Membrane proteins are key players in many biological processes. Since most membrane proteins are assembled into oligomeric complexes it is important to understand how they interact with each other. Unfortunately however, the assembly process (i.e. their social life) remains poorly understood. In the work presented in this thesis I have investigated when and how membrane proteins assemble with each other and their cofactors to form functional units. We have shown that that cofactor insertion in the hetero-tetrameric cytochrome bo3 occurs at an early state in the assembly process. We also found that the pentameric CorA magnesium ion channel is stabilised by different interactions depending on the magnesium ion concentration in the cell. These studies indicate that the assembly of a functional unit is a dynamic process, which is a result of many different forces. By studying the assembly of membrane proteins we have obtained a deeper insight into their function, which cannot be explained by static crystal structures. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.</p>

This dissertation explores the electrochemical behavior of enzymes and their cofactors at carbon nanotube (CNT) and nitrogen-doped carbon nanotube (N-CNT) electrodes. Two common types of oxidoreductases are considered: flavin adenine dinucleotide (FAD)-dependent oxidases and nicotinamide adenine dinucleotide-dependent (NAD⁺)-dehydrogenases. Chapter 1 presents the oxygen reduction reaction (ORR) at N-CNT electrodes as a way to electrochemically measure enzymatic turnover at the electrode surface. The unique peroxide pathway at N-CNT electrodes, which catalytically disproportionates hydrogen peroxide (H₂O₂) back into oxygen, provides an increased ORR current directly proportional to the rate of enzymatic turnover for H₂O₂ producing enzymes, even in an oxygen saturated solution. Biosensing of L-lactate using the increased ORR current is demonstrated using L-lactate oxidase. Chapter 2 explores the surface bound electrochemical signal of FAD when FAD-dependent enzyme or free FAD is allowed to spontaneously adsorb onto the CNT/N-CNT surface. Specifically, the origin of the enzymatically generated FAD signal and the rate constant of the electron transfer are elucidated. Chapter 3 continues the discussion of the cofactor FAD by demonstrating its use as an informative surface specific redox probe for graphitic carbon surfaces. Primarily, FAD can be used to determine the electroactive surface area and the relative hydrophobicity/hydrophilicity of graphitic surfaces. Chapter 4 changes gears to NAD⁺-dependent dehydrogenases by investigating the electrocatalytic oxidation of NADH at N-CNTs in comparison with conventional carbon electrodes or nondoped CNTs. Biosensing of glucose through the oxidation of NADH is demonstrated using glucose dehydrogenase adsorbed onto the N-CNT surface. Chapter 5 continues the discussion of NAD⁺-dependent dehydrogenases by addressing the reaction kinetics of NADH oxidation at N-CNTs as a tool to measure the enzymatic reduction of NAD⁺.

Yes / Understanding skin metabolism is key to improve in vitro to in vivo extrapolations used to inform risk assessments of topically applied products. However, published literature is scarce and usually covers a limited and non-representative number of donors. We developed a protocol to handle and store ex vivo skin samples post-surgery and prepare skin S9 fractions to measure the metabolic activity of Phase II enzymes. Preincubation of an excess of cofactors at 37 °C for fifteen minutes in the S9 before introduction of the testing probe, greatly increased the stability of the enzymes. Using this standardised assay, the rates of sulphation (SULT) and glucuronidation (UGT) of 7-hydroxycoumarin, methylation (COMT) of dopamine and N-acetylation (NAT) of procainamide were measured in the ng/mg protein/h (converted to ng/cm2/h) range in eighty-seven individuals. Glutathione conjugation (GST) of 1-chloro-2,4-dinitrobenzene was assessed in a smaller pool of fifty donors; the metabolic rate was much faster and measured over six minutes using a different methodology to express rates in μg/mg protein/min (converted to μg/cm2/min). A comprehensive statistical analysis of these results was carried out, separating donors by age, gender and metabolic rate measured.

The maintenance of protein homeostasis as a response to changing external conditions is crucial for cellular survival and proper function. Since plants cannot adapt by changing location, their need for a rapid intracellular response is accentuated. The AAA ATPase CDC48 maintains protein homeostasis in conjunction with NPL4 and UFD1 by coupling ATP hydrolysis with mechanical force to extract and unfold ubiquitylated proteins from organelle membranes, chromatin, or protein complexes. Our bioinformatic analysis revealed considerable domain and binding motif differences in A. thaliana NPL4 compared to its orthologs in animals and fungi. Using ITC, MST, and SEC-MALS, we found that NPL4 and UFD1 did not heterodimerize, NPL4 bound to CDC48A in the absence of UFD1, and the complex was not stable in vitro. Additionally, we provided the first medium-high-resolution reconstructions of CDC48A in both an AMP-PNP bound and apo state, using cryo-EM. AMP-PNP bound CDC48A was reconstructed in both a tense (3.3 Å) and relaxed (3.5 Å) conformation with the N domain was positioned above or coplanar with the D1 ring, respectively. Our heterogeneity analysis using CryoDRGN revealed continuous flexibility of the N domains between the two conformations. The apo state was reconstructed as a single conformation at 4.4 Å resolution. A cryo-EM reconstruction of the complex was also obtained at a resolution of ~6 Å, which showed expected cofactor stoichiometry and binding positions. Through our efforts, we have observed differences in the interaction between A. thaliana CDC48A and its cofactors UFD1 and NPL4 that may correspond to functional differences between kingdoms.

