Submitted by LUCAS BOSCOV BRAOS null (lucasbraos@hotmail.com) on 2018-01-05T13:13:58Z No. of bitstreams: 1 Tese_Lucas_Boscov_Braos.pdf: 1554570 bytes, checksum: e5419ca73de20bad4b5d5693b1cbae54 (MD5) / Approved for entry into archive by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br) on 2018-01-08T10:18:47Z (GMT) No. of bitstreams: 1 braos_lb_dr_jabo.pdf: 1554570 bytes, checksum: e5419ca73de20bad4b5d5693b1cbae54 (MD5) / Made available in DSpace on 2018-01-08T10:18:47Z (GMT). No. of bitstreams: 1 braos_lb_dr_jabo.pdf: 1554570 bytes, checksum: e5419ca73de20bad4b5d5693b1cbae54 (MD5) Previous issue date: 2017-12-01 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Conhecer as formas e as transformações do fósforo (P) aplicado via fertilizantes orgânicos e minerais é importante para melhorar o manejo e otimizar o uso do P. Os objetivos com o presente trabalho foram avaliar formas orgânicas e inorgânicas de P em solos adubados com esterco bovino, torta de filtro e superfosfato triplo em função do tempo de contato solo-adubo, e estabelecer relações entre as formas de P e a disponibilidade. As formas de P orgânico (Po) e inorgânico (Pi) foram determinadas em amostras de Latossolo Vermelho argiloso (LV) e de Argissolo Vermelho Amarelo arenoso (PVA), adubadas ou não com 100 mg dm-3 de P nas formas de esterco bovino, torta de filtro e superfosfato triplo, e mantidas em incubação por 15, 45, 90 e 180 dias. O Pi foi fracionado em P solúvel e fracamente retido, P ligado ao Al ou Fe, P ocluso e P ligado ao Ca. O P orgânico foi fracionado em Po lábil, Po da biomassa microbiana, Po moderadamente lábil, Po dos ácidos fúlvicos, Po dos ácidos húmicos e Po residual. Com as amostras de solo também foi conduzido experimento com plantas de milho para determinar a produção de matéria seca e a absorção de P. No latossolo foi observado maior teor de Pi ocluso e Po residual e a adubação também aumentou os teores dessas frações, indicando que o P dos adubos é incorporado às frações menos disponíveis, o que torna os teores de P disponível menores neste solo. No argissolo predominaram Pi ligado ao Fe e Po associado aos ácidos húmicos, e o P adicionado foi incorporado às formas ligadas ao Al e ao Fe, que contribuíram para maior disponibilidade de P neste solo. As frações mais estáveis tanto do Pi quanto do Po não se correlacionaram com o P disponível, e as frações menos estáveis se correlacionaram com a matéria seca acumulada e o P absorvido pelas plantas, indicando que mesmo estando em maior teor, as frações mais estáveis contribuem de forma mais limitada para a absorção de P pelas plantas. No solo latossolo, o acúmulo de P nas formas ligadas ao Al e ao Fe, no tratamento com superfosfato triplo, foi determinante para maior disponibilidade. No solo argissolo, o aumento das formas de P ligado ao Al e ao Fe, junto ao menor acúmulo de P ocluído no tratamento com esterco bovino, resultou na maior disponibilidade. A interação entre tipo de solo e adubo definiu o destino do P aplicado, bem como a disponibilidade / Evaluating the forms and transformations of phosphorus (P) applied via organic and mineral fertilizers is important to improve the management and optimize the use of P. The objectives of the present study were to evaluate organic and inorganic forms of P in two soil types, fertilized with dairy manure, filter cake and triple superphosphate, as a function of the incubation time, and to establish relationships between soil P forms and P available, plant uptake P and growth. The organic (Po) and inorganic (P) forms of P were determined on samples of typic Hapludox clayey and arenic Hapludult sand, fertilized or not with 100 mg dm-3 of P as dairy manure, filter cake and triple superphosphate, and incubated for 15, 45, 90 and 180 days. Pi was fractionated into soluble and weakly bound P, Al or Fe bound P, occluded P and Ca bound P. The organic Po was fractionated into labile Po, microbial Po, moderately labile Po, fulvic acids associate Po, humic acids associate Po and residual Po. In the soil samples, an experiment with maize plants was also carried out to determine the plant dry matter production and the