Carbohydrates are essential biomolecules that decorate cell membranes and proteins in organisms. They are important both as structural elements and as identification markers. Many biological and pathogenic processes rely on the identification of carbohydrates by proteins, thereby making them attractive as molecular blueprints for drugs. This thesis describes how NMR spectroscopy can be utilized to study carbohydrates in solution at a molecular level. This versatile technique facilitates for investigations of (i) shapes, (ii) motions and (iii) interactions. A conformational study of an E. coli O-antigen was performed by calculating atomic distances from NMR NOESY experiments. The acquired data was utilized to validate MD simulations of the LPS embedded in a membrane. The agreement between experimental and calculated data was good and deviations were proven to arise from spin-diffusion. In another study presented herein, both the conformation and the dynamic behavior of amide side-chains linked to derivatives of D-Fucp3N, a sugar found in the O-antigen of bacteria, were investigated. J-couplings facilitated a conformational analysis and 13C saturation transfer NMR experiments were utilized to measure rate constants of amide cis-trans isomerizations. 13C NMR relaxation and 1H PFG diffusion measurements were carried out to explore and describe the molecular motion of mannofullerenes. The dominating motions of the mannofullerene spectral density were found to be related to pulsating motions of the linkers rather than global rotational diffusion. The promising inhibition of Ebola viruses identified for a larger mannofullerene can thus be explained by an efficient rebinding mechanism that arises from the observed flexibility in the linker. Molecular interactions between sugars and caffeine in water were studied by monitoring chemical shift displacements in titrations. The magnitude of the chemical shift displacements indicate that the binding occurs by a face to face stacking of the aromatic plane of caffeine to the ring plane of the sugar, and that the interaction is at least partly driven by solvation effects. Also, the binding of a Shigella flexneri serotype Y octasaccharide to a bacteriophage Sf6 tail spike protein was investigated. This interaction was studied by 1H STD NMR and trNOESY experiments. A quantitative analysis of the STD data was performed employing a newly developed method, CORCEMA-ST-CSD, that is able to simulate STD data more accurately since the line broadening of protein resonances are accounted for in the calculations. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.</p>

Neste trabalho, descrevemos o desenvolvimento do equipamento e o software necessários à implementação da técnica de obtenção de imagens por RMN. Nossos principais objetivos foram a construção de um sistema de controle e aquisição de dados que permitisse operar um espectrômetro de Fourier de RMN pulsada como um tomógrafo de RMN; por outro lado, visamos a construção de um espectrômetro que tivesse seus parâmetros facilmente reconfiguráveis pelo sistema de controle. O resultado foi um sofisticado equipamento que permite, além do proposto, trabalhar com técnicas de espectroscopia de alta resolução e espectroscopia em sólidos. Uma grande ênfase foi dada ao entendimento das técnicas De reconstrução de imagens, desde as convencionais até aquelas que constituem atualmente a fronteira de pesquisa nessa área. Os resultados obtidos com o sistema descrito são considerados bons, comparáveis aos das unidades construídas por empresas que operam comercialmente nessa área, em cooperação com centros localizados em universidades no exterior, pouco devendo a equipamentos similares (protótipos) desenvolvidos naqueles centros. / We describe in this work the development of hardware and software necessary to implement the Magnetic Resonance Imaging (MRI) techniques. Our major subjects were the construction of an acquisition and control system which allowed the operation of a pulsed Fourier NMR spectrometer as a NMR Tomograph; further we oriented the developing of a NMR spectrometer whose parameters could be easily reconfigured by the controlling system. As a result we obtained a sophisticated equipment which allows, more than the proposed, working with high resolution spectroscopic techniques and spectroscopy in solids. Since the basic techniques employed in NMR and CT Tomographs are well known, a great emphasis was also given on the understanding of the image reconstruction techniques that constitutes today the frontier of research in this area. The results obtained with the system described here are considered good, comparable to the results from commercial units developed in cooperation with imaging groups located in universities abroad.

