Les bactéries sont exposées aux perturbations externes causées par les changements environnementaux ou la présence d’agents antibactériens nocifs. L’enveloppe bactérienne forme une barrière entre le milieu externe et l’intérieur de la cellule et se trouve donc potentiellement exposée aux dommages causées par les perturbations et forme la première ligne de défense pour les bactéries. Pour survivre à ces conditions, les bactéries ont développé des systèmes à deux composantes (TCS) qui détectent et permettent la réponse à ces stress.Bien qu’ils soient associés à la protéine périplasmique ZraP, ZraSR constitue un de ces TCS. La présence de cette protéine accessoire associé au système ZraSR montre une homologie avec le système CpxPAR qui capte un grand nombre de stress d’enveloppe. Le système Zra est activé en présence de zinc et cause l’expression de zraP, zraS et zraR. Les protéines ZraP et ZraR ont été étudiées mais aucun travail n’a encore impliqué l’étude de la protéine membranaire ZraS et son mécanisme d’activation. En effet, l’étude des senseurs de TCS s’est beaucoup focalisée sur la compréhension de la partie cytoplasmique mais très peu sur le domaine périplasmique. Dans le cas du système Zra, il y a encore des interrogations sur l’activation ainsi que la régulation de ce système. Lors de ma thèse j’ai concentré mes recherches sur le domaine périplasmique de ZraS. Nous avons d’abord voulu comprendre comment le zinc active le système Zra mais aussi par quel moyen la protéine ZraP influe sur cette activation par le zinc. Pour cela, la caractérisation biochimique du domaine périplasmique de ZraS a été effectué et l’effet du zinc sur ce domaine a été observé. De ce fait, nous avons aussi tenté de déterminer quels sont les résidus de ce domaine qui permettent la liaison du zinc. Par une approche in vivo et in vitro, nous avons voulu comprendre le rôle régulateur de ZraP sur le système Zra. Ce travail s’inscrit dans l’objectif de mieux comprendre les différents mécanismes d’activation des différents ESR. / Bacteria are exposed to external perturbations due to environmental changes or to the presence of noxious agents. Because the bacterial cell envelope forms the barrier between the inside and the outside of the cell it is highly susceptible to be damaged by these perturbations but it is also the first line of defense. To survive gram-negative bacteria have developed two component systems (TCS) that detect and respond to these envelope stresses.ZraSR is one of these TCS, although it is atypical because associated with ZraP, a periplasmic protein. The presence of an accessory protein associated with ZraSR system shows that it is functionally homologous to the CpxPAR system, a sensor of a variety of envelope stress signals. In presence of zinc, Zra system is activated and allows the expression of zraP, zraS and zraR. The periplasmic protein ZraP and the response regulator ZraR have been studied but the activation of the membrane histidine kinase by zinc has not been studied yet. Indeed, studying of TCS sensors was focused on the understanding of the cytoplasmic domain and less on the periplasmic part.During my thesis, I tried to concentrate my study on the periplasmic domain of ZraS. We first tried to understand how the zinc is activating the Zra system but also how ZraP is regulating this activation. For that purpose, we characterized ZraS periplasmic domain and analyzed the effect of zinc binding on it. Hence, we also tried to identify all of ZraS residues that are coordinating the zinc. By combining in vitro and in vivo assays, we tried to determine ZraP role in the regulation of Zra system. This study could help for the understanding of the mechanisms important for the activation of bacterial stress response systems.