absorption of P. It was observed higher levels of occluded Pi and residual Po in the Hapludox. The fertilization also increased the contents of these fractions indicating that P is incorporated to the less available fractions. Therefore, the available P contents were smaller in this soil. In the Hapludult, Fe bound Pi and humic acids associated Po were the predominant P forms. The added P was incorporated into the Al and Fe bound P forms, which contributed to higher P availability in this soil. The more stable fractions of both Pi and Po did not correlate with available P, and the less stable fractions correlated with accumulated dry matter and P uptook by plants, indicating that even having a higher P content, the more stable fractions contribute in a more limited way to the P uptake by plants. In the Hapludox, the increase of Al, Fe bound P in the triple superphosphate treatment was crucial for greater availability. In the Hapludult, the increase of Al, Fe bound P, with lower occlusion of P in cattle manure treatment, resulted in higher availability. The interaction between the soil and fertilizer type defined the fate of the applied P, as well as the availability / FAPESP 2014/11466-3

L’utilisation de détergents est inévitable pour les études structurales des protéines membranaires. Dodecylphosphocholine (DPC) est un des détergents les plus utilisés pour ce type d’études employant la spectroscopie de résonance magnétique nucléaire (RMN) en solution. L’effet des détergents sur la structure et la dynamique des macromolécules est une problématique importante, mais peu étudiée à ce jour. Dans cette étude nous avons caractérisé la dynamique à l’échelle de la milliseconde, la liaison des substrats ainsi que des propriétés structurales de trois protéines membranaires différentes solubilisées dans des micelles de DPC. Ces protéines font partie de la famille des transporteurs mitochondriaux et nous avons choisi les séquences de la levure (ORC1, GGC1, AAC3). Nous avons détecté de la dynamique à l’échelle de la milliseconde qui est distribuée d’une manière asymétrique à travers la structure. En contradiction avec des propos de la littérature, nous montrons que cette dynamique n’est pas corrélée à la fonction, puisqu’elle n’est pas modifiée par des mutations qui inhibent le transport effectué par ces protéines quand elles sont reconstituées dans des liposomes. En plus, nous avons pu montrer que leur spécificité par rapport aux substrats, n’est pas conservée quand ces transporteurs sont reconstitués dans du DPC, mettant en question leur fonctionnalité dans ce détergent. La RMN a aussi permis de démontrer que les structures tertiaire et secondaire sont perturbées dans les micelles avec quelques hélices transmembranaires apparaissant exposées au solvant. Nous avons donc conclu que la présence du détergent a un effet fort sur les trois transporteurs mitochondriaux de notre étude et probablement d’autres protéines similaires, en les rendant très flexible. Nos résultats indiquent un probable effet général de ce détergent sur les protéines membranaires, comme nous le discutons dans une analyse détaillée de quelques études de protéines membranaires décrites dans la littérature. Dans la seconde partie de ce travail, nous avons adressé une question fondamentale de la dynamique des protéines: comment se comportent les protéines dans des cristaux ? Nous avons étudié la dynamique de l’ubiquitine cristalline à l’échelle de la milliseconde afin de comprendre l’influence de la maille cristalline sur ce type de mouvement. Pour ce faire, nous avons employé la RMN à l’état solide et des simulations de dynamique moléculaire de la protéine dans différents réseaux cristallins distincts. Il est intéressant à noter que dans ces cristaux on détecte toujours des processus locaux d’échange dynamique sur une échelle de temps de la milliseconde. Cependant, en comparant les résultats obtenus avec différentes formes cristallines, nous constatons que les paramètres thermodynamiques des différents états en échange et les vitesses d’interconversion entre ces dernières sont significativement modifiés par les contacts cristallins. De