No description available.

Les génomes eucaryotes sont très complexes et peuvent être très grands. Par exemple, le génome humain contient environ de 20 000 à 25 000 gènes codant pour des protéines. L'expression de ces gènes doit être strictement régulée à de nombreux niveaux (tels que l'organisation de la chromatine, la transcription des gènes, le traitement et l'exportation de l'ARN messager ainsi que la traduction) pour le bon fonctionnement de la machinerie cellulaire. De nombreuses protéines et complexes protéiques sont impliqués dans ces processus essentiels de régulation, tels que les remodeleurs de la chromatine, les activateurs, co-activateurs et répresseurs de la transcription et particulièrement la machinerie générale de transcription. Chez les eucaryotes, la transcription de gènes codant pour des protéines est appelée transcription génique de classe II, elle est catalysée par l'ARN polymérase II (Pol II). La transcription des gènes par la polymérase II nécessite l'interaction coopérative de plusieurs protéines et complexes protéiques afin de faciliter l'assemblage d'un complexe de pré-initiation (PIC) au promoteur de base. Le complexe de pré-initiation comprend l'ARN polymérase II et les facteurs de transcription généraux (GTFs) - TFIIA, TFIIB, TFIID, TFIIE, TFIIF et TFIIH ainsi que le complexe de Médiateur et une grande variété de co-activateurs transcriptionnels.Une étape fondamentale dans l'assemblage d'un complexe de pré-initiation est la reconnaissance du promoteur de base par le facteur de transcription général TFIID. TFIID est un complexe multi protéique d'environ 1,6 MDa. Chez l'homme, il comprend une vingtaine de sous-unités constituées de 14 protéines différentes - la protéine de liaison à la boite tata (TBP) et ses facteurs associés (TAFs 1 à 13). Une série d'études sur la TFIID humaine et ses sous-ensembles ont été réalisés depuis sa découverte il y a plus de 20 ans, cherchant à comprendre la structure et le mécanisme de ces facteurs de transcription général essentiel, cependant l'architecture de TFIID, ses activités, ses fonctions, ses rouages et ses mécanismes d'assemblage cellulaire reste largement incompris à ce jour.Cette thèse décrit les études biochimiques que nous avons effectuées sur trois sous-ensembles distincts de TFIID humain. Nous avons utilisé un certain nombre de techniques de biologie structurale : la cristallographie, la spectroscopie à résonance magnétique nucléaire (RMN) et la diffusion des rayons X aux petits angles (SAXs), pour étudier le complexe formé par les facteurs humains, associés à la protéine de liaison à la boite tata, TAF1 et TAF7. Ces études structurelles fournissent un aperçu détaillé sur l'interface d'interaction complexe de TAF1/TAF7, misent de concert avec des données disponibles dans la littérature, elles mettent en évidence la nature dynamique de l'interaction TAF1/TAF7 dans le complexe de TFIID humain.Dans une deuxième étude, nous avons analysé un complexe formé par TAF11, TAF13 et TBP en utilisant un panel de méthodes biophysiques et biochimiques : l'analyse électrophorétique de retard sur gel (EMSA), l'ultracentrifugation analytique (AUC), la chromatographie d'exclusion stérique (SEC) analyse, le pull-down, la spectrométrie de masse native et la spectrométrie de masse chimique à réticulation (CLMS). Ce complexe fait penser au complexe TAF1/TBP qui imite la boite tata.De plus, dans le cadre des efforts en cours au sein du laboratoire du Pr Imre Berger afin de déterminer la structure de l'holo-TFIID humaine, nous avons reconstitué un grand sous-ensemble de TFIID (900 KDa) appelé 9TAF, qui est composé de neuf différents facteurs associés de TBP. Nous avons effectué des études d'électro-microscopie par