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The ability of a cell to facilitate the selective and rapid movement of ions and small molecules across the plasma membrane is one of the most fundamental biological processes. Inward rectifier potassium (Kir) channels are integral membrane proteins that provide K+-selective pathways across the otherwise impermeable cell membrane along the electrochemical gradients. Kir channels support the flow of K+ ions into and out of the cell and regulate various functions in the human body, including heart rate, vascular tone, insulin secretion, and salt and fluid balance. The physiological significance of Kir channels is highlighted by the fact that genetically-inherited defects in these genes result in human diseases (channelopathies). We are particularly interested in Andersen’s syndrome, where mutations in the KCNJ2 gene coding for Kir2.1 protein are directly involved. Andersen’s syndrome (AS) is a rare disease characterized by cardiac arrhythmias, dysmorphic features, and periodic paralysis. The available treatment for AS patients is empirical rather than rational due to the lack of knowledge of this Kir2.1 channel. This thesis aimed to identify the differences between the wild-type Kir2.1 channel and two mutant AS-causing channels to find links between the structure and the function of human Kir2.1 using a combination of biochemical, structural, and functional approaches. In this study, we recombinantly expressed the human Kir2.1 channel in yeast and purified it in detergent. We characterized the interaction between Kir2.1 and the essential activator PIP2, solved the first human Kir channel structure by cryo-EM, and explored reconstitution in detergent-free systems like amphipols and nanodiscs. The findings of this study will provide a structural and functional base to understand better the mechanisms involved in Kir channels and the effects of their mutations. This manuscript is divided into three parts. The first part introduces Kir channels and state-of-the-art. The second part focuses on the characterization of the human potassium channel Kir2.1, the determination of its structure by cryo-EM, and the impact of mutations on its structure and function. The third part presents two mutations in the bacterial homolog KirBac3.1, which shares structural features with Kir2.1, to provide insight into the gating mechanism of Kir channels.; La capacité d'une cellule à faciliter le mouvement sélectif et rapide des ions et des petites molécules à travers la membrane plasmique est un processus biologique indispensable. Les canaux potassiques à rectification entrante (Kir) sont des protéines membranaires intégrales qui fournissent des voies sélectives aux ions K+ à travers la membrane cellulaire autrement imperméable, le long des gradients électrochimiques. Les canaux Kir permettent le passage des ions K+ dans les deux sens et régulent diverses fonctions chez les humains, notamment la fréquence cardiaque, le tonus vasculaire, la sécrétion d'insuline et l'équilibre salin et hydrique. L'importance physiologique des canaux Kir est mise en évidence par le fait que des défauts génétiquement héréditaires de ces gènes entraînent des maladies humaines (canalopathies). Nous nous intéressons particulièrement au syndrome d'Andersen, où des mutations du gène KCNJ2 codant pour la protéine Kir2.1 sont directement impliquées. Le syndrome d'Andersen (AS) est une maladie rare caractérisée par des arythmies cardiaques, des dysmorphies multiples et des paralysies périodiques. Le traitement disponible pour les patients atteints d’AS est empirique plutôt que rationnel en raison de la manque de connaissance de ce canal Kir2.1. Cette thèse visait à identifier les différences entre le canal Kir2.1 de type sauvage et deux canaux mutants causant l’AS afin de trouver des liens entre la structure et la fonction du Kir2.1 humain en utilisant une combinaison d'approches biochimiques, structurelles et fonctionnelles. Dans cette étude, nous avons exprimé le canal Kir2.1 humain dans la levure et l'avons purifié dans un détergent. Nous avons caractérisé l'interaction entre Kir2.1 et l'activateur essentiel PIP2, résolu par cryo-EM la première structure d'un canal Kir humain et exploré la reconstitution dans des systèmes modèles sans détergent comme les amphipols et les nanodisques. Les résultats de cette étude fourniront une base structurale et fonctionnelle pour mieux comprendre les mécanismes impliqués dans les canaux Kir et les effets de leurs mutations. Ce manuscrit est divisé en trois parties. La première partie présente les canaux Kir et l'état de l'art. La deuxième partie porte sur la caractérisation du canal potassique humain Kir2.1, la détermination de sa structure par cryo-EM et l'impact des mutations sur sa structure et sa fonction. La troisième partie présente deux mutations dans l'homologue bactérien KirBac3.1, qui partage des caractéristiques structurelles avec Kir2.1, pour donner un aperçu du mécanisme d’ouverture et fermeture des canaux Kir.

