciais para uma melhor compreensão dos mecanismos das doenças e para testar novas terapias. Recentemente, avanços significativos na avaliação não invasiva de modelos murinos para doenças musculares genéticas foram alcançados. Entretanto, diversas linhagens de camundongos ainda não foram caracterizadas de maneira não invasiva, e ainda é necessário o desenvolvimento de métodos sensíveis para a identificação precoce de alterações sutis no músculo de camundongos afetados. A proposta desta tese é aplicar técnicas não invasivas inovadoras no estudo do músculo de modelos murinos para doenças musculares genéticas com fenótipos variados. Três modelos murinos para distrofias musculares (mdx, Largemyd, mdx/ Largemyd) e um modelo murino para miopatia congênita (KI-Dnm2R465W) foram estudados com métodos de Ressonância Magnética Nuclear (RMN). Duas linhagens distróficas (Largemyd, mdx/ Largemyd) e camundongos normais após injúria foram estudados através de micro-Tomografia Computadorizada (micro-CT). Em RMN, todas as linhagens de camundongos afetados apresentaram aumento de T2 muscular, o que foi relacionado a diversas anomalias na análise histológica, como necrose e inflamação, mas também a conjuntos de fibras em regeneração ou a fibras com citoarquitetura alterada. A combinação de RMN com análise de textura permitiu a identificação não ambígua de todas as linhagens distróficas, sendo que apenas a comparação dos valores de T2 muscular não permitiu esta diferenciação. Camundongos mdx mostraram alterações funcionais e morfológicas na rede vascular do músculo. Estudo piloto em camundongos KI-Dnm2R465W revelou tendências de comprometimento da função muscular. Por fim, imagens de micro-CT não permitiram a detecção de diferenças na composição muscular em camundongos distróficos. Este conjunto de resultados não apenas enriquece o painel de modelos murinos para doenças musculares genéticas caracterizados de maneira não invasiva, mas também demonstra um certo grau de especificidade nas anomalias observadas nas imagens, como revelado pela análise de textura. Estes resultados também mostraram que métodos não invasivos de RMN podem ser suficientemente sensíveis para identificar alterações sutis no fenótipo muscular murino, mesmo em estágios precoces. Esta tese foi desenvolvida sob acordo de co-tutela internacional entre a França e o Brasil, e compreendeu uma importante transferência de conhecimento, com os primeiros estudos não invasivos de músculo murino realizados no Brasil. / Novel therapeutic approaches are being introduced for genetic muscle diseases such as muscle dystrophies and congenital myopathies, all of them having remained without cure so far. These recent developments have motivated a renewed and augmented interest in non-invasive methods for muscle characterization and monitoring, particularly during and after therapeutic intervention. In this context, animal models are essential to better understand the disease mechanisms and to test new therapies. Recently, significant advances in the non-invasive evaluation of mouse models for genetic muscle diseases have been achieved. Nevertheless, there were still several mouse strains not characterized non-invasively, and it was necessary to develop sensitive methods to identify subtle alterations in the murine affected muscle. The purpose of this thesis was to apply non-invasive techniques in the study of murine models for genetic muscle diseases with variable phenotypes. Three mouse models for muscle dystrophy (mdx, Largemyd, mdx/ Largemyd) and one mouse model for congenital myopathy (KI-Dnm2R465W) were studied with Nuclear Magnetic Resonance (NMR) methods. Two dystrophic strains (Largemyd, mdx/ Largemyd) and normal mice after injury were studied through micro-Computed Tomography (micro-CT). On NMR, all affected mouse strains presented increased muscle T2, which could be related to variable features in the histological evaluation, including necrosis and inflammation, but also to clusters of fibers under regeneration or with altered cytoarchitecture. The combination of NMR and texture analyses allowed the unambiguous differential identification of all the dystrophic strains, although it was not feasible when comparing the muscle T2 measurements only. Mdx mice showed functional and morphological alterations of vascular network. In the KI-Dnm2R465W mice, a pilot study revealed tendencies of functional impairment. Finally, micro-CT images were unable to detect differences in muscle´s content in dystrophic mice. Altogether, these results not only increased the number of murine models for genetic muscle diseases non-invasively characterized, it also demonstrated some degree of specificity of the imaging anomalies, as revealed by texture analysis. It also showed that non-invasive NMR methods can be sensitive enough to identify subtle alterations in murine muscle phenotype, even in early stages. This thesis was developed under an international joint supervision between France and Brazil, and comprised an important transfer of technology, with the first non-invasive studies of murine muscles performed in Brazil.

