Ácidos graxos são moléculas hidrofóbicas essenciais para a composição da estrutura física celular, para o metabolismo energético dos seres vivos e também para os caminhos de sinalização molecular no proteoma celular. No caso de deficiência no ácido graxo docosahexaenóico (DHA) e do ácido eicosapentaenoico (EPA) temos a depressão e a mudança do comportamento. O transporte destas moléculas hidrofóbicas no citosol celular é realizado por uma família de proteínas capazes de se ligar a esses ácidos graxos de maneira seletiva, com alta afinidade e de forma reversível. Esta família de proteína é conhecida como FABP, ou proteínas ligantes de ácido graxo. Para realizar esta função, as FABP possuem características únicas tanto na sua estrutura tridimensional quanto na dinâmica experimentada pelos vários elementos estruturais. Diversos trabalhos identificaram regiões relevantes e, com mutações realizadas em resíduos específicos, caracterizaram o mecanismo como a proteína interage com ligantes e com a bicamada lipídica para a realização da sua função, identificando um processo multi-estágio na interação com a bicamada lipídica. Contudo, a não realização de mutações em todos os resíduos da proteína pode deixar não-identificados regiões ou resíduos da proteína também envolvidos na sua função. Além disso, nunca foi caracterizado o que ocorre com os resíduos e com a estrutura da FABP quando a proteína está complexada com uma bicamada lipídica. No presente trabalho, escolhemos a B-FABP para estudar a interação com ligantes e o complexo proteína-membrana desta família de proteínas. Para isto, as técnicas de ressonância magnética nuclear 15N-HSQC e eletrônica (RMN e RPE) foram utilizadas para acompanhar mudanças estruturais e dinâmicas ocorridas quanto de interações moleculares. Com a técnica de RPE e o uso de derivados de ácidos graxos marcados com radicais nitróxidos, monitoramos o sítio de ligação da molécula de ácido graxo e suas alterações quando na presença do surfactante SDS. No caso de RMN, foi usada em proteínas marcadas isotopicamente com 15N na presença de bicelas isotrópicas de DMPC: DHPC na razão igual a um (q = 1), em uma concentração lipídica (CL) de 4%. Nossos resultados além de identificar os mesmos resíduos já conhecidos na interação da FABP com modelos de membrana, também encontrou novos resíduos nunca antes associados à superfície de contato da FABP com a bicamada lipídica. / Fatty acids are hydrophobic molecules essential to the cell structure, to the energetic metabolism of living organisms and to the molecular signaling pathways in the cell proteome. Depression and behavior alteations are two common consequences of deficiencies in docosahexanoic (DHA) and eicosapentaenoic (EPA) acids. The transport of such hydrophobic molecules in the cytosol is the main function of a family of proteins capable of making a selective, high affinity, and reversible binding of fatty acids. This family of proteins is known as FABPs (fatty acid binding proteins). To perform their function, FABPs have unique features in both their tridimensional structure and in the dynamics experienced by the several structural elements. Many reports have identified regions that are relevant to function and, through point mutations of specific residues, have characterized the mechanism used by the protein to bind its ligand and also to interact with lipid bilayers. However, the point mutation strategy relies heavily on the choice of residues such that missing residues can lead to the lack of identification of important elements involved in protein function. Moreover, the characterization of the protein-bilayer complex still deserves a more detailed investigation. In this work, we study the B-FABP protein in terms of its interaction with ligands as well as a membrane model system. We made use of magnetic resonance techniques, nuclear (NMR) and electronic (EPR), to probe structural and dynamical changes occurring upon intermolecular interaction. EPR and spin labeled fatty acids allowed us to monitor the ligand binding site in the protein structure and also its alterations in the presence of the surfactant SDS. NMR HSQC was used to gain information on the conformational changes of isotopically labeled protein in the presence of biceles made of DMPC:DHPC (q = 1 and lipid concentration CL of 4%). Our results confirmed relevant functional residues that had been previously identified and also pointed to new residues that had not been implicated as part of the contact surface before, thus widening our understanding of FABP-bilayer interaction.

