<p>This work studies the effect of dopamine (DA) and adenosine triphosphate (ATP) on lipid membranes using a number of complementary experimental methods. These methods include Dynamic Light Scattering to measure electrostatic surface potentials, solid-state Nuclear Magnetic Resonance to measure the degree of lipid acyl chain order, Electron Paramagnetic Resonance to measure changes in membrane viscosity, and X-ray diffuse scattering to measure structural and material parameters of lipid bilayers. It is shown that both DA and ATP have a measurable affinity to the lipid-water interface even in the absence of specialized biological receptors. These results are important for understanding the function of DA and ATP in cellular processes.</p>

<p>Exchange proteins directly activated by cAMP (EPAC) are guanine nucleotide exchange factors for the small GTPases, Rap1 and Rap2. The central regulatory module of EPAC is a cAMP binding domain (CBD), which in the absence of cAMP provides auto-inhibition of the catalytic guanine nucleotide exchange activity. Binding of the allosteric effector, cAMP, removes the auto-inhibition exerted by the CBD of EPAC. Herein, we investigate through NMR spectroscopy the structural and dynamical basis of auto-inhibition and cAMP-dependent allosteric activation in the CBD of EPAC. Specifically, the work described in this dissertation proposes novel methods that utilize NMR chemical shifts to define the network of residues that mediates long-range intra-molecular signalling, <em>i.e.</em> the chemical shift covariance analysis (CHESCA) and the chemical shift projection analysis (CHESPA). Using CHESCA as explained in Chapter 2, we identified an allosteric network that bridges the sites of cAMP-binding and cAMP-dependent structural changes to those of cAMP-dependent dynamical changes, which are critical for the release of auto-inhibition. The CHESCA results therefore rationalize how cAMP leads to activation through modulation of both structure and dynamics. In order to dissect the determinants of auto-inhibition in the absence of cAMP, several mutations along the signaling pathways identified by CHESCA were implemented and their effect on the auto-inhibitory conformational equilibrium of the apo-CBD was assessed through CHESPA, as outlined in Chapters 3 and 4. Overall, we have shown how CHESCA and CHESPA provide unprecedented insight into the allosteric networks underlying auto-inhibition and cAMP dependent activation in the CBD of EPAC. In addition, the methods employed here to map EPAC allostery are likely to be generally applicable to other systems.</p> / Doctor of Philosophy (PhD)

Il existe un lien étroit entre la structure tridimensionnelle et la fonction cellulaire de l’ARN. Il est donc essentiel d’effectuer des études structurales de molécules d’ARN telles que les riborégulateurs afin de mieux caractériser leurs mécanismes d’action. Une technique de choix, permettant d’obtenir de l’information structurale sur les molécules d’ARN est la spectroscopie RMN. Cette technique est toutefois limitée par deux difficultés majeures. Premièrement, la préparation d’une quantité d’ARN nécessaire à ce type d’étude est un processus long et ardu. Afin de résoudre ce problème, notre laboratoire a développé une technique rapide de purification des ARN par affinité, utilisant une étiquette ARiBo. La deuxième difficulté provient du grand recouvrement des signaux présents sur les spectres RMN de molécules d’ARN. Ce recouvrement est proportionnel à la taille de la molécule étudiée, rendant la détermination de structures d’ARN de plus de 15 kDa extrêmement complexe. La solution émergeante à ce problème est le marquage isotopique spécifique des ARN. Cependant, les protocoles élaborées jusqu’à maintenant sont très coûteux, requièrent plusieurs semaines de manipulation en laboratoire et procurent de faibles rendements. Ce mémoire présente une nouvelle stratégie de marquage isotopique spécifique d’ARN fonctionnels basée sur la purification par affinité ARiBo. Cette approche comprend la séparation et la purification de nucléotides marqués, une ligation enzymatique sur support solide, ainsi que la purification d’ARN par affinité sans restriction de séquence. La nouvelle stratégie développée permet un marquage isotopique rapide et efficace d’ARN fonctionnels et devrait faciliter la détermination de structures d’ARN de grandes tailles par spectroscopie RMN. / The tridimensional structure of a given RNA molecule is closely linked to its cellular function. For this reason, it is crucial to study the structure of RNA molecules, such as riboswitches, to characterize their mechanism of action. To do so, NMR spectroscopy is often used to gather structural data on RNA molecules in solution. However, this approach is limited by two main difficulties. First, the production