A técnica de dupla ressonância unidimensional para alta resolução em líquidos constitui o objetivo deste trabalho. Para isso construiu-se uma sonda de dupla ressonância, apropriada para experiências heteronucleares do tipo 13C-{1H}. Empregam-se algumas sequências de pulsos para permitir as medidas do EON e do desacoplamento nuclear entre 1H e 13C. Emprega-se o EON com a finalidade de obter um aumento na intensidade do sinal de RMN do 13C; emprega-se o desacoplamento para eliminar a estrutura fina que surge devido ao acoplamento nuclear entre 1H e 13C. Inclui-se uma breve revisão sobre a teoria com a fmalidade de unificar o tratamento desta com as aplicações. As técnicas experimentais são discutidas e alguns espectros são mostrados para ilustrar os principais resultados / The one dimensional double resonance technique for high resolition in liquids is the main purpose of this work. For this we have built a double resonance probe, suitable for heteronuclear 13C-{1H} experiment. Some pulse sequences are employed to allow the NOE and decoupling between 1H e 13C to be measured. The NOE is employed in order to obtain a three-fold enhancement of the 13C NMR signal; decoupling is employed to eliminate the fme structW\'e arising from spin coupling between 1H e 13C. A short review about theory is included to provide unified treatment with applications. The experimental techniques are discussed and some spectra are shown to illustrate the main results.

Lithium bis(amido)cuprates are an important class of bimetallic base, which can chemo- and regioselectively metalate aromatic compounds, via directed ortho cupration (DoCu). This thesis begins with an introduction to aspects of the chemistry of organolithium compounds, group 11 organometallic compounds and their lithium 'ate complexes. Examples of such synergic bases are presented and the introduction is concluded with a discussion of lithium bis(amido)cuprate bases, which along with their silver congeners, are the subject of this dissertation. In general, syntheses involve the addition of a lithium amide to a group 11 salt, resulting in the formation of a lithium bis(amido)cuprate or argentate. Structurally focussed work commences with the use of new amide ligands to develop heteroleptic bis(amido)cuprate systems. The reaction of mixtures of lithium amides with CuBr provides a series of novel Lipshutz-type and Gilman cuprates. Interesting structural features are uncovered, which are rationalised in terms of altered steric demands in the newly introduced amide ligands in these systems. CuSCN and CuOCN are investigated as inexpensive and safer alternatives to CuCN in cuprate formation. In the solid state, a series of Lipshutz-type cuprates (TMP)2Cu(SCN)Li2(L) (L = Et2O, THF, THP) are revealed, whose molecular conformations are infuenced by the identity of the Lewis base. However, in benzene solution, in situ conversion of Lipshutz-type to Gilman cuprate is found to occur. Moving to the synthetic setting, derivatisation of chloropyridines is attempted and gives functionalised halopyridines in 51-71 % yield. CuOCN is found to behave quite differently when reacted in the same way as CuSCN, whereby X-ray crystallography reveals structures in which Cu-Li substitution is apparent. The unique reactivity of CuOCN is interpreted with the aid of multinuclear NMR spectroscopy. A new route to Lipshutz-type cuprates is explored by the synthesis of (TMP)2Cu(OCN)Li2(THF) from Gilman cuprate and LiOCN. This avoids Cu-Li substitution. Meanwhile, reaction of lithium N,N-diisopropylamide with CuOCN also avoids metal disorder, to give a novel lithium cuprate-lithium amide adduct. Further advances in our understanding of group 11 'ate complexes are made by introducing silver as a spectroscopically active nucleus in the lithium argentates (TMP)2AgLi and (TMP)2Ag(CN)Li2(THF). In the solid state, these parallel the structures known for Gilman cuprate (TMP)2CuLi and Lipshutz cuprate (TMP)2Cu(CN)Li2(THF), respectively. In solution, NMR spectroscopy reveals features consistent with retention of these structures. Lastly, the formation of mixed Cu-Li aggregates from combining TMPLi and TMPCu in aromatic solvent are investigated. Surprising reactivity is uncovered, in which the aromatic solvent is metalated and incorporated into mixed-metal aggregates. This thesis concludes with a summary of the findings and suggestions for future work, including how the findings presented herein may be transformed into practical improvements to cuprate systems. In particular, the possibility that Gilman cuprate may be activated towards the metalation of aromatic substrates by the addition of sub-stoichiometric or catalytic amounts of a lithium salt additive is explored.