Iron-sulfur clusters biogenesis is a process involving numerous proteins and the defects of one of them lead to severe diseases such as anaemia, neurodegenerative process, diabetes, cardiac hypertrophy and cancers. Iron-sulfur (Fe-S) clusters are critical prosthetic groups of proteins involved in redox processes such as ATP production, enzymatic catalysis, protein synthesis and maintenance of genome integrity. Therapeutic strategies based on the development of drugs mimicking the function of the proteins that perform the synthesis of these clusters are still in their infancy due to the lack of understanding of the exact molecular and biochemical mechanisms of their synthesis. The PhD project has mainly focused on the mechanism of Fe-S cluster biosynthesis by the ISC machinery and the functional role of frataxine in this process, a key regulator of the whole process, for which a defective expression leads to Friedreich's ataxia, a severe neurodegenerative and cardiac disease. Indeed, the assembly sequence of these Fe-S clusters was poorly defined, especially on the coordination of the insertion of iron and sulfur to form a polynuclear Fe-S cluster. Moreover, the nature of the final product of this ISC machinery was subject to debate: [2Fe2S] or [4Fe4S]. The global aim of the PhD project was to reconstitute the Fe-S cluster assembly machinery, eukaryote and prokaryote, with purified proteins to determine the structural basis of the assembly process using a panel of biochemical (kinetics, alkylation assay) and biophysical (Mössbauer, NMR, circular dichroism and EPR spectroscopies and native mass spectrometry) techniques, in order to understand how Fe-S clusters are synthesized and how frataxin regulates this process.; La biosynthèse des centres Fe-S est un processus impliquant un très grand nombre de protéines et la déficience de l’une de ces protéines conduit à des pathologies sévères : anémie, processus neurodégénératif, diabètes, hypertrophie cardiaque et même cancers. Ces centres Fe-S sont des groupements prosthétiques de protéines impliquées dans une multitude de processus redox tels que la production d'ATP, la catalyse enzymatique, la synthèse protéique ou encore la maintenance de l'intégrité du génome. Les stratégies thérapeutiques basées sur le développement de composés capable de mimer la fonction des protéines assurant la synthèse des centres Fe-S sont peu développées en raison du manque d'information sur les mécanismes moléculaires et biochimiques de synthèse de ces cofacteurs métalliques particulièrement versatiles. Le projet de thèse s’est principalement intéressé à l’élucidation du mécanisme de biosynthèse des centres Fe-S par la machinerie ISC et au rôle fonctionnel de la frataxine dans ce processus qui est une protéine centrale dont le défaut d'expression conduit à l'ataxie de Friedreich, une maladie neurodégénérative et cardiaque. En effet, la séquence d’assemblage de ces centres Fe-S était mal défini notamment sur la coordination de l’insertion du fer et du soufre pour former un centre polynucléaire Fe-S. De plus, la nature du produit final de cette machinerie ISC était sujette à débat : [2Fe2S] ou [4Fe4S]. L'objectif principal de ce projet de thèse était de reconstituer in vitro la machinerie d'assemblage des centres Fe-S, eucaryote et procaryote, à partir des protéines purifiées afin de déterminer les bases biochimiques et structurales du processus d'assemblage en utilisant un panel de techniques biochimiques (cinétique d’assemblage, test d’alkylation) et biophysiques (spectroscopies Mössbauer, RMN, RPE, spectrométrie de masse native et dichroïsme circulaire), dans le but de comprendre comment les centres Fe-S sont synthétisés et comment la frataxine régule ce processus.

