Pseudomonas aeruginosa est une bactérie Gram-négative qui présente une grande résistance aux antibiotiques, lui permettant de sévir dans le milieu hospitalier en infectant plus particulièrement les patients immunodéprimés. Cette résistance est principalement due au système d’efflux membranaire MexAB-OprM, capable d’exporter les antibiotiques en dehors de la cellule. Cette pompe à efflux est composée de trois protéines, MexA, MexB et OprM, incorporées dans les membranes internes et externes de la paroi bactérienne. Les structures de MexA, OprM et AcrB -une protéine présente chez E. coli, homologue de MexB- ont été déterminées individuellement par cristallographie des rayons X. Cependant, la structure du complexe entier, regroupant les trois protéines en interaction, ainsi que le mécanisme de cette pompe font toujours défaut. Le renforcement de nos connaissances structurales et fonctionnelles est donc capital pour lutter plus efficacement contre ces bactéries, par de nouvelles stratégies médicamenteuses. Ce travail porte sur l’étude de la structure et de la stœchiométrie de l’assemblage des protéines OprM et MexA au sein d’une membrane lipidique. La caractérisation du complexe OprM/MexA a été réalisée à l’aide de nouvelles techniques de caractérisation physico-chimique des surfaces, telle que la Microbalance à Cristal de Quartz avec Mesure de Dissipation (QCM-D), et par des méthodes d’imagerie, telles que la Cryo-Microscopie Electronique en Transmission (CryoMET) et la Cryo-Tomographie Electronique (CryoTE). En QCM-D, les mesures d’interaction entre OprM et MexA ont été réalisées sur support solide en contrôlant l’orientation d’OprM placée dans un environnement lipidique. Après ajout de la protéine MexA, la formation de complexes OprM/MexA a été mise évidence. Pour comprendre l’organisation de ce complexe, nous avons procédé à une étude comparative de l’organisation des protéines OprM, MexA et du complexe OprM/MexA incorporés dans une membrane lipidique, par CryoMET. Trois types d’organisation, respectivement spécifiques d’OprM, de MexA et du complexe OprM/MexA, ont été mis en évidence. Une analyse structurale de ces trois différents assemblages, pris en sandwich entre deux membranes lipidiques, a été menée par CryoTE. La reconstitution de la protéine OprM conduit à la formation de protéoliposomes, dû à des interactions intervenant entre les protéines OprM au niveau de leurs hélices périplasmiques. La protéine MexA s’organise sous forme d’une structure annulaire de 13 nm de hauteur au sein des membranes lipidiques, et d’une structure plus complexe de 26 nm de hauteur, résultant de l’empilement tête-bêche de deux structures annulaires de 13 nm. Ce travail révèle les dimensions exactes de l’assemblage formé par MexA, et permet de localiser à proximité des membranes les domaines non résolus dans la structure cristallographique. La reconstitution du complexe OprM/MexA révèle une disposition régulière des deux protéines dans les membranes lipidiques. Au sein des complexes, les protéines OprM sont présentes sous forme de trimères. Dans la membrane opposée, à l’aplomb d’une molécule d’OprM, MexA ne forme pas une structure annulaire similaire à celle décrite précédemment, indiquant un état d’oligomérisation différent de celui observé dans les assemblages MexA. Les densités de MexA sont compatibles avec la présence de quelques molécules de MexA. Cependant des structures annulaires de MexA, positionnées à l’aplomb de trois trimères d’OprM sont visibles. Notre étude montre que MexA adopte des structures oligomériques spécifiques en fonction de ses interactions avec les membranes lipidiques ou avec son partenaire OprM. / The structure determination of membrane protein in lipid environment can be carried out using cryo electron microscopy combined with the recent development of data collection and image processing. We describe a protocol to study assemblies or stacks of membrane protein reconstitued into a lipid membrane using both cryo electron tomography and single particle analysis which is an alternative approach to electron crystallography for solving 3D structure. We show the organization of the successive layers of OprM molecules revealing the protein-protein interactions between OprM molecules of two successive lipid bilayers.