<p>An introduction to bacterial polysaccharides and the methods for structural determination are described in the first two parts of the thesis.</p><p>In a structural elucidation of bacterial polysaccharides NMR experiments are important as is component analysis. A short description of immunochemical methods such as enzyme immunoassays is included. Two NMR techniques used for interaction studies, trNOE and STD NMR, are also discussed. </p><p>The third part of the thesis discusses and summarizes the results from the included papers. The structures of the exopolysaccharides produced by two lactic acid bacteria are determined by one- and two dimensional NMR experiments. One is a heteropolysaccharide produced by <i>Streptococcus thermophilus</i> and the other a homopolysaccharide produced by <i>Propionibacterium freudenreichii</i>. The structure of an acidic polysaccharide from a marine bacterium with two serine residues in the repeating unit is also investigated. The structural and immunological relationship between two O-antigenic polysaccharides from <i>Escherichia coli</i> strain 180/C3 and O5 is discussed and investigated. Finally, interaction studies of an octasaccharide derived from the <i>Salmonella enteritidis</i> O-antigen and a bacteriophage are described which were performed with NMR experiments.</p>

<p>Fosfaters reaktioner i energiomvandlingsprocesser är kritisk för den generella processen som helhet, för askrelaterade problem, emissioner liksom för en effektiv och hållbar användning av askan.</p><p>Denna avhandling är en sammanställning och diskussion med utgångspunkt i åtta artiklar som behandlar strukturella och termodynamiska studier på faser i CaO-K₂O-P₂O₅-systemet, vilka är av relevans inom förbränning av biomassa. Målsättningen med denna avhandling var: i) att sammanställa och granska tillgängliga strukturella och termodynamiska data i CaO-K₂O-P₂O₅-systemet samt att identifiera avsaknad av data, ii) att fylla i dessa luckor med grundläggande termodynamiska, strukturella och fasstabilitets studier samt iii) att visa på användning samt fördelarna med dessa nya data vid praktisk tillämpning.</p><p>En initial litteraturundersökning i CaO-K₂O-P₂O₅-systemet visade att det saknades både strukturella och termodynamiska data. När det gällde tillgängliga termodynamiska data var situationen särskilt otillfredsställande. Det fanns endast data för några kalcium– och kaliumfosfater med varierande tillförlitlighet. Situationen beträffande pulverröntgen för fasidentifiering var bättre, fast fördunklad av det faktum att strukturellt liknande fasövergångar ofta förekommer i det undersökta systemet. Däremot fattades det tillfredställande enkristallstrukturdata för ternära faser i det undersökta systemet.</p><p>Enkristallröntgendiffraktion användes för att bestämma strukturerna för CaK₂P₂O₇, CaKP₃O₉, Ca₁₀K(PO₄)₇ och CaKPO₄. Faserna CaK₂P₂O₇ and CaKPO₄ tillsammans med Ca₃(PO₄)₂, KPO₃ och K₄P₂O₇ studerades med pulverröntgendiffraktion och termiska analysmetoder för att klargöra fasmodifikationer och övergångstemperaturer. Gibbs bildningsenergi bestämdes för Ca(PO₃)₂, Ca₂P₂O₇, Ca₃(PO₄)₂, Ca₁₀K(PO₄)₇, CaK₂P₂O₇, CaKPO₄ och CaK₄(PO₄)₂ med ems-metodik och yttriastabiliserad zirkonia som fast elektrolyt och Ni/Ni₃P som hjälpsystem. Både de strukturella och termodynamiska data användes sedan vid analyser i ett förbrännningexperiment av olika sädesslag. Framtagna data användes både vid identifiering och även vid kvantifiering av bildade faser i biomassaresterna.</p> / <p>The behaviour of phosphates in thermochemical biomass conversion processes are critical for the general process chemistry, for ash related problems, for emissions as well as for an efficient, sustainable and beneficial use of the ash residues.</p><p>This thesis is a summary and a discussion of eight papers dealing with structural and thermodynamical studies of phases in the CaO-K₂O-P₂O₅ system, with relevance for biomass combustion. The objectives were: i) to compile and review the available structural and thermodynamical data of phases in the CaO-K₂O-P₂O₅ system as well as to identify existing gaps in the field of these data, ii) to fill in as many as possible of the gaps by fundamental thermodynamic, structural and phase stability studies and iii) to demonstrate the uses and the benefits of the new data in practical applications.