of preparative quantities of natively folded and purified RNA molecules is a long and tedious process. To facilitate this step, our laboratory has developed an RNA-affinity purification method using an ARiBo tag. The second limiting step comes from the extensive signal overlap detected on NMR spectra of large RNA molecules. This overlap is proportional to the length of the RNA, which often prevents high-resolution structure determination of RNAs larger than 15 kDa. To solve this problem, specific isotopic labeling of RNAs can now be achieved. However, existing labeling protocols are expensive, require several weeks of laboratory manipulations and usually provide relatively low yields. This thesis provides an alternative strategy to achieve specific isotopic labeling of RNA molecules, based on the ARiBo tag affinity purification technique. The protocol includes the separation and the purification of isotopically labeled nucleotides, an enzymatic ligation step performed on a solid support and the affinity purification of the RNA of interest, without any sequence restriction. This new strategy is a fast and efficient way to label functional RNAs isotopically and should facilitate NMR structure determination of large RNAs.

Current quantitative nuclear magnetic resonance (NMR) technics offer biomarkers that allow performing non-invasive longitudinal studies for the follow up of therapeutic trials in neuromuscular disorders (NMD). In contrast to fat degeneration, the mechanisms of inflammation/oedema/necrosis and fibrosis are characteristic signs of disease activity, which makes their quantification a promising source of crucial biomarkers for longitudinal studies. This thesis work consisted on the implementation of more precise quantitative NMR methods adapted to the clinical study of skeletal muscle (SKM) for : (i) detection and quantification of sites of disease activity by T2-mapping of muscle water ; (ii) investigation of the different pathophysiological mechanisms underlying T2 alterations ; and (iii) Detection and quantification of muscle fibrosis. We implemented two methods for T2 mapping of muscle water. The first one is based on a multi-spin-echo sequence du type CPMG. In this method the 1H-NMR signals from water and lipids are acquired simultaneously. The acquired data are fitted to a tri-exponential model, in which water and fat signals are separated by exploring the T2 difference between water and fat. This method allows extraction of muscle water T2-value in the presence of fat infiltration. The second method is based on a " partially spoiled steady state free precession " (pSSFP) sequence. In contrast to the first method, which demands a sophisticated post-treatment of images acquired at 17 different echo-times, with the pSSFP a T2-mapping is extracted from two 3D data sets. 3D acquisition is compatible with spectrally selective water excitation, which eliminates signal contribution from lipids. Both methods were validated experimentally on patients and healthy subjects. The results demonstrated their capacity to detect and quantify disease activity sites. This 2 works have been published in two international journals : Azzabou, de Sousa, Araujo, & Carlier, 2014. Journal of Magnetic Resonance Imaging. DOI 10.1002/jmri.24613 (in press); et de Sousa, Vignaud, Araujo, & Carlier . 2012. Magnetic Resonance in Medicine. 67:1379-1390. Although it was shown to reveal disease activity, mono-exponential T2 of muscle water is non-specific to what concerns the mechanisms underlying its alterations. It has been long known that T2 relaxation in SKM tissue is multi-exponential. This is currently accepted to reveal anatomical compartmentation of myowater. We implemented a method for localized spectroscopic CPMG acquisition. CPMG data respect echo-time sampling and signal to noise ration limits for allowing robust multiexponential analysis. This work allowed us to establish a compartmentation model that perfectly explains the multi-exponential T2 relaxation observed in SKM tissue. This work was published in the " Biophysical Journal " (Araujo, Fromes & Carlier 2014. New Insights on skeletal muscle tissue compartments revealed by T2 NMR relaxometry. (In press)). Pilot studies performed in patients show promising results and suggest potential application of the method in clinical studies. Fibrosis starts with an excessive accumulation of intramuscular connective tissue (IMCT). We have explored the " Ultrashort time to echo " (UTE) method with the aim to detect and characterize the signal from IMCT. In a first study we characterized in vivo a short T2 component (~500 µs) in SKM, and we collected evidences suggesting that this component might reflect IMCT. Then we implemented a methodology that allowed imaging this short component in SKM tissue for the first time.