Much of our knowledge of cellular biology arises from direct observation of active cellular functions. Tools and techniques have steadily developed over the past several hundreds of years to aid in our understanding and control of the nanoworld and are referred to as nanotechnologies. In the context of nanotechnology, DNA is not used as a carrier for genetic information (as it is in cell), but as a construction material. DNA offers unprecedented control over the construction of simplified biomimetic models for the study of biological processes. This thesis first introduces and defines the field of DNA nanotechnology, with particular emphasis on the interaction of snthetic DNA nanostructures with biological membranes. Inspired by the protein clathrin, three-fold symmetric DNA tile made of eight, short DNA strands and capable of polymerising is described and studied, with the aim to interact with and controllably bend a membrane bilayer. This structure presented challenges during construction so an enhanced three-armed DNA structure built with DNA origami was designed. The succesful assembly of a rigid and functionalisable nanostructure is described. This origami structure was polymerised into large constructs in solution and on a supported lipid membrane. The shape of the structure was modulated to vary its curvature and apply a bending force to a lipid vesicle when anchored to it. Following the conclusion of this study, we present the construction of a small, unique DNA structure for enhanced electron microscopy imaging in cell lysate. This project is part of a developing technique to couple the interaction specificity of dyes in super-resolution microscopy and the high-resolution output of electron microscopy. Finally, the optimisation procedures and recommendations for TEM imaging of samples of DNA origami and lipid structures are discussed.

Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this work, a summary is provided of our current understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria (Chapter 1). The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities. Although this thesis primarily explores structure and function, it also elucidates the hidden regulatory mechanism (post-translational) behind the association of a small protein called AcrZ with the tripartite complex AcrAB/TolC, in connection with the lipid environment, and the resulting changes in the latter's functionality (Chapter 2). A regulatory role of the native membrane lipid environment as well as of small proteins for efflux pump activity have previously been hypothesised. I present the first example of a function-regulating role of the lipid cardiolipin in combination with a small protein binding partner (AcrZ) for the substrate selectivity and transport activity of an efflux pump protein (AcrB). This regulation happens through induced structural changes which have remained unseen so far. Alongside with these results, a nanodisc reconstitution method was experimentally adapted for a structure-function investigation of an efflux pump (complex) using cryo-EM (Chapter 2). Beyond some fundamental regulatory insights, hidden intrinsic transport mechanisms for some transporters have also remained to be explored and studied. The discovery of a mechanism for active influx by a prominent efflux pump model system (Chapter 3) provides hope that this phenomenon is more common amongst multidrug transporters and that it could be utilised for drug discovery purposes. This novel feature explains the contradictory findings on this transporter in the past and raises new questions about the little-known physiological role and evolution of efflux pumps. The development and evolution of antimicrobial resistance has frequently shown to be a multifactorial and fast-moving process. One of these factors is the evolution of pumps itself towards an altered functionality (e.g. towards a broader or altered substrate spectrum or higher efflux rates). Against this background, the role of key carboxylate residues for efflux-energising proton trafficking was investigated for a prominent study model of a secondary-active transporter (Chapter 4). The re-allocation and/or addition of acidic residues was demonstrated to result in the preservation of wild type activity or the generation of hyper-efflux activity, respectively. These findings suggest that rapid emergence of antimicrobial resistance could be enhanced by the 'plasticity' in the location of key carboxylate residues with a role in proton coupling. It also demonstrates the necessity of antimicrobial drug design programmes to anticipate possible trajectories of an adaptive evolution of efflux pump. The 'cryo-EM revolution' has boosted the pace at which new structural and functional insights into multidrug efflux pumps are gained. Nevertheless, in order to derive the structure of individual pump components or of a full assembly, it is sometimes necessary to identify and characterise homologues and mutants, which would allow the application of cryo-EM for obtaining near-atomic maps. Functional analyses presented in this work helped to characterise a homologue and mutants of the MacAB/TolC tripartite complex to justify the obtained protein structures and strategies for further functional characterisation (Chapter 5). Given (1) the unusual stoichiometry of a MacB dimer in complex with a hexameric membrane-fusion protein (MacA), which leads to a seeming leakiness of the assembly, and (2) the fact that substrate has to pass through a narrow aperture in the membrane-fusion protein for extrusion, it is rather surprising that MacB was previously shown to transport an entire toxin. An experimental approach was developed that could enable the structure determination of a toxin-bound full assembly of MacAB/TolC (Chapter 5). Finally, the role of multidrug efflux pumps for the evolution of multidrug resistance is yet to be studied and better explored. For instance, evolutionary trajectories of pump overexpression, as compared to those of regular expression or no expression, are unknown yet could have the potential to reveal useful insights for spread prevention and drug design. The outline of an experimental design with some preliminary validating data is presented in Chapter 6.