</p><p>An initial review of the CaO-K₂O-P₂O₅ system showed that both structural information and thermodynamic data were lacking. The situation regarding the available thermodynamic data was especially unsatisfactory, data could only be found for some few calcium phosphates and a few potassium phosphates with varying reliability. Concerning powder X-ray diffraction patterns for phase identification the situation was better, though obscured by the fact that structurally close related phase transitions often occur in the studied system. However, adequate single crystal structural data of ternary phases in the system was completely missing.</p><p>Crystal structures of CaK₂P₂O₇, CaKP₃O₉, Ca₁₀K(PO₄)₇ and CaKPO₄ were determined by single-crystal X-ray diffraction. The phases CaK₂P₂O₇ and CaKPO₄ were together with Ca₃(PO₄)₂, KPO₃ and K₄P₂O₇, investigated by powder X-ray diffraction and thermal analysis to elucidate phase modifications and transitions temperatures. Gibbs standard energy of formation was determined for Ca(PO₃)₂, Ca₂P₂O₇, Ca₃(PO₄)₂, Ca₁₀K(PO₄)₇, CaK₂P₂O₇, CaKPO₄ and CaK₄(PO₄)₂ by solid state emf measurements with yttria stabilised zirconia as solid electrolyte and Ni/Ni₃P as auxiliary solid couple. Both the structural and thermodynamical data were subsequently utilised in analysis of a combustion experiment of cereal grains. The data were also used to both identify and quantify the phases formed in biomass combustion residues.</p>

An introduction to bacterial polysaccharides and the methods for structural determination are described in the first two parts of the thesis. In a structural elucidation of bacterial polysaccharides NMR experiments are important as is component analysis. A short description of immunochemical methods such as enzyme immunoassays is included. Two NMR techniques used for interaction studies, trNOE and STD NMR, are also discussed. The third part of the thesis discusses and summarizes the results from the included papers. The structures of the exopolysaccharides produced by two lactic acid bacteria are determined by one- and two dimensional NMR experiments. One is a heteropolysaccharide produced by Streptococcus thermophilus and the other a homopolysaccharide produced by Propionibacterium freudenreichii. The structure of an acidic polysaccharide from a marine bacterium with two serine residues in the repeating unit is also investigated. The structural and immunological relationship between two O-antigenic polysaccharides from Escherichia coli strain 180/C3 and O5 is discussed and investigated. Finally, interaction studies of an octasaccharide derived from the Salmonella enteritidis O-antigen and a bacteriophage are described which were performed with NMR experiments.

Fosfaters reaktioner i energiomvandlingsprocesser är kritisk för den generella processen som helhet, för askrelaterade problem, emissioner liksom för en effektiv och hållbar användning av askan. Denna avhandling är en sammanställning och diskussion med utgångspunkt i åtta artiklar som behandlar strukturella och termodynamiska studier på faser i CaO-K2O-P2O5-systemet, vilka är av relevans inom förbränning av biomassa. Målsättningen med denna avhandling var: i) att sammanställa och granska tillgängliga strukturella och termodynamiska data i CaO-K2O-P2O5-systemet samt att identifiera avsaknad av data, ii) att fylla i dessa luckor med grundläggande termodynamiska, strukturella och fasstabilitets studier samt iii) att visa på användning samt fördelarna med dessa nya data vid praktisk tillämpning. En initial litteraturundersökning i CaO-K2O-P2O5-systemet visade att det saknades både strukturella och termodynamiska data. När det gällde tillgängliga termodynamiska data var situationen särskilt otillfredsställande. Det fanns endast data för några kalcium– och kaliumfosfater med varierande tillförlitlighet. Situationen beträffande pulverröntgen för fasidentifiering var bättre, fast fördunklad av det faktum att strukturellt liknande fasövergångar ofta förekommer i det undersökta systemet. Däremot fattades det tillfredställande enkristallstrukturdata för ternära faser i det undersökta systemet. Enkristallröntgendiffraktion användes för att bestämma strukturerna för CaK2P2O7, CaKP3O9, Ca10K(PO4)7 och CaKPO4. Faserna CaK2P2O7 and CaKPO4 tillsammans med Ca3(PO4)2, KPO3 och K4P2O7 studerades med pulverröntgendiffraktion och termiska analysmetoder för att klargöra fasmodifikationer och övergångstemperaturer. Gibbs