plus, nous avons détecté des mouvements globaux de type «rocking» des ces molécules à l’état cristallin qui surviennent également à l’échelle de la milliseconde. Ceci suggère que les mouvements globaux et locaux sont corrélés. Cette observation ouvre la discussion de l’importance de ce type de mouvements pour la qualité et l’interprétation des données des expériences de diffraction des rayons-X. / The use of detergents is often unavoidable in the structural studies of membrane proteins. Dodecylphosphocholine (DPC) is one of the most commonly used detergents for such studies in solution state NMR spectroscopy. The effect of detergent on structure and dynamics remains an important and poorly understood question. In this study we have investigated millisecond dynamics, substrate binding and structural features of three different yeast proteins from mitochondrial carrier family (GGC1, ORC1 and AAC3) in DPC micelles. We have detected millisecond dynamics, which are asymmetrically distributed across the structure. Contrary to previous claims, we show that these dynamics are unrelated to function, as they are not affected by the substitutions which abolish mitochondrial carrier transport in proteoliposomes. Furthermore, we could show that the very well-defined substrate specificity of these proteins in membranes is abolished when they are reconstituted in DPC, questioning their functionality. Structural investigations have revealed that both tertiary and secondary structures of these carriers are perturbed in DPC micelles, with some TM helices showing substantial solvent exposure. We have concluded from these observations that DPC detergent strongly perturbs these, and likely other mitochondrial carriers by rendering them very flexible. Our findings point to a possibly general effect of this detergent on membrane proteins, as we discuss with examples of previously studied membrane proteins. In the second part we have addressed a fundamental question of protein dynamics: how do proteins move inside crystals? We have investigated ms dynamics in a crystalline ubiquitin to gain the insight on the impact of the crystalline lattice on such motions, using solid-state NMR and ms long MD simulations of explicit crystal arrangements. Interestingly a local dynamic exchange process on a ms time scale is still present in crystals. However, by comparing different crystal forms we establish that the thermodynamics of the exchanging states and their interconversion rate constants are significantly altered by the crystal contacts. Furthermore, we detect overall "rocking" motion of molecules in the crystal, occurring on a tens-of-ms time scale, and provide evidence that overall and local motion are coupled. We discuss the implications of ms dynamics on the data quality in X-ray diffraction experiments.

Title: The Study of Dynamic Behaviour and Interactions During the Tempera- ture-Induced Phase Separation in Polymer Solutions Author: Hana Kouřilová Department / Institute: Charles University in Prague, Faculty of Mathemat- ics and Physics, Department of Macromolecular Physics Supervisor of the doctoral thesis: doc. RNDr. Lenka Hanyková, Dr. Abstract: 1 H and 13 C high-resolution NMR spectroscopies were used for the phase separation investigation in three types of polymer solutions: i) poly(N -isopropylmethacrylamide)/D2O/ethanol with or without negatively charged comonomer sodium methacrylate, ii) random copolymers poly(N -isopro- pylmethacrylamide-co-acrylamide) in D2O, D2O/ethanol and D2O/acetone and iii) D2O solutions of polymer mixtures poly(N -isopropylmethacrylamide)/poly(N - vinylcaprolactam). For i) cononsolvency effect and influence of temperature on the phase separation was studied. Differences between mesoglobules formed as a consequence of cononsolvency effect and of temperature were found. While inside the cononsolvency-induced mesoglobules no bound ethanol molecules were detect- ed, in the mesoglobules formed by the effect of temperature ethanol molecules were present. The charge introduced into the polymer chains strenghtens polymer- solvent interactions. For ii) mesoglobules were found to be...