We present here a novel method measuring interactions between biological molecules. This is useful in medical research, to determine if a drug will work on a target, for example. To do that, we stick two molecules we want to study to a molecular "scaffold" we can observe under the microscope. Thus, we can see if the molecules bind or separate, and at which speeds. In addition, the scaffold being magnet-sensitive, we can "pull" on those molecules with a magnetic tweezer and apply force, or add other molecules (for example, other drugs) in the medium and compare the efficiency of different molecules. This thesis focuses on the design and improvement of this tool and of the associated data analysis tools. We apply our technique to the study of the FKBP12- Rapamycin system, essential for the regulation of metabolism and immune responses., Nous présentons ici une nouvelle méthode de mesure des interactions entre molécules biologiques. Ceci est utilisé dans la recherche médicale, pour savoir si un médicament va fonctionner sur une cible par exemple. Pour cela, nous accrochons deux molécules que nous voulons étudier à un "échafaudage" moléculaire observable au microscope. Ainsi, nous pouvons voir si les molécules accrochées se lient ou se détachent, et à quelle vitesse. De plus, l'échafaudage étant aimanté, nous pouvons "tirer" sur ces molécules avec une pince magnétique et donc appliquer une force, ou encore ajouter d'autres molécules (par exemple, un autre médicament) dans le milieu et comparer l'efficacité de différentes molécules. Le travail présenté ici se concentre sur le développent de cet outil et sur les outils d'analyse informatique associés. Nous appliquons ces techniques à l'étude du système FKBP12-Rapamycine, central dans la régulation du métabolisme et de la réponse immunitaire.

We present here a novel method measuring interactions between biological molecules. This is useful in medical research, to determine if a drug will work on a target, for example. To do that, we stick two molecules we want to study to a molecular "scaffold" we can observe under the microscope. Thus, we can see if the molecules bind or separate, and at which speeds. In addition, the scaffold being magnet-sensitive, we can "pull" on those molecules with a magnetic tweezer and apply force, or add other molecules (for example, other drugs) in the medium and compare the efficiency of different molecules. This thesis focuses on the design and improvement of this tool and of the associated data analysis tools. We apply our technique to the study of the FKBP12- Rapamycin system, essential for the regulation of metabolism and immune responses., Nous présentons ici une nouvelle méthode de mesure des interactions entre molécules biologiques. Ceci est utilisé dans la recherche médicale, pour savoir si un médicament va fonctionner sur une cible par exemple. Pour cela, nous accrochons deux molécules que nous voulons étudier à un "échafaudage" moléculaire observable au microscope. Ainsi, nous pouvons voir si les molécules accrochées se lient ou se détachent, et à quelle vitesse. De plus, l'échafaudage étant aimanté, nous pouvons "tirer" sur ces molécules avec une pince magnétique et donc appliquer une force, ou encore ajouter d'autres molécules (par exemple, un autre médicament) dans le milieu et comparer l'efficacité de différentes molécules. Le travail présenté ici se concentre sur le développent de cet outil et sur les outils d'analyse informatique associés. Nous appliquons ces techniques à l'étude du système FKBP12-Rapamycine, central dans la régulation du métabolisme et de la réponse immunitaire.

We present ten insights that can be gained from computational models based on molecular mechanisms for the mammalian circadian clock. These insights range from the conditions in which circadian rhythms occur spontaneously to their entrainment by the light–dark (LD) cycle and to clock-related disorders of the sleep-wake cycle. Endogenous oscillations originate spontaneously from transcription-translation feedback loops involving clock proteins such as PER, CRY, CLOCK and BMAL1. Circadian oscillations occur in a parameter domain bounded by critical values. Outside this domain the circadian network ceases to oscillate and evolves to a stable steady state. This conclusion bears on the nature of arrhythmic behavior of the circadian clock, which may not necessarily be due to mutations in clock genes. Entrainment by the LD cycle occurs in a certain range of parameter values, with a phase that depends on the endogenous period of the circadian clock. A decrease in PER phosphorylation is accompanied by a decrease in endogenous period and a phase advance of the clock; this situation accounts for the familial, advanced sleep