bildningsenergi bestämdes för Ca(PO3)2, Ca2P2O7, Ca3(PO4)2, Ca10K(PO4)7, CaK2P2O7, CaKPO4 och CaK4(PO4)2 med ems-metodik och yttriastabiliserad zirkonia som fast elektrolyt och Ni/Ni3P som hjälpsystem. Både de strukturella och termodynamiska data användes sedan vid analyser i ett förbrännningexperiment av olika sädesslag. Framtagna data användes både vid identifiering och även vid kvantifiering av bildade faser i biomassaresterna. / The behaviour of phosphates in thermochemical biomass conversion processes are critical for the general process chemistry, for ash related problems, for emissions as well as for an efficient, sustainable and beneficial use of the ash residues. This thesis is a summary and a discussion of eight papers dealing with structural and thermodynamical studies of phases in the CaO-K2O-P2O5 system, with relevance for biomass combustion. The objectives were: i) to compile and review the available structural and thermodynamical data of phases in the CaO-K2O-P2O5 system as well as to identify existing gaps in the field of these data, ii) to fill in as many as possible of the gaps by fundamental thermodynamic, structural and phase stability studies and iii) to demonstrate the uses and the benefits of the new data in practical applications. An initial review of the CaO-K2O-P2O5 system showed that both structural information and thermodynamic data were lacking. The situation regarding the available thermodynamic data was especially unsatisfactory, data could only be found for some few calcium phosphates and a few potassium phosphates with varying reliability. Concerning powder X-ray diffraction patterns for phase identification the situation was better, though obscured by the fact that structurally close related phase transitions often occur in the studied system. However, adequate single crystal structural data of ternary phases in the system was completely missing. Crystal structures of CaK2P2O7, CaKP3O9, Ca10K(PO4)7 and CaKPO4 were determined by single-crystal X-ray diffraction. The phases CaK2P2O7 and CaKPO4 were together with Ca3(PO4)2, KPO3 and K4P2O7, investigated by powder X-ray diffraction and thermal analysis to elucidate phase modifications and transitions temperatures. Gibbs standard energy of formation was determined for Ca(PO3)2, Ca2P2O7, Ca3(PO4)2, Ca10K(PO4)7, CaK2P2O7, CaKPO4 and CaK4(PO4)2 by solid state emf measurements with yttria stabilised zirconia as solid electrolyte and Ni/Ni3P as auxiliary solid couple. Both the structural and thermodynamical data were subsequently utilised in analysis of a combustion experiment of cereal grains. The data were also used to both identify and quantify the phases formed in biomass combustion residues.

Le protéasome est responsable de la dégradation régulée d'une majeure partie des protéines intracellulaires. Cette machinerie multimoléculaire est composée d'un cœur catalytique, le protéasome 20S, qui peut être activé par plusieurs types de protéines régulatrices, en particulier la particule régulatrice 19S ou PA700, les complexes heptamériques formés par les membres de la famille 11S (ou PA28) et PA200. Au cours de ce travail, nous nous sommes focalisés sur PA28gamma, un régulateur nucléaire du protéasome, qui active la dégradation de plusieurs substrats par le protéasome 20S de façon indépendante de l'ubiquitine et de l'ATP. Malgré de multiples études montrant l'implication de PA28gamma dans de nombreux processus cellulaires essentiels tels que le cycle cellulaire, la prolifération, l'apoptose, l'architecture nucléaire, la dynamique de la chromatine, les infections virales et la réponse au stress, ses fonctions exactes ne sont pas encore comprises. De plus, les mécanismes impliqués dans la régulation de l'activité de PA28gamma et de son association avec le protéasome 20S restent mystérieux. Une analyse SILAC des partenaires d'interaction de PA28gamma endogène a révélé l'existence d'un nouveau facteur, non caractérisé, que nous avons appelé PIP30 (PA28gamma Interacting Protein 30 kDa). Le gène PIP30 contient un domaine très conservé chez les Eucaryotes. Nous avons produit et purifié la protéine PIP30 recombinante et montré qu'elle est faiblement structurée, malgré le fait qu'elle puisse se dimériser. Nous avons confirmé, aussi bien in vitro qu'in cellulo, que PIP30 interagit directement et spécifiquement avec PA28gamma. En analysant la co-immunoprécipitation de