Le Cancer, l’une des pathologies les plus fréquentes au sein de la population, possède encore actuellement un taux de morbi-mortalité important tous sexes confondus, et ce malgré les importants progrès diagnostiques et thérapeutiques réalisés. D’un point de vue diagnostique, dans une approche dite de « Biologie de systèmes », en complément de l’étude anatomo- pathologique qui reste la référence, de nouvelles techniques ont été développées pour la caractérisation de profils métaboliques (Métabolomique) d’échantillons tissulaires pathologiques ou non, parmi lesquelles la Spectroscopie RMN HRMAS. Après un bref rappel théorique et avoir dressé le bilan des applications de cette technique en Cancérologie, nous avons exposé les différentes étapes du protocole à mettre en place afin d’envisager son implémentation dans un cadre hospitalier. L’ensemble des résultats présentés permettent d’envisager l’utilisation de cette technique en pratique clinique courante. Il faut néanmoins valider la robustesse des modèles statistiques élaborés et confirmer ces résultats sur de plus grandes cohortes d’échantillons. Des développements technologiques, analytiques et statistiques sont également nécessaires. / Cancer, one of the most frequent pathologies among the population, has still an important morbidity-mortality rate all sex confounded, despite the important diagnostical and therapeutical progresses achieved. From a diagnostical point of view, in a so called “Systems Biology approach”, as a complement of the gold standard histopathological study, some new techniques have been developed for the characterization of metabolic profiles (Metabolomics) of tissular samples pathological or not, among which HRMAS NMR Spectroscopy. After some brief theoretical considerations and after reporting the applications of this technique in Cancerology, we exposed the different steps of the protocol to design in order to consider its implementation in a hospital set up. All the results presented allow considering the use of this technique in a clinical routine. Nevertheless, it is necessary to validate the robustness of the statistical models built and to confirm these results on much larger cohorts of samples. Some technical, analytical and statistical developments are also needed.

La maladie de Parkinson est une maladie neurodégénérative du système cerveau central conduisant à l'apparition des troubles moteurs caractéristiques de la maladie : akinésie, rigidité et tremblement de repos. La perte des neurones dopaminergiques de la voie nigro-striée va conduire à des modifications biochimiques au niveau du putamen. Notamment, les travaux réalisés en électrophysiologie, microdialyse et spectroscopie par résonance magnétique (SRM) suggèrent une hyperactivité de la voie glutamatergique cortico-striatale associée à un changement du microenvironnement glial au niveau du putamen. Ces observations conduisent à penser à une adaptation du cycle glutamate-glutamine ayant lieu entre les neurones et les astrocytes en réponse à la perte neuronale. Ainsi, dans ce travail de thèse, deux approches ont été développées afin de suivre par SRM les changement métaboliques impliqués dans la pathologie parkinsonienne, notamment les variations des concentrations en glutamate et glutamine dans le putamen. Une première approche de la quantification des métabolites cérébraux par spectroscopie du 1H, technique couramment utilisée en clinique, a été utilisée pour suivre l'évolution des métabolites d'intérêt chez des patients parkinsoniens à jeun ou suite à la prise d'un traitement dopaminergique. Si cette étude a révélé des changements de concentration en N-acetylaspartate, créatine et myoinositol chez les patiens parkinsoniens, aucun changement du métabolisme glutamatergique n'a pu être observé par cette technique, peut-être à cause d'un manque de sensibilité de la technique pour discriminer les pools de glutamate et de glutamine. De ce fait, une nouvelle approche de SRM du Carbone 13C a été développée pour le suivi du cycle glutamate-glutamine in vivo, c'est la polarisation dynamique nucléaire (PDN). Grâce à la haute sensibilité de cette technique, il est désormais possible de suivre des voies métaboliques in vivo en temps réel. La mise en place et l'optimisation de la PDN pour le suivi du cycle glutamate-glutamine a été un des objectifs au cours de ce projet de thèse. Validée sur un groupe d'animaux contrôle, cette technique offre un avenir prometteur pour l'analyse de ce flux dans les pathologies neurodégénératives. En conclusion, les stratégies diagnostiques en clinique par SRM du 1H restent, à l'heure actuelle, peu sensibles pour l'étude des modifications du cycle glutamate-glutamine in vivo chez l'homme. Les développements technologiques réalisés au cours de ce travail de thèse notamment avec la PDN du 13C laissent entrevoir une nouvelle approche pour le suivi en temps réel de ce métabolisme cérébral. Si la PDN est