Ce travail de thèse a porté sur l’étude structurale de peptides urotensinergiques humains par DC, RMN etmodélisation moléculaire. L’hUII (11 aa) et son analogue l’URP (8 aa) sont considérés comme les peptides vasoactifs les plus puissants connus à ce jour et sont impliqués dans divers systèmes biologiques, notamment le système cardiovasculaire et la prolifération des cellules tumorales. Ces deux peptides sont des ligands endogènes d'un RCPG, l’UT. Ils peuvent exercer des actions physiologiques communes mais aussi divergentes. Afin d’apporter des éléments permettant une meilleure compréhension de leurs activités biologiques, nous avons, dans un premier temps, déterminé la structure 3D de trois agonistes (hUII4-11, URP,P5U) et d’un antagoniste (urantide) dans un milieu micellaire mimant les membranes des cellules eucaryotes, le DPC. Dans les quatre peptides, nous avons observé la présence de deux conformations majoritaires du pont disulfure, RHStaple et LHHook, qui sont connues pour être essentielles à l’activité biologique. Nous avons mis en évidence une différence de nature de coude entre les agonistes (coude β de type I) et l’antagoniste (coude β de type II’). Nos analyses ont également permis de montrer l’existence de variations d’orientation des chaînes latérales des résidus F6, Y9 et plus spécialement celle de W7 entre les agonistes etl’antagoniste. Le groupe indole du D-W7 présente ainsi une rotation de 180°. Dans un deuxième temps, nous avons mis en évidence un impact de la concentration sur la conformation de l’hUII qui n’est pas observé pour l’URP. Ce phénomène d’auto-association pourrait avoir une influence sur l’interaction avec le récepteur et être à l’origine des divergences d’activités biologiques entre l’hUII et l’URP. / This work aims to characterize the structure of human urotensinergic peptides by CD, NMR and molecular modelling. hUII (11 aa) and its analogue URP (8 aa) are considered as the most potent vasoactive peptides known so far and are involved in various biological systems, including the cardiovascular system and tumor cell proliferation. These two peptides are endogenous ligands of a GPCR, UT, and exert common but also divergent physiological actions. In order to gain a better understanding of their biological activities, we determined the structures of three agonists (hUII4-11, URP, P5U) and one antagonist (urantide), in DPC micelles, a cellular eukaryotic mimetic membrane. For all peptides, we observed the presence of two major forms of the disulfide bridge, RHStaple and LHHook, which are known to be essential for biological activity. We showed a difference in the turn nature between agonists (type I β turn) and the antagonist (type II’ β turn). Our analyses also revealed that, in agonists and antagonist, the side chain orientations of residues F6, Y9 and more specifically W7 were different. Indeed, the indole group of D-W7 exhibited a 180° rotation. Secondly, we showed that, contrary to URP, the conformation of hUII was dependent on concentration. This selfassembly phenomenon may impact the interaction with the receptor and be responsible for the differential biological activities of hUII and URP.