Il existe un lien étroit entre la structure tridimensionnelle et la fonction cellulaire de l’ARN. Il est donc essentiel d’effectuer des études structurales de molécules d’ARN telles que les riborégulateurs afin de mieux caractériser leurs mécanismes d’action. Une technique de choix, permettant d’obtenir de l’information structurale sur les molécules d’ARN est la spectroscopie RMN. Cette technique est toutefois limitée par deux difficultés majeures. Premièrement, la préparation d’une quantité d’ARN nécessaire à ce type d’étude est un processus long et ardu. Afin de résoudre ce problème, notre laboratoire a développé une technique rapide de purification des ARN par affinité, utilisant une étiquette ARiBo. La deuxième difficulté provient du grand recouvrement des signaux présents sur les spectres RMN de molécules d’ARN. Ce recouvrement est proportionnel à la taille de la molécule étudiée, rendant la détermination de structures d’ARN de plus de 15 kDa extrêmement complexe. La solution émergeante à ce problème est le marquage isotopique spécifique des ARN. Cependant, les protocoles élaborées jusqu’à maintenant sont très coûteux, requièrent plusieurs semaines de manipulation en laboratoire et procurent de faibles rendements. Ce mémoire présente une nouvelle stratégie de marquage isotopique spécifique d’ARN fonctionnels basée sur la purification par affinité ARiBo. Cette approche comprend la séparation et la purification de nucléotides marqués, une ligation enzymatique sur support solide, ainsi que la purification d’ARN par affinité sans restriction de séquence. La nouvelle stratégie développée permet un marquage isotopique rapide et efficace d’ARN fonctionnels et devrait faciliter la détermination de structures d’ARN de grandes tailles par spectroscopie RMN. / The tridimensional structure of a given RNA molecule is closely linked to its cellular function. For this reason, it is crucial to study the structure of RNA molecules, such as riboswitches, to characterize their mechanism of action. To do so, NMR spectroscopy is often used to gather structural data on RNA molecules in solution. However, this approach is limited by two main difficulties. First, the production of preparative quantities of natively folded and purified RNA molecules is a long and tedious process. To facilitate this step, our laboratory has developed an RNA-affinity purification method using an ARiBo tag. The second limiting step comes from the extensive signal overlap detected on NMR spectra of large RNA molecules. This overlap is proportional to the length of the RNA, which often prevents high-resolution structure determination of RNAs larger than 15 kDa. To solve this problem, specific isotopic labeling of RNAs can now be achieved. However, existing labeling protocols are expensive, require several weeks of laboratory manipulations and usually provide relatively low yields. This thesis provides an alternative strategy to achieve specific isotopic labeling of RNA molecules, based on the ARiBo tag affinity purification technique. The protocol includes the separation and the purification of isotopically labeled nucleotides, an enzymatic ligation step performed on a solid support and the affinity purification of the RNA of interest, without any sequence restriction. This new strategy is a fast and efficient way to label functional RNAs isotopically and should facilitate NMR structure determination of large RNAs.

