PagP is an integral outer membrane enzyme that transfers a palmitoyl group from a phospholipid to lipid A and the polar headgroup of phosphatidylglycerol (PG). Palmitoyl-lipid A and palmitoyl-PG (PPG) have been implicated in resistance to host immune defenses. PagP proteins are diverse, the E. coli PagP belongs to the major clade of PagP homologs and palmitoylates lipid A regiospecifically at the 2-position, whereas P. aeruginosa PagP belongs to the minor clade of PagP homologs and instead palmitoylates lipid A regiospecifically at the 3’-position. Our objective was to understand how PagP has been adapted in nature to interact with multiple lipid substrates and products. We investigated the structure-function relationships of key major clade homologs, to show that Bordetella PagP palmitoylates lipid A at the 3’-position and employs surface residue T29 in its palmitoyltransferase reaction. Legionella PagP palmitoylates lipid A at the 2-position and was confirmed to select a palmitate chain from a pool including iso-methyl branched phospholipids characteristic of this species. PagP is usually encoded as a single copy on the chromosome in most bacteria, but two copies of pagP are found in endophytic bacteria. These duplicated PagP homologs from the major clade branch into two subclades, namely chromosomal and plasmid-based PagP homologs. The chromosomal PagP homologs exhibit interacting periplasmic D61 and H67 residues, which are naturally mutated in plasmid-based PagP homologs, and are associated with a conformational change in the -barrel that determines its ability to palmitoylate PG. Chromosomal PagPs can convert PPG to bis(monoacylglycero)phosphate (BMP) and lysophosphatidylglycerol (LPG) through a periplasmic active site controlled by the invariant Y87 residue of E. coli PagP. Plasmid-based PagP homologs appear to have been adapted instead as monofunctional lipid A palmitoyltransferases. These results points to a common ancestor for PagP proteins. Knowledge gained from these studies can be applied to protein engineering. / Thesis / Doctor of Philosophy (PhD)

Yes / In Escherichia coli, the biogenesis of both cytochrome bd-type quinol oxidases and periplasmic cytochromes requires the ATP-binding cassette-type cysteine/GSH transporter, CydDC. Recombinant CydDC was purified as a heterodimer and found to be an active ATPase both in soluble form with detergent and when reconstituted into a lipid environment. Two-dimensional crystals of CydDC were analyzed by electron cryomicroscopy, and the protein was shown to be made up of two non-identical domains corresponding to the putative CydD and CydC subunits, with dimensions characteristic of other ATP-binding cassette transporters. CydDC binds heme b. Detergent-solubilized CydDC appears to adopt at least two structural states, each associated with a characteristic level of bound heme. The purified protein in detergent showed a weak basal ATPase activity (approximately 100 nmol Pi/min/mg) that was stimulated ∼3-fold by various thiol compounds, suggesting that CydDC could act as a thiol transporter. The presence of heme (either intrinsic or added in the form of hemin) led to a further enhancement of thiol-stimulated ATPase activity, although a large excess of heme inhibited activity. Similar responses of the ATPase activity were observed with CydDC reconstituted into E. coli lipids. These results suggest that heme may have a regulatory role in CydDC-mediated transmembrane thiol transport. / This work was supported by Biotechnology and Biological Sciences Research Council grant BBS/B/14418 (Membrane Protein Structure Initiative).