phase syndrome (FASPS). The mirror delayed sleep phase syndrome (DSPS) can be accounted for, similarly, by an increase in PER phosphorylation and a rise in autonomous period. Failure of entrainment by the LD cycle in the model corresponds to the non-24 h sleep-wake cycle syndrome, in which the phase of the circadian clock drifts in the course of time. Quasi-periodic oscillations that develop in these conditions sometimes correspond to long-period patterns in which the circadian clock is nearly entrained for long bouts of time before its phase rapidly drifts until a new regime of quasi-entrainment is re-established. In regard to jet lag, the computational approach accounts for the two modes of re-entrainment observed after an advance or delay which correspond, respectively, to an eastward or westward flight: the clock adjusts in a direction similar (orthodromic) or opposite (antidromic) to that of the shift in the LD cycle. Computational modeling predicts that in the vicinity of the switch between orthodromic and antidromic re-entrainment the circadian clock may take a very long time to resynchronize with the LD cycle. Repetitive perturbations of the circadian clock due, for example, to chronic jet lag —a situation somewhat reminiscent of shift work— may lead to quasi-periodic or chaotic oscillations. The latter irregular oscillations can sometimes be observed in normal LD cycles, raising the question of their possible relevance to fragmented sleep patterns observed in narcolepsy. The latter condition, however, appears to originate from disorders in the orexin neural circuit, which promotes wakefulness, rather than from an irregular operation of the circadian clock., SCOPUS: re.j, info:eu-repo/semantics/published

RelA-SpoT Homolog (RSH) enzymes control bacterial physiology through synthesis and degradation of the nucleotide alarmone (p)ppGpp. We recently discovered multiple families of small alarmone synthetase (SAS) RSH acting as toxins of toxin-antitoxin (TA) modules, with the FaRel subfamily of toxSAS abrogating bacterial growth by producing an analog of (p)ppGpp, (pp)pApp. Here we probe the mechanism of growth arrest used by four experimentally unexplored subfamilies of toxSAS: FaRel2, PhRel, PhRel2, and CapRel. Surprisingly, all these toxins specifically inhibit protein synthesis. To do so, they transfer a pyrophosphate moiety from ATP to the tRNA 3′ CCA. The modification inhibits both tRNA aminoacylation and the sensing of cellular amino acid starvation by the ribosome-associated RSH RelA. Conversely, we show that some small alarmone hydrolase (SAH) RSH enzymes can reverse the pyrophosphorylation of tRNA to counter the growth inhibition by toxSAS. Collectively, we establish RSHs as RNA-modifying enzymes., SCOPUS: ar.j, info:eu-repo/semantics/published

Chagas disease is one of the most common parasitic infections in Latin America, which istransmitted by hematophagous triatomine bugs, of which Rhodnius prolixus is the vector prototype forthe study of this disease. The protozoan parasite Trypanosoma cruzi, the etiologic agent of this disease,is transmitted by the vector to humans through the bite wound or mucosa. The passage of the parasitethrough the digestive tract of its vector constitutes a key step in its developmental cycle. Herewith,by a using high-throughput proteomic tool in order to characterize the midgut proteome of R. prolixus,we describe a set of functional groups of proteins, as well as the biological processes in which theyare involved. This is the first proteomic analysis showing an elaborated hematophagy machineryinvolved in the digestion of blood, among which, several families of proteases have been characterized.The evaluation of the activity of cathepsin D proteases in the anterior part of the digestive tract ofthe insect suggested the existence of a proteolytic activity within this compartment, suggesting thatdigestion occurs early in this compartment. Moreover, several heat shock proteins, blood clottinginhibitors, and a powerful antioxidant enzyme machinery against reactive oxygen species (ROS) andcell detoxification have been identified. Highlighting the complexity and importance of the digestivephysiology of insects could be a starting point for the selection of new targets for innovative controlstrategies of Chagas disease., info:eu-repo/semantics/published

