The size and conformational complexity of proteins and other large systems represent major challenges for today's methods of quantum chemistry.This thesis is centered around the development of new computational tools to gain molecular-level insight into electronic transitions in such systems. To meet this challenge, we focus on the polarizable embedding (PE) model, which takes advantage of the fact that many electronic transitions are localized to a smaller part of the entire system.This motivates a partitioning of the large system into two regions that are treated at different levels of theory:The smaller part directly involved in the electronic process is described using accurate quantum-chemical methods, while the effects of the rest of the system, the environment, are incorporated into the Hamiltonian of the quantum region in an effective manner. This thesis presents extensions of the PE model with theaim of expanding its range of applicability to describe electronic transitions in large molecular systemsin the optical and X-ray regions. The developments cover both improvements with regardto the quantum region as well as the embedding potential representing the environment.Regarding the former, a damped linear response formulation has been implemented to allow for calculations of absorption spectra of large molecular systems acrossthe entire frequency range. A special feature of this development is its abilityto address core excitations that are otherwise not easily accessible.Another important development presented in this thesis is the coupling of the PE model to a multi-configuration self-consistent-field description of the quantum region and its further combination with response theory. In essence, this extends the PE model to the study of electronic transitions in large systems that are prone to static correlation --- a situation that is frequently encountered in biological systems. In addition to the direct environmental effects on the electronic structure of the quantum region, another important component of the description of electronic transitions in large molecular systems is an accurate account of the indirect effects of the environment, i.e., the geometrical distortions in the quantum region imposed by the environment. In thisthesis we have taken the first step toward the inclusion of geometry distortions in the PE frameworkby formulating and implementing molecular gradients for the quantum region. To identify critical points related to the environment description, we perform a theoretical analysis of the PE model starting from a full quantum-mechanicaltreatment of a composite system. Based on this, we present strategies for an accurate yet efficient construction of the embedding potentialcovering both the calculation of ground state and transition properties. The accurate representation of the environment makes it possible to reduce the size of the quantum region without compromising the overall accuracy of the final results. This further enables use of highly accurate quantum-chemical methods despite their unfavorable scaling with the size of the system. Finally, some examples of applications will be presented to demonstrate how the PE model may be applied as a tool to gain insight into and rationalize the factors influencing electronic transitions in large molecular systems of increasing complexity. / <p>The dissertation was awarded the best PhD thesis prize 2016 by the Danish Academy of Natural Sciences.</p><p></p><p>QC 20170209</p>

Les peptides aldéhydes sont connus comme inhibiteurs de protéases et précurseurs de différentes classes de composés biologiquement actifs. Les méthodes pour leur synthèse impliquent classiquement la transformation d'un précurseur (amide de Weinreb, ester, alcool, acétal) en aldéhyde en étape finale pour éviter l'épimérisation du stéréocentre en position α de l'aldéhyde. En revanche, les β-peptides aldéhydes, plus stables à l’épimérisation, ont été relativement peu explorés. Ils sont généralement obtenus par homologation de l'acide aminé correspondant malgré les faibles rendements, les problèmes d’épimérisation et de nombreuses étapes. Par conséquent, un nouvel accès synthétique aux β-peptides aldéhydes reste toujours un challenge difficile. Sur la base des travaux antérieurs dans notre équipe en hétérocycloaddition diastéréosélective [4+2] et [3+2], nous avons développé au cours de ce doctorat de nouvelles stratégies pour l'accès asymétrique à ces dérivés de β-aminoacides par deux voies complémentaires :1) Une voie utilisant les hétérocycles à six chaînons de type 6-ATO (6-alcoxytétrahydrooxazinone) qui ont été préparés par une réaction d’hétérocycloaddition hautement stéréosélective avec de bons rendements et ed. Ces cycloadduits ont été transformés par transacétalisation vers les aminoacétals intermédiaires «mixtes» ou «symétriques». Ces nouveaux acétals sont des intermédiaires parfaits pour la N-élongation par couplage peptidique, conduisant finalement aux aldéhydes peptidiques β3-C-terminaux monosubstitués. 