Ce manuscrit décrit la synthèse et l’étude physico-chimique de tensioactifs innovants utilisés comme outils biochimiques pour le maintien et la cristallisation de protéines membranaires en solution aqueuse. Un premier chapitre présente les moyens techniques actuels à disposition pour la manipulation et l’étude des protéines membranaires ainsi que les problèmes rencontrés concernant leur inactivation et les alternatives actuelles. Une seconde partie décrit la synthèse d’un lipide hémifluoré possédant un ligand métallique spécifique, qui a été utilisé pour la formation d’un film de Langmuir. Les propriétés du film lipidique (stabilité et fluidité) ont été étudiées et des essais de cristallisation 2D suivant le concept interfacial ont été réalisés sur une protéine recombinante SUR1 « his tag » solubilisée dans des micelles de détergents hydrocarbonés. Le troisième chapitre aborde la notion d’amphiphilie faciale et décrit la synthèse de tensioactifs glucosidiques par « click chemistry » basés sur corps aromatique central. La persubsitution sélective de têtes hydrophiles sur les positions 1,3,5 et de parties hydrophobes sur les positions 2,4,6 apporte une amphiphilie aux molécules via une ségrégation faciale. Enfin, le dernier chapitre est dédié à l’étude du comportement et des propriétés physico-chimiques des tripodes amphiphiles faciaux en solution aqueuse grâce à différentes techniques : tensiométrie, diffusion de la lumière, CPLH,... / This thesis deals with the synthesis and the physico-chemical study of new surfactants used as tools for holding membrane proteins in aqueous media. A first part presents the existing methods that allow the manipulation of the membrane proteins and describes the current issues encountered which lead to its denaturation. In a second chapter, the synthesis of a hemifluorinated lipid with a specific ligand is presented in order to form a film of Langmuir. The stability and fluidity of the monolayer lipid is monitored and used in experiments of cristallisation 2D following the interfacial concept on the recombinant membrane protein SUR1 « his tag » keep soluble in water with hydrocarbonated detergents. The third part defines the term associated to facial amphiphile and presents a synthesis by « click chemistry » of glucosidic surfactants with an aromatic core persubstitued. The alternated and selective substitution on 1,3,5 and 2,4,6 positions of the aromatic ring by respectively hydrophilic heads and hydrophobic tails induces a facial segregation. The last chapter concerns the study of facial amphiphiles behavior and its physico-chemical properties in aqueous solution by using several methods : tensiometry, dynamic diffusion light scattering, HPLC,...

Les transporteurs à ATP binding cassette (ABC) peuvent transporter une grande variété de substrats utilisant l'ATP-Mg2+ comme source d'énergie. Ces transporteurs sont présents dans toutes les formes de vie et sont impliqués dans la résistance aux médicaments, comprenant les anticancéreux et les antibiotiques. Mes travaux de thèse se concentrent sur le transporteur BmrA (130 kDa) de Bacillus subtilis utilisé en tant que système modèle et homologue de la P-glycoprotéine humaine impliquée dans la multirésistance aux anticancéreux. Dans ces travaux nous montrons que la reconstitution de cette protéine dans les lipides de Bacillus subtilis répond aux deux exigences centrales pour RMN: haut rapport signal sur bruit et la stabilité de l'échantillon sur une période de plusieurs années. Les spectres obtenus indiquent une protéine bien repliée et une préparation très homogène, comme en témoignent les lignes de résonance étroites et la dispersion du signal typique de la distribution de structure secondaire attendue de la protéine membranaire. Nous avons adapté la méthode GRecon utilisée dans les études de microscopie électronique pour la reconstitution des protéines membranaires pour la RMN à l'état solide. Nous avons suivi en détail la reconstitution du transporteur ABC BmrA par dialyse comme référence, et établi des conditions optimales de reconstitution en utilisant un gradient combiné de saccharose / cyclodextrine / lipide caractérisant GRecon. Les spectres RMN de