A Ressonância Magnética Nuclear (RMN) é uma das técnicas mais versáteis de investigação científica experimental, com destaque para o estudo da dinâmica, estrutura e conformação de materiais. Em particular, sua utilização na ciência do petróleo é uma de suas primeiras aplicações rotineiras. Metodologias desenvolvidas especificamente para atender esta comunidade científica mostraram-se desde cedo muito úteis, sendo o estudo da interação rocha/fluido uma de suas vertentes mais bem sucedidas. Desde então, importantes propriedades petrofísicas de reservatórios de óleo e gás têm sido determinadas e entendidas, tanto em laboratório quanto in-situ, nas próprias formações geológicas que armazenam esses fluidos. Entre estas propriedades, a permeabilidade, porosidade e molhabilidade de um reservatório figuram dentre as mais importantes informações estimadas. Com essa finalidade, a determinação e correlação dos possíveis efeitos que a interação rocha/fluido pode causar nos fenômenos de relaxação magnética e difusão molecular, tais como influência da susceptibilidade magnética e geometria do espaço poroso, foram estudados em onze rochas sedimentares retiradas de afloramentos, que possuem propriedades petrofísicas similares àquelas apresentadas por rochas reservatório de petróleo. Os resultados mostraram que os tipos de interação rocha/fluido, detectáveis pelos experimentos de RMN, são por sua vez influenciados pelas características geométricas e estruturais do meio poroso, sendo possível obter essas informações pelos resultados de RMN. Assim, este trabalho teve como objetivo principal estudar e estabelecer essas correlações, afim de se obter informações petrofísicas com maior acurácia e abrangência. Em particular, o estudo da razão T1/T2, que é a razão entre os tempos de relaxação longitudinal e transversal, típicos parâmetros envolvidos numa medida de RMN, mostrou ser um parâmetro útil no estabelecimento destas correlações. Ainda, diferentes metodologias para se medir estes e outros parâmetros de RMN foram estudadas e propostas, cuja interpretação conjunta mostrou ser fundamental para o entendimento dessas correlações. A permeabilidade das rochas, importante parâmetro que define as propriedades de transporte de fluidos dentro da matriz porosa, foi estimada aplicando-se essas metodologias propostas, mostrando excelentes resultados. Através do uso da técnica de RMN em estado-estacionário, esses resultados podem ser estendidos para a escala de well-logging, fato que aumenta consideravelmente a importância desses resultados. Uma vez consolidadas as medidas in-situ, as metodologias propostas deverão auxiliar a indústria de exploração e produção de petróleo a otimizar seus métodos e estratégias de produção, reduzindo seus custos e aumentando a vida útil de seus reservatórios. / The Nuclear Magnetic Resonance (NMR) technique is one of the most versatile techniques for scientific research, specially for the study of dynamics, structure and conformational of materials. In particular, its application in oil science is one of its first routine applications. Methodologies developed specifically to match this scientific community proved to be very useful, and the study of rock/fluid interactions is one of its most successful cases. Since then, important petrophysical properties of oil and gas reservoirs have been determined and understood both in the laboratory and inside the geological formations that store those fluids. Among these properties, the permeability, porosity and wettability of a reservoir formation are the most important information to be estimated. For this purpose, the determination and correlation of possible rock/fluid interaction effects that cause alterations on magnetic relaxation phenomena and molecular diffusion, such as the influence of the magnetic susceptibility and geometry of the porous space, were studied in eleven sedimentary rock cores taken from outcrops, since they have the same petrophysical properties presented by oil reservoir rocks. The results obtained confirmed that the types of rock/fluid interactions, detectable by the NMR experiments, are for instance influenced by the porous media geometry and structure, being possible so to obtain such information using those NMR results. Thus, the main goal of this work was the study and establishment of these correlations, in order to obtain petrophysical information with greater accuracy and comprehensiveness. In particular, the study of the T1/T2 ratio, which is the ratio of longitudinal and transverse relaxation times, common parameters strongly involved in a typical NMR measurement, was found to be useful in establishing those correlations. Moreover, different methodologies to measure this and other NMR parameters were studied and proposed, whose joint interpretation proved to be fundamental for the success of these correlations. The permeability of the rocks, an important parameter that controls the fluid transport properties inside the porous matrix, was estimated using the proposed methodologies, showing excellent results. Appling the steady-state NMR technique, those results could be extended to the well-logging scale, which could improve considerably the importance of that results. Once confirmed in measurements in-situ, the proposed methodologies will be able to help the production and exploration industry to optimize their production methods and strategies, thereby reducing production costs and increasing the reservoir lifetimes.