2) Sur une autre approche, les hétérocycles à cinq chaînons 5-AISO (3,3'-disubstitué 5-alcoxy-isoxazolidines) ont été obtenus par cycloaddition dipolaire-1,3 entre des cétonitrones esters et des éthers vinyliques. Ces composés ont été utilisés avec succès en tant que précurseurs d'aminoaldéhydes β3-disubstitués après l’étape de transprotection de l'atome d'azote, suivie par la copure de la liaison N-O. L’extension asymétrique de l'étape de cycloaddition a été étudiée par des voies énantiosélective et diastéréosélective, ouvrant ainsi l'entrée vers les peptides aldéhydiques β3-disubstitués-C-terminaux énantioenrichis. / Peptide aldehydes are known as protease inhibitors and precursors for many biologically active compounds. Methods for their synthesis involve classically the transformation of a precursor (Weinreb amide, ester, alcohol, acetal) into an aldehyde as one of the final steps to prevent epimerization of the carbon α to the aldehyde. By contrast, β-peptide aldehydes, more stable to epimerization, have been relatively unexplored. They are usually obtained by homologation of the corresponding amino acid despite low yielding steps, an epimerization problem and low number of accessible amino acids. Therefore, new synthetic access to β-peptide aldehydes is still a challenging problem. On the basis of previous work in our team concerning [4+2] and [3+2] diastereoselective cycloadditions, we have developed during this PhD thesis new strategies for the asymmetric access of β-amino acid derivatives by two complementary ways :1) Original six-membered heterocycles 6-ATO (6-alkoxy-tetrahydrooxazinone ) were prepared by a highly stereoselective heterocycloaddition reaction with good yields and de. These cycloadducts were transformed via transacetalisation into both «mixed» and «symmetrical» aminoacetals. Moreover, these new acetals are ideal intermediates for further peptide coupling, leading ultimately to monosubstituted β3-C-terminal peptide aldehydes. 2) By another approach five-membered heterocycles 5-AISO (3,3’-disubstituted 5-alkoxy-isoxazolidines) were obtained via 1,3-dipolar cycloaddition between α-keto ester nitrones and vinyl ether. These compounds were successfully used as precursors of disubstituted β-amino aldehydes after transprotection of the nitrogen atom and N-O cleavage of the isoxazolidine ring. Asymmetric extension of the cycloaddition step was studied by enantioselective and diastereoselective pathways, thus opening unprecedented entry to enantioenriched disubstituted β3,β3-C-terminal peptide aldehydes.

Les nano-Oscillateurs à transfert de spin (STNOs) sont des dispositifs capables d'émettre une onde hyperfréquence lorsqu'ils sont pompés par un courant polarisé grâce au couple de transfert de spin. Bien qu'ils offrent de nombreux avantages (agilité spectrale, intégrabilité, etc.) pour les applications, leur puissance d'émission et leur pureté spectrale sont en général faibles. Une stratégie pour améliorer ces propriétés est de synchroniser plusieurs oscillateurs entre eux. Une première étape est de comprendre la synchronisation d'un STNO unique à une source externe. Pour cela, nous avons étudié une vanne de spin Cu60|NiFe15|Cu10|NiFe4| Au25 (épaisseurs en nm) de section circulaire de 200 nm. Dans l'état saturé perpendiculaire (champ appliqué > 0.8 T), nous avons déterminé la nature du mode qui auto-Oscille et son couplage à une source externe grâce à un microscope de force par résonance magnétique (MRFM). Seul un champ micro-Onde uniforme permet de synchroniser le mode oscillant de la couche fine car il possède la bonne symétrie spatiale, au contraire du courant micro-Onde traversant l'échantillon. Ce même échantillon a ensuite été étudié sous faible champ perpendiculaire, les deux couches magnétiques étant alors dans l'état vortex. Dans ce cas, il est possible d'exciter un mode de grande cohérence (F/ ∆F >15000) avec une largeur de raie inférieure à 100 kHz. En analysant le contenu harmonique du spectre, nous avons déterminé que le couplage non-Linéaire amplitude-Phase du mode excité est quasi nul, ce qui explique la grande pureté spectrale observée, et qu'en parallèle, la fréquence d'oscillation reste ajustable sur une grande gamme grâce au champ d'Oersted créé par le courant injecté. De plus, la synchronisation de ce mode à une source de champ micro-Onde est très robuste, la largeur de raie mesurée diminuant de plus de cinq ordres de grandeur par rapport au régime autonome. Nous concluons de cette étude que le couplage magnéto-Dipolaire entre STNOs à base de vortex est très prometteur pour obtenir une synchronisation mutuelle, le champ dipolaire rayonné par un STNO sur ses voisins jouant alors le rôle de la source micro-Onde. Nous sommes donc passés à l'étape suivante, à savoir la mesure expérimentale de deux STNOs similaires séparés latéralement de 100 nm. En jouant sur les différentes configurations de polarités des vortex, nous avons réussi à observer la synchronisation mutuelle de ces deux oscillateurs. / Spin transfer nano-Oscillators (STNOs) are nanoscale devices capable of generating high frequency microwave signals through spin momentum transfer. Although they offer decisive advantages compared to existing technology (spectral agility, integrability, etc.), their emitted power and spectral purity are quite poor. In view of their applications, a promising strategy