l‘échantillon reconstitué par GRecon sont très similaire à ceux obtenus précédemment sur des échantillons reconstitués par dialyse. La préparation d'échantillons par GRecon présente un gain de temps de près d'un ordre de grandeur. Afin d'étudier les états ouvert vers l'intérieur (inward-facing IF) et ouvert vers l'extérieur (outward-facing OF) du transporteur, nous avons développé un protocole reproductible et quantitatif induisant l'état OF. Nous avons enregistré des spectres bidimensionnels RMN à l'état solide avec différents temps de mélange (20 et 200 ms) afin de suivre les changements des déplacements chimiques et d'identifier les résidus par des corrélations séquentielles. L'apparition très apparente de nouveaux signaux concomitants à la grande amplitude des perturbations de déplacement chimique (CSP) met en évidence l'importante flexibilité et les changements conformationnels de la protéine en présence d'ATP: Mg2+. Afin d'identifier les résidus apparaissant dans les spectres, nous avons utilisé le remplacement paramagnétique du co-facteur Mg2+ par du Mn2+. Cette méthode a révélé que les acides aminés apparaissant dans les spectres sont situés à proximité du site de liaison de l'ATP. En outre, les mesures EPR ont confirmé l'état fermé de la protéine en identifiant la distance correspondant à 1,8 nm entre deux atomes de Mn2+. Nous avons étudié les différences conformationnelles entre l'état IF et OF de BmrA. L'observation de nombreux CSP, ainsi que l'apparition de nouveaux signaux sont observés pour un mutant ne pouvant pas hydrolyser l'ATP, indiquant que l'hydrolyse n'est pas nécessaire pour la transition IF à OF dans BmrA. Nous avons également analysé le mécanisme lié au motif X-loop décrit comme étant impliqué dans la communication entre deux domaines de la protéine. Nous avons observé pour une protéine mutante dans laquelle le transport est aboli mais qui reste ATPase active, une transition incomplète puisque seul un sous-ensemble de CSPs est observé, ainsi qu'un manque de rigidification. Ces mesures suggèrent que la flexibilité semble être le point central dans la transmission des changements conformationnels nécessaires de la partie motrice à la partie d'exportation de molécules. Ces observations montrent que ce système serait semblable à un moteur tournant à plein régime qui ne serait pas connecté de manière rigide à un arbre de transmission le reliant au système de transport / ATP binding cassette (ABC) transporters can translocate a variety of molecules by coupling drug/lipid efflux with an ATP-Mg2+ fuelled engine. They are found in all forms of life and they are involved in a number of drug resistances including anti-cancer drugs and antibiotics. My studies focus on the drug exporter BmrA (130 kDa) from Bacillus subtilis as a model system and homologue of the human P-glycoprotein that is involved in multidrug resistance in cancer. We show that the reconstitution of this protein in lipids from Bacillus subtilis at a lipid-protein ratio of 0.5 m/m allows an optimal protein insertion into lipid bilayer as well as it complies with the two central NMR requirements: high signal-to-noise in the spectra and sample stability over a time period of years. The obtained spectra point to a well-folded protein and a highly homogenous preparation, as witnessed by the narrow resonance lines and the signal dispersion typical of the expected secondary structure distribution of the membrane protein. In the same time, we adapted the GRecon method used in electron microscopy studies for membrane protein reconstitution to the needs of solid-state NMR sample preparation. We followed in detail the reconstitution of the ABC transporter BmrA by dialysis as a reference, and established optimal reconstitution conditions using the combined sucrose/cyclodextrin/lipid gradient characterizing GRecon. NMR spectra recorded on a sample produced by GRecon showed a highly similar fingerprint as those recorded previously on samples reconstituted by dialysis. GRecon sample preparation presents a gain in time of nearly an order of magnitude for reconstitution. In order to study the inward-facing (IF) and the outward-facing (OF) state of the transporter, we