L'organisation de la chromatine eucaryote ainsi que les mécanismes qui régulent sa compaction restent discutés. Nous proposons de comprendre le rôle de variations locales de charges et de concentrations ioniques dans l'organisation supramoléculaire de la chromatine. Nous utilisons un système modèle, la particule cœur de nucléosome (NCP) constituée de 146pb d'ADN qui s'enroulent autour d'un octamère d'histones sur un 1.75 tours. Les extensions terminales des histones, les queues, sont mobiles et positivement chargées. A l'aide de NCPs reconstituées à partir d'ADN et d'histones intactes ou globulaires recombinants, nous montrons que les queues des histones H3 et H4 sont essentielles pour l'établissement d'interactions attractives entre NCPs, en solution diluée. Le rôle d'ions multivalents dans les interactions entre NCPs et la formation de précipités ont été étudiés. Le rôle des queues d'histones est également abordé pour la formation de phases denses obtenues sous stress osmotique.

<p>Physico-chemical characterisation of structure and stability of liposomes intended for drug delivery is the central issue in this thesis. In addition, targeted liposomes to be used in boron neutron capture therapy (BNCT) were developed.</p><p>Lysolipids and fatty acids are products formed upon hydrolysis of PC-lipids. The aggregate structure formed upon mixing lysolipids, fatty acids and EPC were characterised by means of cryo-TEM. A relatively monodisperse population of unilamellar liposomes was detected in mixtures containing equimolar concentration of the three components. </p><p>The interactions between alternative steric stabilisers (PEO-PPO-PEO copolymers) and conventional PC-and pH-sensitive PE-liposomes were investigated. Whereas the PE-liposomes could be stabilised by the PEO-PPO-PEO copolymers, the PC-liposomes showed an enhanced permeability concomitant with the PEO-PPO-PEO adsorption.</p><p>Permeability effects induced by different PEG-stabilisers on EPC liposomes were shown to be dependent on the length of the PEG chain but also on the linkage used to connect the PEG polymer with the hydrophobic membrane anchor.</p><p>An efficient drug delivery requires, in most cases, an accumulation of the drug in the cell cytoplasm. The mechanism behind cytosolic drug delivery from pH-sensitive liposomes was investigated. The results suggest that a destabilisation of the endosome membrane, due to an incorporation of non-lamellar forming lipids, may allow the drug to be released. </p><p>Furthermore, sterically stabilised liposomes intended for targeted BNCT have been characterised and optimised concerning loading and retention of boronated drugs. </p>