to improve the coherence and increase the emitted microwave power of these devices is to mutually synchronize several of them. A first step is to understand the synchronization of a single STNO to an external source. For this, we have studied a circular nanopillar of diameter 200~nm patterned from a Cu60|Py15|Cu10|Py4|Au25 stack, where thicknesses are in nm. In the saturated state (bias magnetic field > 0.8 T), we have identified the auto-Oscillating mode and its coupling to an external source by using a magnetic resonance force microscope (MRFM). Only the uniform microwave field applied perpendicularly to the bias field is efficient to synchronize the STNO because it shares the spatial symmetry of the auto-Oscillation mode, in contrast to the microwave current passing through the device. The same sample was then studied under low perpendicular magnetic field, with the two magnetic layers in the vortex state. In this case, it is possible to excite a highly coherent mode (F/∆F>15000) with a linewidth below 100 kHz. By analyzing the harmonic content of the spectrum, we have determined that the non-Linear amplitude-Phase coupling of the excited mode is almost vanishing, which explains the high spectral purity observed. Moreover, the oscillation frequency can still be widely tuned thanks to the Oersted field created by the dc current. We have also shown that the synchronization of this mode to a microwave field source is very robust, the generation linewidth decreasing by more than five orders of magnitude compared to the autonomous regime. From these findings we conclude that the magneto-Dipolar interaction is promising to achieve mutual coupling of vortex based STNOs, the dipolar field from a neighboring oscillator playing the role of the microwave source. We have thus experimentally measured a system composed of two STNOs laterally separated by 100 nm. By varying the different configurations of vortex polarities, we have observed the mutual synchronization of these two oscillators.

Ce travail de thèse a été réalisé au Laboratoire de Physique Subatomique et de Cosmologie (IN2P3) deGrenoble en collaboration avec le groupe Thalès avec pour objectif le développement d’une nouvellegénération de plasmas micro-onde fonctionnant sur une gamme de pression étendue allant de 0,5 mtorrà 10 torr en argon. La travail présenté porte donc en : i) la conception des applicateurs basés sur destronçons de longueur λ/4 faisant office de transformateurs d’impédance entre le générateur et leplasma d’impédance supposée donnée (adaptation d’impédance approchée); ii) la déterminationexpérimentale de l’impédance réelle du plasma (partie réelle et partie imaginaire) par mesure dumodule et de la phase du coefficient de réflexion dans des conditions opératoires définies; iii) leredimensionnement des différents tronçons de l’applicateur par simulation numérique en tenantcompte de l’impédance réelle du plasma; iv) la validation expérimentale de l’adaptation d’impédanceentre générateur et plasma. Les résultats obtenus démontrent clairement qu’il est possible, à fréquencedonnée (2.45 GHz dans le cas présent), de concevoir et de dimensionner une source plasma avec uneefficacité énergétique supérieure à 80% pour des fenêtres en pression (d’au moins une décade)équivalentes à des fenêtres opératoires en termes de paramètres plasma. Ces sources individuelles àabsorption localisée de micro-ondes peuvent être utilisées en nombre pour la réalisation des plasmasuniformes de grandes dimensions par leur distribution selon des réseaux à deux dimensions (sourcesplanes) ou à trois dimensions (volumes de plasma), et donc pour des applications industrielles auxtraitements de surface. / This work was done in the « Laboratoire de Physique Subatomique et de Cosmologie (IN2P3,Grenoble) » during a collaboration with Thales. The aim of the project was the development of a newgeneration of microwave plasma with extended operating conditions in the pressure range 0.5 mtorr to10 torr in argon. The presented work consists of: i) designing applicators based on sections of λ/4length serving as impedance transformers between the generator and the plasma with impedance ofgiven assumed value (approximate impedance adaptation); ii) experimentally determine the realplasma impedance (the real part and the imaginary part) for given operating conditions from themeasurement of modulus and phase of the reflection coefficient S11; iii) resize the different sections ofthe applicator by digital simulation taking the real plasma impedance into account; iv) finally, verifyexperimentally that the impedance adaptation between the generator and the plasma is correct. Theobtained results clearly demonstrate that it is possible, at a given frequency (here 2.45 GHz), to designand size a plasma source with an efficiency greater than 80 % for a window in pressure (at least onedecade) equivalent to an operating window in terms of plasma parameters. These individual sourceswith localized absorption of microwaves can be used in numbers to achieve uniform plasmas via theirdistribution over two-dimensional (planar sources) or tri-dimensional (volume plasma) networks, andthus for industrial surface treatments.