Cette thèse s’inscrit dans le cadre de la thématique du Laboratoire de Pharmacognosie de l’UFR Pharmacie, au sein de l’Université de Bourgogne. Elle vise essentiellement la recherche de molécules d’origine végétale issues de la biodiversité tropicale dont principalement des saponines. Ces composés suscitent un grand intérêt de par leur large éventail d’applications pharmacologiques. Dans ce contexte l’étude de trois espèces végétales appartenant à deux familles, à savoir Chlorophytum blepharophyllum Schweinf. ex Baker, Ornithogalum dubium Houtt (Asparagaceae) et Weigela × « kosteriana variegata » (Caprifoliaceae), a conduit à l’isolement de 16 glycosides naturels par les techniques chromatographiques (Chromatographie liquide sous vide, Chromatographie d’exclusion moléculaire, Chromatographie liquide moyenne pression). Les structures de ces derniers ont été élucidées principalement par les techniques spectroscopiques de RMN1D et -2D, et de spectrométrie de masse. Il s’agit de 4 glycosides phénoliques de structure connue, 8 saponines stéroïdiques parmi lesquelles 6 sont de structure nouvelle, ainsi que 4 saponines triterpéniques dont une nouvelle. 5 saponines stéroïdiques ont été testées en vue d’évaluer leur activité cytotoxique sur deux lignées cellulaires cancéreuses (A549 et HL 60). Les résultats ont montré une faible sensibilité de ces deux lignées cellulaires à ces saponines. Les effets toxiques et tératogènes des 3 saponines triterpéniques ont été également déterminés à l’aide d'un test in vivo de poisson-zèbre (zebrafish). Les résultats ont montré un effet létal à de faibles concentrations des 3 saponines. Des relations structure/activité ont été ainsi proposées. / This thesis was carried out in the Laboratory of Pharmacognosy, in health department of the University of Burgundy. The principal theme of this Laboratory is the research of natural compounds from tropical biodiversity, mainly saponins. These molecules are known for their various pharmacological activities. The study of 3 species belonging to 2 different families: Chlorophytum blepharophyllum Schweinf. ex Baker, Ornithogalum dubium Houtt (Asparagaceae) and Weigela × « kosteriana variegata » (Caprifoliaceae), led to the isolation and characterization of 16 natural glycosides by column chromatography, medium pressure liquid chromatography, and vacuum liquid chromatography. The spectral analysis was achieved using mainly 2D NMR and mass spectrometry. Among them, 4 were phenolic glucosides, 8 were steroidic saponins with 6 new structures and 4 were triterpenic saponins with one new structure. The cytotoxic activities of 5 isolated steroidic saponins were evaluated on 2 strains cancer cells (A549 and HL 60). The results showed a low sensitivity of these two cell lines to these saponins. The toxic and teratogenic effects of 3 triterpenic saponins were also determined in by using an in vivo zebrafish assay. The results showed a lethal effect at low concentrations of these 3 saponins. Structure / activity relationships have been proposed.