Les fonctions d'une molécule d'ARN dans les processus cellulaires sont très étroitement liées à sa structure tridimensionnelle. Il est donc essentiel de pouvoir prédire cette structure pour étudier sa fonction. Le repliement de l'ARN peut être vu comme un processus en deux étapes : le repliement en structure secondaire, grâce à des interactions fortes, puis le repliement en structure tridimensionnelle par des interactions tertiaires. Prédire la structure secondaire a donné lieu à de nombreuses avancées depuis plus de trente ans. Toutefois, la prédiction de la structure tridimensionnelle est un problème bien plus difficile. Nous nous intéressons ici au problème de prédiction de la structure 3D d'ARN sous la forme d'un jeu. Nous représentons la structure secondaire de l'ARN comme un graphe : cela correspond à une modélisation à gros grain de cette structure. Cette modélisation permet de réaliser un jeu de repliement dans l'espace. Notre hypothèse consiste à voir la structure 3D comme un équilibre en théorie des jeux. Pour atteindre cet équilibre, nous utiliserons des algorithmes de minimisation de regret. Nous étudierons aussi différentes formalisations du jeu, basées sur des statistiques biologiques. L'objectif de ce travail est de développer une méthode de repliement d'ARN fonctionnant sur tous les types de molécule d'ARN et obtenant des structures similaires aux molécules réelles. Notre méthode, nommée GARN, a atteint les objectifs attendus et nous a permis d'approfondir l'impact de certains paramètres pour la prédiction de structure à gros grain des molécules. / The functions of RNA molecules in cellular processes are related very closely to its three dimensional structure. It is thus essential to predict the structure for understanding RNA functions. This folding can be seen as a two-step process: the formation of a secondary structure and the formation of three-dimensional structure. This first step is the results of strong interactions between nucleotides, and the second one is obtain by the tertiary interactions. Predicting the secondary structure is well-known and results in numerous advances since thirty years. However, predicting the three-dimensional structure is a more difficult problem due to the high number of possibility. To overcome this problem, we decided to see the folding of the RNA structure as a game. The secondary structure of the RNA is represented as a graph: its corresponds to a coarse-grained modeling of this structure. This modeling allows us to fold the RNA molecule in a discrete space. Our hypothesis is to understand the 3D structure like an equilibrium in game theory. To find this equilibrium, we will use regret minimization algorithms. We also study different formalizations of the game, based on biological statistics. The objective of this work is to develop a method of RNA folding which will work on all types of secondary structures and results more accurate than current approaches. Our method, called GARN, reached the expected objectives and allowed us to deepen the interesting factors for coarse-grained structure prediction on molecules.

La protéine Bcd1 est un facteur nucléaire essentiel à la viabilité cellulaire de la levure Saccharomyces cerevisiae. Il est décrit comme requis pour assurer la stabilité des snoRNA à boîtes C/D. Ces petits ARN non codants s’assemblent à un jeu de 4 protéines invariables pour former les snoRNP à boîtes C/D qui sont des acteurs cruciaux de la biogenèse des ribosomes. En effet, quelques-unes de ces particules participent aux mécanismes assurant la maturation du précurseur des ARN ribosomiques et la grande majorité des autres particules sont des catalyseurs de la modification par 2’-O-méthylation des riboses. Bcd1p n’est pas présente au sein des particules matures, mais fait partie de ses facteurs d’assemblage, au même titre que les sous-complexes Rsa1p:Hit1p et R2TP (Rvb1p:Rvb2p:Tah1p:Pih1p). Notre analyse de différents fragments de Bcd1p a dans un premier temps montré que sa région N-terminale (résidus 1 à 96) suffit à lui conférer son caractère essentiel. Cette région comprend un domaine à double doigt à zinc de la famille zf-HIT, également présent chez un autre facteur d’assemblage des snoRNP à boîtes C/D, la protéine Hit1. Nous avons résolu la structure 3D en solution de ces doigts à zinc et montré que ce