Les faisceaux d’électrons et d’ions sont au cœur de nombreuses techniques instrumentales servant à explorer, analyser et agir sur des matériaux à l’échelle du micromètre au nanomètre (Microscopie électronique, spectrométrie d’électrons, techniques de « FIB »). Les limites de résolution spatiale et énergétique de ces techniques dépendent en grande partie des propriétés des sources qu’elles utilisent et en particulier de leur température de fonctionnement. De fait, depuis plus de 10 ans, le potentiel des atomes froids ionisés comme nouveau type de source d’électrons ou d’ions est intensivement exploré.Le projet expérimental réalisé au LAC et décrit dans cette thèse utilise un jet d’atomes de césium issu d’un piège magnéto-optique à deux dimensions. La température transverse du jet est de l’ordre de 100 µK. Malgré cela, le jet est encore trop divergent après la sortie de la zone de refroidissement pour notre expérience. Afin guider le jet d’atomes jusqu’à la zone d’ionisation, nous avons étudié une méthode particulière de guidage dipolaire. L’utilisation d’un seul laser convenablement réglé nous a permis de guider et pousser les atomes du jet en même temps tout en limitant le chauffage. Nous avons ainsi pu compresser avec ce laser pousseur-guideur le jet d’atomes sur un diamètre de 400 µm à 60 cm de la zone de refroidissement du PMO-2D.Le jet est ensuite ionisé par la méthode d’ionisation en champ électrique statique d’atomes de Rydberg. Les atomes sont tout d’abord excités par laser sur un état de Rydberg (n~30) en présence d’un champ électrique uniforme et homogène. Les atomes du jet ainsi excités voyagent vers une zone présentant un fort gradient de champ où ils vont alors s’ioniser autour de la même valeur de potentiel, réduisant ainsi la taille de la zone d’ionisation et donc de la dispersion en énergie potentielle initiale du faisceau d’électron. La probabilité d’ionisation des atomes dans le champ dépend grandement de l’état de Rydberg préalablement excité. Le choix de l’état de Rydberg optimal, i.e. qui a une probabilité d’ionisation la plus grande possible, nécessite une étude de l’ionisation des états de Rydberg du césium. Un modèle à deux niveaux est présenté dans cette thèse qui permet de retrouver le comportement d’ionisation d’état de Rydberg observé expérimentalement. Ce modèle simple nous a permis de comprendre quel type d’état nous devions exciter. Enfin une étude expérimentale est également présentée. / Electron and Ion beams are at the base of many instrumental techniques used to explore, to analyse and to modify materials from the micrometer to the manometer scale (Electronic Microscopy, Electron Spectrometry, Focused Ion beams techniques…). Spatial and Energetic resolutions of these techniques are strongly dependent on its source‘s properties and particularly their working temperature. In fact, for more than ten years, the potential of ionised cold atoms have been intensively studied. Our experiment at LAC, described in this thesis, uses a 2 dimensional magneto-optical trap (2D-MOT) to create a caesium atomic beam. The transverse temperature of the beam is around 100 µK. Despite this, the beam is still too divergent after exiting the cooling area. To guide the atomic beam up to the ionisation area, we have studied and implemented a particular method of dipolar guiding. The use of a unique laser properly set allowed us to push and guide altogether the atoms of the beam while limiting the heating effect. Thus, we have managed to compress the atomic beam’s size to 400 µm at 60 cm from the output of the MOT.Afterward, the atomic beam is ionised by the method of Rydberg (static) field ionisation. The atoms are firstly excited by laser on a Rydberg state (n~30) as a static homogeneous and uniform electric field is applied. The excited atoms of beam travel therefore to a high-gradient field area where they ionise around the same electric potential value, therefore reducing the ionisation area’s size and the initial potential energy spread of the electron beam. The ionisation probability of the atoms in the field depends greatly on the excited Rydberg state. The choice of an optimal Rydberg state , i.e. with the highest probability of ionisation, needs better knowledge of the ionisation of cesium Rydberg states. A two levels model us to describe the ionisation behaviour of some Ryberg. This simple models helps to understand what kind of states we want to excite in order to optimise the ionisation area‘s size. An experimental study of cesium Rydberg states is also presented.