Group living animals form aggregations and flocks that remain cohesive in spite of internal movements of individuals. This is possible because individual group members repeatedly adjust their position and motion in response to the position and motion of other group members. Here, we develop a theoretical approach to address the question, what general features—if any—underlie the interaction rules that mediate group stability in animals of all species? We do so by considering how the spatial organization of a group would change in the complete absence of interactions. Without interactions, a group would disperse in a way that can be easily characterized in terms of Fick’s diffusion equations. We can hence address the inverse theoretical problem of finding the individual-level interaction responses that are required to counterbalance diffusion and to preserve group stability. We show that an individual-level response to neighbour densities in the form of Weber’s Law (a ‘universal’ law describing the functioning of the sensory systems of animals of all species) results in an ‘anti-diffusion’ term at the group level. On short timescales, this anti-diffusion restores the initial group configuration in a way that is reminiscent of methods for image deblurring in image processing. We also show that any non-homogeneous, spatial density distribution can be preserved over time if individual movement patterns have the form of a Weber’s Law response. Weber’s Law describes the fundamental functioning of perceptual systems. Our study indicates that it is also a necessary—but not sufficient—feature of collective interactions in stable animal groups., SCOPUS: ar.j, info:eu-repo/semantics/published

PaaR2 is a putative transcription regulator encoded by a three-component parDE-like toxin-antitoxin module from Escherichia coli O157:H7. Although this module's toxin, antitoxin, and toxin-antitoxin complex have been more thoroughly investigated, little remains known about its transcription regulator PaaR2. Using a wide range of biophysical techniques (circular dichroism spectroscopy, size-exclusion chromatography-multiangle laser light scattering, dynamic light scattering, small-angle x-ray scattering, and native mass spectrometry), we demonstrate that PaaR2 mainly consists of α-helices and displays a concentration-dependent octameric build-up in solution and that this octamer contains a global shape that is significantly nonspherical. Thermal unfolding of PaaR2 is reversible and displays several transitions, suggesting a complex unfolding mechanism. The unfolding data obtained from spectroscopic and calorimetric methods were combined into a unifying thermodynamic model, which suggests a five-state unfolding trajectory. Furthermore, the model allows the calculation of a stability phase diagram, which shows that, under physiological conditions, PaaR2 mainly exists as a dimer that can swiftly oligomerize into an octamer depending on local protein concentrations. These findings, based on a thorough biophysical and thermodynamic analysis of PaaR2, may provide important insights into biological function such as DNA binding and transcriptional regulation., SCOPUS: ar.j, info:eu-repo/semantics/published

Bacterial pathogens are a major cause of foodborne diseases and food poisoning. To cope with the acid conditions encountered in different environments such as in fermented food or in the gastric compartment, neutralophilic bacteria have developed several adaptive mechanisms. One of those mechanisms, the amino acid dependent system, consumes intracellular protons in biochemical reactions. It involves an antiporter that facilitates the exchange of external substrate amino acid for internal product and a cytoplasmic decarboxylase that catalyzes a proton-consuming decarboxylation of the substrate. So far, four acid resistance antiporters have been discovered, namely the glutamate-γ-aminobutyric acid antiporter GadC, the arginine-agmatine antiporter AdiC, the lysine-cadaverine antiporter CadB, and the ornithine-putrescine antiporter PotE. The 3D structures of AdiC and GadC, reveal an inverted-repeat fold of two times 5 transmembrane helices, typical of the amino acid-polyamine-organocation (APC) superfamily of transporters. This review summarizes our current knowledge on the transport mechanism, the pH regulation and the selectivity of these four acid resistance antiporters. It also highlights that AdiC is a paradigm for eukaryotic amino acid transporters of the APC superfamily as structural models of several of these transporters built using AdiC structures were exploited to unveil their mechanisms of amino acid recognition and translocation., SCOPUS: ar.j, info:eu-repo/semantics/published