La variabilité des propriétés du bois ainsi que son hygroscopicité pourraient être un frein à son utilisation dans la construction, même s’il peut être considéré comme un matériau de choix dans le contexte environnemental et économique actuel. Il est donc primordial de mieux comprendre les origines physiques du comportement du bois pour être capable d’améliorer la prédiction de ses propriétés, et pouvoir ainsi le rendre plus compétitif par rapport aux autres matériaux de construction. Le comportement hygromécanique du bois, caractérisé par des variations dimensionnelles en présence de variations d’hygrométrie, est particulièrement difficile à prédire, du fait de sa microstructure multi-échelle et de ses interactions complexes avec l’eau.Dans ce contexte, la thèse vise à comprendre et enrichir les relations entre la microstructure du bois, ses propriétés de sorption et son comportement hygromécanique, en étudiant l’influence de l’hétérogénéité de l’accroissement annuel (cerne), constitué de bois initial et de bois final dont la structure et les propriétés présentent de nombreuses différences. Cette étude est menée sur du Douglas (Pseudotsuga menziesii (Mirb.) Franco), actuellement référencé comme un matériau de structure intéressant. Des outils de caractérisation avancés sont utilisés : la Résonance Magnétique Nucléaire (RMN) du proton pour caractériser les mécanismes de sorption ; la corrélation d’images volumiques (DVC) pour mesurer les champs de déformations à partir d’images 3D de microtomographie aux rayons X (µTRX), donnant aussi accès à la densité locale du bois.Après une introduction sur le matériau bois et un état de l’art sur son comportement hygromécanique, une caractérisation préliminaire de la microstructure (angle des microfibrilles, largeur de cerne, densité) et du comportement hygromécanique d’échantillons de bois initial et de bois final prélevés dans différents cernes est menée. Une forte anisotropie du bois initial est mise en évidence en opposition au comportement isotrope transverse du bois final. Les déformations suivant la direction des fibres présentent aussi de fortes non-linéarités peu discutées dans la littérature. Une discussion sur la variabilité des propriétés est par ailleurs engagée, ainsi que sur les relations structure-propriétés à l’échelle macroscopique.L’origine des différences de comportement hygromécanique entre le bois initial et le bois final est tout d’abord recherchée au niveau des mécanismes de sorption, au travers une étude de relaxométrie RMN du proton en 2D (cartes T1-T2). Deux types d’eau liée situés dans des environnements distincts sont mis en évidence et leur isotherme de sorption diffère dans les deux types de bois. Une hypothèse sur leur localisation dans la paroi cellulaire est proposée, puis une modélisation simplifiée 2D est effectuée pour évaluer leur impact respectif sur le comportement hygromécanique du bois initial et du bois final, en particulier dans la direction des fibres.Enfin, les champs de déformations locaux et globaux sont étudiés en analysant par DVC des images de µTRX de bois initial et de bois final soumis à différentes sollicitations hydriques. Le couplage entre ces deux matériaux est aussi étudié pour évaluer leurs interactions et comprendre le comportement du bois à l’échelle du cerne. Un protocole de DVC adapté aux images de bois est proposé. Les comportements hygromécaniques du bois initial, du bois final et du cerne sont comparés. A l’échelle locale, des hétérogénéités du champ de déformations sont mises en évidence et corrélées à la densité locale. Leur effet sur le comportement du cerne et sur la courbure des échantillons induite par le chargement hydrique est analysé. Une modélisation 3D par éléments finis, tenant compte des gradients locaux de propriétés, vient enfin compléter cette étude pour améliorer la compréhension des interactions mécaniques entre le bois initial et le bois final / Wood has highly variable properties and is also hygroscopic. These characteristics may restrict its use in construction even if it can be considered as a material of choice with the current environmental and economical concerns. Therefore, it is essential to better understand the physical origins of the behavior of wood in order to improve the prediction of its properties, and making it competitive with respect to other building materials. Dimensional changes of wood appear when it is subjected to relative humidity variations. This hygromechanical behavior is particularly difficult to predict because of the multiscale structure of wood and its complex interactions with water.In this context, the present work aims to understand and enrich relationships between microstructure, sorption properties and hygromechanical behavior of wood. More specifically, it is focused on the influence of the growth-ring heterogeneity, constituted of earlywood and latewood which have different structures and properties. The study is performed on Douglas fir (Pseudotsuga menziesii (Mirb.) Franco), which is a species of significant interest for structural applications. Advanced characterization tools are used: proton Nuclear Magnetic Resonance (NMR) to characterize sorption mechanisms; digital volume correlation (DVC) to measure deformation fields from X-Ray microtomography 3D images (XRµT), also providing local density of wood.At first wood properties and its hygromechanical behavior are described through a literature overview. Preliminary microstructural (microfibril angle, growth-ring width, density) and hygromechanical behavior characterizations of earlywood and latewood samples with different cambium age are performed. Earlywood reveals a strong anisotropic behavior compared to latewood which is isotropic in the transversal plane. Moreover, strains along the fiber direction nonlinearly evolve with moisture content. This phenomenon has been hardly reported and studied in the literature. Discussions on variability of properties and on relationships between structure and properties are also initiated.Sorption mechanisms are then studied by 2D NMR relaxometry (T1-T2 correlation spectra) in order to investigate differences between earlywood and latewood hygromechanical behaviors. Two types of bound water located in distinct environments are highlighted and their sorption isotherms are shown to be different in the two types of wood. A hypothesis on their location in the cell-wall is proposed and a simple 2D model is developed to evaluate their respective effect on the hygromechanical behavior of earlywood and latewood, especially in the fiber direction.Furthermore, local and global strains fields are studied using DVC from XRµT images of earlywood and latewood subjected to relative humidity variations. The coupling of these two materials is also investigated in order to evaluate their mechanical interactions and to understand the behavior at the growth-ring scale. A specific DVC procedure is developed for images of wood. The hygromechanical behaviors of earlywood, latewood and a growth-ring are compared. At the local scale, strains fields heterogeneities are highlighted and correlated to the local density. Their effect on the growth-ring behavior and the samples curvature is analyzed. A 3D finite elements model which takes into account local gradients of properties is finally developed to better understand earlywood-latewood mechanical interactions

O sistema especialista SISTEMAT tem por objetivo auxiliar pesquisadores da área de produtos naturais no processo de determinação estrutural de substâncias. Para tanto, utilizando dados provenientes de várias técnicas espectrométricas e espectroscópicas, principalmente RMN 13C, inúmeros programas foram desenvolvidos com a finalidade de propor o provável esqueleto de uma substância. Essa informação, juntamente com as substruturas apresentadas a partir de um conjunto de dados, é utilizada por geradores estruturais como grandes restrições, a fim de impedir a explosão combinatória e a geração de propostas estruturais incompatíveis com produtos naturais, além de reduzir o elevado tempo computacional gasto durante uma análise. Esse trabalho descreve o desenvolvimento e utilização dos módulos de reconhecimento de esqueletos, determinação e geração estrutural e simulação de dados de RMN 13C de esteróides. Assim, foi elaborada uma base de dados com 1436 substâncias distribuídas entre 119 tipos de esqueletos provenientes das mais diversas fontes naturais. Vários testes foram realizados e bons percentuais de acerto foram obtidos para o reconhecimento de esqueletos e geração de propostas estruturais através da sobreposição dos tipos de anéis encontrados em esqueletos de esteróides. Para validar as propostas estruturais apresentadas pelo gerador, bem como para prever os dados de deslocamentos químicos de novos esteróides, o simulador de dados de RMN 13C foi usado e, quando comparado a um programa comercial de mesma finalidade, apresentou maior exatidão na previsão dos dados. / The aim of the expert system SISTEMAT is to aid natural product researchers in the process of structural determination of organic substances. For that, using data from various spectrometric and spectroscopic techniques, mainly 13C NMR, countless programs were developed to propose the most probable skeleton of a substance. This information together with the substructures shown from the data set are utilized by structural generators as important constraints in order to avoid the combinatorial explosion problem and the generation of incompatible structural proposals for natural products, besides reducing the computational time spent during the analysis. This work describes the development and use of the modules of skeleton identification, structural determination and generation, and the 13C NMR data prediction of steroids. Thus, was built a database containing 1436 steroids distributed in 119 different skeletons originated from the most varied natural sources. Several tests were performed, wherein good hit percentuals were obtained for the skeleton identification and structural generation through the overlapping of the types of rings found in the steroid skeletons. For validation of the structural proposals shown by the generator as well as for prediction of the chemical shift data of new substances, the simulator of 13C NMR data was used and next compared with a commercial program of the same purpose, and exhibited higher accuracy in the data prediction.