Proper control of gene expression is important for coordinating biological processes. Transcription factors (TFs) play a critical role in maintaining proper gene expression by binding their specific binding sites at cis-regulatory elements (CREs) and recruiting cofactors (COFs). Given their important roles in mediating gene expression, there is a need for methods that can profile TF-COF binding to DNA in a high throughput (HT) manner. In this thesis, I present two novel, array-based, HT methods – CASCADE (Customizable Approach to Survey Complex Assembly at DNA Elements) and CoRec (Cofactor Recruitment) – to profile the indirect recruitment of any COF in any cell type or cell state in a HT manner. CASCADE is a technique to profile the indirect recruitment of COFs to DNA via TFs in a stimulus-dependent manner. We demonstrate how CASCADE can be used to characterize COF recruitment at single nucleotide resolution to CREs in LPS-stimulated macrophages and demonstrate how it can be applied to characterize COF recruitment to ~1700 non-coding single nucleotide polymorphisms (ncSNPs). To understand genetic alterations that drive cancer, we apply CASCADE to cancer-associated non-coding variants (NCVs). Using our newly developed genetic burden test, we predict 2,555 driver NCVs and find that 765 candidate drivers altered transcriptional activity, 510 led to differential binding of TF-COF complexes, and that they primarily impact the binding to ETS factors. Lastly, I introduce the CoRec technique for profiling COF recruitment to a broad set of TF families. I show how CoRec can be used to develop cell type-specific TF-COF interaction “fingerprints” and reveal distinct COF recruitment preferences at single-nucleotide resolution. I integrate the findings from CoRec with genomic accessibility and gene expression data and demonstrate that COF-recruitment motifs captured with CoRec are enriched at promoters and significantly related to highly expressed genes. Taken together, the CASCADE and CoRec approaches are powerful methods to investigate TF-COF complex binding and their use will add to our understanding of CRE regulation, uncover biophysical mechanisms of NCVs, and characterizations of cell state-specific TF-COF complexes.

La mise en conformation de l’α et β tubulines en hétérodimeres polymérisables nécessite l’intervention de cinq protéines « Tubulin Binding Cofactors » (TBCA a TBCE) dont TBCC qui joue un rôle indispensable. Dans des cellules humaines d’adénocarcinome mammaire, nous avons modifié le niveau d’expression de TBCC et nous avons montre que ceci avait un impact sur le contenu des fractions de tubuline, la dynamique des microtubules ainsi que sur le phénotype et chimiosensibilité des cellules. La distribution en cycle cellulaire et les durées de la mitose et de la phase S ont été altérées. La modification de TBCC avait un faible effet sur la vitesse de prolifération in vitro par contre les cellules présentaient des différences significatives de croissance tumorale in vivo. Les réponses aux agents antimicrotubulaires et à la gemcitabine ont montrées une chimiosensibilité dépendante de la distribution en cycle cellulaire. Tous ces résultats montrent l’importance de la régulation du contenu en tubulines et l’impact de ceci sur le comportement de la cellule en général et vis-à-vis des traitements / The proper folding pathway of α and β-tubulin into the α/β-tubulin heterodimers involve five Tubulin Binding Cofactors (TBCA to TBCE). TBCC plays a crucial role in the formation of polymerization-competent the α/β-tubulin heterodimers. To evaluate the impact of microtubule mass and dynamics on the phenotype and chemosensitivity of breast cancer cells, we targeted TBCC in human breast adenocarcinoma and developed variants of breast cancer cells with modified content of TBCC. We have shown that the modifications in TBCC expression level influenced tubulin fraction distribution and microtubule dynamics. Cell cycle distribution and the durations of mitosis and S-phase were altered. The proliferation rate in vitro was slightly modified whereas in vivo the TBCC variants presented major differences in tumor growth capacity. Chemosensitivity to antimicrotubule agents (paclitaxel and vinorelbine) as well as to gemcitabine was observed to be dependent on the cell cycle distribution of the TBCC variants. These results underline the essential role of fine tuned regulation of tubulin content in tumor cells and the major impact of dysregulation of tubulin dimer content on tumor cell phenotype, cell cycle progression and response to chemotherapy. A better understanding of how the microtubule cytoskeleton is dysregulated in cancer cells would greatly contribute to a better understanding of tumor cell biology and characterization of resistant phenotypes