sont des modules d’interaction avec les protéines Rvb1/2. Dans un second temps nous avons identifié la région C-terminale (résidus 120 à 303) de la protéine Bcd1 comme étant suffisante pour interagir avec la chaperonne d’histone Rtt106p. La structure 3D en solution de ce domaine a été déterminée par RMN. Différentes approches de cinétique d’échange hydrogène/deutérium et d’expériences de cross-link suivies par des analyses par spectrométrie de masse, des expériences de titrage par RMN et de SAXS nous ont permis d’obtenir des informations sur les surfaces d’interaction de chacune de ces deux protéines. Un fragment, défini à partir des données de RMN de Bcd1p libre, nous a permis d'obtenir des cristaux du complexe Bcd1p:Rtt106p ouvrant la perspective de résoudre sa structure 3D par diffraction aux rayons X. De plus, des études fonctionnelles ont débuté visant à déterminer l’importance de la formation de ce complexe sur la biogenèse des snoRNP à boîtes C/D et l’impact de Bcd1p sur l’interaction entre Rtt106p et les nucléosomes / The protein Bcd1 is a nuclear factor essential for the cellular viability of the yeast Saccharomyces cerevisiae. It is described as required to ensure box C/D snoRNA stability. These small non-coding RNAs associate with an invariable set of 4 proteins to form the box C/D snoRNPs that are crucial players in ribosome biogenesis. Indeed, some of these particles participate in mechanisms for the maturation of the ribosomal RNA precursor (prerRNA) and the vast majority of the other particles are catalysts of 2’-O-methylation of riboses. Bcd1p is not present in mature particles, but is one of the assembly factors in addition to the Rsa1p:Hit1p and R2TP (Rvb1p:Rvb2p:Tah1p:Pih1p) sub-complexes. Our analysis of the different Bcd1p fragments has firstly shown that the essential function of Bcd1p relies on its N-terminal region (residues 1 to 96). It comprises a double zinc finger domain from the zf-HIT family, also present in another box C/D snoRNP assembly factor, the protein Hit1. We solved the 3D solution structure of these two zinc fingers and showed that these are modules for the interaction of Bcd1p with the Rvb1/2 proteins. Secondly, we identified the C-terminal region (residues 120 to 303) of Bcd1p as being sufficient to interact with the histone chaperone Rtt106p. The 3D solution structure of this domain of Bcd1p was determined by NMR. Different approaches of hydrogen/deuterium kinetic exchange and cross-link experiments followed by mass spectrometry analysis, NMR titration, and SAXS allowed us to obtain information about the interaction surfaces on each of the two proteins. A fragment defined from NMR data on the free Bcd1p allowed us to obtain crystals of the Bcd1p:Rtt106p complex, opening the perspective to solve its 3D structure by X-ray diffraction. Furthermore, functional studies started in order to determine the importance of this complex formation in box C/D snoRNP biogenesis and the impact of Bcd1p on the interaction of Rtt106p with nucleosomes

Title: Anisotropic tomography of the European upper mantle Author: Helena Žlebčíková Department: Department of Geophysics, Faculty of Mathematics and Physics, Charles University Training institution: Institute of Geophysics of the Czech Academy of Sciences (IG CAS) Supervisor: RNDr. Jaroslava Plomerová, DrSc., IG CAS Consultants: RNDr. Vladislav Babuška, DrSc., IG CAS RNDr. Luděk Vecsey, Ph.D., IG CAS Abstract: Large-scale seismic anisotropy of the continental mantle lithosphere derived from joint inversion/interpretation of directional variations of P-wave travel-time residuals and SKS-wave splitting calls for orientation of the symmetry axes to be treated generally in 3D. Nevertheless, most of the tomography studies neglect the anisotropy of the body waves completely or they are limited to either azimuthal or radial anisotropy. Therefore, we have developed a code called AniTomo for coupled anisotropic-isotropic travel-time tomography of the upper mantle. The novel code allows inversion of relative travel-time residuals of teleseismic P waves simultaneously for 3D distribution of P-wave isotropic- velocity perturbations and anisotropy of the upper mantle. We assume weak anisotropy of hexagonal symmetry with either the 'high-velocity' a axis or the 'low-velocity' b axis. The symmetry axis is allowed to be...