Le virus d'Epstein-Barr (EBV) est un herpèsvirus humain qui infecte plus de 90% de la population généralement de façon bénigne et asymptomatique. Cependant, de nombreuses données démontrent que ce virus peut également contribuer à certains processus de cancérisation. En effet, l'EBV est associé à de nombreuses pathologies malignes telles que le lymphome de Burkitt, le lymphome hodgkinien et le carcinome du nasopharynx. Dans la grande majorité de ces cancers associées à ce virus, l'EBV exprime un programme de latence de type II durant lequel la protéine LMP1 est exprimée. Elle est décrite comme l'oncogène majeur de l'EBV car son expression est nécessaire à la survie et à la prolifération des lignées transformées in vitro. Cette protéine membranaire est fonctionnellement apparentée aux membres de la famille des récepteurs du TNF. LMP1 est constitutivement active et son expression conduit à l'activation de voies de signalisation telles que les voies NF-κB, PI3K et des MAPK. L'activation de ces voies de signalisation cellulaire confère à LMP1 des propriétés oncogéniques, cependant, des effets toxiques liés à son expression ont également été décrits. Effectivement, LMP1 est capable d'induire l'apoptose dans différents types cellulaires. Dans ce contexte, nous avons d'abord développé et caractérisé, des variants dérivés de LMP1 constitués de sa partie C-terminale signalisatrice, complète ou partielle, fusionnée à la protéine GFP. Nous montrons que ces variants sont capables de séquestrer les protéines adaptatrices se fixant à LMP1 ou au récepteur TNFR1, et d'inhiber le signal et les phénotypes induits par ces derniers. Ces protéines à effet dominant négatif peuvent ainsi contrecarrer les effets transformants de LMP1 dans des modèles de latence II et III. Ces dominants négatifs peuvent aussi inhiber l'activation du TNFR1 et les phénotypes qui en découlent. Puis, nous avons étudié les propriétés de LMP1 en dehors d'un contexte infectieux et son rôle dans la transformation épithéliale. Nous démontrons que LMP1 induit la mort des cellules épithéliales MDCK mais certaines cellules outrepassent ses effets cytotoxiques générant des lignées qui expriment stablement LMP1 et dans lesquelles cet oncogène viral favorise la survie et exacerbe les phénotypes induits par le facteur de croissance HGF. Le caractère ambivalent de LMP1 pourrait limiter le pouvoir oncogène de l'EBV mais en contrepartie favoriser l'émergence de cellules résistantes à l'apoptose et capables de répondre de façon accrue à des facteurs de croissance. Nos travaux ont permis de mieux comprendre la dualité fonctionnelle de LMP1, d'une part ses effets oncogènes favorisant la survie cellulaire et d'autre part ses propriétés pro-apoptotiques, induites directement ou révélées suite à son inhibition, limitant la tumorigenèse. La caractérisation des mécanismes moléculaires impliquant LMP1 pourrait ainsi participer à la définition de potentielles stratégies thérapeutiques pour le traitement de cancers associés à l'EBV et où LMP1 est exprimée.

Bacteriorhodopsin (bR) is a 7TM membrane protein expressed in Halobacterium salinarum. Due to its stability and high expression levels, bR serves as a model for other 7TM membrane proteins. Neurotensin receptor 1 (NTS1) is a member of pharmacologically relevant G protein-coupled receptor superfamily, and is the high affinity receptor for neurotensin, a 13mer peptide that can be found in the brain, gut, and central nervous system. NTS1 is a target for Parkinson’s, Schizophrenia, and drug addiction. This thesis aims to develop pulsed magnetic resonance techniques and sample preparation forms for high resolution structural studies on 7TM proteins. In this thesis, pulsed dipolar distance electron paramagnetic resonance (EPR) methods for the study of proteins in their native membrane are established. bR is spin-labeled, and a wellresolved distance distribution is measured in excellent agreement with other structural data. Preliminary distance data for a photoexcited state of bR suggests quaternary rearrangements in the native membrane that are agreement with published AFM results. A fitting method is developed to enable measurements of systems with rapid signal decay, a common feature in reconstituted systems studied by pulsed EPR methods. A physical chemical characterization of nanosized-bilayer discs termed Lipodisqs®, and the successful incorporation of bR is presented. Lipodisqs® are formed from DMPC and a polymer that is able to solubilize DMPC vesicles into discrete particles. Lipodisqs® possess a broad phase transition with increased lipid ordering compared to a DMPC dispersion. The SMA polymer interacts with the lipid tails, but does not perturb the headgroup. BR is incorporated in the monomeric form, and EPR dynamic and distance measurements confirm that Lipodisqs® preserve the native structure of bR, whilst detergent solubilisation increases the overall mobility compared to bR in its native membrane, suggesting that Lipodisqs® serve as an excellent medium for EPR studies on 7TM membrane proteins. A cysteine-depleted mutant of active, ligand binding NTS1 is constructed. Cysteines are reintroduced at positions that may be able to monitor agonist and inverse-agonist induced conformational and dynamic changes. A spin-labeling protocol is developed, and preliminary EPR measurements are discussed. Dynamic nuclear polarization (DNP) results are presented with uniformly-¹³C-labelled