Les verres sont des matériaux utilisés dans de très nombreux domaines. Cependant leur structure reste à ce jour peu connue du fait de l’absence d’ordre à longue distance rendant difficile la résolution de la structure à l’échelle atomique. Il est admis que les verres sont constitué d’un enchainement désordonné d’unités élémentaires par exemple des triangles et tétraèdres de bore dans le cas des verres de borates. La résonance magnétique nucléaire (RMN) a démontré être une technique de choix pour l’étude des verres, permettant de mesurer la proportion de chaque unités. Toutefois, la résolution structurale du verre reste aujourd’hui un enjeu scientifique majeur afin de mieux comprendre les relations propriétés-composition. Cette thèse a pour objectif de développer des méthodes combinant des expériences de RMN 1D et 2D avec des calculs DFT de paramètres RMN effectués sur des modèles numériques afin de caractériser la signature spectrale de l’ordre à moyenne distance. Sur une première série de verres de borates de sodium, il a été mis en évidence que seul la dynamique moléculaire (DM) ab-initio permet de reproduire des unités superstructurale telle que des anneaux, qui ont pu être caractérisées expérimentalement notamment grâce à la prise en compte fine des effet de distributions des paramètres RMN. La deuxième série sont des verres d’aluminoborate de lanthane pour laquelle les simulations par DM ne permettent pas un accord satisfaisant avec l’expérience. De ce fait, nous avons exploré une méthode par Reverse Monte Carlo contraintes par les données expérimentales. Cette méthode permet d’améliorer significativement l’accord des modèles avec l’expérience et reste donc à poursuivre. / Glasses are materials used in many fields. However, their structures still not well known because of the lack of long range order, making it difficult to extract the structural information of these materials. It is accepted that the glassy network is made of many elementary unit chains, being boron triangles and tetrahedron in the case of borate glasses. Nuclear magnetic resonance (NMR) has proven to be a vital characterization technique for the glasses study. It allows the measurement of proportion of each unit. The determination of the structural resolution of glasses remains a major scientific challenge for understanding of the relationship between the glass properties and it elemental compositions. This thesis aims to develop new NMR approach combining 1D, 2D and oxygen-17 NMR with DFT-GIPAW calculations on numerical models in order to characterize the intermediate ranger order NMR fingerprint. The first study is on sodium borate glasses. It highlighted that only ab-initio molecular dynamics (MD) can reproduce the boron rings, which have been confirmed by the NMR data, taking into account of the fine NMR parameters distributions effects. The second study is on aluminoborate glasses. Unlike the previous, the computed MD structures are not in agreement with NMR data. Thereby, a diferente stuctural simulation is applied. Refined models have been determined by Reverse Monte Carlo by constraining few experimental NMR data. This method allows to significantly improve the agreement between sumulated models and the experiment.

La Spectroscopie par Résonance Magnétique Nucléaire (NMRS) est une technique largement connue pour l'analyse de molécules chimique et biologiques. Cependant, en raison de la faible intensité des signaux de RMN, il est très difficile de travailler sur des volumes inférieurs à un mm³. Cette limitation a conduit à la mise au point de capteurs miniaturisés tels que les microbobines, les centres NV et des magnétomètres atomiques. Au cours de cette thèse nous avons développé une approche basée sur l'utilisation de capteurs à MagnétoRésistance Géante (GMR), capteurs magnétiques à large de la bande, capable de détecter localement le signal RMN. Les capteurs GMR, sur différents substrats tels que le silicium, le verre et l’alumine, ainsi que la configuration du montage RMN ont été spécifiquement conçus pour avoir une détectivité dans la gamme de 20pt/sqrt(Hz) et capable de travailler avec un champ magnétique externe jusqu'à 1 Tesla. Nous allons d’abord présenter les résultats obtenus à 0.3T sur de l’eau, dans la configuration où la RMN locale est effectuée dans un grand volume, mettant en évidence le caractère fonctionnel du montage. Puis les résultats obtenus, également à 0.3T, de la spectroscopie RMN de liquides modèle comme l'éthanol où le volume sondé estimé est de l’ordre de 20x20x20μm³. Finalement un résultat à un champ magnétique plus élevé, 0.6T, a également été montré sur de l’eau. / Nuclear Magnetic Resonance Spectroscopy (NMRS) is a widely known technique for chemical and biological molecule analysis. However due to the weakness of the NMR signals, it is very difficult to work on volumes lower than a mm³. That limitation has led to the development of miniaturized sensors such as microcoils, NV centers and atomic magnetometers. We will present our approach based on the use of Giant Magnetoresistive sensors (GMR) as wide band magnetic sensors to detect locally the NMR signal. GMR sensors and NMR set up have been specifically designed to have a detectivity in the range of 20pt/sqrt(Hz) and able to work with external magnetic field up to 1T. We will first present the results obtained at 0.3T on water, in the configuration where the local NMR is done on a high volume, highlighting the functionality of the set-up. Then we will show the results obtained also at 0.3T, of NMR spectroscopy of model liquids like Ethanol on a volume of the order of 20x20x20μm³. Finally, a result at a higher magnetic field, 0.6T, has also been obtained on water.