<p>The focus of this thesis has been on the effects of segregation in mixtures of amphiphilic molecules. Two different systems were investigated: fluorocarbon-hydrocarbon surfactant mixtures and lipid-surfactant mixtures.</p><p>In fluorocarbon-hydrocarbon surfactant mixtures the repulsive interactions between the chains can lead to a demixing into different types of coexisting micelles, fluorocarbon rich and hydrocarbon rich. From NMR self-diffusion measurements such a demixing was found to occur in the mixture of the partially fluorinated surfactant HFDePC and C₁₆TAC. We furthermore suggested a demixing also within the micelles to explain ¹⁹F-NMR line width data and results from neutron scattering.</p><p>In lipid-surfactant mixtures, a segregation of the molecules may instead be caused by a difference in the preferred curvature of the lipid and the surfactant residing within the same aggregate. Using a surfactant selective electrode, binding isoterms of four different cationic surfactants (C₁₂TAC, C₁₄TAC, C₁₆TAC and HFDePC) to preformed lipid (GMO) vesicles were determined. Perforated vesicles were observed by cryo-TEM in the mixture with C₁₆TAC. To explain the results from the binding isoterms, the formation of pores in the bilayer was regarded as a cooperative process, similar to micelle formation. The surfactant accumulates at the edges of the pores, and increasing the surfactant concentration results in an increased number of pores with a constant surfactant/lipid ratio at the edges.</p><p>The lipid-surfactant mixtures were also studied at the solid/solution interface using AFM. An adsorbed mesh structure, a counterpart to the bulk perforated lamellar phase, was observed for the first time.</p>

Physico-chemical characterisation of structure and stability of liposomes intended for drug delivery is the central issue in this thesis. In addition, targeted liposomes to be used in boron neutron capture therapy (BNCT) were developed. Lysolipids and fatty acids are products formed upon hydrolysis of PC-lipids. The aggregate structure formed upon mixing lysolipids, fatty acids and EPC were characterised by means of cryo-TEM. A relatively monodisperse population of unilamellar liposomes was detected in mixtures containing equimolar concentration of the three components. The interactions between alternative steric stabilisers (PEO-PPO-PEO copolymers) and conventional PC-and pH-sensitive PE-liposomes were investigated. Whereas the PE-liposomes could be stabilised by the PEO-PPO-PEO copolymers, the PC-liposomes showed an enhanced permeability concomitant with the PEO-PPO-PEO adsorption. Permeability effects induced by different PEG-stabilisers on EPC liposomes were shown to be dependent on the length of the PEG chain but also on the linkage used to connect the PEG polymer with the hydrophobic membrane anchor. An efficient drug delivery requires, in most cases, an accumulation of the drug in the cell cytoplasm. The mechanism behind cytosolic drug delivery from pH-sensitive liposomes was investigated. The results suggest that a destabilisation of the endosome membrane, due to an incorporation of non-lamellar forming lipids, may allow the drug to be released. Furthermore, sterically stabilised liposomes intended for targeted BNCT have been characterised and optimised concerning loading and retention of boronated drugs.

The focus of this thesis has been on the effects of segregation in mixtures of amphiphilic molecules. Two different systems were investigated: fluorocarbon-hydrocarbon surfactant mixtures and lipid-surfactant mixtures. In fluorocarbon-hydrocarbon surfactant mixtures the repulsive interactions between the chains can lead to a demixing into different types of coexisting micelles, fluorocarbon rich and hydrocarbon rich. From NMR self-diffusion measurements such a demixing was found to occur in the mixture of the partially fluorinated surfactant HFDePC and C16TAC. We furthermore suggested a demixing also within the micelles to explain 19F-NMR line width data and results from neutron scattering. In lipid-surfactant mixtures, a segregation of the molecules may instead be caused by a difference in the preferred curvature of the lipid and the surfactant residing within the same aggregate. Using a surfactant selective electrode, binding isoterms of four different cationic surfactants (C12TAC, C14TAC, C16TAC and HFDePC) to preformed lipid (GMO) vesicles were determined. Perforated vesicles were observed by cryo-TEM in the mixture with C16TAC. To explain the results from the binding isoterms, the formation of pores in the bilayer was regarded as a cooperative process, similar to micelle formation. The surfactant accumulates at the edges of the pores, and increasing the surfactant concentration results in an increased number of pores with a constant surfactant/lipid ratio at the edges. The lipid-surfactant mixtures were also studied at the solid/solution interface using AFM. An adsorbed mesh structure, a counterpart to the bulk perforated lamellar phase, was observed for the first time.