bR in the PM, resulting in a DNP enhancement of 16 using the biradical nitroxide polarizing agent, TOTAPOL. DNP-enhanced solid state NMR (ssNMR) is typically carried out at cryogenic temperatures, resulting in poor spectral resolution compared to ambient temperatures. Two different forms of samples are prepared that could potentially lead to better-resolved DNP spectra. BR is reverse labelled by adding natural abundance amino acids to isotopically labelled growth medium, resulting in the partial depletion of resonance signals that may obscure and crowd the NMR spectra. A crystalline sample of bR is prepared using the LCP method for crystallization, which is to date the most successful method for the crystallization of GPCRs. In summary, the first pulsed dipolar measurements of a protein in its native membrane are shown, Lipodisqs® are characterized and found to be a suitable medium for structural and functional studies of 7 TM membrane proteins, the first preliminary EPR studies on a ligand binding GPCR are presented, and novel sample preparation techniques are developed for the nitroxide-based DNP enhancement of ssNMR data. This thesis opens up several avenues for future research into 7TM membrane proteins.

A large number of proteins interact with biological membranes, either integrated in the membrane (PepTSo2), embedded on a membrane surface (5-lipoxygenase) or encircling a cutout of lipid bilayer (apolipoprotein1 (apoA-I). They function as transporters, receptors or biocatalysts in cellular processes like inflammation or cholesterol transport which are touched upon here. Malfunction of specific membrane proteins are the cause for several diseases or disorders. Knowledge of protein structure supports understanding of its mechanism of function. Here, transmission electron microscopy (TEM) was used for structure determination. To obtain structure information to high resolution for membrane proteins, normally surrounded by lipids, demands specific methods and materials for stabilization. Stabilized in detergent the structure of the bacterial transporter PepTSo2 was shown to form a tetramer even bound to substrate. However, with a protein based stabilizer, Salipro, the structure of PepTSo2 could be determined to high resolution. High density lipoprotein (HDL) in blood plasma, involved in the removal of cholesterol from peripheral tissues, have a central role in cardiovascular function, metabolic syndrome and diabetes. The HDL-particle is composed of two copies of ApoA1 and around hundred lipid molecules. From TEM data, for the first time the clearly discoidal shape could be shown by 3-dimendional reconstructions. These were used for modelling the ApoA1 protein dimer by a "biased fitting" procedure. The results indicate how ApoA1 folds around a lipid bilayer in a disc-shaped structure. Modified HDL called nanodiscs were here used to show the Ca2+ dependent binding of 5-lipoxygenase on the nanodisc bilayer and thereby increased production of the inflammatory mediator leukotrieneA4. Dimerization of 5-lipoxygenase inactivates these functions. / <p>QC 20170323</p>

Anaplasma phagocytophilum and A. marginale are the etiologic agents of bovine anaplasmosis and human granulocytic anaplasmosis, respectively. As obligate intracellular pathogens, binding and entry of host cells is a prerequisite for survival. The molecular events associated with these processes are poorly understood. Identifying the adhesins mediating binding, delineating their key functional domains, and determining the molecular determinants to which they bind not only benefits better understanding of Anaplasma spp. pathobiology, but could also benefit the development of novel approaches for protecting against infection. We previously demonstrated that A. phagocytophilum outer membrane protein A (ApOmpA) is critical for bacterial binding and entry host through recognition of α2,3-sialic acid and α1,3-fucose of its receptors, including 6-sulfo-sLex. In this study, we determined that two amino acids, G61 and K64, within its binding domain (ApOmpA59-74), are essential for ApOmpA function. We also confirmed the ability of ApOmpA to act as an adhesin and invasin as it conferred adhesiveness and invasiveness to inert beads. We next extended our studies to A. marginale as it also expresses OmpA (AmOmpA) and its role in infection has not been studied. Molecular models of ApOmpA and AmOmpA were nearly identical, especially in the ApOmpA binding domain and its counterpart in AmOmpA. Antisera raised against AmOmpA or its putative binding domain inhibit A. marginale infection. AmOmpA G55 and K58 are contributory and K59 is essential for AmOmpA to bind to host cells. AmOmpA binding is dependent on α2,3-sialic acid and α1,3-fucose. Coating inert beads with AmOmpA conferred the ability to bind to and be taken up by host cells, confirming that it acts as an adhesin and invasin. 6-sulfo-sLex is dispensable for AmOmpA binding and A. marginale infection. ApOmpA works cooperatively with Asp14 (14-kDa A. phagocytophilum surface protein) to promote optimal infection of host cells. We found that Asp14 is conserved across A. phagocytophilum strains and in A. marginale and confirmed the ability of Asp14 to act as an adhesin and invasin as it conferred adhesiveness and invasiveness to inert beads. Collectively, this work advances our understanding of A. phagocytophilum and A. marginale adhesion and invasion of host cells.