Les récepteurs couplés aux protéines G (RCPGs), constituent la plus grande famille de protéines membranaires dans le génome humain. Les RCPGs sont des protéines de signalisation, qui exercent leur action à la surface des cellules, en réponse à une grande variété de stimuli extérieurs. Ils jouent un rôle primordial dans de nombreuses fonctions physiologiques et sont donc impliqués dans une multitude de pathologies comme les maladies cardiovasculaires, métaboliques, neurodégénératives, psychiatriques et oncologiques. L'attribution du prix Nobel de chimie 2012 aux professeurs Robert Lefkowitz et Brian Kobilka pour leurs travaux et avancées spectaculaires dans le champ de recherches des RCPGs, souligne encore leur importance. Les RCPGs constituent également la plus importante cible thérapeutique, avec 30% des médicaments actuellement disponibles sur le marché qui exercent leur action via un RCPG. Cependant, la découverte de nouveaux ligands reste un chalenge. Le but est de développer des approches basées sur la RMN à l’état liquide, qui auront un impact positif sur la recherche de ligand de RCPGs, grâce à l’étude et la caractérisation de récepteur pleine taille, solubilisés en micelles de détergents ou enchâssés en bicouches lipidiques natives / G protein-coupled receptors (GPCRs) are the largest class of membrane proteins in the human genome. GPCRs act as cell surface signalling proteins and respond to a variety of external signals. They play a pivotal role in many physiological functions and are therefore associated with a multitude of diseases, including cardiovascular, metabolic, neurodegenerative, psychiatric, and oncologic diseases. The 2012 noble Prize in Chemistry was awarded jointly to Robert J. Lefkowitz and Brian K. Kobilka for studies of GPCRs, highlighting the importance of this protein superfamily. GPCRs constitute also the most important family of drug targets in the human body, with 30% of current drugs acting on GPCRs. However, drug discovery targeting GPCRs remains difficult, owing to the restricted structural information on GPCRs related to the instability of these proteins when isolated from their cell membrane environments. There is also a lack of knowledge for the structural and functional consequences of the interactions of small-molecule compounds with GPCR. The aim is to develop methods to study and characterize a full GPCR solubilized in detergents or in native lipid bilayers, both in its free form and in small molecule bound forms, using liquid-state NMR experiments. The aim is to develop NMR-based approaches that will strongly impact the structure-based drug discovery process for the GPCR family

Le bactériophage T5, qui infecte la bactérie Escherichia coli, est constitué d’une capside icosaédrique renfermant un ADN double brin et d’une queue permettant le transfert de son ADN dans le cytoplasme de la cellule hôte. Au cours de la morphogénèse, la capside et la queue sont assemblées séparément puis connectées pour former les particules infectieuses. La capside de T5 est d'abord assemblée sous forme d'une procapside vide constituée de 775 copies d’une protéine unique qui s'organise en hexamères et pentamères pour former respectivement les faces et les sommets de l’icosaèdre. Un des sommets est occupé par la protéine portale qui constitue un pore d’entrée pour l’ADN. L’encapsidation du génome à travers le canal portal, assurée par un moteur moléculaire, provoque l’expansion de la procapside. La capside pleine d'ADN est ensuite décorée par la protéine pb10 qui se fixe sur sa surface externe, au centre des 120 hexamères, et elle est fermée par la protéine p144 qui constitue le point d'ancrage pour la queue.Les objectifs de ma thèse étaient de déterminer