coloration négative sur le complexe 9TAF qui nous ont fourni des informations à faible résolution. Ces études ouvrent la voie à de futures études de cryo-EM sur le complexe 9TAF pour obtenir un modèle de plus haute resolution. / Eukaryotic genomes are highly complex and can be very large. For example, the human genome contains approximately 20,000-25,000 protein coding genes. Expression of these genes needs to be tightly regulated at many levels, including chromatin organization, gene transcription, mRNA processing and export and translation, for proper functioning of cellular machinery. Many proteins and protein complexes are involved in these essential regulatory processes, examples include chromatin remodelers, transcriptional activators and coactivators, transcriptional repressors and notably the general transcription machinery. Transcription of protein coding genes in eukaryotes is called Class II gene transcription, and is catalyzed by RNA polymerase II (Pol II). Gene transcription by Pol II requires the cooperative interaction of multiple proteins and protein complexes to facilitate the assembly of a preinitiation complex (PIC) at the core promoter. The PIC comprises Pol II and the General Transcription Factors (GTFs)- TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH, together with the Mediator complex and a large variety of transcriptional coactivators.A fundamental step in PIC assembly is recognition of the core promoter by GTF TFIID, a magdalton sized multiprotein complex. In humans, TFIID comprises about twenty subunits made up of 14 different proteins – the TATA box binding protein (TBP) and its associated factors (TAFs, numbered 1 to 13). A range of studies on human TFIID and its subassemblies have been carried out since its discovery more than two decades ago, to understand the structure and mechanism of this essential GTF, but the architecture of TFIID, its activities, its functions, its inner workings and the mechanisms of its cellular assembly have eluded detailed understanding to date.This thesis describes biochemical, biophysical, structural and functional studies carried out on three distinct human TFIID subassemblies. We used a number of structural biology techniques, including crystallization, nuclear magnetic resonance (NMR) spectroscopy and small angle X-ray scattering (SAXS) to analyse a complex formed by the human TBP associated factors TAF1 and TAF7. These structural studies provide detailed insights into the intricate interaction interface formed by TAF1 and TAF7, and, together with other data available from the literature, highlight the dynamic nature of the TAF1/TAF7 interaction in the human TFIID complex.In a second study, we analyzed a novel complex formed by TAF11, TAF13 and TBP using a range of biophysical and biochemical methods including electrophoretic mobility shift assay (EMSA), analytical ultracentrifugation (AUC), size exclusion chromatography (SEC) analysis, pull-down assay, native mass-spectroscopy and chemical cross-linking mass spectroscopy (CLMS). This complex is reminiscent of a so-called TATA-box mimicry discovered previously in a TAF1/TBP complex.As part of the ongoing efforts in the Berger laboratory to determine the structure of human holo-TFIID, we furthermore produced and purified a large (~900 kDa) TFIID subassembly called 9TAF, which is composed of nine different TBP associated factors. We carried out negative stain EM studies and random conical tilt (RCT) analysis on 9TAF to obtain low resolution structural information. These studies set the stage for future cryo-EM studies of this 9TAF complex to obtain a high(er) resolution model to decipher the inner workings of human TFIID.

No description available.