The rapid pace of scientific advances is enabling a greater understanding of diseases at the molecular level. In turn, the process for researching and developing new medicines is growing in difficulty, costs, and length as a result of the scientific, technical, and regulatory challenges related to the development process. In light of these challenges, drug repositioning, the utilization of known drugs for a new medical indication, has emerged as an increasingly important strategy for the new drug discovery. Availability of prior knowledge regarding safety, efficacy and the appropriate administration route significantly reduces the development costs and cuts down the development time resulting in less effort to successfully bring a repositioned drug to market. In another aspect, a protein’s shape is closely linked with its function; thereby, the ability to predict this structure unlocks a greater understanding of what it does and how it works. Nowadays, more than 10,000 biologically relevant protein structures are yearly released and available to the scientific community. A number suspected to triple over the following years due to the recent breakthroughs in structure prediction techniques. This work introduces a novel structure-based drug repositioning approach, exploiting the similarities of drugs’ binding mode via identification and virtual screening of interaction patterns. Such patterns are uncovered with the use of PLIP, an automated tool for the in silico detection of non-covalent interactions defining the binding mode between drugs and their protein targets. Besides, the approach has been applied to a series of case studies with tangible results: the uncovering of an antimalarial drug as potential chemoresistance treatment, the explained binding mode of ibrutinib to the target VEGR2 as potential B-cells deactivator in autoimmune diseases, and three over the counter drugs with a proved anti-trypanocidal activity as treatments for Chagas disease. Overall the structure-based approach with interaction patterns proved to be a suitable framework for identifying novel repositioning candidates. The uncovered candidates were structurally unrelated to the currently available treatments, and experimental assays successfully demonstrated their inhibitory activity on the protein targets of interest. Furthermore, the approach represents a promising option for the 'in high demand' diseases and all rare and neglected diseases for which no reliable treatment has yet been found and for which the pharmaceutical industry makes only a little investment.

Concrete’s great vulnerability against impact demonstrates significant risks of injury for workers and occupants in all building types, especially existing concrete structures in which protection measures were not originally integrated. Beside the social and economic costs directly associated with impact accidents, the reconstruction or replacement of buildings damaged by impact negatively affects the environment and resources. In response to the increasing public concern for safety and sustainability, the DFG Research Training Group GRK 2250 is formed with the core aim to develop significant improvements in the impact resistance of existing concrete buildings by applying thin strengthening layers made of innovative mineral-bonded composites. The introduction of textile-based high-performance reinforcement is highly instrumental in realizing the required functions of thin mineral-bonded strengthening layers. Novel impact-resistant 3D reinforcement is developed on the basis of the innovative 3D cellular weaving technology in this dissertation. Woven 3D cellular structures are characterized by outstanding and customizable mechanical characteristics, owning to the flexible incorporation of elements with different materials and geometries both in in-plane and out-of-plane directions. Based on a systematic and partly iterative development process, impact-resistant woven 3D cellular reinforcements containing impact-load-oriented elements and impact-appropriate material combination are successfully designed and optimized. On the one hand, a series of experiments are