La spectroscopie RMN est un moyen unique d’évaluer l’environnement cellulaire in vivo. En effet, les molécules observées sont exclusivement intracellulaires, et ont en général un rôle biochimique ainsi qu’une compartimentation cellulaire spécifique. C’est donc un outil potentiellement utile pour comprendre le fonctionnement des cellules dans leur environnement. Mon travail de thèse consistait à développer de nouvelles séquences en spectroscopie de diffusion et en spectroscopie du phosphore 31.Mon premier travail a été de développer une séquence de spectroscopie de diffusion à temps de diffusion ultra-court pour observer la diffusion anormale dans le cerveau de rat. L’évolution de l’ADC en fonction du temps de diffusion montre que le transport des métabolites dans le cerveau se fait essentiellement par diffusion aléatoire et que la contribution des transports actifs (s’ils existent) est négligeable. La modélisation de ces données a mis en évidence que la spectroscopie de diffusion à court temps de diffusion était sensible à la viscosité du cytoplasme et à l’encombrement à courte échelle. Cette technique a donc été choisie lors d’une collaboration avec la firme Eli Lilly pour le suivi de souris transgéniques (rTg4510), modèle de taupathie. Les résultats préliminaires font apparaitre des différences significatives d’ADC à un stade précoce de la neurodégénérescence (3 et 6 mois). La spectroscopie RMN du phosphore 31 permet d’observer des métabolites directement impliqués dans le processus énergétique. Au cours de cette thèse, des séquences de localisation ont été développées pour pouvoir mesurer le pH intracellulaire dans le striatum de macaque. A terme, ces séquences seront utilisées pour évaluer l’utilité potentielle du pH comme biomarqueur de la neurodégénérescence dans un modèle phénotypique de la maladie de Huntington chez le macaque. / NMR spectroscopy is a unique modality to evaluate intracellular environment in vivo. Indeed observed molecules are specifically intracellular and generally have a biochemistry role and a specific cellular compartmentation. That could be a useful tool to understand cell functioning in their environment. My thesis work consisted in development of new sequence in both diffusion and phosphorus NMR spectroscopy.My first study was to develop a diffusion-weighted spectroscopy at ultra-short diffusion time to look at the anomalous diffusion in the rat brain. ADC evolution as a function of time shows that brain metabolites motion is mainly due to random diffusion and that active transport (if exist) are negligible. Data modeling evidences that diffusion at short diffusion time is sensitive to cytoplasm viscosity and short scale crowding. In collaboration with the pharmaceutical company, this technique was chosen to follow up transgenic mice (rTg4510), model of tau pathology. Preliminary results show significant differences of ADC at an early stage of neurodegenerescence (3 and 6 months).Phosphorus spectroscopy allows observation of metabolites directly implicated in energetic processes. During this thesis, localization sequences were developed to measure intracellular pH in the primate striatum. These sequences are supposed to be used to evaluate the potential of pH as a biomarker of neurodegenerescence in a phenotypic model of the Huntington disease in the non-human primate.

Inhibition of the intrinsically disordered proteins (IDP) is a recognized issue in drug research. Standard approaches, based on key-lock model, cannot be used in the absence of rigid structure and defined active site. Here a basic helix-loop-helix leucine zipper (bHLHZip) domain of c-Myc was studied, which is intrinsically disordered and prone to aggregation. Chemical denaturation of proteins is a widely accepted technique to study protein folding, but here this methodology was applied to IDP, observing its effect on the structural ensemble of c-Myc by NMR spectroscopy. Nonlinear chemical shift changes indicated cooperative unfolding of the helical structure of the part of the leucine zipper domain in parallel with the melting of the N-terminal helix. Paramagnetic relaxation enhancement (PRE) was used to probe long-range structure and revealed presence of long-range contacts. The following search for inhibitors can be directed to the search for ligands, locking c-Myc in its more compact conformation. Protein self-association is a problem typical for IDPs and intrinsic process for all proteins at high concentrations. It leads to increased viscosity, gelation and possible precipitation, which cause problems in protein manufacturing, stability and delivery. If protein drugs require high dosing, special approaches are needed. At high concentrations proteins experience conditions close to the crystal state, therefore interactions in solution could potentially coincide with crystal lattice contacts. A range of diverse methods is used to study this process, but the complexity of the mechanism makes it hard to build a reliable model. Here, the self-association of streptococcal Protein G (PrtG) was studied using Nuclear Magnetic Resonance (NMR) spectroscopy in solution. The properties of protein-protein interactions at high concentration, up to ~ 160 mg/ml, were studied at residue-level resolution. Residue specific information on protein dynamics was obtained using 15N relaxation measurements. The experiments were carried out at multiple concentrations. Variation in the rotational correlation time over these concentrations showed changes in the protein dynamics, which indicated weak protein-protein interactions occurring in solution. Pulsed-field gradient NMR spectroscopy was used to monitor translational diffusion coefficients in order to estimate the degree of protein self-association. Oligomer formation was also monitored by looking at variations in 1H and 15N amide chemical shifts. Better understanding of protein self-association mechanisms under different conditions could assist in developing methods to reduce the level of reversible protein self-association in solution at high protein concentrations.