principalement utilisée dans des études précliniques, la disponibilité de nouveaux systèmes cliniques pourrait permettre son avènement en tant que nouvelle stratégie de diagnostic en imagerie clinique. / Parkinson's disease is a neurodegenerative disorder characterized by motor troubles such as akinesia, rigidity and tremor. The loss of dopaminergic neurons from the nigro-striatal pathway will lead to biochemical changes in the putamen. Especially, works on electrophysiology, micro dialysis and magnetic resonance spectroscopy (MRS) suggests hyperactivity of the glutamatergic cortico-striatal pathway associated with glial microenvironment changes. These observations suggest a modification of the glutamate-glutamine cycle occurring between neurons and astrocytes in response to neuronal loss.In this thesis, two approaches have been developed in order to follow by MRS the metabolic changes occuring in Parkinson's disease. In particular, we want to follow the changes in glutamate-glutamine cycle inside the putamen.in a first study, a a 1H MRS approach was used to assess the metabolic changes inside the putamen of Parkinson's disease without or under dopaminergic treatment. In this study, changes in N-acetylaspartate, creatine and myo-inositol were observed in Parkinsonian patients, but no change in glutamatergic metabolism was observed. This could be due to the lack of sensitivity of the technique to differentiate glutamate and glutamine pools.Thus, we chose to use a new 13C carbon MRS approach in order to follow dynamically in vivo the glutamate-glutamine cycle inside the brain: dynamic nuclear polarization (DNP). Thanks to the high sensitivity of this technique, it is now possible to follow metabolic pathways in vivo in real time. The implementation of DNP was assessed under a control group of animals. This technique offers a new promising tool for the analysis of this flow under pathologic conditions.To conclude, the MRS strategies for clinical diagnostic strategies remain, at present, poorly sensitive for the study of glutamate-glutamine cycle in vivo in humans. The development of DNP opens the door to a new approach for real-time monitoring of this cerebral metabolism Even if DNP is mainly used in preclinical studies at present, the development of new clinical systems could lead to its emergence as a new diagnostic strategy in clinical imaging.

Le cancer est la première cause de morbi-mortalité dans le monde. La recherche de biomarqueurs diagnostiques, pronostiques et prédictives de la réponse aux traitements est capitale dans l’amélioration de la prise en charge de ce fléau mondial. Nous avons choisi une technique récente qui est la spectroscopie RMN HRMAS et des méthodes d’analyse statistique robustes (PCA et PLS-DA), afin d’établir les profils métaboliques des cancers épithéliaux de l’ovaire et des cancers mammaires. Nous avons établi, après un rappel théorique de la spectroscopie RMN HRMAS, un état d’art des applications médicales de cette technique, notamment gynécologiques chez la femme et urogénitales chez l’homme. Nous avons décrit les différentes étapes de la démarche établie pour l’analyse spectrale : préparation de l’échantillon tissulaire, acquisition RMN et analyse statistique. Nous avons montré que cette technique, permettant une analyse rapide (20 min) et non destructive d’échantillons tissulaires intacts, est applicable à la prise en charge thérapeutique des patientes atteintes de carcinomes ovariens et mammaires. Elle a permis, dans le cas des cancers de l’ovaire, de caractériser métaboliquement les trois types histologiques (séreux, endométrioïdes et mucineux) et le tissu ovarien sain, de générer des modèles statistiques permettant de classer les tumeurs borderline et de prédire la survie des patientes et la réponse à la chimiothérapie. Dans le cas des cancers du sein, elle a permis de discriminer métaboliquement les carcinomes mammaires, les fibroadénomes et le tissu sain et d’étudier métaboliquement les différents indicateurs histologiques des ces carcinomes. Nous projetons de confirmer ces résultats préliminaires très encourageants sur une plus grande cohorte. / Cancer is the leading cause of morbidity and mortality worldwide. The search for diagnostic, prognostic and predictive biomarkers of response to treatment is crucial in improving the management of this global scourge. We chose a new technique that is HRMAS NMR spectroscopy and robust statistical analysis methods (PCA and PLS-DA), to establish the metabolic profiles ofepithelial ovarian and breast cancers. We have determined, after a theoretical reminder of HRMAS NMR spectroscopy, a state of the art including medical applications of this technique, mainly gynecological in woman and uro-genital in man. We describe the different steps of the process established for spectral analysis : preparation of tissue sample, NMR acquisition and statistical analysis. We showed that this technique, allowing a rapid analysis (20 min) and non-destructive of intact tissue samples, is applicable to the therapeutic management of patients with breast and ovarian carcinomas. It has, in the case of ovarian cancer, characterize metabolically the three histological types (serous, endometrioid and mucinous) and healthy ovarian tissue, generate statistical models to classify borderline tumors and predict survival patients and response to chemotherapy. In the case of breast cancer, it could discriminate metabolically breast carcinomas, fibroadenomas and healthy tissue and study metabolically different histological indicators of these carcinomas. We plan to confirm these very encouraging preliminary results in a larger cohort.