A signifficant obstacle facing the healthcare industry is the phenomenon of multidrug resistance (MDR) in which a cell acquires simultaneous resistance to many unrelated drugs that it has never been exposed to. At the molecular level, MDR can be characterised by a reduction of intracellular drug levels due to their active efflux by multidrug transporters such as P-glycoprotein (Pgp). Pgp is able to efflux a phenomenally wide variety of chemically unrelated drugs and causal relationships have been established between its expression and the acquisition of MDR to numerous anticancer and central nervous system (CNS) drugs. There has thus been much effort to understand the molecular biology of Pgp and how it functions. However, many aspects of its functioning remain unclear. From a drug discovery viewpoint, we have yet to fully understand what features make some drugs susceptible to Pgp-mediated efflux (substrates) and what makes others able to inhibit Pgp function (inhibitors). From a mechanistic viewpoint, it is still uncertain what the exact nature of Pgp's binding site is, the role of ATP binding and hydrolysis in transport and how both of these interplay with ligand binding. The work presented in this thesis attempts to answer these questions from two perspectives. Firstly the mouse Pgp crystal structure [PDB 3G60] was used as a unique starting point for molecular dynamics (MD) simulations to characterise the dynamics and conformational exibility of Pgp, properties believed to be integral to its function. The simulations revealed Pgp to be a highly dynamic molecule at both its transmembrane (TM) and nucleotide binding domains (NBDs). The latter exhibited a conformational asymmetry that supports the Constant Contact model of ATPase activity. In the presence of the Pgp substrate, daunorubicin, the NBDs exhibited tighter asymmetric dimerisation leading to increased affinity for ATP. In contrast, the presence of the Pgp inhibitor, QZ59-RRR led to NBD conformational changes that reduced their affinity for ATP. Thus providing an appealing mechanism for how QZ59-RRR inhibits Pgp ATPase activity. MD simulation was also used to provide atomic-detail interpretations of multiple binding stoichiometries of drug and lipid molecules observed by collaborator-led mass spectrometry experiments. This also provided opportunity to validate the Pgp simulations against novel experimental data. The second strand of the thesis explored the membrane permeation dynamics of CNS therapeutics in order to identify differences in protonation states, conformations, orientations and membrane localisation that might distinguish those that are Pgp substrates and from those that are not. These properties were studied using complementary MD simulation and nuclear magnetic resonance (NMR) techniques. The simulations revealed a novel set of criteria that in uence the likelihoodof a drug to 'flip-flop' across a membrane, a behaviour that may make drugs more susceptible to Pgp efflux. These observations were broadly consistent with the NMR experiments. However, the NMR data also highlighted limitations in the simulation approaches used in this thesis and emphasised the need to also consider the kinetics of permeation in addition to its thermodynamics.