The creation of new protein functions based on recognition and molecular assembly is not only a major goal in biotechnology but is also a means to understand the relation structure/function of proteins involved in interaction processes. Today, libraries of artificial proteins obtained by engineering can be a source of proteins with recognition properties similar to the properties of antibodies.The team Protein Engineering and Modeling has thus created a library of proteins with structural repeats called the “alphaReps”. The alphaReps present remarkable properties in terms of production and stability. Unlike most of the antibodies and their derivatives, they can even be expressed and functional in the cytoplasm of eukaryotic cells. Such objects can therefore be used as building bricks in modular engineering. The construction of new optimized recognition functions both in specificity and in affinity can then be possible by rearranging or duplicating these elementary bricks.The first part of this thesis project consisted in the construction and study of the biophysical properties of bidomain proteins based on alphaRep in order to have a better understanding of the behaviour of such constructions. Beside the fundamental aspect of this question, this study will give the “rules” to modulate the interactions between these proteins in a controlled way. The results show that it is possible to create new functions such as avidity, cooperativity, conformational change, simply by adding a linker between two alphaReps.In a second step, the goal was to develop, with the bidomain proteins previously studied, new biosensors based on the FRET (Förster Resonance Energy Transfer) which can be used in vivo and in vitro. This second part presents two biosensors with limits of detection in the nanomolar range. Since the alphaReps used in these constructions can be changed depending on the chosen target, it is a proof of concept which can be adapted to any desired target.Finally, the third part of this thesis focused on the development of genetically codable biosensors. These biosensors have the particular advantage of being usable directly after production and therefore no longer require a chemical coupling step. The results show that the development of such biosensors is worth considering but an optimization is still required in order to improve their specificity, their stability and their detection capacity.; La création de nouvelles fonctions basées sur la reconnaissance protéique et sur l'assemblage de domaines est un enjeu majeur en biotechnologie et est un moyen de comprendre les relations structures/fonctions des protéines engagées dans des processus d'interactions. Aujourd’hui, des bibliothèques de protéines artificielles obtenues par ingénierie peuvent être sources de protéines aux propriétés de reconnaissance analogues à celles des dérivés d’anticorps.L’équipe Modélisation et Ingénierie des Protéines a ainsi construit une banque de protéines à motifs structuraux répétés appelées « alphaReps ». Les alphaReps présentent des propriétés remarquables en termes de production et de stabilité. Contrairement à la plupart des anticorps et dérivés d’anticorps, elles peuvent même s’exprimer sous forme fonctionnelle dans le cytoplasme de cellules eucaryotes. De tels objets peuvent donc maintenant être utilisés comme des briques élémentaires en vue d’une ingénierie modulaire. Ainsi la construction de nouvelles fonctions de reconnaissance optimisées tant au niveau de la spécificité que de l’affinité sera possible en réarrangeant et/ou dupliquant ces briques élémentaires.Un premier volet de ce projet de thèse a consisté à construire puis étudier les propriétés biophysiques de protéines bidomaines basées sur les alphaReps afin de mieux comprendre les comportements adoptés par de telles constructions. Outre l’aspect fondamental de cette question, cette étude donnera « les règles » pour moduler de façon contrôlée les interactions entre ces protéines. Les résultats montrent qu'il est possible de créer de nouvelles fonctions par simple ajout d'un linker entre deux alphaReps : avidité, coopérativité, changement de conformation.Dans un second temps, l’objectif a été de développer, à partir des protéines bidomaines précédemment étudiées, de nouveaux biosenseurs basés sur le FRET (Förster Resonance Energy Transfer) pouvant être utilisés in vivo et in vitro. Cette deuxième partie présente deux biosenseurs avec des limites de détection de l'ordre du nanomolaire. Les alphaReps utilisées dans ces constructions pouvant être changées en fonction de la cible souhaitée, il s'agit ici d'une preuve de concept pouvant être généralisée à n'importe quelle cible.Enfin la dernière partie de cette thèse s'est portée sur la conception et l'étude de nouveaux biosenseurs génétiquement codables. Ces biosenseurs présentent notamment l’avantage d’être utilisables immédiatement après production et ne nécessitent donc plus d’étape de couplage chimique. Les résultats obtenus montrent que la création de tels biosenseurs est possible mais qu’une optimisation reste encore nécessaire pour améliorer leur spécificité, leur stabilité et leur capacité de détection.