Carbohydrates are ubiquitous components in nature involved in a range of tasks. They cover every cell and contribute both structural stability as well as identity. Lipopolysaccharides are the outermost exposed part of the bacterial cell wall and the primary target for host-pathogen recognition. Understanding the structure and biosynthesis of these polysaccharides is crucial to combat disease and develop new medicine. Structural determinations can be carried out using NMR spectroscopy, a powerful tool giving information on an atomistic scale. This thesis is focused on method development to study polysaccharide structures as well as application on bacterial lipopolysaccharides. The focus has been to incorporate a bioinformatics approach prior to analysis by NMR spectroscopy, and then computer assisted methods to aid in the subsequent analysis of the spectra. The third chapter deals with the recent developments of ECODAB, a tool that can help predict structural fragments in Escherichia coli O-antigens. It was migrated to a relational database and the aforementioned predictions can now be made automatically by ECODAB. The fourth chapter gives insight into the program CASPER, a computer program that helps with structure determination of oligo- and polysaccharides. An approach to determine substituent positions in polysaccharides was investigated. The underlying database was also expanded and the improved capabilities were demonstrated by determining O-antigenic structures that could not previously be solved. The fifth chapter is an application to O‑antigen structures of E. coli strains. This is done by a combination of NMR spectroscopy and bioinformatics to predict components as well as linkages prior to spectra analysis. In the first case, a full structure elucidation was performed on E. coli serogroup O63, and in the second case a demonstration of the bioinformatics approach is done to E. coli serogroup O93. In the sixth chapter, a new version of the CarbBuilder software is presented. This includes a more robust building algorithm that helps build sterically crowded polysaccharide structures, as well as a general expansion of possible components. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 5: Manuscript.</p>

NMR chemical shifts have an extremely high information content on the behaviour of macromolecules, owing to their non-trivial dependence on myriads of structural and environmental factors. Although such complex dependence creates an initial barrier for their use for the characterisation of the structures of protein and nucleic acids, recent developments in prediction methodologies and their successful implementation in resolving the structures of these molecules have clearly demonstrated that such barrier can be crossed. Furthermore, the significance of chemical shifts as useful observables in their own right has been substantially increased since the development of the NMR techniques to study low populated 'excited' states of biomolecules. This work is aimed at increasing our understanding of the multiple factors that affect chemical shifts in proteins and nucleic acids, and at developing high-quality chemical shift predictors for atom types that so far have largely escaped the attention in chemical shift restrained molecular dynamics simulations. A general approach is developed to optimise the models for structure-based chemical shift prediction, which is then used to construct CH3Shift and ArShift chemical shift predictors for the nuclei of protein side-chain methyl and aromatic moieties. These results have the potential of making a significant impact in structural biology, in particular when taking into account the advent of recent techniques for specific isotope labelling of protein side-chain atoms, which make large biomolecules accessible to NMR techniques. Through their incorporation as restraints in molecular dynamics simulations, the chemical shifts predicted by the approach described in this work create the opportunity of studying the structure and dynamics of proteins in a wide range of native and non-native states in order to characterise the mechanisms underlying the function and dysfunction of these molecules.