conducted to capture the working mechanism of woven 3D cellular structure in mineral-bonded composites loaded under impact, and to understand the effects of critical structure features. On the other hand, feasible weave patterns and effective technological solutions are worked out and implemented to enable a reliable and low-damage manufacturing process. Through a series of impact experiments, it can be strongly evidenced that the developed 3D cellular reinforcement pronouncedly enhances the load bearing capacity, ductility and energy dissipation of mineral-bonded composite undergoing impact, thus, remarkably enhances its impact resistance. The development of impact-resistant woven 3D cellular reinforcements in this dissertation introduces a completely new and unique class of textile-based reinforcement for concrete, as well as mineral-bonded composites, with numerous benefits over the presently available reinforcing structures. A major advantage of the novel 3D cellular reinforcement is the capability to activate and exploit multiple energy dissipation mechanisms using both material and structure properties, through which remarkable impact resistance can be obtained. Thanks to a high degree of versatility and flexibility in material combination and structure design, in combination with a high degree of automation and flexibility of the weaving technology, impact-resistant woven 3D cellular reinforcement that is highly customized to specific impact scenarios can be produced with a significant time and cost efficiency. Furthermore, impact-resistant woven 3D cellular reinforcements possess an integral 3D architecture that ensures a high structure stability, allowing for a speedy casting process with a high placement-accuracy. On that basis, a reasonable production cost and a stable performance of designed functions can be obtained. The successful development of impact-resistant woven 3D cellular reinforcement essentially facilitates the successful creation of high-performance mineral-bonded strengthening layers, through the use of which the impact resistance of existing concrete structures, thus, their sustainable use, significantly enhances.:1 INTRODUCTION AND MOTIVATION 1 2 LITERATURE REVIEW 7 2.1 Fundamentals of concrete and reinforced concrete 7 2.1.1 Normal concrete 7 2.1.2 Structural concrete family 10 2.1.3 Steel reinforced concrete 11 2.1.4 Concrete and reinforced concrete under impact loading 14 2.1.5 Fiber-based reinforcing materials for concrete 18 2.1.6 Fiber reinforced concrete 21 2.1.7 Textile reinforced concrete 22 2.2 Two-dimensional textile concrete reinforcements 24 2.2.1 Welded metal wire mesh 24 2.2.2 Expanded metal mesh 25 2.2.3 Woven 2D reinforcing structures 25 2.2.4 Warp knitted 2D reinforcing structures 27 2.2.5 Stitched 2D reinforcing structures 28 2.2.6 Adhesively-bonded 2D reinforcing structures 29 2.2.7 Discussion of 2D reinforcing structures 30 2.3 Three-dimensional textile concrete reinforcements 33 2.3.1 Assembled 3D reinforcing structures 33 2.3.2 Woven 3D reinforcing structures 34 2.3.3 Warp knitted 3D reinforcing structures 35 2.3.4 Stitched 3D reinforcing structures 36 2.3.5 Adhesively-bonded 3D reinforcing structures 36 2.3.6 Discussion of available 3D reinforcing structures 36 2.4 Woven 3D cellular structures 37 2.5 Conclusion based on literature review 37 3 RESEARCH AIMS AND OBJECTIVES 39 4 PRELIMINARY INVESTIGATION INTO IMPACT BEHAVIOR OF MINERAL-BONDED COMPOSITE REINFORCED WITH WOVEN 3D CELLULAR STRUCTURE 41 4.1 Introduction 41 4.2 Materials under investigation 43 4.2.1 Reinforcement - Reference woven 3D cellular structure 3DWT Ref 43 4.2.2 Matrix - Fine-grained concrete Pagel TF10 44 4.2.3 Comparing reinforcement - Warp knitted 2D structure 2D BZT2 44 4.3 Specimen labeling 45 4.4 Methodology of small-scale plate impact test 46 4.4.1 Specimen preparation 46 4.4.2 Test setup 47 4.5 Preliminary small-scale plate impact test results 47 4.6 Summary and conclusion of preliminary investigation 58 4.7 Derivation of requirements and procedure for developing impact-resistant woven 3D cellular reinforcement 59 5 DEVELOPMENT OF STRUCTURE SYSTEMATICS FOR IMPACT-RESISTANT WOVEN 