The study of quadrupolar nuclei using NMR spectroscopy in the solid state significantly increased in popularity from the end of the 20th century, with the introduction of specific methods to acquire spectra free from the effects of the quadrupolar interaction, that results in broadened lineshapes that cannot be completely removed by spinning the sample at the magic angle (MAS), unlike most of the other interactions present in the solid state. The first technique which allows, without any specific hardware, the removal of this broadening has been the Multiple-Quantum MQMAS experiment. The method quickly gained a popularity within the NMR community, with numerous successful applications published. However, the multiple-quantum filtration step in this experiment relies on severely limits sensitivity, restricting application to the most sensitive nuclei. Extending the applicability of MQMAS to less receptive nuclei requires the use of signal improvement techniques. There are multiple examples of such approaches in the literature, but most of these require additional optimisation that may be time-consuming, or simply impossible, on less receptive nuclei. This work introduces a novel signal improvement technique for MQMAS, called FAM-N. Its optimisation is solely based on density matrix simulations using SIMPSON, implying no additional experimental optimisation is required, while improving the signal in MQMAS spectra by equivalent or higher amounts than other common methods. In order to prove the applicability of this method on virtually any system, FAM-N has been investigated by simulation, and tested experimentally using a number of model samples, as well as samples known to be challenging to study by NMR. This work also explores other aspects of NMR spectroscopy on quadrupolar nuclei. Adiabatic inversion of the satellite populations can be performed to improve the central transition signal in static or MAS spectra. A range of methods has been tested and compared, with particular attention given to hyperbolic secant-shaped pulses, for which its performance have been described. Finally, cross-polarisation from a spin I = 1/2 nucleus to a quadrupolar nucleus has been investigated. After reviewing the theory for the static case, simulations have been performed under MAS in order to identify the conditions for efficient magnetisation transfer, with applications in spectral editing or for the combination with MQMAS.

The thesis entitled "Pushing the Limits of NMR Sensitivity and Chiral Analysis: Design of New NMR Methods and Bio-molecular Tools" consists of six chapters. The research work reported in this thesis is focused on the development of novel chemical and NMR methodological approaches for enantiomeric analysis and mea- surement of residual dipolar couplings (RDCs), and the development of sensitivity enhanced slice selective NMR experiments for obtaining pure shift 1H spectra and the measurement of scalar couplings. The thesis is divided into two parts. The Part I comprises chapters 2-4, where the enantiomeric analysis is discussed, which includes newly developed chiral reagents, two new weak chiral aligning media and design of novel NMR techniques. Part II comprises chapters 5 and 6, which discusses new sensitivity enhanced slice selective NMR techniques. Chapter 1 gives a general introduction to NMR and the problems investigated in the remaining chapters of the thesis. The chapter starts with a brief discussion on the introduction, advancements and general applications of NMR, discussion is also given on the NMR approaches for enantiomeric analysis both in isotropic and anisotropic phases and the measurement of RDCs, including the benefits and limitations associated with each approach. The chapter sets the tone by discussing limitations of the existed NMR enantiomeric approaches and slice-selective techniques, and builds the bridge for the rest of the chapters by addressing these limitations. The chapter also introduces slice selective experiments, their benefits over other conventional methods and limitations. Additional introductory notes are also given on some related concepts. Part I : NMR Chiral analysis and RDCs measurements Chapter 2 discusses chiral sensing properties of RNA nucleosides and their utility as chiral derivatizing agents for the enantio-discrimination of 1o-amines using one dimensional 1H NMR. A three component protocol has been proposed for the complexation of nucleosides with amines, which is rapid, economical and provides maximum diastereomeric conversion. The chiral differentiating ability of nucleosides are examined for different amines based on the 1H NMR chemical shift differences between the diastereomers (∆δ R, S ). Enantiomeric differentiation has been observed at multiple chemically distinct proton sites. It is observed that adenosine and guanosine exhibit large chiral differentiation (∆δ R, S ) due to the presence of a purine ring. The comparison of the diastereomeric excess (de) measured by NMR with those of the gravimetrically prepared ratios are in excellent agreement with each other confirming