abstract: Coronaviruses are the causative agents of SARS, MERS and the ongoing COVID-19 pandemic. Coronavirus envelope proteins have received increasing attention as drug targets, due to their multiple functional roles during the infection cycle. The murine coronavirus mouse hepatitis virus strain A59, a hepatic and neuronal tropic coronavirus, is considered a prototype of the betacoronaviruses. The envelope protein of the mouse hepatitis virus (MHV-E) was extensively screened with various membrane mimetics by solution state nuclear magnetic resonance spectroscopy to find a suitable mimetic, which allowed for assignment of ~97% of the backbone atoms in the transmembrane region. Following resonance assignments, the binding site of the ion channel inhibitor hexamethylene amiloride (HMA) was mapped to MHV-E using chemical shift perturbations in both amide and aromatic transverse relaxation optimized spectroscopy (TROSY) spectra, which indicated the inhibitor binding site is located at the N-terminal opening of the channel, in accord with one of the proposed HMA binding sites in the envelope protein from the related SARS (severe acute respiratory syndrome) betacoronavirus. Structure calculation of residues M1-K38 of MHV-E, encompassing the transmembrane region, is currently in progress using dihedral angle restraints obtained from isotropic chemical shifts and distance restraints obtained from manually assigned NOE cross-peaks, with the ultimate aim of generating a model of the MHV-E viroporin bound to the inhibitor HMA. This work outlines the first NMR studies on MHV-E, which have provided a foundation for structure based drug design and probing interactions, and the methods can be extended, with suitable modifications, to other coronavirus envelope proteins. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2020

Les chaperons moléculaires, une famille de protéines diverses en structure et taille, sont dédiés à accompagner, replier et protéger d’autres protéines afin qu’elles atteignent leur conformation finale et leur emplacement dans la cellule. Dans ce but, les chaperons moléculaires doivent être hautement spécialisés dans l’exécution de tâches spécifiques, telles que le repliement, le transport ou la désagrégation, et polyvalents dans leur motifs de reconnais- sance, afin de pouvoir interagir avec un grand nombre de protéines di érentes. Di érents chaperons moléculaires collaborent au sein de la cellule, formant ainsi un réseau complexe qui assure le contrôle de la qualité du protéome. Les interactions entre les di érents partenaires de ce réseau et entre les chap- erones et leurs substrats sont souvent dynamiques, ce qui rend leur obser- vation structurale particulièrement di cile pour les techniques de biologie structurale. Par conséquent, il y a à ce jour peu d’information sur les struc- tures et mécanismes d’interaction au sein des complexes chaperon-substrate. Dans cette thèse, je présente des études sur la structure, la dynamique et les interactions entre les substrats de deux chaperons moléculaires, en utilisant diverses méthodes biophysiques et in vivo.Dans la première partie, je montre que la chaperone TIM910, située dans l’espace inter-membranaire des mitochondries, lie ses substrats, des protéines membranaires destinées aux deux membranes mitochondriales, d’une manière très dynamique. Non seulement le complexe TIM910 est en échange constant entre les espèces monomèriques et hexameriques, mais aussi le substrat lié échange entre mulitples conformations à une échelle de millisecondes. Sur la base de la résonance magnétique nucléaire (RMN), de small-angle X-ray scat- tering (SAXS), de l’ultracentrifugation analytique (AUC) et des expériences mutationnelles in vivo et des tests fonctionnels d’import dans les mitochon- dries, je propose un modèle structurale de l’interaction entre le chaperon et la protéine membranaire. TIM910 lie ses substrats dans une poche hydrophobe à l’extérieur du chaperon. Cette interaction est modulaire et se fait avec un ou deux hexamères de TIM910, en fonction de la longueur du substrat.Dans la deuxième partie, nous avons étudié le comportement du récepteur