developed a reproducible and quantitative protocol of ATP:Mg2+:VO43- addition inducing the OF state. We used selectively labelled samples obtained by the addition of natural abundance residues in the bacterial medium in order to reduce the number of signals in the spectra of this large protein. We recorded solid-state NMR two-dimensional spectra with different mixing times (20 and 200 ms) in order to follow chemical shift changes and identify residues by sequential correlations. The very noticeable apparition of new signals concomitant with the large amplitude of chemical shift perturbations (CSPs) highlight the important flexibility and conformational changes of the protein in presence of ATP:Mg2+:VO43- substrate. In order to identify the residues appearing in the spectra, we use paramagnetic replacement by Mn2+ of the Mg2+ acting as a co-factor in the active site. The paramagnetic relaxation enhancements caused the Mn2+ revealed that the amino acids appearing in the spectra are located in proximity to the ATP binding pocket. Besides, EPR measurements confirmed the closed state of the protein by identifying the corresponding 1.8 nm distances between two Mn2+. We investigate on the conformational differences identified between the IF and OF state in the ABC transporter BmrA reconstituted in its natural lipids. The observation of numerous CSPs, as well as the apparition new signals are observed for a hydrolysis-incompetent mutant on addition of ATP, indicating that hydrolysis is not required for the IF to OF transition in BmrA. We also analyze the mechanistic of the X-loop motif described to be involved in the communication between two domains of the protein. We observe for a mutant protein in which transport is abolished, but which remains ATPase active, an incomplete transition since only a subset of CSPs is observed, as well as lack of rigidification. This suggests that the change in dynamics might be central for transmitting the relevant conformational changes to the part of the protein driving transport, concomitant of an engine which is turning an input shaft, but which fails to connect in a rigid manner, trough adequate gears, with the output shaft driving the pump

>Magister Scientiae - MSc / Acute respiratory infections (ARI) continue to be the leading cause of acute illnesses worldwide and remain the most important cause of infant and young children mortality. Many viruses such as rhinoviruses, influenza viruses, parainfluenza viruses, respiratory syncytial viruses, adenoviruses and coronaviruses are deemed to be the etiological agents responsible for ARI’s in children. The recently discovered coronaviruses HCoV-HKU1 and HCoV-NL63 contribute significantly to the hospitalization of children with ARI’s. HCoV-NL63 was first identified in 2004, as the pathogen responsible for the hospitalization of a 7 month old child presenting with coryza, conjunctivitis and fever. Since then a significant amount of knowledge has been gained in the clinical spectrum on this virus, however HCoV-NL63 is still not well characterized on the molecular and proteomic level. This dissertation focuses on bringing about this characterization by cloning the HCoV-NL63 Nucleocapsid gene to be expressed in a bacterial system and transfecting the Nucleocapsid, Membrane and Envelope genes into a Mammalian cell culture system in order for its respective proteins to be expressed. With the use of Bioinformatic analytic tools certain characteristics of HCoV-NL63 Nucleocapsid, Membrane and Envelope proteins are able to be identified, as well as certain motifs and/or regions that are important in the functioning of these proteins. By comparing the results obtained for HCoV-NL63 N,M and E to other well studied coronavirus homologous will enlighten us on the potential role(s) of these proteins in determining HCoV-NL63 pathogenicity and infectivity. vi Although certain functions of these proteins can be deduced by the means of bioinformatics analysis, it is still imperative for it to be extensively characterized In Vitro. This will therefore form a fundamental step in the development of many other projects, which unfortunately fall outside the scope of this M.Sc thesis.