3D CELLULAR REINFORCEMENT 63 5.1 Fundamentals of woven 3D cellular structure 64 5.1.1 Conventional woven structure 64 5.1.2 Elements of woven 3D cellular structure 65 5.1.3 Formation principles of woven 3D cellular structure 66 5.1.4 Variation possibilities within woven 3D cellular structure 68 5.2 Design concept of mineral-bonded strengthening layers against impact 71 5.3 Requirements for impact-resistant woven 3D cellular reinforcement 73 5.4 Two-plane woven 3D cellular reinforcements 77 5.4.1 Two-plane woven 3D cellular reinforcements with biaxial grids 77 5.4.2 Two-plane woven 3D cellular reinforcements with triaxial grids 81 5.4.3 Two-plane woven 3D cellular reinforcements with quadriaxial grids 82 5.5 Three-plane 3D cellular reinforcements 83 5.6 Material variation 85 5.6.1 Double yarns 85 5.6.2 Hybrid yarns 86 5.7 Selected impact-resistant woven 3D cellular reinforcements for realization and investigation 86 6 DEVELOPMENT OF WEAVE PATTERN FOR IMPACT-RESISTANT WOVEN 3D CELLULAR REINFORCEMENT 89 6.1 Introduction 89 6.2 Two-plane reference structure 3DWT Ref 90 6.3 Two-plane double yarn structure 3DWT DbWi 92 6.4 Three-plane structure 3DWT DbLyr 93 6.5 Two-plane pyramid structure 3DWT Pyr 95 7 DEVELOPMENT OF TECHNOLOGICAL SOLUTIONS FOR THE MANUFACTURE OF IMPACT-RESISTANT WOVEN 3D CELLULAR REINFORCEMENT 101 7.1 3D cellular weaving technology 101 7.2 Manufacture of two-plane double yarn structure 3DWT-DbWi 107 7.3 Manufacture of three-plane structure 3DWT-DbLyr 108 7.4 Manufacture of two-plane pyramid structure 3DWT-Pyr 112 8 TENSILE BEHAVIOR OF SHCC CONTAINING IMPACT-RESISTANT WOVEN 3D CELLULAR REINFORCEMENT 117 8.1 Quasi-static tension tests 117 8.1.1 Specimen preparation 117 8.1.2 Test setup 118 8.1.3 Quasi-static tension test results 119 8.2 High-speed tension tests 126 8.2.1 Specimen preparation 126 8.2.2 Test setup 126 8.2.3 High-speed tension test results 127 9 ENHANCEMENT OF IMPACT-RESISTANT WOVEN 3D CELLULAR REINFORCEMENT 131 9.1 Concept of enhanced impact-resistant 3D cellular reinforcement 131 9.2 Weave pattern development of enhanced impact-resistant reinforcement 3DWT Pyr Hyb 134 9.3 Manufacture of enhanced impact-resistant reinforcement 3DWT Pyr Hyb 136 9.3.1 Material selection 136 9.3.2 Carbon rovings impregnation 142 9.3.3 Steel wires straightening and preshaping 142 9.3.4 Weaving and realized structure 143 10 PERFORMANCE OF MINERAL-BONDED STRENGTHENING LAYER WITH IMPACT-RESISTANT WOVEN 3D CELLULAR REINFORCEMENT 147 10.1 Tensile behavior of SHCC reinforced with 3DWT Pyr Hyb 147 10.1.1 Specimen preparation 147 10.1.2 Quasi-static tension test results 148 10.1.3 Dynamic tension test results 154 10.2 Impact behavior of SHCC reinforced with 3DWT Pyr Hyb 157 10.2.1 Materials under investigation 157 10.2.2 Small-scale plate impact test results 159 10.3 SHCC reinforced with 3DWT Pyr Hyb as strengthening layer on the impacted side of concrete core 169 10.4 Summary and conclusion of the performance investigation on mineral-bonded strengthening layer reinforced with 3DWT Pyr Hyb 173 11 CONCLUSIONS AND RECOMMENDATIONS 175

La RMN est une méthode de choix pour la détermination de la structure tridimensionnelle des protéines et des acides nucléiques en solution. Cependant, la taille des systèmes que l'on peut étudier actuellement par RMN est limitée. Dans la première partie de ce travail, la structure du répresseur BlaI de la beta-lactamase de B. licheniformis 749/I et son interaction avec l'ADN ont été étudiées par RMN avec des méthodes classiques. Ces résultats ont permis de mieux caractériser la répression des gènes de plusieurs mécanismes de résistance aux antibiotiques, incluant la résistance à la méthicilline de la souche pathogène S. aureus. Le deuxième volet de ce travail concerne l'implémentation de filtres Hadamard qui augmentent la résolution des spectres dans certaines expériences de RMN multidimensionnelle. Ces filtres permettent de séparer les pics de corrélation des protéines et des acides nucléiques selon le type d'acide aminé et le type de base, respectivement. Ces développements ouvrent de nouveaux horizons vers l'étude de macromolécules biologiques de plus grosse taille par RMN.