PA28gamma avec différents mutants tronqués de GFP-PIP30, nous avons pu identifier la séquence de PIP30 responsable de l'interaction avec PA28gamma dans sa partie C-terminale. Nous essayons maintenant d'identifier la séquence de PA28gamma impliquée dans la liaison de PIP30 et de cristalliser le complexe PA28gamma/PIP30. L'élaboration d'un anticorps anti-PIP30 « maison » nous a permis de montrer que PIP30 est une protéine nucléaire stable. Son niveau d'expression diminue en réponse à la déplétion de PA28gamma, ce qui suggère que PIP30 est stabilisée par son interaction avec PA28gamma in cellulo. Nous avons démontré in vitro que PIP30 inhibe partiellement l'activation médiée par PA28gamma des activités de type chymotrypsine et caspase, mais pas trypsine, du protéasome. Cependant, nous avons montré, par une approche ELISA, que PIP30 n'affecte pas la liaison de PA28gamma au protéasome 20S. Par ailleurs, nous avons testé l'effet de PIP30 sur la dégradation de p21 par le complexe PA28gamma/protéasome 20S et observé que PIP30 augmente la vitesse de dégradation de p21 dans ce test. Nos tentatives pour élucider la fonction exacte de PIP30 in cellulo n'ont jusqu'ici pas abouti à une conclusion convaincante. L'ensemble de ces résultats suggère que PIP30 pourrait être impliqué dans le recrutement sélectif des substrats de PA28gamma et/ou dans la modulation de l'activation du protéasome par PA28gamma. / The proteasome is responsible for the regulated degradation of most intracellular proteins. This multi-subunit machinery is composed of a common catalytic core, the 20S proteasome, which can be activated by various types of regulators, notably the 19S regulatory particle or PA700, the heptameric complexes formed by the members of the 11S (or PA28) family and PA200. This work has been focused on PA28gamma, a nuclear regulator of the proteasome, which has been shown to activate degradation of several proteasomal substrates in an ATP- and ubiquitin- independent manner. Despite many evidences revealing the involvement of PA28gamma in many essential cellular processes, such as cell cycle progression, proliferation, apoptosis, nuclear architecture, chromatin dynamics, viral infection and stress response, its exact function(s) remain to be understood. In addition, how PA28gamma activity and association to the 20S proteasome are regulated is completely unclear. A SILAC-based analysis of endogenous PA28gamma interaction partners revealed the existence of a novel, completely uncharacterized protein, which we called PIP30 (PA28gamma Interacting Protein 30 kDa). Evolutionary analysis indicates that PIP30 gene contains a domain highly conserved in Eukaryotes, without any alternative splicing or gene duplication evidences. We produced and purified the recombinant PIP30 protein and showed that it is poorly structured, although it is able to make dimers. We confirmed both in vitro and in cellulo that PIP30 directly and specifically interacts with PA28gamma. By analyzing the co-immunoprecipitation of PA28gamma with various GFP-PIP30 truncation mutants, we identified the sequence of PIP30 responsible for PA28gamma binding in its C-terminal part. Ongoing analyses now focus on the identification of PIP30 binding motif on PA28gamma sequence and the crystallization of the PA28gamma-PIP30 complex. Using homemade anti-PIP30 antibodies, we showed that PIP30 is a stable nuclear protein. Its expression level is decreased in response to PA28gamma depletion, suggesting that it is stabilized by its interaction with PA28gamma in cellulo. We demonstrated in vitro that PIP30 partially inhibits PA28gamma-mediated activation of the chymotrypsin- and caspase-, but not the trypsin-like, activities of the proteasome. However, we showed by an ELISA-based approach that PIP30 does not affect PA28gamma binding to 20S. Considering the limitations of probing proteasome activity with small fluorogenic substrates, we tested the effect of PIP30 on the PA28gamma-dependent proteasomal degradation of in vitro translated p21, a known protein substrate of PA28gamma. We unexpectedly found that PIP30 enhanced the rate of p21 degradation. Our attempts to elucidate the exact functions of PIP30 in cellulo were unsuccessful so far. Altogether, our results suggest that PIP30 could be involved in the selective recruitment of PA28gamma protein substrates and/or modulate PA28gamma-mediated proteasome activation.