Mitochondrion is an endosymbiotic organelle synthesizing ~1% of its proteome, while remaining ~99% of the proteins are encoded by the nuclear genome and translated on the cytosolic ribosome. Therefore active mitochondrial biogenesis requires efficient protein transport destined for the different sub-compartments. Mitochondrion contains specialized translocation machineries in the outer and in the inner membrane known as TOM40 and TIM23-complex respectively. Import of a majority of mitochondrial proteome is mediated by inner membrane presequence translocase (TIM23 complex). However, the structural organization of Tim23-complex and mechanisms of mitochondrial inner membrane protein translocation is still elusive. Therefore, the present thesis addresses above elusive questions. Chapter 2 highlights the functional significance of different segments of Tim23 in regulating the conformational dynamics of the presequence-translocase- Tim23 is the central channel forming subunit of the presequence-translocase which recruits additional components for the assembly of the core complex. However the functional significance of different segments of Tim23 was not understood due to the lack of suitable conditional mutants. Our study has reported many conditional mutants from different segments of Tim23 which are precisely defective in the organization of the core complex and in the recruitment of the import motor component which enhances our understanding of protein translocation across mitochondrial inner membrane. Chapter 3 highlights the functional cooperativity among mtHsp70 paralogs and orthologs using Saccharomyces cerevisiae as a model organism- mtHsp70s are implicated in a broad spectrum of functions inside the mitochondria. In case of lower eukaryotes gene duplication event has given rise to multiple copies of Hsp70s thereby presenting an opportunity of division of function among these paralogs. The mitochondria of yeast Saccharomyces cerevisiae contains three Hsp70s, including Ssc1, Ssq1 and Ssc3 (Ecm10). The Ssc1 is essential for protein translocation and de novo protein folding functions while Ssq1 is needed for the Fe/S cluster biogenesis inside the mitochondria. Although it has been proposed earlier that, Ssc1 and Ssc3 possesses overlapping functions in protein translocation as a part of import motor in the Tim23-complex. However the physiological relevance and experimental evidences in favor above hypothesis was not established clearly. Our study has reported Ssc3 as an ‘atypical chaperone’ which cannot perform the generalized chaperone functions due to the conformational plasticity associated with both the domains of Ssc3 resulting into weaker client protein affinity, altered interaction with cochaperones and dysfunctional allosteric interface. Additionally, we have also highlighted the role of Nucleotide-binding domain in determining the functional specificity among Hsp70 paralogs and orthologs.

G protein-coupled receptors (GPCRs) are eukaryotic integral membrane proteins that perform transmembrane signal transduction. Due to their pivotal role in a wide range of essential physiological functions GPCRs represent a high proportion of all drug targets. High resolution X-ray structures of GPCRs are however underrepresented in the Protein Data Bank. This is due to their instability in detergent, low expression levels and the presence of misfolded receptors in many heterologous expression systems. The objective of this project was to engineer the angiotensin II type 1 receptor (AT1R), a human GPCR, to make it suitable for structural studies. It was determined that detergentsolubilised AT1R was thermostable with antagonist bound with an apparent Tm of ~45°C, which was sufficiently stable for purification without further thermostabilisation by rational mutagenesis. Two expression systems were then evaluated for large-scale production of AT1R, namely baculovirus-mediated expression in insect cells and mammalian expression in HEK293 cells. Radioligand binding assays showed that only the mammalian system produced sufficient quantities of active AT1R for structural studies. Expression in the mammalian system was further optimised to approximately 6 mg/L. An AT1R-GFP fusion was created to examine membrane localisation using confocal laser scanning microscopy, to assay expression levels, to select highly expressing monoclonal cell lines using fluorescence activated flow cytometry and to develop a fluorescence size-exclusion chromatographybased assay to examine the suitability of 12 different ligands for co-crystallization. AT1R was also engineered to facilitate crystallisation, including C-terminal truncations to remove predicted disordered regions and bacteriophage T4-lysozyme being added to the third intracellular loop to provide additional points of contact for crystallisation, which increased the apparent Tm by approximately 10°C. All modified versions of AT1R were assessed for expression, stability and monodispersity. Additionally a rapid western blotting based assay was developed for the detection of unfolded membrane proteins, which will have wide applicability in the field.