Les flavan-3-ols et leurs polymères, les proanthocyanidines, appartiennent à une famille de flavonoïdes appelée les tannins condensés. Ces composés polyphénoliques jouent un rôle essentiel dans la qualité phytosanitaire des baies de raisin ainsi que dans les propriétés organoleptiques du vin (flaveur, astringence et couleur). La connaissance des mécanismes qui régissent leur biosynthèse est donc primordiale afin de mieux comprendre la mise en place de la typicité d’un vin. Ce mémoire est consacré à l’étude de l’une des enzymes responsables de la synthèse des flavan-3-ols : la leucoanthocyanidine réductase 1 de Vitis vinifera (VvLAR1). Dans une première partie, nous décrivons les conditions d’expression, de purification et de stabilité de l’enzyme recombinante. L’activité enzymatique est démontrée et la configuration 2R,3S des produits réactionnels caractérisée. La seconde partie de ce manuscrit décrit l’étude structurale de l’enzyme. Des monocristaux d’apoenzyme, de complexes binaires (VvLAR1 / NADPH) et d’un complexe ternaire (VvLAR1 / NADPH / (+)-catéchine) ont été obtenus. Les différentes structures permettent de décrire les modifications structurales associées à la fixation du coenzyme puis du produit. Un mécanisme catalytique basé sur les interactions intermoléculaires observées au sein du complexe ternaire est proposé. La troisième partie de ce mémoire est consacrée à la recherche de conditions expérimentales permettant la production et la stabilisation de la leucocyanidine en solution, un des substrats naturels de l’enzyme. Les résultats obtenus permettent une première approche de l’étude des propriétés cinétiques de la VvLAR1. / Flavan-3-ols and their polymerisation products, proanthocyanidins, belong to a flavonoid family named condensed tannins. These polyphenolic compounds play a major role in the protection of grape berries to intruders and in the organoleptic properties of wine (flavour, astringency and colour). Knowledge of the mechanisms which govern their biosynthesis is thus essential to better understand wine typical composition. The present thesis is devoted to the investigation of one of the two enzymes which catalyse the flavan-3-ols formation: leucoanthocyanidin reductase 1 from Vitis vinifera (VvLAR1). In the first part of the manuscript, we describe the expression, purification and stability conditions of the recombinant enzyme. The enzyme activity is demonstrated and the reaction product 2R,3S configuration is characterised. The second part of this report describes the structural studies of the enzyme. Monocrystals of the apoenzyme and of binaries (VvLAR1 / NADPH) and a ternary (VvLAR1 / NADPH / (+)-catechin) complexes were obtained. These different structures allow the description of the structural changes associated with the coenzyme and then the substrate binding. A catalytic mechanism, based on the intermolecular interactions within the ternary complex, is proposed. The last part of the work is devoted to the investigation of the experimental conditions leading to the stability of leucocyanidin in solution, one of the natural substrates of the enzyme. The results obtained allow a first study of the VvLAR1 kinetic properties.

The aim of diploma thesis is to design steel roof structure of minimum dimensions 45 m x 50 m and minimum height 12 m. The plan of the building design has dimensions of 52,14 m x 70, 00 m and height is 18,68 m. The roofing was design as 3D truss girders with two lower chords and one upper chord. The shape of 3D truss girder consists of three circular arcs of radius 69,88m, 12,43 m and 33,45 m. Between main girders is 3D bracing. The structure is pin-supported.