Membrane proteins of the rhomboid-family are evolutionarily widely conserved and include rhomboid intramembrane serine proteases and rhomboid-like proteins. The latter have lost their catalytic activity in evolution but retained the ability to bind transmembrane helices. Rhomboid-family proteins play important roles in intercellular signalling, membrane protein quality control and trafficking, mitochondrial dynamics, parasite invasion and wound healing. Their medical potential is steeply increasing, but in contrast to that, their mechanistic and structural understanding lags behind. Rhomboid protease GlpG from E.coli has become the main model rhomboid-family protein and the main model intramembrane protease - it was the first one whose X-ray structure was solved. GlpG cleaves single-pass transmembrane proteins in their transmembrane helix, but how substrates bind to GlpG and how is substrate specificity achieved is still poorly understood. This thesis investigates the importance of the transmembrane helix of the substrate in its recognition by GlpG using mainly enzyme kinetics and site-directed mutagenesis. We find that the transmembrane helix of the substrate contributes significantly to the binding affinity to the enzyme, hence to cleavage efficiency, but it also plays a role in cleavage site...

Après le génome, le nouveau défi est celui du protéome. Nous avons progressé vers la mise au point de la séparation électrophorétique des protéines membranaires dans un milieu qui leur conviendrait, type bicouche lipidique supportée. La grandeur principale, mesurée par FRAPP, a été le coefficient de diffusion de lipides ainsi que des protéines. L'étude du comportement de la bicouche supportée a permis de mettre en évidence, pour certains supports et dans certaines conditions de température, la formation d'une phase ondulée (ou ripple) malgré la proximité du support. La diminution de la portée des interactions coulombiennes par adjonction de sel se traduit par une augmentation de plusieurs ordres de grandeur du coefficient de diffusion, approchant au final le comportement d'une bicouche libre, tout en conservant les étapes caractéristiques de la transition gel/fluide. L'ordre de grandeur de ces énergies d'interactions a été estimé à partir des courbes D= f(T) et validé par une étude préliminaire originale de DSC sur des bicouches lipidiques supportées. L'&#945;-Hémolysine s'insère spontanément sous forme d'un pore heptamérique dans nos bicouches supportées et diffuse librement. En l'incubant en phase mixte (zones gel+ zones fluide), nous observons la formation de complexes de protéines. La dépendance du coefficient de diffusion avec la taille de l'objet est en 1/R2, R étant le rayon équivalent de la partie insérée de l'objet. L'application d'un champ électrique montre un transport électrophorétique dont la direction et l'importance sont modulées par la charge de l'objet. La mobilité électrophorétique varie également en 1/R2. / After the genome, the new challenge is the proteome. We have progressed toward electrophoretic separation of membrane proteins in a medium that they love, a supported lipid bilayer. The main parameter, measured by FRAPP, was the diffusion coefficient of different objects (lipids, proteins). Studying bilayer behaviour has showed that, on particular supports and in a given temperature range, ripple phase can exist, despite the proximity of the support. Adding salt decreases coulombic interactions which turns to increase the diffusion coefficient over several orders of magnitude, reaching the value for a free-standing bilayer in the fluid phase, meanwhile the main characteristic steps of the global gel/fluid transition are still observed. Estimation of the value of the interaction energy has been made and compared to results of a preliminary DSC study. &#945;-Hémolysin self-inserts spontaneously as an heptameric pore in supported bilayers and diffuses freely. Incubating in a gel/fluid mixture leads to protein complex formation. Diffusion varies with size as 1/R2, R being the equivalent radius of the inserted part of the object. Applying an electric field results in an electrophoretic motion where direction and magnitude are modulated by the charge of the object. Electrophoretic mobility varies also as 1/R2. Size dependence, magnitude of mobilities and a simple building protocol allow to hope carrying out soon a real electrophoretic separation of a protein mixture.