This thesis focuses on the structural and functional characterization of two integral membrane proteins; CfrA, an outer membrane TonB-dependent transporter (TBDT) from Campylobacter jejuni, and ELIC, a pentameric ligand-gated ion channel (pLGIC) from Erwinia Chrysanthemi. The spectroscopic characterization of CfrA revealed a fold consistent with the structural and biophysical properties observed for other TBDT. Both a homology model of CfrA and sequence alignments of CfrA with other ferric-enterobactin transporters suggested a unique mode of ligand binding, thus raising the possibility that C. jejuni can be specifically inhibited. To investigate the molecular determinates of binding to CfrA, I set out to crystallize CfrA. Hundreds of crystal trials led to crystals diffracting to 3.6 Å resolution, with a complete data set acquired at 5 Å resolution that led to a structural model of the CfrA β-barrel. In the second part of this thesis, I reconstituted ELIC into model membranes in order to test the role of intramembrane aromatic interactions in ELIC gating and lipid sensing. ELIC was reconstituted into both asolectin (aso-ELIC) and 1-palmitoyl-2-oleoyl phosphatidylcholine (PC-ELIC), membranes that stabilize the homologous nicotinic acetylcholine receptor (nAChR) in functional coupled versus non-functional uncoupled conformations, respectively. In both membrane environments, ELIC exhibits a mixed α-helical and β-sheet secondary structure, with a thermal denaturation intermediate between those of the nAChR and the close prokaryotic homolog, GLIC, in similar membranes. The data suggest that although ELIC has a decreased propensity to adopt an uncoupled conformation relative to the nAChR, its ability to undergo cysteamine-induced channel gating is sensitive to its lipid environment. The decreased propensity to uncouple may reflect an increased level of aromatics at the interface between the transmembrane α-helices, M1, M3, and M4. To test this hypothesis further, the level or aromatic residues at the M1, M3, and M4 interface in both GLIC and ELIC were varied, and in both cases the levels of intramembrane aromatic interactions correlated with the efficiency of coupling binding to gating. The data provide further evidence for a role of intramembrane aromatics in channel gating and in dictating the propensity of pentameric ligand-gated ion channels to adopt an uncoupled conformation.

As proteínas de classe 3 são candidatas na preparação de uma vacina contra a doença meningocócica. O objetivo deste estudo é determinar a imunogenicidade da proteína de classe 3 purificada da cepa de Neisseria meningitidis do sorogrupo B juntamente com a capacidade adjuvante de whole cells de Bordetella pertussis. Foram imunizados camundongos BALB/c neonatos em um intervalo de 3 a 12 dias entre 1 e 4 doses da proteína de classe 3 mais adjuvante, pela via intranasal e no 21º dia pela via intramuscular com a proteína de classe 3 emulsificada com hidróxido de alumínio. Os resultados demonstraram que após 2 doses pela via intranasal e 1 dose pela via intramuscular houve rápido estímulo das células imunes nos camundongos adultos BALB/c e neonatos BALB/c e outbred. Todos os soros foram analisados por ELISA e immunoblot. O adjuvante B. pertussis administrado pelas vias intranasal ou intramuscular, aumentou a resposta imune comparada com os controles. Anticorpos bactericidas e de alta afinidade foram produzidos. / Proteins of class 3 sound candidates in the preparation of vaccine against meningococcal illness. The aim of this study was to determine the immunogenicity of class 3 proteins purified of Neisseria meningitidis of the serogroup B along with whole cells of Bordetella pertussis as adjuvant. BALB/c and outbred neonate mice between 3 and 12 days old were immunized with 1 to 4 doses of the purified class 3 proteins with or without adjuvant given by the intranasal route, and on the 21st day the animals received an intramuscular dose of the class 3 proteins with or without aluminum hydroxide. The results demonstrated that after 2 doses by the intranasal route and 1 dose intramuscular there was a rapid stimulation of the immune cells in BALB/c adult mice as well as BALB/c and outbred neonates mice. All sera were analyzed by ELISA and immunoblot. The adjuvant B. pertussis used in the present investigation and given via the intranasal or intramuscular route increased the immune response compared with the controls. High affinity and bactericidal antibodies were produced.