L’objectif de cette thèse est de proposer un Alphabet Structural (AS) permettant une caractérisation fine et précise des structures tridimensionnelles (3D) des protéines, à l’aide des chaînes de Markov cachées (HMM) qui permettent de prendre en compte la logique issue de l’enchaînement des fragments structuraux en intégrant l’augmentation des conformations 3D des structures protéiques désormais disponibles dans la banque de données de la Protein Data Bank (PDB). Nous proposons dans cette thèse un nouvel alphabet, améliorant l’alphabet structural HMM-SA27,appelé SAFlex (Structural Alphabet Flexibility), dans le but de prendre en compte l’incertitude des données (données manquantes dans les fichiers PDB) et la redondance des structures protéiques. Le nouvel alphabet structural SAFlex obtenu propose donc un nouveau modèle d’encodage rigoureux et robuste. Cet encodage permet de prendre en compte l’incertitude des données en proposant trois options d’encodages : le Maximum a posteriori (MAP), la distribution marginale a posteriori (POST)et le nombre effectif de lettres à chaque position donnée (NEFF). SAFlex fournit également un encodage consensus à partir de différentes réplications (chaînes multiples, monomères et homomères) d’une même protéine. Il permet ainsi la détection de la variabilité structurale entre celles-ci. Les avancées méthodologiques ainsi que l’obtention de l’alphabet SAFlex constituent les contributions principales de ce travail de thèse. Nous présentons aussi le nouveau parser de la PDB (SAFlex-PDB) et nous démontrons que notre parser a un intérêt aussi bien sur le plan qualitatif (détection de diverses erreurs)que quantitatif (rapidité et parallélisation) en le comparant avec deux autres parsers très connus dans le domaine (Biopython et BioJava). Nous proposons également à la communauté scientifique un site web mettant en ligne ce nouvel alphabet structural SAFlex. Ce site web représente la contribution concrète de cette thèse alors que le parser SAFlex-PDB représente une contribution importante pour le fonctionnement du site web proposé. Cette caractérisation précise des conformations 3D et la prise en compte de la redondance des informations 3D disponibles, fournies par SAFlex, a en effet un impact très important pour la modélisation de la conformation et de la variabilité des structures 3D, des boucles protéiques et des régions d’interface avec différents partenaires, impliqués dans la fonction des protéines / The purpose of this PhD is to provide a Structural Alphabet (SA) for more accurate characterization of protein three-dimensional (3D) structures as well as integrating the increasing protein 3D structure information currently available in the Protein Data Bank (PDB). The SA also takes into consideration the logic behind the structural fragments sequence by using the hidden Markov Model (HMM). In this PhD, we describe a new structural alphabet, improving the existing HMM-SA27 structural alphabet, called SAFlex (Structural Alphabet Flexibility), in order to take into account the uncertainty of data (missing data in PDB files) and the redundancy of protein structures. The new SAFlex structural alphabet obtained therefore offers a new, rigorous and robust encoding model. This encoding takes into account the encoding uncertainty by providing three encoding options: the maximum a posteriori (MAP), the marginal posterior distribution (POST), and the effective number of letters at each given position (NEFF). SAFlex also provides and builds a consensus encoding from different replicates (multiple chains, monomers and several homomers) of a single protein. It thus allows the detection of structural variability between different chains. The methodological advances and the achievement of the SAFlex alphabet are the main contributions of this PhD. We also present the new PDB parser(SAFlex-PDB) and we demonstrate that our parser is therefore interesting both qualitative (detection of various errors) and quantitative terms (program optimization and parallelization) by comparing it with two other parsers well-known in the area of Bioinformatics (Biopython and BioJava). The SAFlex structural alphabet is being made available to the scientific community by providing a website. The SAFlex web server represents the concrete contribution of this PhD while the SAFlex-PDB parser represents an important contribution to the proper function of the proposed website. Here, we describe the functions and the interfaces of the SAFlex web server. The SAFlex can be used in various fashions for a protein tertiary structure of a given PDB format file; it can be used for encoding the 3D structure, identifying and predicting missing data. Hence, it is the only alphabet able to encode and predict the missing data in a 3D protein structure to date. Finally, these improvements; are promising to explore increasing protein redundancy data and obtain useful quantification of their flexibility