A tese de doutorado tem como foco o desenvolvimento de nanopartículas superparamagnéticas (Fe3O4 - magnetita) hidrofílicas e lipofílicas aplicadas à nanotecnologia do petróleo. Inicialmente, os objetivos foram voltados para a elaboração e transferência de tecnologia envolvendo uma rota de síntese de nanopartículas lipofílicas, em escala semi-industrial. Para isso, foram realizados ensaios piloto num reator com capacidade de uma tonelada, visando a produção de nanopartículas magnéticas recobertas com ácido esteárico. Mais tarde, esse trabalho foi otimizado, permitindo sua execução em laboratório, prosseguindo depois, com um escopo mais amplo, incluindo a síntese de nanopartículas recobertas com polímero hidrofílico. Nesse sentido, foram desenvolvidas duas rotas inéditas para produção desses nanomateriais. Em um segundo estágio, as investigações foram voltadas para a utilização das nanopartículas sintetizadas, em estudos de avaliação das condições dos reservatórios de petróleo. Para isso, a técnica de ressonância magnética nuclear (RMN) foi explorada, monitorando o efeito da concentração dessas nanopartículas superparamagnéticas sobre o tempo de relaxação dos prótons, e o consequente efeito de contraste nas imagens em função da magnetização. A aplicação desse tipo de ferramenta (RMN) já vem sendo feita (sem nanopartículas magnéticas) pelas empresas prestadoras de serviço ao setor de petróleo e gás, na avaliação e perfilagem de reservatórios. Isso motivou o estudo dos nanomateriais magnéticos como sondas para melhorar o mapeamento de fluidos em meio poroso. Eles seriam aplicados como aditivos em fluidos de injeção em reservatórios, tanto para imageamento, como para a obtenção de parâmetros petrofísicos. Por fim, devido à presença de grupos carboxílicos na superfície das nanopartículas hidrofílicas, foram investigadas suas interações com microcristais de carbonato de cálcio, pensando no modelo de reservatório petrolífero do tipo carbonáceo. Explorando técnicas de microscopia eletrônica de varredura (MEV) e de microscopia Raman confocal, a presença das nanopartículas magnéticas sobre a superfície da matriz mineral foi constatada, confirmando sua interação efetiva com o CaCO3. Abordando a síntese, caracterização e aplicações das nanopartículas superparamagnéticas, esta tese proporciona uma base para estudos de aplicação de nanomateriais, assunto cada vez mais relevante, diante dos inúmeros problemas e desafios enfrentados pelo setor de petróleo e gás. / The Ph.D thesis is focused on the preparation of hydrophilic and lipophilic superparamagnetic nanoparticles (Fe3O4 - magnetite) for application in oil nanotechnology. The initial efforts have been directed to the upscaling of a laboratory route of synthesis of lipophilic nanoparticles, aiming technology transfer to the industry. Accordingly, a pilot process, involving a one ton reactor, has been tested for the production of magnetic nanoparticles coated with stearic acid. After this, the research has evolved, allowing the production in the laboratory scale, and continued, pursuing the development of nanoparticles coated with a hydrophilic polymer. Two new routes for the production of these nanomaterials have been developed. In a second step, the investigations were directed to the application of these nanoparticles to the evaluation of oil reservoirs, by monitoring the proton relaxation times, using nuclear magnetic resonance (NMR), and the consequent contrasting effects observed on the images, as a function of the magnetization and the concentration of these particles. Currently, NMR tools are being employed in the oil and gas sector for the evaluation and profiling of reservoirs. This fact has stimulated the use of such nanomaterials for improving the mapping of the fluids in porous media. Introduced as additives for fluid injection into reservoirs, they can enhance the imaging and also perform the rating of petrophysical parameters. Finally, the presence of carboxylic groups on the surface of the hydrophilic nanoparticles has been explored in studies of interaction with calcium carbonate, simulating a carbonaceous type reservoir. Based on electron microscopy (SEM) and confocal Raman microscopy, the presence of magnetic nanoparticles on the surface of the mineral matrix has confirmed the interaction of these particles with the CaCO3 surface. By developing the synthesis, characterization and application of superparamagnetic nanoparticles, this work provides a useful starting point for further research on the use nanoparticles, for solving problems and challenges in the oil and gas sector.