N-terminal du unfoldase ClpC1 de M. tuberculosis en présence d’antibiotiques et de ligands di érents. Le domaine N-terminal de ClpC1 est le site de liai- son de divers antibiotiques nouveaux contre M. tuberculosis. L’antibiotique Cyclomarin A supprime complètement la dynamique induite par le ligand arginine-phosphate. Nous proposons que cette suppression de la dynamique soit le principe fondamental du mécanisme d’action de cet antibiotique.Dans les deux cas, les structures X-ray des chaperons dans leur état apo et la structure de ClpC-NTD liée à des antibiotiques étaient disponibles, mais ces structures statiques ne su sent pas pour expliquer le mécanisme d’action. La structure X-ray de TIM910 n’a pas fourni d’ indication sur l’endroit ou la façon dont les substrats sont liés. De même, les structures X-ray du domaine N-terminal de apo et de Cyclomarine A de ClpC1 ne présentent que des di érences de structure mineures. Les deux exemples montrent que les données structurelles statiques souvent ne permettent pas d’expliquer le fonctionnement d’un système moléculaire, donc la combinaison de di érentes techniques et le développement de nouvelles méthodes pour étudier les complexes chaperon-substrat sont primordiaux pour comprendre leur fonction. / The diverse group of molecular chaperones is dedicated to accompany, fold and protect other proteins until they reach their final conformation and loca- tion inside the cell. To this end, molecular chaperones need to be specialized in performing specific tasks, like folding, transport or disaggregation, and versatile in their recognition pattern to engage many di erent client pro- teins. Moreover, molecular chaperones need to be able to interact with each other and with other components of the protein quality control system in a complex network. Interactions between the di erent partners in this network and between the substrate and the chaperone are often dynamic processes, which are especially di cult to study using standard structural biology tech- niques. Consequently, structural data on chaperone/substrate complexes are sparse, and the mechanisms of chaperone action are poorly understood. In this thesis I present investigations of the structure, dynamics and substrate- interactions of two molecular chaperones, using various biophysical and in vivo methods.In the first part I show that the mitochondrial membrane protein chap- erone TIM910 binds its substrates in a highly dynamic manner. Not only is the TIM910 complex in constant exchange between monomeric and hex- americ species, but also the bound substrate samples multiple conformations on a millisecond timescale. Based on nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), analytical ultracentrifugation (AUC) and in vivo mutational experiments I propose a structural model of the chap- erone/membrane protein interaction. TIM910 binds its substrates in a hy- drophobic pocket on the exterior of the chaperone in a modular fashion, where the number of TIM910 complexes bound depends on the length of the substrate.In the second part I studied the behavior of the N-terminal receptor do- main of the ClpC1 unfoldase from M.tuberculosis in the presence of di erent antibiotics and ligands. The N-terminal domain of ClpC1 is the binding site for various new antibiotics against M.tuberculosis. The antibiotic cyclomarin completely abolishes dynamics induced by the ligand arginine-phosphate. We propose that this suppression of dynamics is the underlying principle for the mechanism of action of this antibiotic.In both cases X-ray structures of the apo or antibiotic bound form were available, but not su cient to explain the mechanism of action. The X- ray structure of TIM910 provided no evidence on where or how substrates are bound. Likewise, X-ray structures of the apo and cyclomarin-bound N-terminal domain of ClpC1 show only minor di erences in structure.Both examples show that static structural data is often not enough to explain how a molecular system works, and only the combination of di er- ent techniques, including newly developed methods enable the atomic-level understanding of chaperone/substrate complexes.