Le fer est un élément essentiel à la vie car il possède un rôle clé dans de nombreux processus biologiques.Malgré son abondance au niveau de la croûte terrestre, le fer est très faiblement biodisponible. Pour contourner ce problème, la majorité des micro-organismes a développé différents systèmes particulièrement efficaces pour l’acquisition de cet élément. Le mécanisme le plus répandu implique la production et la sécrétion de petites molécules chélatrices ayant une forte affinité pour le fer. Après sécrétion dans le milieu extracellulaire, ces composés chélatent le Fe3+ et le transportent ensuite au travers de la membrane externe via des transporteurs TonB-dépendants (TBDT). Durant cette thèse, nous avons mis en place un protocoleefficace permettant d’aller rapidement du clonage à la cristallisation de ces cibles afin d’étudier la structure tridimensionnelle de cette famille de protéines. Ainsi, nous avons pu résoudre et étudier la structure de plusieurs TBDT, de bactéries Gram-négatives. Ainsi nous avons mis en évidence un mouvement du domaine de signalisation en présence du ligand, proposé un mécanisme de transporteur de la molécule d’hème par le système shu chez Shigella dysenteriae. Chez les bactéries du genre Pseudomonas, nous avons élucidé et caractérisé au niveau structural les mystères de l’énantiosélectivité des pyochélines. En parallèle, nous nous sommes intéressé au devenir du ferri-sidérophore au niveau du périplasme, chez P. aeruginosa, ainsi qu’au transport du fer au travers de la membrane interne grâce à un transporteur ABC FpvCDEF ayant laparticularité de posséder deux protéines périplasmiques associées capables d’interagir avec le sidérophore. / Iron is essential for life because it has a key role in many biological processes. Despite its abundance in the earth's crust, iron is poorly bioavailable. To circumvent this problem, most micro-organisms have developed different systems particularly effective for the acquisition of this element. The most common mechanism involves the production and secretion of small chelating molecules having high affinity for iron. After secretion into the extracellular medium, these compounds chelate and transport ferric iron through the outer membrane via TonB-dependent transporters (TBDTs). In this thesis, we have developed an efficient protocol to easily go from cloning to crystallization of these targets and then studied the three-dimensional structure of this protein family. Thus, we were able to solve and study the structure of several TBDT of Gram-negative bacteria. We have identified a movement of the signaling domain in the presence of ligand. We proposed a mechanism for heme translocation through the shu system, in Shigella dysenteriae. In Pseudomonas species, we elucidated and characterized at the structural level the mysteries of the pyochelin enantioselectivity. In Pseudomonas aeruginosa, we studied the ferri-siderophore become in the periplasmic space, as well as iron transport across the inner membrane by an ABC transporter, named FpvCDEF, with the particularity of having two periplasmic proteins associated able to interact with the siderophore.