the robustness of these RNA nucleosides in discriminating primary amines. Chapter 3 establishes the smooth connectivity with the chapter 2 by discussing the limitations of the enantiomeric discrimination using NMR in isotropic solutions. This chapter discusses two new water compatible aligning media that were developed based on self-assembling strategy of small bio-molecules. The self-assembled folic acid, and the binary mixture of 50-GMP and guanosine are introduced as two novel weak aligning media. The properties of these low ordered media have been systematically studied for their easy preparation, physical parameter dependent tunability of their degree of alignment, mesosphere sustainability over a broad range of temperature and the concentration of the ingredients, and the phase reproducibility. The applications of both these new media are demonstrated for chiral and pro-chiral discrimination and also for the measurement of RDCs. Both these liquid crystalline media could be tuned to very low degree of alignment (order parameter of the order of 10−4), which provides simple first order spectra of molecules aligned in them, the analysis provide order dependent NMR spectral parameters. The 50-GMP:guanosine orienting medium can be prepared in less than 1 hour, and has been demonstrated to be an ideal medium for the determination of RDCs that are used as restraints in the structure calculations of small molecules. Chapter 4 describes 1H NMR spectral complexity in isotropic and anisotropic phases and its consequences on enantiomeric analysis. In circumventing such problems, new NMR techniques have been developed and the spin dynamics involved in the designed sequences are discussed. The newly developed 2D 1H NMR experimental method termed as RES-TOCSY, and its applicability for resolving R and S enantiomeric or diastereomeric peaks of all the coupled proton spins in isotropic phase is discussed. The utility of the developed method is demonstrated in diverse situations, such as, for suppressing impurities peaks, resolving the severely overlapped peaks and unraveling the peaks masked due to severe line broadening when metal complexes are used as chiral auxiliaries. The advantages and limitations of the method over other methods available in the literature are discussed and the significant advantage of the present method is illustrated by spectral comparison with J-resolved experiment. The appli- cation of the method for the accurate measurement of enantiomeric excess has also been demonstrated. The chapter also introduces another NMR experimental technique developed for resolving enantiomeric peaks and complete unraveling of R and S spectra in anisotropic phase. The developed 2D NMR method is cited in the literature as CH-RES-TOCSY. In addition to spectroscopic visualization of R and S spectra, the method also yields C-H RDCs. The applicability of the new experiment has been demonstrated on a chosen example. The wide utility of the method has also been demonstrated for the assignment of symmetric cis- and trans- isomers. Part II : Sensitivity Enhancement of Slice selective NMR Experiments Chapter 5 describes applications of slice selective NMR experiments over conven tional NMR methods and their limitations as far as the sensitivity of signal detection is concerned, especially in low concentrated samples. The chapter introduces the implementation of Acceleration by Sharing Adjacent Polarization (ASAP) technique in slice selective experiments. It is convincingly demonstrated that ASAP helps in reducing inter scan relaxation delay and consequently permits acquisition of more number of scans in a given time, resulting in the gain in signal enhancement by a factor of two. The pulse sequences have been suitably designed for obtaining the pure shift 1H spectra and in G-SERF experiment for the measurement of 1H-1H couplings, both with significantly enhanced signal intensities. Chapter 6 describes new sensitivity enhanced slice selective NMR methods for mea- surement of scalar couplings. A new experiment has been developed which is named as Quick G-SERF (QG-SERF). It is a 1D NMR slice selective method developed based on real time spin manipulation technique. The method gives multiple scalar couplings of a selected spin with simplified multiplets, which is analogous to the 2D G-SERF but with considerable saving in instrument time by 1-2 orders of magnitude. The rapidness of the experiment arises due to reduced dimensionality. The spin dynamics involved in the pulse sequence and its working principle have been described. The application of the method is illustrated for the measurement of 1H-1H couplings. The sequence has been further improved to obtain the heteronuclear couplings between two abundant spins in an orchestrated manner and has been demonstrated for measurement of 1H-19F couplings. This sequence cited as HF-QG-SERF has been implemented on the molecules containing number of chemically non-equivalent fluorine atoms.

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.

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.