O trocador de Na+/Ca2+ (NCX) constitui um dos principais mecanismos de extrusão de Ca2+ intracelular em células excitáveis. Foi demonstrado que alterações no funcionamento do NCX estão relacionadas a diversas situações patológicas. Por este motivo, o entendimento do mecanismo molecular da manutenção da concentração de Ca2+ intracelular via NCX é importante para a compreensão do funcionamento do trocador, bem como para o desenvolvimento de fármacos. Além de transportar Na+/Ca2+, o NCX também é regulado por esses íons. Este trocador é composto por dois domínios transmembranares, cada um deles contendo 5 &#945;-hélices (TM), e uma grande alça intracelular que conecta as hélices TM5 e TM6. O domínio transmembranar é responsável por catalisar o transporte de Na+/Ca2+ através da bicamada lipídica, enquanto que a alça citoplasmática está envolvida com a regulação do trocador. Esta alça contém dois domínios sensores de Ca2+ adjacentes, denominados CBD1 e CBD2. Apesar da importância fisiológica do NCX, o mecanismo de regulação alostérica do trocador por Ca2+ intracelular permanece desconhecido. Neste trabalho, a espectroscopia de ressonância magnética nuclear (RMN) de alta resolução foi utilizada para investigar a conformação e a dinâmica de CBD1 e CBD2 do trocador de Na+/Ca2+ de Drosophila melanogaster (CALX), isolados ou conectados covalentemente em uma construção denominada CBD12. Um total de 98% das ressonâncias da cadeia principal de CBD1 isolado na presença de Ca2+ foi assinalado, enquanto que na ausência de Ca2+, assinalamentos para apenas uma parte da cadeia principal puderam ser obtidos. Os assinalamentos adquiridos para CBD12 foram baseados na análise de um conjunto de espectros de RMN tridimensional heteronuclear e por comparação com os espectros dos domínios isolados. Uma análise preliminar dos deslocamentos químicos e dos parâmetros de relaxação de 15N obtidos para CBD1 indicou que este domínio é flexível na ausência de Ca2+, mas torna-se rígido após a adição deste íon. As medidas das velocidades de relaxação de 15N e de acoplamentos dipolares residuais (RDCs) de 1H-15N realizadas para CBD12 nas formas apo e holo indicaram que a ligação de Ca2+ em CBD1 estabiliza uma orientação rígida entre os domínios. A análise dos RDCs de 1H-15N mostrou ainda que a orientação média entre CBD1 e CBD2 é praticamente linear na ausência de Ca2+, enquanto que um ângulo menor é assumido após a adição deste íon. Os dados descritos nesta tese suportam um modelo de regulação alostérica em que a modulação da plasticidade de CBD12 pela ligação de Ca2+ no domínio CBD1 controla a abertura e o fechamento do trocador. / The Na+/Ca2+ exchanger (NCX) is a major mechanism for the extrusion of intracellular Ca2+ in excitable cells. It was demonstrated that altered functioning of this protein is related to various pathological situations. Therefore, the understanding of the molecular mechanism for maintaining the intracellular Ca2+ concentration by means of the NCX is important to understand the functioning of the exchanger and to develop drug-based therapies. Besides transporting Na+/Ca2+, the exchanger is also regulated by these ions. The NCX is composed of two transmembrane domains, each of them containing 5 transmembrane alpha-helices (TM), and a very large cytosolic loop that connects TM5 to TM6. The transmembrane domains are responsible for catalyzing the transport of Na+ and Ca2+ ions across the lipid bilayer, while the cytosolic loop is involved in regulation of the exchanger activity. It contains two regulatory Ca2+- binding domains, called CBD1 and CBD2, that appear in tandem. Despite the physiological importance of the NCX, the mechanism of allosteric regulation of the exchanger by intracellular calcium remains unclear. In this work we used high-resolution NMR spectroscopy to study the conformation and the dynamics of the two Ca2+-binding regulatory domains of Drosophila\'s Na+/Ca2+ exchanger (CALX), CBD1 and CBD2, in isolation as well as in a covalent construct called CBD12. Complete backbone NMR resonance assignments were obtained for the isolated CBD1 domain in the Ca2+-bound state, while partial assignments were obtained for CBD1 in the free state. Partial backbone NMR resonance assignments were obtained for the CBD12 construct through the analysis of a standard set of triple resonance NMR spectra. Additional assignments were obtained by comparison with the isolated CBD1 and CBD2 domains. A preliminary analysis of NMR chemical shifts and 15N relaxation data obtained for CBD1 indicates that this domain displays considerable amount of flexibility in the free state, but becomes more rigid upon Ca2+-binding. NMR 15N relaxation rates and 1H-15N residual dipolar couplings (RDCs) obtained for the Apo and Ca2+-bound states of the CBD12 domain indicate that calcium binding stabilizes a rigid inter-domain orientation. Analysis of 1H-15N RDCs further shows that Drosophila\'s CBD12 domain assumes an almost linear inter-domain orientation in the absence of Ca2+, while a smaller inter-domain angle was found in its presence. These findings support a model in which modulation of CBD12 plasticity by the binding of Ca2+ to the CBD1 domain controls the opening and closing of the exchanger.