Dynamic structural fluctuations occurring over a broad range of timescales are now known to facilitate the catalytic function of enzymes, but there is less comprehensive experimental evidence linking fast-timescale, high frequency motions to the reaction coordinate. Interest in the role of such motions has recently surged and been the subject of intensive experimental efforts, in part due to the identification of enzymatic hydride tunnelling reactions. This mechanism involves transiently degenerate product and reactant states, which enable H-transfer to occur instantaneously without the need to surmount the activation barrier associated with traditional transition-state based models of enzyme catalysis. The primary gauge of tunnelling in enzyme-catalysed reactions is the identification of temperature dependent kinetic isotope effects (KIEs), i.e. the relative rates of a reaction where the transferred atom is substituted for an alternate isotope. The identification of temperature-, and also pressure-, dependent KIEs has resulted in the emergence of new models of describing enzymatic H-transfer. These invoke a role for fast-timescale protein motions that 'promote' transfer via tunnelling. A popular model system for studying enzymatic H-tunnelling reactions is Pentaerythritol tetranitrate reductase, which belongs to the Old Yellow Enzyme (OYE) family of ene-reductases. These nicotinamide coenzyme dependent oxidoreductases catalyse the stereospecific reduction of alpha/β-unsaturated alkene containing substrates. Here, the importance of donor-acceptor distances in determining the observed rate of PETNR reduction with NAD(P)H is probed via a detailed structural and kinetic analysis of site-directed variants. In addition, an investigation of distance-dependent Nuclear Overhauser effects via Nuclear Magnetic Resonance (NMR) spectroscopy is undertaken to assess active site organisation and measure donor-acceptor distances in PETNR-substrate complexes. A variable pressure NMR study reveals how NOE build- up is perturbed in high-energy conformers favoured as a result of the application of increased hydrostatic pressures. Recently there has been interest in exploiting the stereoselective properties of reactions catalysed by ene-reductase enzymes for use in biocatalytic reactions to produce industrially valuable compounds from renewable sources. The reactions of PETNR and additional OYE enzymes, Thermophilic old yellow enzyme and Xenobiotic reductase A, with both natural coenzymes and a set of synthetic Nicotinamide Coenzyme Biomimetics (NCBs) are also characterised. The NCBs represent affordable and fast-reacting alternatives to the physiological coenzymes. Reactions with NCBS are also shown to proceed via a tunnelling mechanism and furthermore, that enhanced donor-acceptor sampling correlates with the faster reactivity seen with these compounds.