Abstract Wood is an essential material that has many applications in the fields of engineering and especially in the forest industry, which is particularly important in Fennoscandia. Among the various modification methods for wood, thermal modification has grown substantially over the past decades. It is an environmentally friendly method for increasing the lifetime and usability of timber. The aim of this thesis is to characterize the properties of thermally modified wood as well as to obtain new information on the changes taking place in pinewood due to the thermal modification process. Several NMR methods were used to gain information on the effect of thermal modification on the microstructure and moisture components of Pinus sylvestris pinewood. Pinewood samples thermally modified at different temperatures were studied and compared to corresponding unmodified wood samples. Diffusion of water and methane was studied using pulsed-field-gradient stimulated-echo measurements to determine the highly anisotropic size distribution of pores in different cell structures of pinewood. NMR cryoporometry and relaxometry measurements were conducted to gain information on the amounts and environments of both the bound and free water absorbed into the wood samples. Cryoporometry measurements resulted in an upper limit value for the size of bound water sites and the combination of cryoporometry and relaxometry data enabled the size determination of cell wall micropores. Magnetic resonance imaging was used to visualize the spatial distribution of absorbed free water in the studied samples. Together these methods give a broad overall picture of the effects of the modification process. The results of this work give new insight into the microstructure of thermally modified pinewood and its relationship to moisture, which is of importance for both wood science as well as industry. The applicability of the NMR techniques used here to the study of wood is also proven in this work. Using the techniques developed, it is possible to determine the optimal modification temperature, which is high enough to obtain the desired effects, but low enough not to destroy the microstructure of wood. / Tiivistelmä Puuta pystytään hyödyntämään useilla eri aloilla ja se on materiaalina tärkeä etenkin Fennoskandiassa merkittävälle metsäteollisuudelle. Useiden erilaisten puun käsittelymenetelmien joukossa lämpökäsittely on kasvattanut voimakkaasti suosiotaan viime vuosikymmeninä. Kyseessä on ympäristöystävällinen menetelmä, jolla voidaan pidentää puun käyttöikää sekä käytettävyyttä erilaisissa sovelluskohteissa. Tämän väitöskirjan päämääränä on ollut lämpökäsitellyn puun ominaisuuksien tutkiminen ja uuden tiedon saaminen puussa lämpökäsittelyprosessin myötä tapahtuvista muutoksista. Työssä käytettiin useita eri NMR-menetelmiä lämpökäsitellyn mäntypuun (Pinus sylvestris) mikrorakenteen sekä puussa olevan kosteuden aiheuttamien vaikutusten tutkimiseksi. Työssä tutkittiin eri lämpötiloissa käsiteltyjä mäntypuunäytteitä, joita verrattiin vastaaviin käsittelemättömiin näytteisiin. Veden ja metaanin diffuusiota tutkittiin PGSTE-menetelmällä puun erittäin anisotrooppisen solurakenteen sisältämien huokosten mittojen määrittämiseksi. NMR-kryoporometria- ja -relaksometriamittaukset antoivat tietoa puuhun imeytyneen sidotun ja vapaan veden määrästä ja esiintymisympäristöstä. Kryoporometria-mittausten tuloksista saatiin yläraja sidotun veden esiintymispaikkojen koolle, ja kryoporometria- ja relaksometriamittausten tuottaman tiedon yhdistäminen mahdollisti soluseinämien mikrohuokosten koon määrittämisen. Magneettikuvausta käytettiin näytteisiin absorboituneen veden avaruudellisen jakauman määrittämiseen. Käytetyt menetelmät tarjoavat laajan kokonaiskuvan lämpökäsittelyprosessin vaikutuksista puulle. Tämän työn tulokset antavat puutiedettä ja -teollisuutta hyödyttävää uutta tietoa lämpökäsitellyn männyn mikrorakenteesta sekä sen suhteesta kosteuteen. Väitöskirja myös osoittaa käytettyjen NMR-menetelmien soveltuvan hyvin puun tutkimiseen. Tämän tutkimuksen myötä kehitettyjen menetelmien avulla voidaan määrittää mm. optimaalinen lämpökäsittelylämpötila, joka on riittävän korkea haluttujen ominaisuuksien kannalta aiheuttamatta kuitenkaan puun mikrorakenteen hajoamista.