la structure, la fonction et le mécanisme de fixation à la capside des deux protéines pb10 et p144. J’ai produit et purifié la protéine de fermeture p144 dont la structure et les caractéristiques de fixation sur la capside seront prochainement étudiées. J’ai résolu la structure de la protéine de décoration pb10 en solution par résonance magnétique nucléaire (RMN), ce qui a révélé une protéine formée de deux domaines. Le domaine N-terminal structuré en hélices alpha se fixe à la capside, alors que le domaine C-terminal, de type immunoglobuline, est exposé au solvant. La détermination des constantes cinétiques d'association et de dissociation par résonance plasmonique de surface (SPR) a permis de montrer que pb10 se fixe sur la capside de T5 de manière quasi-irréversible, avec une affinité de l’ordre du picomolaire. Des expériences de mutagenèse dirigée sur le domaine de fixation de pb10 indiquent que cette forte affinité repose sur un réseau d’interactions électrostatiques et hydrophobes. J’ai démontré que pb10 participe à la stabilisation de la capside de T5 par des techniques de calorimétrie différentielle à balayage (DSC) et thermo-fluorescence (FTSA). Par ailleurs, j'ai démontré qu’il était possible de fusionner des protéines de grande taille au domaine C-terminal de pb10 sans affecter sa haute affinité pour la capside. J’ai ainsi pu fonctionnaliser des capsides avec une protéine d’intérêt fusionnée à pb10. Ces résultats ouvrent la voie vers diverses applications, dont la présentation d’antigènes en vue de créer de nouveaux vaccins. / Bacteriophage T5, a lytic phage which infects the bacterium Escherichia coli, is composed of an icosahedral capsid containing a double stranded DNA and a tail responsible for DNA transfer into the host cell cytoplasm. The capsid and the tail are assembled separately and then connected to form infectious viruses. The T5 capsid is first assembled as an empty procapsid composed of 775 copies of the major head protein organized in hexamers on the faces and pentamers on the vertices of the icosahedron. A single vertex is occupied by the portal protein which forms an entry channel for DNA. DNA is packaged through the portal channel by a molecular motor thus triggering procapsid expansion. The DNA-filled capsid is then decorated by the protein pb10 which binds on the outer surface in the center of each hexamer, and closed by the connector protein p144 needed for tail attachment.The goals of my PhD were to characterize the structure, function and mechanisms of capsid binding of both pb10 and p144 proteins. I have produced and purified the head completion protein p144 for future exploration of its structure and capsid binding properties. I have solved the solution structure of the decoration protein pb10 by nuclear magnetic resonance (NMR), thus unravelling that pb10 has two domains. The alpha-helical N-terminal domain binds to the capsid and the immunoglobulin-like C-terminal domain is exposed to the environment. Surface plasmon resonance (SPR) showed that that pb10 attachment to the T5 capsid is quasi-irreversible with a picomolar affinity. Site-directed mutagenesis of the binding domain of pb10 suggested that the decoration mechanism is driven by both hydrophobic and electrostatic interactions. Differential scanning calorimetry (DSC) and fluorescence thermal shift assays (FTSA) demonstrated the role of the decoration protein in capsid stabilization. I have also demonstrated that a large protein can be fused to the C-terminal end of pb10 without affecting its high affinity for the T5 capsid. Capsids can thus be functionalized with a protein of interest fused to pb10. Possible applications of this work include antigen presentation for new vaccines.