Les systèmes quantiques à N corps en interaction sont au cœur des problèmes actuels de la recherche en physique quantique. La compréhension de tels systèmes est un enjeu crucial pour le développement des connaissances en physique de la matière condensée. De nombreux efforts de recherche visent à la construction d'un « simulateur quantique » : une plateforme permettant de modéliser, grâce à un système quantique bien contrôlé, un système quantique dont l'accès expérimental est difficile. Les fortes interactions dipolaires entre atomes de Rydberg représentent un objet d'étude choix pour ce type de problème. Nous présentons dans le présent manuscrit une étude des conditions d'excitation d'un nuage dense d'atomes de Rydberg en interaction, permise par le dispositif expérimental dont nous disposons, qui mêle les techniques de piégeage et de refroidissement d’atomes sur puce avec les techniques de manipulation des niveaux de Rydberg. Les résultats de cette étude nous permettent de formuler une proposition expérimentale complète de développement d'un simulateur quantique fondé sur le piégeage d'atomes de Rydberg circulaires. Le simulateur que nous proposons est très prometteur, grâce à sa flexibilité et aux longs temps de simulation qu’il permettrait. Nous terminons ce manuscrit par la description détaillée de la première étape sur le chemin vers ce simulateur : l'excitation d’atomes de Rydberg circulaires sur puce. / Interacting many-body quantum systems are at the heart of contemporary research in quantum physics. The understanding of such systems is crucial to the development of condensed-matter physics. Many research efforts aim at building a "quantum simulator": a platform which allows to model a hard-to-access quantum system with a more controllable one. Ensembles of Rydberg atoms, thanks to their strong dipolar interactions, make for an excellent system to study many-body quantum physics. We present here a study of the excitation of a dense cloud of interacting Rydberg atoms. This study was conducted on an experimental setup mixing on-chip cold atoms techniques with Rydberg atoms manipulation techniques. The result of this study leads us to make a full-fledged proposal for the realisation of a quantum simulator, based on trapped circular Rydberg atoms. The proposed simulator is particularly promising due to its flexibility and to the long simulation times for which it would allow. We conclude this manuscript with a detailed description of the first experimental step towards building such a simulator: the on-chip excitation of circular Rydberg atoms.

O trocador de Na+/Ca2+ (NCX) constitui um dos principais mecanismos de extrusão de Ca2+ intracelular em células excitáveis. Foi demonstrado que alterações no funcionamento do NCX estão relacionadas a diversas situações patológicas. Por este motivo, o entendimento do mecanismo molecular da manutenção da concentração de Ca2+ intracelular via NCX é importante para a compreensão do funcionamento do trocador, bem como para o desenvolvimento de fármacos. Além de transportar Na+/Ca2+, o NCX também é regulado por esses íons. Este trocador é composto por dois domínios transmembranares, cada um deles contendo 5 &#945;-hélices (TM), e uma grande alça intracelular que conecta as hélices TM5 e TM6. O domínio transmembranar é responsável por catalisar o transporte de Na+/Ca2+ através da bicamada lipídica, enquanto que a alça citoplasmática está envolvida com a regulação do trocador. Esta alça contém dois domínios sensores de Ca2+ adjacentes, denominados CBD1 e CBD2. Apesar da importância fisiológica do NCX, o mecanismo de regulação alostérica do trocador por Ca2+ intracelular permanece desconhecido. Neste trabalho, a espectroscopia de ressonância magnética nuclear (RMN) de alta resolução foi utilizada para investigar a conformação e a dinâmica de CBD1 e CBD2 do trocador de Na+/Ca2+ de Drosophila melanogaster (CALX), isolados