Les membranes biologiques, qui compartimentent les différents éléments du vivant, jouent un rôle essentiel dans les processus biologiques comme la signalisation, le transport, la transmission du message nerveux, etc. Envisagées comme des fluides à deux dimensions, l’étude de leurs propriétés physiques peut nous aider à comprendre certains mécanismes biologiques. Ce travail de thèse s’est intéressé à la mobilité des molécules au sein des membranes, et notamment à deux paramètres essentiels, la viscosité membranaire, et la diffusion latérale. Après avoir optimisé la technique de recouvrement de fluorescence après photoblanchiment (FRAP) au microscope confocal, nous avons étudié la mobilité des molécules au sein de deux types de membranes modèles in vitro : la phase éponge d’un surfactant non-ionique (C12E5) et les vésicules géantes unilamellaires (GUVs) lipidiques. 1) La phase éponge (ou L3) : après avoir déterminé son diagramme de phase et montré que les protéines membranaires restent actives dans cette phase, nous avons mesuré la mobilité de protéines par recouvrement de fluorescence après photoblanchiment sur un motif à franges (FRAPP). Cela nous a permis d’obtenir les constantes d’association de protéines de la pompe d’efflux OprM-MexAB, impliquée dans la résistance aux antibiotiques de la bactérie Pseudomonas aeruginosa. Ces interactions dépendent très fortement du degré de confinement de chacune des protéines. 2) Les GUVs : après avoir développé une méthode simple de formation des GUVs, au sein desquelles les protéines membranaires restent actives, nous avons mesuré la diffusion des lipides par FRAP, et montré que dans certaines conditions, ils se déplacent en groupe, ce qui permet d’expliquer la diversité des résultats de la littérature. En mesurant la viscosité membranaire par imagerie microscopique du temps de vie de fluorescence (FLIM), nous avons également montré qu’elle ne se déduit pas nécessairement des modèles hydrodynamiques de diffusion. / Biological membranes, which divide the elements of life, are a key factor in biological processes such as signaling, transport, transmission of an nerve impulse, etc. Seen as two-dimensional fluids, the study of their physical properties could help us understand some unsolved biological mechanisms. This work focused on molecule mobility within membranes, and specifically on two essential parameters: membrane viscosity and lateral diffusion. After optimizing the Fluorescence Recovery After Photobleaching (FRAP) technique on confocal microscopes, we studied the mobility of molecules within two types of in vitro model membranes: the sponge phase made of a non-ionic surfactant (C12E5) and the giant unilamellar lipidic vesicles (GUVs). 1) Sponge phase (or L3) : after having established its phase diagram and shown that membrane proteins stay active in this phase, we measured protein mobility by Fluorescence Recovery After fringe Pattern Photobleaching (FRAPP). This allowed us to obtain the association constants of the proteins of the efflux pump OprM-MexAB involved in the resistance to antibiotics of the bacteria Pseudomonas aeruginosa. These interactions heavily depend on the degree of confinement of each protein. 2) GUVs : after having developed a simple method for the formation of GUVs, in which membrane proteins stay active, we measured the lipid diffusion by FRAP. We showed that, under certain conditions, they can move together, which explains the diversity of results in the literature. By measuring membrane viscosity by Fluorescence Lifetime Imaging Microscopy (FLIM), we also showed that viscosity should not be necessarily deduced from hydrodynamic diffusion models.