Les lamines sont le principal composant du nucléosquelette. Elles sont principalement localisées à l’enveloppe nucléaire, où elles interagissent avec la membrane nucléaire interne, les protéines associées à la chromatine ainsi qu’avec des modulateurs de la signalisation cellulaire. Le gène LMNA code pour la prélamine A et la lamine C. La région C-terminale de la prélamine A est prédite pour être désordonnée et est la cible de plusieurs événements de maturation. En effet, la protéine est farnésylée, coupée, carboxyméthylée, puis coupée à nouveau ; perdant finalement son groupement farnésyl. Un mutant de cette protéine, dont 50 acides aminés sont manquants, est responsable du syndrome d’Huchtinson-Gilford, appelé progéria (Eriksson et al., 2003). Chez ce mutant, appelé progérine, le site de coupure finale est absent et la protéine reste constitutivement farnésylée. La lamine A est connue pour interagir avec la protéine de la membrane nucléaire interne, l’émerine. L’absence d’émerine est responsable de la dystrophie musculaire d’Emery Dreifuss. L’émerine contient un LEM, suivi d’une région prédite comme désordonnée, essentielle pour l’auto-assemblage de l’émerine (Berk et al., 2014). L’oligomérisation de l’émerine régule ses interactions avec plusieurs partenaires à la membrane nucléaire interne et à la chromatine. Nous avions auparavant démontré que la région nucléoplasmique de l’émerine peut s’auto-associer pour former des filaments in vitro (Herrada et al., 2015) et nous avons récemment révélé que ces filaments sont capables d’interagir directement avec la queue de la lamine A (Samson et al., 2018). Ici, je me suis intéressé à l’analyse structurale des régions prédites comme désordonnées chez (1) l’émerine (2) la prélamine A. Dans le cas de l’émerine, j’ai analysé la conformation de la région nucléoplasmique d’émerine avant et après auto-assemblage, en travaillant avec l’émerine sauvage et plusieurs mutants entraînant des myopathies. J’ai montré que deux fragments de l’émerine 1-187 et 67-221 peuvent polymériser, tandis que leur région commune 67-187, reste toujours monomérique dans nos conditions (Samson et al., 2018). Nous avons aussi montré que le domaine LEM est au moins partiellement déplié au cours de l’assemblage de la région 1-187. J’ai également attribué les signaux RMN de la région désordonnée 67-170, dans le but d’étudier par la suite l’impact des phosphorylations de cette région sur la structure de l’émerine et sur ses propriétés d’auto-assemblage (Samson et al., 2016). Dans le cas de la lamine A, j’ai étudié la région C-terminale de la prélamine A, prédite comme dépliée et qui est le siège de nombreuses modifications post-traductionnelles. J’ai attribué les signaux RMN du peptide prélamine A ainsi que de son mutant progérine (Celli et al., 2018). J’ai montré que ces deux peptides sont en effet déplés et possèdent une hélice  transitoire très conservée. Je propose cette hélice comme site de liaison pour un partenaire encore non identifié. J’ai également démontré que le peptide prélamine A possède une tendance à s’auto-assembler. Cependant, la prélamine A et le peptide progérine sauvages et farnésylés, n’interagissent pas avec le domaine IgFold de la lamine A ni avec BAF, deux domaines associés avec la progéria. J’ai étudié par la suite les interactions de ces peptides avec deux autres partenaires associés à la progéria : la protéine de la membrane nucléaire interne SUN1 et la protéine associée à la chromatine RBBP4. SUN1 est également intrinsèquement désordonnée et très peu soluble dans nos conditions. Les résultats montrent que le peptide prélamine A ne lie pas RBBP4 mais pourrait avoir besoin de la partie C-terminale qui la précède. Cependant, RBBP4 lie directement le partenaire de la lamine BAF. Sur les bases de ces résultats, je propose une série d’expériences pour identifier les détails moléculaires des interactions entre la queue C-terminale de la lamine A, BAF et RBBP4. / Lamins are the main components of the nucleoskeleton. They are primarily located at the nuclear envelope, where they interact with inner nuclear membrane proteins, chromatin-associated proteins and cell signaling modulators. The LMNA gene codes for prelamin A and lamin C. The C-terminal region of prelamin A is predicted to be unfolded and is the target of several maturation events. Indeed, the protein is farnesylated, cleaved, carboxymethylated and cleaved again; losing eventually its farnesyl group. A mutant of this protein, lacking 50 amino acids, is responsible for the Hutchinson-Gilford Progeria Syndrome (Eriksson et al., Nature 2003). In this mutant, called progerin, the final cleavage site is absent and the protein stays constitutively farnesylated. Lamin A is reported to interact with the inner nuclear membrane protein emerin. Lack of emerin is responsible for Emery Dreifuss Muscular Dystrophy. Emerin contains a folded LEM domain, followed by a region that is predicted to be disordered and is essential for emerin self-assembly (Berk et al., 2014). Emerin oligomerization regulates its interaction with several partners at the inner nuclear membrane and at the chromatin. We previously showed that the nucleoplasmic region of emerin can self-assemble to