Le lactate est considéré comme un métabolite déchet depuis de très nombreuses années. Cependant, cette vision semble revisitée depuis quelques temps, avec l'apparition de la notion de glycolyse aérobie et de navettes lactate dans différents types cellulaires (muscle, cerveau et sperme). Concernant le cerveau, des études in vitro, ex vivo et in vivo réalisées ces 20 dernières années ont montré, d'une part, que les astrocytes produisent du lactate et d’autre part que le lactate pouvait être un substrat énergétique pour le système nerveux central (SNC), et plus particulièrement les neurones. Cette notion de navette lactate entre astrocyte et neurone a été proposée pour la première fois en 1994 par Pellerin et Magistretti (ANLS, pour astrocyte-neuron lactate shuttle). Malgré de nombreuses recherches depuis, l'existence d'un transfert net de lactate entre les astrocytes et les neurones n'a toujours pas pu être démontrée in vivo. Dans cet optique, la visualisation de la production de lactate in vivo dans le cerveau activé est essentielle. Le rôle des transporteurs au lactate, MCTs (Monocarboxylate Transporters), dans la détection de ce signal est également un point capital. L’objectif de cette thèse a été de développer la spectroscopie de RMN in vivo localisée dans le cortex somato-sensoriel du rat en condition d’activation cérébrale. Dans un premier temps, un travail de développement a été effectué afin de mettre au point le protocole de stimulation neuronale et d’obtenir un rapport signal sur bruit suffisant pour pouvoir quantifier de façon fiable le lactate. Une fois le protocole établi sur des rats contrôles, l’étude a été réalisée sur des rats modifiés génétiquement et réprimés pour le MCT, soit neuronal, soit astrocytaire. Le but était de déterminer si ce partenaire clef de l’ANLS avait une influence sur les fluctuations de lactate lors de l'activation cérébrale. En plus de la spectroscopie proton in vivo et de l’IRM fonctionnelle, des études de RMN du carbone-13 ont été réalisées ex vivo. Le résultat majeur de cette thèse montre qu’en l’absence du transporteur de lactate neuronal, non seulement on perd l’augmentation de lactate lors de la stimulation cérébrale mais on perd également le signal BOLD sur l’IRMf. Ce résultat suggère, et ce pour la première fois, que l’activité neuronale est fortement dépendante du transporteur au lactate. / Lactate has been considered as a waste metabolite for many years. However, this vision has been reconsidered recently, with the appearance of the notion of aerobic glycolysis and lactate shuttles in different cell types (muscle, brain, and sperm). Concerning the brain, in vitro, ex vivo and in vivo studies carried out over the last 20 years have shown, on the one hand, that astrocytes produce lactate and, on the other hand, that lactate can be an energetic substrate for the central nervous system (CNS), and more particularly neurons. This lactate shuttle between astrocyte and neuron was first proposed in 1994 by Pellerin and Magistretti (called ANLS, for astrocyte-neuron lactate shuttle). Despite many studies since then, the existence of a net transfer of lactate between astrocytes and neurons has still not been demonstrated in vivo. In this regard, visualization of lactate production in vivo in the activated brain is essential. The role of lactate transporters, MCTs (Monocarboxylate Transporters), in detecting this signal is also a key issue. The objective of this thesis was to develop in vivo NMR spectroscopy located in the somato-sensory cortex of rats under brain activation conditions. First, experiments were carried out to develop the neural stimulation protocol and to obtain a sufficient signal-to-noise ratio to be able to quantify lactate. Once the protocol was established on control rats, the study was performed on genetically modified rats and down-regulated for MCT, either neuronal or astrocytic. The aim was to determine whether this key partner of the ANLS has an influence on lactate fluctuations during brain activation. In addition to in vivo proton spectroscopy and functional MRI, carbon-13 NMR studies were performed ex vivo. The major result of this thesis shows that in the absence of the neuronal lactate transporter, not only is the increase in lactate lost during brain stimulation but the BOLD signal on the fMRI is also lost. This result suggests, for the first time, that neural activity is highly dependent on the lactate transporter.

β-glucan is a major component of the fungal cell wall consisting of (1→3)-β linked glucose polymers with (1→6)-β linked side chains. The published classical isolation procedure of β-glucan from Saccharomyces cerevisiae is expensive and time-consuming. Thus, the aim of this research was to develop an effective procedure for the extraction of glucans. We have developed a new method for glucan extraction that will be cost effective and will maintain the native structure of the glucan. The method that we developed is 80% faster and utilizes 1/3 of the reagents compared to the published classical method. Further, the method developed increases the yield from 2.9 % to 10.3 %. Our new process has a branching frequency of 18.4 down from 197 and a side chain of 5.1 up from 2.5. The data indicate a more preserved native structure of isolated glucans.

No description available.