The creation of new protein functions based on recognition and molecular assembly is not only a major goal in biotechnology but is also a means to understand the relation structure/function of proteins involved in interaction processes. Today, libraries of artificial proteins obtained by engineering can be a source of proteins with recognition properties similar to the properties of antibodies.The team Protein Engineering and Modeling has thus created a library of proteins with structural repeats called the “alphaReps”. The alphaReps present remarkable properties in terms of production and stability. Unlike most of the antibodies and their derivatives, they can even be expressed and functional in the cytoplasm of eukaryotic cells. Such objects can therefore be used as building bricks in modular engineering. The construction of new optimized recognition functions both in specificity and in affinity can then be possible by rearranging or duplicating these elementary bricks.The first part of this thesis project consisted in the construction and study of the biophysical properties of bidomain proteins based on alphaRep in order to have a better understanding of the behaviour of such constructions. Beside the fundamental aspect of this question, this study will give the “rules” to modulate the interactions between these proteins in a controlled way. The results show that it is possible to create new functions such as avidity, cooperativity, conformational change, simply by adding a linker between two alphaReps.In a second step, the goal was to develop, with the bidomain proteins previously studied, new biosensors based on the FRET (Förster Resonance Energy Transfer) which can be used in vivo and in vitro. This second part presents two biosensors with limits of detection in the nanomolar range. Since the alphaReps used in these constructions can be changed depending on the chosen target, it is a proof of concept which can be adapted to any desired target.Finally, the third part of this thesis focused on the development of genetically codable biosensors. These biosensors have the particular advantage of being usable directly after production and therefore no longer require a chemical coupling step. The results show that the development of such biosensors is worth considering but an optimization is still required in order to improve their specificity, their stability and their detection capacity.; La création de nouvelles fonctions basées sur la reconnaissance protéique et sur l'assemblage de domaines est un enjeu majeur en biotechnologie et est un moyen de comprendre les relations structures/fonctions des protéines engagées dans des processus d'interactions. Aujourd’hui, des bibliothèques de protéines artificielles obtenues par ingénierie peuvent être sources de protéines aux propriétés de reconnaissance analogues à celles des dérivés d’anticorps.L’équipe Modélisation et Ingénierie des Protéines a ainsi construit une banque de protéines à motifs structuraux répétés appelées « alphaReps ». Les alphaReps présentent des propriétés remarquables en termes de production et de stabilité. Contrairement à la plupart des anticorps et dérivés d’anticorps, elles peuvent même s’exprimer sous forme fonctionnelle dans le cytoplasme de cellules eucaryotes. De tels objets peuvent donc maintenant être utilisés comme des briques élémentaires en vue d’une ingénierie modulaire. Ainsi la construction de nouvelles fonctions de reconnaissance optimisées tant au niveau de la spécificité que de l’affinité sera possible en réarrangeant et/ou dupliquant ces briques élémentaires.Un premier volet de ce projet de thèse a consisté à construire puis étudier les propriétés biophysiques de protéines bidomaines basées sur les alphaReps afin de mieux comprendre les comportements adoptés par de telles constructions. Outre l’aspect fondamental de cette question, cette étude donnera « les règles » pour moduler de façon contrôlée les interactions entre ces protéines. Les résultats montrent qu'il est possible de créer de nouvelles fonctions par simple ajout d'un linker entre deux alphaReps : avidité, coopérativité, changement de conformation.Dans un second temps, l’objectif a été de développer, à partir des protéines bidomaines précédemment étudiées, de nouveaux biosenseurs basés sur le FRET (Förster Resonance Energy Transfer) pouvant être utilisés in vivo et in vitro. Cette deuxième partie présente deux biosenseurs avec des limites de détection de l'ordre du nanomolaire. Les alphaReps utilisées dans ces constructions pouvant être changées en fonction de la cible souhaitée, il s'agit ici d'une preuve de concept pouvant être généralisée à n'importe quelle cible.Enfin la dernière partie de cette thèse s'est portée sur la conception et l'étude de nouveaux biosenseurs génétiquement codables. Ces biosenseurs présentent notamment l’avantage d’être utilisables immédiatement après production et ne nécessitent donc plus d’étape de couplage chimique. Les résultats obtenus montrent que la création de tels biosenseurs est possible mais qu’une optimisation reste encore nécessaire pour améliorer leur spécificité, leur stabilité et leur capacité de détection.