ou conectados covalentemente em uma construção denominada CBD12. Um total de 98% das ressonâncias da cadeia principal de CBD1 isolado na presença de Ca2+ foi assinalado, enquanto que na ausência de Ca2+, assinalamentos para apenas uma parte da cadeia principal puderam ser obtidos. Os assinalamentos adquiridos para CBD12 foram baseados na análise de um conjunto de espectros de RMN tridimensional heteronuclear e por comparação com os espectros dos domínios isolados. Uma análise preliminar dos deslocamentos químicos e dos parâmetros de relaxação de 15N obtidos para CBD1 indicou que este domínio é flexível na ausência de Ca2+, mas torna-se rígido após a adição deste íon. As medidas das velocidades de relaxação de 15N e de acoplamentos dipolares residuais (RDCs) de 1H-15N realizadas para CBD12 nas formas apo e holo indicaram que a ligação de Ca2+ em CBD1 estabiliza uma orientação rígida entre os domínios. A análise dos RDCs de 1H-15N mostrou ainda que a orientação média entre CBD1 e CBD2 é praticamente linear na ausência de Ca2+, enquanto que um ângulo menor é assumido após a adição deste íon. Os dados descritos nesta tese suportam um modelo de regulação alostérica em que a modulação da plasticidade de CBD12 pela ligação de Ca2+ no domínio CBD1 controla a abertura e o fechamento do trocador. / The Na+/Ca2+ exchanger (NCX) is a major mechanism for the extrusion of intracellular Ca2+ in excitable cells. It was demonstrated that altered functioning of this protein is related to various pathological situations. Therefore, the understanding of the molecular mechanism for maintaining the intracellular Ca2+ concentration by means of the NCX is important to understand the functioning of the exchanger and to develop drug-based therapies. Besides transporting Na+/Ca2+, the exchanger is also regulated by these ions. The NCX is composed of two transmembrane domains, each of them containing 5 transmembrane alpha-helices (TM), and a very large cytosolic loop that connects TM5 to TM6. The transmembrane domains are responsible for catalyzing the transport of Na+ and Ca2+ ions across the lipid bilayer, while the cytosolic loop is involved in regulation of the exchanger activity. It contains two regulatory Ca2+- binding domains, called CBD1 and CBD2, that appear in tandem. Despite the physiological importance of the NCX, the mechanism of allosteric regulation of the exchanger by intracellular calcium remains unclear. In this work we used high-resolution NMR spectroscopy to study the conformation and the dynamics of the two Ca2+-binding regulatory domains of Drosophila\'s Na+/Ca2+ exchanger (CALX), CBD1 and CBD2, in isolation as well as in a covalent construct called CBD12. Complete backbone NMR resonance assignments were obtained for the isolated CBD1 domain in the Ca2+-bound state, while partial assignments were obtained for CBD1 in the free state. Partial backbone NMR resonance assignments were obtained for the CBD12 construct through the analysis of a standard set of triple resonance NMR spectra. Additional assignments were obtained by comparison with the isolated CBD1 and CBD2 domains. A preliminary analysis of NMR chemical shifts and 15N relaxation data obtained for CBD1 indicates that this domain displays considerable amount of flexibility in the free state, but becomes more rigid upon Ca2+-binding. NMR 15N relaxation rates and 1H-15N residual dipolar couplings (RDCs) obtained for the Apo and Ca2+-bound states of the CBD12 domain indicate that calcium binding stabilizes a rigid inter-domain orientation. Analysis of 1H-15N RDCs further shows that Drosophila\'s CBD12 domain assumes an almost linear inter-domain orientation in the absence of Ca2+, while a smaller inter-domain angle was found in its presence. These findings support a model in which modulation of CBD12 plasticity by the binding of Ca2+ to the CBD1 domain controls the opening and closing of the exchanger.