Die Anaphylaxie, eine potentiell lebensbedrohliche Reaktion, kann durch Kofaktoren beeinflusst werden. ACE-Inhibitoren, ß-Blocker und Acetylsalicylsäure (ASS) werden häufig in der Therapie von Herz-Kreislauferkrankungen eingesetzt. In der vorliegenden Arbeit wurde überprüft, ob diese anaphylaktische Reaktionen begünstigen. Das Modell der passiv systemischen Anaphylaxie (PSA) wurde speziell angepasst, um die Behandlung einer Herz-Kreislauf-Therapie nachzubilden. Die orale Gabe von Metoprolol oder Ramipril verstärkte die Anaphylaxie geringfügig. Die Kombination der Medikamente steigerte die Anaphylaxie deutlich, was im Modell der passiv kutanen Anaphylaxie (PCA) bestätigt werden konnte. Gleichzeitig waren Mastzellmediatoren im Serum der Tiere erhöht. Die Inkubation muriner Mastzellen (MZ) mit den Medikamenten, steigerte die FcεRI-vermittelten Histaminfreisetzung in vitro. ASS-Vorbehandlung der Mäuse verstärkte die Ausprägung der PSA und der PCA, was mit einer Steigerung von MZ-Mediatoren im Serum assoziiert war. Die FcεRI-induzierte Histaminfreisetzung muriner MZ wurde hingegen nach ASS-Inkubation gehemmt, was auf einen indirekten Mechanismus hinweist. Die Reduktion der Prostaglandine (PG) durch ASS ist mit einer gesteigerten Leukotriensynthese verbunden. Der Leukotrienantagonist Montelukast konnte die, durch ASS verstärkte, PSA nicht mildern, was zeigt, dass dieser Effekt unabhängig von Leukotrienen ist. PGE2 kann die MZ-Degranulation über EP1-EP4-Rezeptoren modulieren. Tatsächlich schwächten EP3- und EP4-Rezeptoragonisten die durch ASS gesteigerte Anaphylaxie ab. PGE2 nimmt somit eine wichtige Rolle in der pro-anaphylaktischen Wirkung von ASS ein. Zusammenfassend wurde erstmals gezeigt, dass Metoprolol und Ramipril die Anaphylaxie über eine Steigerung der MZ-Reaktivität verstärken. ASS hingegen erhöht anaphylaktische Reaktionen über einen indirekt steigernden Effekt auf die MZ. PGE2 ist zumindest teilweise an der pro-anaphylaktischen Wirkung von ASS beteiligt. / Cofactors contribute to the severity of anaphylaxis, a potential life-threatening hypersensitivity reaction. ACE-inhibitors, ß-blockers and acetylsalicylic acid (asa) are frequently used drugs in cardiovascular therapy. Whether they affect systemic anaphylactic reactions has been addressed within this thesis. To this aim, the passive systemic anaphylaxis model (PSA) was employed here and specially designed to mimic a long term treatment in cardiovascular therapy. The data demonstrate that oral treatment of mice with ramipril or metoprolol alone slightly aggravated anaphylaxis. However, the combination clearly potentiated anaphylactic reactions, which was also confirmed in the passive cutaneous anaphylaxis model (PCA). In line with this, elevated amounts of mast cell (MC) mediators were detected in mice sera upon combined drug treatment. In vitro, FcεRI-mediated histamine release of murine MCs was likewise enhanced by the respective drugs. Pre-treatment of mice with asa aggravated the symptoms of PSA and PCA; simultaneously MC-mediators in sera were elevated. In contrast, FcεRI-mediated histamine release of MCs was reduced by asa in vitro, pointing to an indirect mechanism. Asa reduces prostaglandins (PGs) and increases leukotriene synthesis. The leukotriene antagonist montelukast failed to attenuate PSA, aggravated by asa, suggesting that the pro-anaphylactic effect of asa might be independent of leukotrienes. PGE2 can modulate MC degranulation via EP1-EP4 receptor. Indeed, EP3 and EP4 receptor agonists alleviated anaphylaxis enhanced by asa. Therefore PGE2 might play an important role in the pro-anaphylactic effect of asa. In conclusion, the data demonstrate for the first time that metoprolol and ramipril exacerbate anaphylactic symptoms by a direct increase in MC reactivity. In contrast, asa aggravates anaphylactic reactions by priming MCs through an indirect mechanism. PGE2 is at least partly involved in this process.