ErbB2/HER2 est un récepteur tyrosine kinase de la famille d'EGFR (ErbB1) surexprimé dans plus de 20% des cancers du sein et associé à une forme particulièrement agressive de la maladie. Les récepteurs ErbBs sont actifs seulement sous forme de dimères, permettant la phosphorylation de leur queue C-terminale par leur domaine tyrosine kinase. La phosphorylation entraine l'interaction avec des protéines adaptatrices et l'activation de voies de signalisation, Ras/MAPK et PI3K/Akt principalement. Ces voies contrôlent la prolifération, la motilité cellulaire et la résistance à l'apoptose. Contrairement à ErbB1/3/4, ErbB2 dimérise en l'absence de ligand. Comprendre les autres mécanismes de régulation de la phosphorylation de ses tyrosines et de ses interactions est donc particulièrement intéressant.ErbB2 a fait l'objet de nombreuses études structurales et fonctionnelles. Elles ont permis la mise au point de traitements ciblés efficaces mais sujets à l'apparition de résistance, dont l'anticorps Trastuzumab, ciblant sa partie extracellulaire. La queue C-terminale d'ErbB2 (CtErbB2) a été très souvent ignorée dans ces études. Cette partie étant intrinsèquement désordonnée, il a fallu attendre ces dernières années pour que les concepts et les outils permettant de l'étudier émergent.Dans cette thèse, j'ai d'abord effectué la caractérisation structurale et dynamique de CtErbB2. J'ai montré que bien qu'étant dépourvue de toute structure stable, cette région riche en prolines possède plusieurs structures secondaires transitoires et un contact longue-distance participant très probablement à la régulation de ses interactions intra- et inter-moléculaires. Dans une deuxième partie je me suis intéressée à la caractérisation de la protéine adaptatrice Grb2, partenaire essentiel de ErbB2 pour l'activation de la voie des MAP kinases. L'organisation en solution des domaines de cette protéine modulaire dans sa forme libre était jusque là inconnue. J'ai ensuite étudié l'interaction entre Grb2 et CtErbB2, et montré que CtErbB2 interagit non seulement avec le domaine SH2 de Grb2 (par l'intermédiaire d'une phosphotyrosine), mais aussi avec son domaine SH3 N-terminal (grâce à un motif polyproline). Enfin, j'ai mis en place plusieurs stratégies de phosphorylation des tyrosines de CtErbB2, dans le but d'étudier plus largement l'effet des phosphorylations sur l'ensemble de cette région. / ErbB2/HER2 is a receptor tyrosine kinase of the EGFR (ErbB1) family overexpressed in 20% of breast cancers and associated to a particularly aggressive form of the disease. ErbB receptors are only active upon dimerization that enables phosphorylation of their C-terminal tail by their tyrosine kinase domain. Phosphorylation then triggers interaction with adaptor proteins and activation of signaling pathways, mainly Ras/MAPK and Akt/PI3K. Those pathways control cell proliferation, motility and resistance to apoptosis. Contrary to ErbB1/3/4, ErbB2 can dimerize without any ligand. Understanding other mechanisms of regulation of its tyrosine phosphorylation and of its interactions is thus particularly interesting.ErbB2 structure and function have been extensively studied. This has led to the development of several FDA-approved targeted drugs, that are effective but to which resistance occurs, amongst which the Trastuzumab antibody that targets ErbB2 extracellular domain. The C-terminal tail of ErbB2 (CtErbB2) has been widely ignored in these studies. Since it is intrinsically disordered, the concepts and tools to study it have only emerged in the last few years.In the present work, I have performed the structural and dynamic study of CtErbB2. I showed that despite its lack of any stable structure, this proline-rich region exhibits several transient secondary structures and a long-range contact that might participate in the regulation of its intra- and inter-molecular interactions. Then, I characterized the adaptor protein Grb2, which is a partner of ErbB2 that is essential for the activation of the MAPK pathway. The solution organization of the domains of this modular protein in its apo-form was unknown so far. I also studied the interaction between Grb2 and CtErbB2, showing that in addition to the known SH2-phosphotyrosine interaction, a polyproline motif of CtErbB2 binds to the N-terminal SH3 domain of Grb2. Finally, I implemented several strategies to phosphorylate CtErbB2 tyrosines, to study more extensively the effect of phosphorylation on the whole tail.