PEG-lipid stabilized bilayer disks have been found in lipid mixtures containing polyethylene glycol (PEG)-lipids where the combination of a high bending rigidity and low PEG-lipid/lipid miscibility favours disk formation. The disks are planar and circular in shape and their long-term stability is excellent. Theoretical calculations and experimental observations suggest that the micelle forming PEG-lipid are situated at the rim of the aggregate, protecting the hydrophobic lipid chains in the bulk of the aggregate from contact with water. This thesis deals with fundamental aspects concerning the lipid distribution in the disks, as well as with development, optimization, and initial evaluation of the disks as model membranes in partition and interaction studies. Small angle neutron scattering was used to study the partial segregation of components within the bilayer disk. The experiments verified that the PEG-lipids segregate and accumulate at the bilayer disk rim. The proof of component segregation is important from a fundamental point of view and useful, as exemplified in the below-mentioned study of melittin-lipid interaction, when interpreting partition or binding data obtained from studies based on bilayer disks. Today liposomes are often used as model membranes in partition and interaction studies. Using liposomes to predict, e.g., drug partitioning can however have certain drawbacks. In this thesis the disks were proven to be attractive alternatives to liposomes as model membranes in partition studies. The formation of bilayer disks by a technique based on detergent depletion enabled incorporation of a transmembrane protein in the bilayer disks and opened up for the use of disks as model membranes in membrane protein studies. Further, bilayer disks were used in a comparative study focused on the effect of aggregate curvature on the binding of the peptide melittin. Various techniques were used to perform initial evaluations of the bilayer disks as model membranes. Of these, capillary electrophoresis and biosensor-based technology had not been used before in combination with bilayer disks.

Le monoxyde d'azote est exclusivement synthétisé chez les mammifères par une famille d'hémoprotéines, les NO-Synthases. Le cœur de l'activité des NO-Synthases est l'activation de l'oxygène c'est-à-dire l'activation de l'intermédiaire réactionnel FeIIO2. Cette étape est contrôlée par la réactivité intrinsèque du fer, par les transferts de proton et les transferts d'électron. Elle doit être parfaitement maîtrisée car elle contrôle le chemin catalytique emprunté et la nature du produit final. Comprendre l'étape d'activation de l'oxygène est essentiel à la compréhension du rôle biologique et/ou pathologique de la NO-Synthase de mammifère. Cette question s'étend aux NO-Synthases bactériennes pour lesquelles on ne connait ni le mécanisme moléculaire ni la fonction biologique. Ce manuscrit propose une analyse approfondie de l'étape d'activation de l'oxygène de la NO-Synthase. Dans un premier temps, nous avons étudié l'influence de l'environnement proximal sur la réactivité intrinsèque du fer et l'activation de l'oxygène. Nous avons généré des protéines mutées qui modifient les propriétés électroniques de la liaison proximale de l'hème. Ces protéines mutées ont été caractérisées par différentes spectroscopies (résonance paramagnétique électronique, Raman de résonance). Dans un second temps nous avons directement étudié le complexe FeIIO2, en présence d'analogues de substrat, grâce à des analyses de cinétique rapide en flux continu et en flux arrêté (stopped-flow). Dans un troisième temps, le rôle du cofacteur tetrahydrobioptérine dans le transfert de proton et d'électron a été étudié par une méthode de piégeage à des temps très courts : le freeze-quench. L'ensemble de nos résultats montrent que l'activation de l'oxygène est régulée par les propriétés électro-donneuses du ligand proximal et par le réseau de liaisons H distal. Nous mettons en évidence des différences dans le rôle redox du cofacteur tetrahydrobioptérine entre la NO-Synthase de mammifère et la NO-Synthase bactérienne. La difficulté majeure pour comprendre l'étape d'activation de l'oxygène de la NO-Synthase réside dans la complexité et la rapidité de la réaction catalytique. Dans ce contexte, nous avons cherché à adapter une méthodologie qui a prouvé son efficacité dans le cas des cytochromes P450 : la cryo-réduction couplée à des sauts en température.