La mise en conformation de l'α et β tubulines en hétérodimeres polymérisables nécessite l'intervention de cinq protéines " Tubulin Binding Cofactors " (TBCA a TBCE) dont TBCC qui joue un rôle indispensable. Dans des cellules humaines d'adénocarcinome mammaire, nous avons modifié le niveau d'expression de TBCC et nous avons montre que ceci avait un impact sur le contenu des fractions de tubuline, la dynamique des microtubules ainsi que sur le phénotype et chimiosensibilité des cellules. La distribution en cycle cellulaire et les durées de la mitose et de la phase S ont été altérées. La modification de TBCC avait un faible effet sur la vitesse de prolifération in vitro par contre les cellules présentaient des différences significatives de croissance tumorale in vivo. Les réponses aux agents antimicrotubulaires et à la gemcitabine ont montrées une chimiosensibilité dépendante de la distribution en cycle cellulaire. Tous ces résultats montrent l'importance de la régulation du contenu en tubulines et l'impact de ceci sur le comportement de la cellule en général et vis-à-vis des traitements.

La mise en conformation de l'α et β tubulines en hétérodimeres polymérisables nécessite l'intervention de cinq protéines " Tubulin Binding Cofactors " (TBCA a TBCE) dont TBCC qui joue un rôle indispensable. Dans des cellules humaines d'adénocarcinome mammaire, nous avons modifié le niveau d'expression de TBCC et nous avons montre que ceci avait un impact sur le contenu des fractions de tubuline, la dynamique des microtubules ainsi que sur le phénotype et chimiosensibilité des cellules. La distribution en cycle cellulaire et les durées de la mitose et de la phase S ont été altérées. La modification de TBCC avait un faible effet sur la vitesse de prolifération in vitro par contre les cellules présentaient des différences significatives de croissance tumorale in vivo. Les réponses aux agents antimicrotubulaires et à la gemcitabine ont montrées une chimiosensibilité dépendante de la distribution en cycle cellulaire. Tous ces résultats montrent l'importance de la régulation du contenu en tubulines et l'impact de ceci sur le comportement de la cellule en général et vis-à-vis des traitements.

L’intégrase (IN) du VIH-1 est une enzyme clé du cycle viral catalysant l’insertion stable de l’ADN viral dans le génome de la cellule infectée. L’IN participe également à de nombreuses étapes du cycle viral telles que la transcription inverse ou la maturation virale. Ainsi, la compréhension des mécanismes régulant l’intégration du VIH-1 représente un enjeu majeur dans le cadre notamment d’approches thérapeutiques. En effet, les études montrent que ces mécanismes sont finement régulés dans la cellule par des facteurs viraux et cellulaires agissant à différentes étapes du cycle viral. C’est donc dans ce contexte que nous avons étudié les facteurs à la fois viraux et cellulaires régulant ce processus. Dans un premier temps, les déterminants viraux modulant l’intégration dans la chromatine ont été analysés dans le cas de plusieurs modèles rétroviraux. Puis, dans un second temps, nous avons étudié l’impact de facteurs cellulaires, identifiés au laboratoire, sur les mécanismes d’insertion de l’ADN viral dans le génome cellulaire. Mon travail de thèse s’est ainsi articulé en trois axes majeurs aboutissant à : ● La démonstration de la régulation de l’intégration rétrovirale par la structure chromatinienne de l’hôte ● L’identification de nouveaux cofacteurs cellulaires participant à la régulation de l’intégration dans la chromatine dont le complexe de remodelage FACT « Facilitates Chromatin Transcription » ● L’identification d’une nouvelle interaction fonctionnelle entre l’IN du VIH-1 et la queue amino-terminale de l’histone humaine H4 et de son rôle dans la sélectivité de l’intégration / HIV-1 integrase (IN) is a key enzyme of the viral cycle that catalyzes the stable insertion of viral DNA into the genome of the infected cell. IN also participates in many stages of the viral cycle such as reverse transcription or viral maturation. Thus, an understanding of the mechanisms regulating the integration of HIV-1 is a major challenge, particularly in the context of therapeutic approaches. Indeed, studies show that these mechanisms are finely regulated in the cell by viral and cellular factors acting at different stages of the viral cycle. It is in this context that we studied both viral and cellular factors regulating this process. Initially, the viral determinants modulating the integration in chromatin were analyzed in the case of several retroviral models. Then, we studied the impact of cellular factors, identified in the laboratory, on the mechanisms of insertion of the viral DNA in the cellular genome. My thesis work has thus been articulated in three major axes leading to: • The demonstration of the regulation of retroviral integration by the chromatin structure of the host • The identification of new cellular cofactors participating in the regulation of chromatin integration, including the FACT remodeling complex "Facilitates Chromatin Transcription" • The identification of a new functional interaction between the HIV-1 IN and the amino-terminal tail of human H4 histone and its role in the selectivity of integration.