Pantothenate synthetase (PS), which catalyzes the last step in the pantothenate (vitamin B5) biosynthesis, is a dimeric enzyme present in bacteria, fungi and plants. The enzymatic properties of PS from Escherichia Coli, Mycobacterium tuberculosi, Fusarium Oxysporum, Lotus japonicus, Oryza sativum, Brassica napus and Arabidopsis thaliana have been characterized. The chemical reaction and the proposed mechanism of reaction are identical for PS, irrespective of the source. However, from an enzyme mechanistic point of view, plant PS’s are dissimilar to their bacterial counterparts, in that they exhibit “allosteric behavior”, a property that has not been observed in the bacterial enzyme. The behavior is quite remarkable when one takes into consideration the fact that plant PS’s share a high degree of sequence identity (~ 40%) with the bacterial enzymes. Even more intriguing is the structural mechanism proposed to explain the observed differences in structure between the PS’s from E.Coli and M.tb, which share a 42% sequence identity. Till date there is no structural information available on the plant PS’s and of the substrate bound conformation of E.coli PS. This thesis aims to provide an understanding on some aspects of the structure – function relationship of this physiologically important enzyme. Specifically, the solution properties of E. coli PS have been examined using high-resolution multinuclear, multidimensional NMR methods. Given the large size of the full-length protein (~ 63 KDa), the structurally distinct N and C-terminal domains were cloned and expressed as individual proteins and their properties investigated. Towards this end, the tertiary fold of the 40 kDa dimeric amino-terminal domain of E. coli pantothenate synthetase has been determined using multidimensional multinuclear nuclear magnetic resonance (NMR) methods (PDB entry 2k6c). Sequence specific resonance assignments for backbone HN, 15N, 13Cα, 13C', sidechain 13Cβ and aliphatic 13CH3 (of isoleucine, leucine and valine residues) were obtained using perdeuterated ILV-methyl protonated samples (BMRB entry 6940). Secondary structure of nPS was determined from 13C secondary chemical shifts and from short and medium range NOEs. Global fold of the 40 kDa homo-dimeric nPS has been determined using a total of 1012 NOEs, 696 dihedral angles, 260 RDCs, 155 hydrogen bonds, radius of gyration potential, non-crystallographic symmetry potential and database derived potential based upon the Ramachandran map. The calculated structures, which show that the N-terminal domain forms a homo-dimer in solution, is of high stereochemical quality as judged by the Ramachandran statistics (70% of the residues have backbone dihedral angles in the allowed region, 25.5% in the additionally allowed region, 4.0% in generously allowed region, and only 0.5% in disallowed region). Dynamics of nPS, which has rotational correlation time τc of 17.3 ns, was investigated by 15N relaxometry measurements. Results of these studies indicate that the E. coli protein exhibits dynamic nature at the dimer interface. These structural and dynamic features of the protein were found to be of interest when correlated with NMR based substrate binding studies. Interaction of homo-dimeric amino-terminal domain (nPS) of E. coli pantothenate synthetase (PS; encoded by the gene panC; E.C. 6.3.2.1) with the substrates pantoate, β-alanine, ATP and the product pantothenate has been studied using isotopically edited solution NMR methods. Addition of pantoate prior to ATP has led to the interesting observation that pantoate binds each monomer of nPS at two sites. ATP displaces a molecule of pantoate from the ATP binding site. β-alanine and pantothenate do not bind the protein under the condition studied. Binding of pantoate and ATP also manifests as changes in residual dipolar couplings (RDCs) of backbone 1H-15N pairs in nPS when compared to the free form of the protein. Structures of homo-dimeric nPS bound to two molecules of pantoate (PDB entry 2k6e) as well as to pantoate + ATP (PDB entry 2k6f) were calculated by inclusion of hydrogen bonds between the ligands and backbone 1H-15N pairs of nPS in addition to other NMR derived restraints. The ligand bound structures have been compared to the similar forms of the M. tb PS. Structure of each monomer of nPS bound to pantoate and ATP shows the substrates in a favorable orientation for the intermediate pantoyl adenylate to form. Moreover, at all stages of substrate binding the symmetry of the dimer was preserved. A single set of resonances was observed for all protein-ligand complexes implying symmetric binding with full-occupancy of the ligands bound to the protein. In an effort to understand the structural basis of the observed enzymatic properties of plant PS’s, a structural model of the Arabidopsis PS was constructed. The results of these structural and substrate binding studies strongly suggest that 1 Substrate binding to PS occurs only at the active site. 2 There are no additional substrate binding sites which could potentially participate as regulatory sites. 