form curvilinear filaments in vitro (Herrada et al., 2015) and we recently revealed that these filaments are able to directly bind to the lamin A tail (Samson et al., 2018).Here I focused on the structural analysis of regions that are predicted to be unfolded in (1) emerin, (2) prelamin A. In the case of emerin, I analysed the conformation of the nucleoplasmic region of emerin before and after self-assembly, working on wild-type emerin as well as several mutants causing myopathies. I showed that the two fragments of emerin 1-187 and 67-221 were able to self-assemble, whereas their common region, 67-187, is always a monomer in our conditions (Samson et al., 2018). I also revealed that the LEM domain is at least partially unfolded during self-assembly of region 1-187, as a mutant with a destabilized LEM domain self-assembles faster and a mutant with a LEM domain locked in its folded conformation cannot self-assemble (Samson et al., 2017). I also assigned all the NMR signals of the unfolded region 67-170, in order to further study by NMR the impact of phosphorylation of this region on emerin structure and self-assembly properties (Samson et al., 2016). In the case of lamin A, I studied the C-terminal region of prelamin A that is predicted as unfolded and is heavily post-translationally modified. I assigned the NMR signals of this prelamin A peptide as well as its mutant peptide corresponding to the progerin sequence (Celli et al., 2018). I showed that both peptides are indeed unstructured and exhibit a partially populated  helix that has a highly conserved sequence. I propose that this helix is a binding site for a yet unidentified partner. I also revealed that the prelamin A peptide has a tendency to self-assemble. However, the monomeric prelamin A and progerin peptides, wild-type as well as farnesylated, do not interact with the immunoglobulin-like domain of lamin A/C and with BAF, two domains associated with progeria. Then, I investigated the interactions mediated by these peptides and two other important partners associated to progeria: the inner nuclear membrane SUN1 and the chromatin-associated protein RBBP4. However, SUN1 is also intrinsically disordered and poorly soluble in our conditions. First results showed that the prelamin peptide does not bind to RBBP4 but might need the remaining part of the lamin A tail for this interaction. However, RBBP4 directly binds to the lamin partner BAF. Based on my results, I propose a set of experiments to identify the molecular details of the interactions between the lamin A tail, BAF and RBBP4.

Dans un marché globalisé où 40% du vin consommé est importé, le contrôle de la traçabilité est un enjeu majeur de la filière viti-vinicole. L'authentification du vin est le processus pouvant faire appel à différentes méthodes analytiques devant pouvoir contrôler trois paramètres fondamentaux : l’origine géographique, le cépage et le millésime. La spectroscopie RMN 1H quantitative (RMNq) est aujourd'hui considérée comme un outil très prometteur pour l'étude de l'authenticité des vins. Lors de cette thèse, une technique de dosage de 40 composés majoritaires des vins par RMN 1H a été développée. Elle permet l’acquisition d’une information riche et complexe en une seule analyse non-spécifique. La capacité de cette technique à authentifier un vin a été démontrée suite à une collaboration avec le Château Mouton-Rothschild, par comparaisons avec des analyses officielles réalisées par la DGDDI et DGCCRF de Pessac (SCL). La détermination d’un seuil de conformité a été établie en prenant en compte l’évolution naturelle des vins en bouteille. Une étude de caractérisation des vins rouges de Bordeaux a été menée. La singularité de ces vins a été observée par comparaison avec d’autres vins français, mettant en évidence des métabolites caractéristiques des vins de Bordeaux. Les résultats fournissent une description globale du potentiel de la RMN 1H pour l’authentification des vins. / In a globalized market where 40% of the wine consumed is imported, traceability control is a major challenge for the wine industry. Wine authentication is the process that can use different analytical methods able to control three fundamental parameters: geographical origin, grape variety and vintage. Quantitative 1H NMR spectroscopy (qNMR) is now considered as a very promising tool for studying wine authenticity. During this thesis, a technique was developed for the determination of 40 major wine compounds by 1H NMR. It allows the acquisition of rich and complex information in a single non-specific analysis. The ability of this technique to authenticate a wine has been demonstrated following a collaboration with Château Mouton-Rothschild, by comparison with official analyses carried out by the DGDDI and DGCCRF of Pessac (SCL).The determination of a compliance threshold has been established by taking into account the natural evolution of bottled wines. A characterization study of Bordeaux red wines was carried out. The singularity of these wines was observed in comparison with other French wines, highlighting the characteristic metabolites of Bordeaux wines. The results provide a global description of the potential of 1H NMR for wine authentication.