Ce travail de thèse porte sur l’analyse conformationelle de biomolécules en phase gazeuse. L’étude d’objets complexes en phase gazeuse permet de connaître les facteurs intrinsèques stabilisant leur structure. La première étape de mes travaux a été le couplage entre un appareil de mobilité ionique (IMS) et un appareil de spectrométrie de masse (MS). Nous avons simulé (SimIon) et développé différentes optiques ioniques fonctionnant à haute pression (entonnoirs à ions, piège ionique). Ces modifications expérimentales nous ont permis de commencer des études conformationnelles de biomolécules en phase gazeuse.Les premières expériences avaient pour objectif d’observer les facteurs stabilisants une structure secondaire sur des séries de peptides analogues. La première étude a été réalisée sur des séries de polyalalanines et de polyglycines de formules Arg(Ala)4XxxAla4Lys et Arg(Gly)4Xxx(Gly)4Lys, où Xxx est l’un des 20 acides aminés naturels. Nous nous sommes intéressés à l’influence de l’acide aminé central sur la conformation globale. Puis nous avons observés la stabilité de l’hélice de la partie transmembranaire de la protéine M2 du virus de la grippe A et de différents mutants. Ces études ont permit de montrer l’importance de la solvatation des charges en phase gazeuse.Enfin nous avons initié une étude sur le repliement des protéines en utilisant une protéine modèle, le lysozyme. Nous nous sommes plus particulièrement intéressés aux mécanismes de repliements en fonction du degré d’oxydation de cette dernière / This work deals with the conformational studies of biomolecules in gas phase. The gas phase allows observing the intrinsic factors that stabilize the structure.The first step of this work consisted in coupling an ion mobility tube and a mass spectrometer (IM-MS). Especially, ion optics working at high pressure had to be developed (ion funnels, cylindrical ion trap). These experimental modifications allowed us to realising conformational studies in vacuo.This work is build around two major axes. The first one deals with the understanding of the factors that stabilize the secondary structure in gas phase. We have studied series of peptides with similar sequences. We studied a series of polyalanines and polyglycines who have the following formula Arg(Ala)4XxxAla4Lys et Arg(Gly)4Xxx(Gly)4Lys, where Xxx is one of the 20 natural amino acids. We are looking the influence of central amino acid on the global structure of peptides. After that we have observed the stability of the helix of the transmembran domain of the M2 protein of virus Influenza A and some mutants. These studies allow showing the importance of the charge solvatation in the gas phase.Finally, we are initiated a study on the refolding of proteins and more particularly on a model protein: the Lysozyme. We are studied the refolding in function of oxide degrees

Le déficit en 21-hydroxylase est la cause la plus fréquente des hyperplasies congénitales des surrénales. Un grand nombre de nouvelles mutations a été trouvé dans le laboratoire qui centralise la plus grande cohorte de familles au niveau international et l’évaluation de leur sévérité était primordiale pour optimiser la prise en charge des patients (thérapeutique, conseil génétique). Grâce à l’analyse approfondie du phénotype des patients et au développement d’études fonctionnelles (in vitro, in silico), nous avons pu évaluer le retentissement de la plupart des 85 nouvelles mutations ; nous avons choisi comme témoins des mutations fréquentes de sévérité connue et nous avons comparé nos résultats avec ceux de la littérature. L’analyse plus approfondie d’une quinzaine de mutations rares a confirmé l’existence de bonnes corrélations phénotype-génotype comme ceci est décrit dans cette pathologie. Par ailleurs, les études structurales que nous avons développées ont permis d’améliorer les connaissances sur les relations structure-fonction des cytochromes P450 en général. / Steroid 21-hydroxylase deficiency is the most common enzymatic defect causing congenita ladrenal hyperplasia. A large number of new mutations has been detected in the laboratory, which centralizes the biggest cohort of families in the world, and evaluation of their severity wasessential to optimize the care of the patients (treatment, genetic counselling). Thanks to detailed analysis of the patients phenotype and to the development of functional studies (in vitro, in silico), we were able to evaluate the severity of most of the 85 novel mutations; we decided touse as controls frequent known mutations and to compare our results with those of literature. Themore detailed analysis of about fifteen rare mutations confirmed the existence of goodcorrelations phenotype-genotype as this is described in this pathology. Moreover, the structural studies we developed led to improve the knowledge on structure-function relationship of theP450 cytochromes family.

Sequence-specific interactions between proteins and nucleic acids play an essential role in the cell biology. While several molecular mechanisms contributing to the binding speci- ficity have been identified empirically, no general protein-DNA recognition code has been described to date. In this thesis, I explore selected characteristics of protein-DNA inter- actions using computational methods. First, the pairwise interactions between the basic biomolecular building blocks-amino acids and nucleotides-are investigated. It is shown that several statistically enriched, biologically relevant interaction motifs correspond to the most energetically favorable configurations of the respective binding partners. In ad- dition, a relationship between the physico-chemical properties of the amino acid residues found at the protein-DNA interface and the local geometric features of the DNA helix is presented. Next, the applicability of molecular dynamics-based setups to the description of binding equilibria in protein-DNA systems is investigated. Discrepancies are observed between the description offered by the computer simulations and experimental results, as well as between the results obtained using two molecular mechanical force fields. Finally, the more general evolutionary aspects of protein organization...