A la suite des nombreux travaux sur l’inhibition de la glycogène phosphorylase (GP) menés au laboratoire et au travers de diverses collaborations, cette thèse décrit en cinq chapitres suivis d’une partie expérimentale détaillée, les dernières avancées en termes de synthèse et d’évaluation biologique des inhibiteurs du site catalytique de la GP. La chapitre I de ce manuscrit est consacrée à la présentation des diabètes et plus particulièrement du diabète de type II dont le traitement, motivation première de ce projet, repose sur la connaissance des mécanismes complexes régulant la glycémie. Les différents inhibiteurs synthétisés sont classés par famille selon leur structure qui associe un aglycone hétérocyclique, susceptible d’affinité pour le canal β proche du site actif de l’enzyme, avec un motif glycopyranosidique, ou glycopyranosylidène dans le cas des motifs spiro. Le chapitre II est consacré aux inhibiteurs spiro-bicycliques tels que les glucopyranosylidène-spiro-1,4,2-oxathiazoles et les glucopyranosylidène-spiro-isoxazolines. Le chapitre III décrit la synthèse de C- et N-glycosyles hétérocycles, principalement des glycopyranosyl-1,2,3-triazoles. Enfin le chapitre IV décrit la fonctionnalisation de 5-halogéno-1,2,3-triazoles 4-substitués par couplages pallado-catalysés qui ont constitué un développement imprévu mais original des travaux. Pour terminer, le chapitre V décrit l’évaluation des molécules préparées en tant qu’inhibiteurs de la glycogène phosphorylase. Les expériences et résultats d’enzymologie, de cristallographie ainsi que les tests cellulaires in vitro et in vivo sur le rat sont présentés / Following many studies lead on the inhibition of glycogen phosphorylase (GP) in our laboratory an trough several collaborations, this thesis describes in five chapters and a detailed experimental section, the most recent advances in the areas of synthesis and biological evaluation of GP’s catalytic site inhibitors. Chapter I is dedicated to the description of diabetes and especially type 2 diabetes of which treatment, the main goal of this project, requires knowledge of the complex mechanisms that regulates glycemia. Synthesized inhibitors are broken down into families according to their structure which associates an heterocyclic aglycon, prone to binding in the β pocket lining the active site, with a glycopyranoside or glycopyranosylidene moiety in the case of spiro compounds. Chapter II focuses on spiro-bicyclic inhibitors such as glucopyranosilidene-spiro-1,4,2-oxathiazoles and glucopranosylidene-spiro-isoxazolines. Chapter III describes the synthesis of C- and N-glycosyl-heterocycles, mainly glycopyranosyl-1,2,3-triazoles. Finally, chapter IV studies the palladium-mediated cross coupling fonctionalization of 4-substituted-5-halogenated-1,2,3-triazoles that represents an unexpected but interesting development of the project. To conclude, chapter V gathers the evaluation of synthesized molecules as GP inhibitors. Enzymology and crystallography as well as in vitro and in vivo experiments are presented

Près de 40% des protéines présentes dans les cellules sont prédites partiellement ou complètement désordonnées. Ces protéines dépourvues de structure tridimensionnelle à l'état natif sont impliquées dans de nombreux mécanismes biologiques, la flexibilité jouant un rôle moteur dans les mécanismes de reconnaissance moléculaire. La prise en considération de l'existence de flexibilité au sein des protéines et des interactions protéines-protéines a nécessité le renouvellement de nos connaissances, de notre appréhension des fonctions biologiques ainsi que des approches pour étudier et interpréter ces phénomènes. La méthode retenue pour étudier ces transitions conformationnelles est la spectroscopie par résonance magnétique nucléaire. Elle dispose d'une sensibilité unique, d'une résolution à l'échelle atomique et permet par diverses expériences d'accéder à l'ensemble des échelles de temps définissant les mouvements de ces protéines. Nous combinons ces mesures expérimentales à un modèle statistique représentant l'ensemble du paysage énergétique des protéines désordonnées : la description par ensemble explicite de structures. Ce modèle est une représentation discrète des différents états échantillonnés par ces protéines. Il permet, combinant les déplacements chimiques, les couplages dipolaires et la relaxation paramagnétique, de développer une description moléculaire de l'état déplié en caractérisant à la fois l'information locale et l'information à longue portée présente dans les protéines intrinsèquement désordonnées. / Around 40% of the human genome does not fold into stable three-dimensional structures but are either unfolded, or contain unfolded regions of significant length. The inherent flexibility of this class of proteins is essential for their function in a vast range of biomolecular process such as molecular recognition. In order to take into account the specificity of these interactions, it has been necessary to invent new approaches to study and interpret their behaviour. Nuclear magnetic resonance spectroscopy is a unique atomic resolution probe which is sensitive to a very large range of time scales. We combine experimental NMR data with a statistical model describing the energy landscape of unfolded state : the explicit ensemble description. This model is a discrete representation of the different states of theses proteins. Combining chemical shifts, residual dipolar couplings and paramagnetic relaxation enhancement, it is then possible to develop a molecular description of the unfolded state caracterising both the local and long-range information of intrinsically disordered proteins.