La génération des cellules hématopoïétiques, aussi connue sous le nom d'hématopoïèse, est contrôlée par l’activité conjuguée de facteurs de transcription lignée-spécifiques permettant l’expression, en temps et lieu, de gènes spécifiques nécessaires pour le développement cellulaire. Dans le cadre de notre étude, nous avons étudié les facteurs de transcription KLF2 et KLF4 qui jouent des rôles cruciaux dans la formation des lymphocytes B et T. KLF2 et KLF4 activent la transcription de gènes spécifiques via leur interaction avec le co-activateur (CBP). Leurs interactions avec CBP requièrent le domaine de transactivation (TAD) qui est localisé dans la région N-terminal des facteurs KLF2 et KLF4. Des études préalables ont montré que des domaines TAD sont aussi présents chez la protéine suppresseur de tumeur p53 et que ces domaines sont requis pour les interactions entre la protéine p53 et le co-activateur CBP. Récemment, plusieurs structures des TADs de p53 en complexe avec les domaines TAZ2 et KIX de CBP ont permis de démontrer que ces TADs sont de nature acide et contiennent un motif ΦΧΧΦΦ crucial pour la formation des interactions. De plus, il s’avère que ces TADs sont similaires aux TADs de KLF2 et KLF4. L’étude présentée dans ce mémoire relate la caractérisation structurelle et fonctionnelle des interactions formées par les facteurs de transcription KLF2 et KLF4 avec leur partenaire d'interaction, CBP, pour activer la transcription de gènes spécifiques. Nos analyses ont été faites en utilisant différentes techniques telles que le titrage calorimétrique isotherme (ITC), la résonance magnétique nucléaire (RMN) ainsi que des expériences de transactivation chez la levure. Notre étude permet une meilleure compréhension des rôles opposés mais complémentaires qu'ont les protéines KLF2 et KLF4 au cours du développement et de la différentiation des lymphocytes B et T en plus de fournir les détails mécanistiques à la base de leurs interactions. Ces informations seront potentiellement utiles pour le développement d'outils à des fins thérapeutiques dans le cadre des leucémies, notamment. / Hematopoietic development is regulated through a combinatorial interplay between lineage-specific activators and the general transcription factors that enables cell-specific patterns of gene expression. In this study, the transcription factors KLF2 and KLF4 play crucial roles in lymphocytes B and T development by activating transcription of specific genes through interactions with the co-activator (CBP). These interactions involve the transactivation domains (TAD) localized in the N-terminal region of KLF2 and KLF4 factors. Previous studies have shown that TADs are also found in the tumor suppressor protein p53 and these TADs are responsible for the interactions between the p53 protein and the coactivator CBP. Recently, several structures of p53TADs in complex with the TAZ2 and KIX domains of CBP have shown that these TADs are acidic and possess a ΦΧΧΦΦ motif crucial for the formation of the interaction. Interestingly, these TADs are similar to the ones found on KLF2 and KLF4. This thesis provides a structural and functional characterization of the interactions formed by the transcription factors KLF2 and KLF4, which have opposing roles, and competes for the same interacting partner CBP to activate transcription. The analysis is done using isothermal titration calorimetry (ITC), nuclear magnetic resonance (NMR) spectroscopy and a yeast activation assay. This study brings a greater understanding on the opposing roles yet complementary of KLF2 and KLF4 proteins involved in B and T lymphocytes specific lineages selection and also provides information for potential therapeutic research regarding disease such as leukemia.