A Periodontite Agressiva (PA), que atualmente pertence ao grupo das Periodontites estágios 3 e 4, distingue-se dos demais tipos de doença periodontal por seu início precoce, agregação familiar dos casos e por afetar pacientes sistemicamente saudáveis. Além disso, pode ser subclassificada em duas formas, localizada (PAL) e generalizada (PAG), em função de sua extensão. Muitas vezes, os depósitos de biofilme bacteriano são desproporcionais à quantidade de destruição óssea e perda de inserção que o paciente apresenta, independente da subclassificação. O microrganismo mais relacionado à etiopatogênese da doença é o Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans), incluindo os seus principais sorotipos a, b e c, amplamente estudados. Associado a estas condições, A. actinomycetemcomitans apresenta alguns fatores de virulência como uma leucotoxina, principalmente ligada ao sorotipo b - clone JP2 (que é altamente leucotóxico) e proteínas de membrana externa (OMPs), especialmente Omp29. A resposta de imunoglobulina G (IgG) sérica contra este patógeno foi anteriormente associada à ambas as formas de PA, porém, são escassos os estudos que avaliaram longitudinalmente a resposta sérica frente a variáveis como estas. Dessa maneira, o objetivo desse estudo foi avaliar a resposta sérica, de 27 pacientes com PA e 10 pacientes periodontalmente saudáveis, contra Omp29 e sorotipos de A. actinomycetemcomitans, através de um ensaio ELISA, correlacionando com o número de cópias de JP2 (obtidos por qPCR em tempo real) e parâmetros clínicos, a partir de dados anteriormente coletados por nosso grupo. Todos os dados foram obtidos antes do início do tratamento e um ano após seu término. O tratamento consistiu de orientações de higiene bucal, tratamento mecânico e antibioticoterapia. Os dados resultantes do estudo mostraram que em ambas as formas de PA houve uma redução significativa na profundidade clínica de sondagem (PCS)(p<0,001), nível clínico de inserção (NCI)(p<0,001) e na resposta sérica contra Omp29 e sorotipo c de A. actinomycetemcomitans(p>0,005). Após 1 ano, os valores de densidade óptica (D.O.) normalizados para Omp29 e sorotipos de A. actinomycetemcomitans, bem como o número de cópias do clone JP2 tornaram-se similares aos níveis encontrados nos controles. A redução no número de cópias do clone JP2 foi correlacionada com redução da PCS em PAL(r=0.80,p=0.0042) e valores de D.O. normalizados de Omp29 em PAG(r=0.66,p=0.005). O estudo concluiu que o tratamento periodontal foi eficaz em alterar a resposta sérica contra Omp29 e sorotipos de A. actinomycetemcomitans, além de reduzir o número de cópias do clone JP2 e melhorar os parâmetros clínicos. / Aggressive Periodontitis (AP), which currently belongs to the group of Periodontites stages 3 and 4, is distinguished from other types of periodontal disease due to its early onset, familial aggregation of cases and to affect systemically healthy patients. In addition, it can be sub classified into two forms, localized (PAL) and generalized (PAG), depending on its extent. Often, bacterial biofilm deposits are disproportionate to the amount of bone destruction and loss of insertion that the patient presents, regardless of sub classification. The most important microorganism related to the etiopathogenesis of the disease is Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans), including its main serotypes a, b and c, widely studied. Associated with these conditions, A. actinomycetemcomitans presents some virulence factors such as leukotoxin, mainly linked to serotype b - clone JP2 (which is highly leukotoxic) and outer membrane proteins (Omp\'s), especially Omp29. Serum immunoglobulin G (IgG) response against this pathogen was previously associated with both forms of BP; however, there are few studies that longitudinally evaluated the serum response to variables such as these. Thus, the objective of this study was to evaluate the serum response of 27 patients with AP and 10 periodontally healthy patients against Omp29 and A. actinomycetemcomitans serotypes by an ELISA, correlating with the number of copies of JP2 (obtained by qPCR in real time) and clinical parameters, from data previously collected by our group. All data were obtained prior to initiation of treatment and one year after its completion. The treatment consisted of oral hygiene guidelines, mechanical treatment and antibiotic therapy. Data from the study showed that in both forms of BP there was a significant reduction in clinical depth of sampling (PCS) (p<0,001),, clinical level of insertion (NCI)(p<0,001) and serum response against Omp29 and serotype c of A. actinomycetemcomitans(p>0,005). After 1 year, normalized optical density (O.D.) values for Omp29 and A. actinomycetemcomitans serotypes, as well as the number of copies of clone JP2 became similar to the levels found in the controls. The reduction in copy number of clone JP2 was correlated with reduction of PCS in PAL(r=0.80,p=0.0042) and O.D. normalized from Omp29 to PAG(r=0.66,p=0.005). The study concluded that periodontal treatment was effective in altering the serum response against Omp29 and A. actinomycetemcomitans serotypes, in addition to reducing the number of copies of clone JP2 and improving clinical parameters.