Le système de sécrétion de type II (SST2) permet la sécrétion de protéines repliées à travers la membrane externe chez les bactéries à Gram-négatif. Le SST2 est une nano-machine enchâssée dans l’enveloppe bactérienne, proche par sa composition et structure aux systèmes d’assemblage des pili de type IV (PT4) impliqués, entre autres, dans d’adhésion et motilité. Chez Klebsiella oxytoca, la surexpression des gènes pul codant le SST2 permet l’assemblage de pili composées des sous-unités PulG. Ceci suggère qu’en conditions physiologiques l’assemblage d’un pseudopilus périplasmique permet la sécrétion du substrat spécifique du SST2, la pullulanase. Dans ce projet nous avons exploré le mécanisme moléculaire de l’assemblage du pseudopilus en se focalisant sur les interactions de PulG avec les composants du SST2 dans la membrane interne. En utilisant l’approche de double-hybride bactérien, nous avons établi le réseau d’interactions de PulG avec les pseudopilins mineures PulH, I, J et K et avec la plateforme d’assemblage (PA). Pour valider ces interactions, nous avons combiné des techniques de biochimie (co-purification par affinité, pontage cystéine et chimique) avec des analyses fonctionnelles de sécrétion et de formation du pseudopilus. Nous avons mis en évidence des interactions entre PulG et les protéines de la PA, PulF et PulM, et nous avons analysé en détail l’interface PulG-PulM. Les résultats suggèrent la formation d’un complexe PulK-I-J-H-G dans la membrane interne impliqué dans des étapes précoces de la formation du pseudopilus, à travers les interactions de PulG et PulH avec PulM et PulF. Nos données expérimentales suggèrent un rôle majeur de PulM dans la sécrétion, vraisemblablement durant l’assemblage du SST2 et l’élongation du pseudopilus. Nos travaux collaboratifs mettant en jeu l'analyse par spectroscopie de masse et en dynamique moléculaire in silico révèlent le rôle essentiel des résidus conservés Glu5 et Thr2 de PulG, requis pour l’interaction avec PulM. Ces données suggèrent que Glu5 participe à l'extraction de PulG de la membrane, en neutralisant la charge positive de son peptide N-terminal par des interactions intramoleculaires. Ces résultats permettent d'établir un modèle détaillant les étapes initiales de l’assemblage des pseudopili dans la membrane interne, relevant pour de futures études sur le SST2 et nanomachines homologues. sécrétion de protéinespili de type 4 assemblage de fibres complexes protéiques membranairesinteractions protéine-protéinemicroscopie à immuno-fluorescence simulations en dynamique moléculairedouble-hybride bactérien spectrométrie de masse nanomachines bacteriennes / The type II secretion system (T2SS) drives the translocation of folded, periplasmic proteins across the outer membrane in Gram-negative bacteria. Secretion is carried out by an envelope-spanning nanomachine that is similar to the apparatus that builds type IV pili (T4P), bacterial surface filaments involved in adhesion, motility and other functions. In the Pul T2SS of Klebsiella oxytoca, overexpression of pul genes in plate-grown bacteria allows the assembly of T4P-like surface fibres made of PulG subunits, suggesting that a periplasmic pseudopilus fibre plays a role in the secretion of the type II substrate pullulanase under physiological conditions. In this project, we explored the molecular mechanism of pseudopilus assembly by focusing on the interaction between PulG and the T2SS inner membrane and pseudopili components. The network of interactions of PulG with the minor pseudopilins PulH, I, J and K and the assembly platform (AP) components was established using bacterial two-hybrid analysis. To validate these interactions, we combined biochemical approaches (affinity co-purification, chemical or cysteine cross-linking) with functional assays of secretion and pseudopilus formation. We provide evidence of the interaction between PulG and the AP proteins PulF and PulM, and delve into the PulG-PulM interface. Our results point to the formation of a PulK-I-J-H-G complex in the plasma membrane involved in early steps of fibre assembly, with a determinant role for PulG and PulH interaction with PulM and PulF. We obtained experimental evidence supporting a major role for PulM in pseudopilus assembly and protein secretion, probably by intervening in the assembly of the T2SS apparatus and in pseudopilus elongation. The results of experimental and in silico studies in collaboration with experts in mass spectrometry and molecular dynamics support the essential role of the highly conserved PulG residues Glu5 and Thr2, which participate in PulM binding. In addition, Glu5 probably favours PulG membrane extraction by neutralising its N-terminal positive charge through intra-molecular interaction. These findings shed new light on early membrane events during fibre assembly, and open new and exciting avenues in research on T2SSs and related nanomachines.protein secretiontype 4 pilifibre assemblymembrane protein complexprotein-protein interactionsimmunofluorescence microscopymolecular dynamics simulationsbacterial two-hybrid assaymass spectrometrybacterial nanomachines