3 Pantoate does not bind at the dimer interface to induce the observed homotropic effects. 4 The structural results presented on the substrate bound forms of nPS have direct implication for the development of novel antibacterial and herbicidal agents. Recently a great deal of interest has been evinced on the effects of molecular crowding on protein folding / unfolding pathways. Nuclear magnetic resonance is the only method by which high resolution structural information can be obtained on partially denatured states of a protein under equilibrium condition. Recent methodological advances have enabled the determination of high resolution structures using information embedded in the residual dipolar couplings. Molecular crowding using confinement may thus reveal important details about chaperone mediated protein folding. We have attempted to develop a protocol to study the effects of molecular confinement by sequestering proteins in poly-acrylamide gels and then subjecting these protein molecules to denaturation and then characterize these states by nuclear magnetic resonance. The preliminary results of these studies are described here.

Nous étudions le ribozyme VS de Neurospora, en tant que système modèle, pour augmenter nos connaissances sur la relation entre la structure et la fonction chez les ARNs, ainsi que pour mieux comprendre le mécanisme de clivage de ce ribozyme. Il a été proposé précédemment que la boucle interne A730 dans la tige-boucle VI (SLVI) contient le site actif du ribozyme et lie un ou plusieurs ions métalliques qui pourraient participer au mécanisme réactionnel. Nous avons déterminé par spectroscopie RMN la structure de la tige-boucle SLVI contenant la boucle A730 afin d’éclaircir ce mécanisme. La structure obtenue est en accord avec les études biochimiques antérieures et présente un ou plusieurs sites de liaison au magnésium associé à la boucle interne. Suite à des études de cinétique et de mutagenèse, il a été proposé qu’une adénine localisée dans le site actif, A756, participe à la catalyse par acide/base générale. Des études de pH effectuées précédemment ont identifié un pKa catalytique (5.2-5.8) qui correspond probablement à l’équilibre de protonation du A756. À l’aide de méthodes utilisant le carbone-13, nous avons identifié un pKa modifié appartenant au A756, ce qui supporte le rôle de ce résidu dans la catalyse par acide/base générale. Les études structurales présentées ici aident donc à augmenter notre compréhension du mécanisme de clivage chez le ribozyme VS. / We are studying the Neurospora VS ribozyme as a model system to increase our knowledge of the structure-function relationship in RNA and to better understand the mechanism of the cleavage reaction. It has been previously postulated that the A730 internal loop of stem-loop VI (SLVI) forms the active site of the VS ribozyme and binds magnesium ion(s) that may participate in catalysis. To get insights into the catalytic mechanism, we have determined by NMR spectroscopy the structure of a SLVI fragment containing the A730 loop. The structure we obtained is in agreement with previous biochemical studies and contains one or more magnesium-ion binding sites in the active site. Based on kinetic and mutagenesis studies, it has been proposed that an adenine in the A730 loop, A756, is important for catalysis and may participate in general acid/base catalysis. Previous pH-dependent enzymatic studies identified a catalytic pKa of 5.2-5.8, which likely corresponds to the protonation equilibrium of this A756 adenine in the A730 loop. Using 13C NMR methods, we have identified a shifted pKa for A756, which gives additional support to the role of this residue in the general acid/base mechanism. The NMR studies presented here therefore increase our understanding of the cleavage reaction in the VS ribozyme.