The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Herein, we disclose EthR structures in complex with 18 different small molecules and then performed in-depth analysis on the complete set of EthR structures that provides insights on EthR-ligand interactions. The 81 molecules solved in complex with EthR show a large diversity of chemical structures that were split up into several chemical clusters. Two of the most striking common points of EthR-ligand interactions are the quasi-omnipresence of a hydrogen bond bridging compounds with Asn179 and the high occurrence of π-π interactions involving Phe110. A systematic analysis of the protein-ligand contacts identified eight hot spot residues that defined the basic structural features governing the binding mode of small molecules to EthR. Implications for the design of new potent inhibitors are discussed., SCOPUS: ar.j, info:eu-repo/semantics/published

UPF1 (Up-Frameshift 1) is a multifunctional helicase that unwinds nucleic acids and is conserved throughout the eukaryote kingdom. UPF1 is required for the Nonsense Mediated mRNA Decay (NMD) surveillance pathway, which degrades mRNAs carrying premature termination codons, among other substrates. UPF1 is the archetype of a family of 11 helicases sharing similar cores but involved in various cellular pathways. However, the structure-function relationship and intrinsic biophysical properties of these molecular engines remain poorly described. In vitro, the UPF1 helicase core is highly processive, it travels along thousands of RNA or DNA bases and unwinds double-strands. In this work, we looked for key factors governing this remarkable processivity. We combined biochemical and biophysical techniques. In particular, we used magnetic tweezers to study helicases in real time at a single molecule scale. In contrast to UPF1, the related IGHMBP2 is not processive, thus processivity is not a shared family trait. Based on the 3D structures of both proteins, we designed various mutants and used them to identify structural elements that modulate processivity. Our approach reveals that UPF1 has a very firm grip on nucleic acids, guaranteeing long binding lifetimes and action times that dictate its high processivity. Thanks to the variety in mutant behaviors, we built a novel mechanistic model linking binding energy to processivity. Furthermore, we show that UPF1 processivity is required for an efficient NMD in vivo. In addition, we used the same biochemical and biophysical tools to investigate a natural human UPF1 isoform moving faster than the major isoform, and to compare the regulation of human andyeast UPF1 by their flanking domains. We also characterized the interaction of yeast UPF1 with new NMD partners. Our work shows how a combination of biochemical, biophysical, structural and in vivo tools can offer unexpected insights into the operating mode of molecular motors., UPF1 (Up-Frameshift 1) est une hélicase multifonctionnelle conservée chez tous les eucaryotes. Elle est essentielle à la voie de surveillance du NMD (Nonsense Mediated mRNA Decay), qui dégrade des ARNm portant un codon stop prématuré. UPF1 est l’archétype d’une famille d’hélicases qui partagent des corps similaires mais sont impliquées dans des voies cellulaires variées. Cependant, les relations structure-fonction et les caractéristiques biophysiques intrinsèques de ces moteurs moléculaires restent à ce jour peu connues. In vitro, le coeur hélicase d’UPF1 est hautement processif, il traverse des milliers de bases sur l’ARN ou l’ADN et déroule des doubles brins. Dans ce travail, nous avons cherché les facteurs clés régissant cette remarquable processivité en combinant des techniques de biochimie et de biophysique. En particulier, nous avons utilisé des pinces magnétiques pour étudier en temps réel des hélicases à l’échelle de la molécule unique. Contrairement à UPF1, l’hélicase IGHMBP2 de la famille UPF1-like n’est pas processive ; la processivité n’est donc pas un trait conservé au sein de la famille. Grâce à une étude fine de la structure 3D des deux hélicases, nous avons conçu divers mutants que nous avons utilisés pour identifier les éléments structuraux qui modulent la processivité. Notre approche révèle qu’UPF1 a une prise très ferme sur les acides nucléiques, garantissant de longs temps de résidence et d’action qui dictent sa haute processivité. Grâce à la variété de comportements des mutants, nous avons construit un modèle mécanistique expliquant le lien entre énergie d’interaction et processivité. Nous démontrons aussi que la processivité d’UPF1 est requise pour un processus de NMD efficace in vivo. Nous avons utilisé les mêmes outils biochimiques et biophysiques pour étudier une isoforme naturelle d’UPF1 humaine se déplaçant plus vite que l’isoforme majeure, et pour comparer la régulation d’UPF1 humaine et de levure par leurs domaines flanquants. Nous avons également caractérisé l'interaction d’UPF1 de levure avec de nouveaux partenaires. Nos travaux montrent comment la combinaison d'outils biochimiques, biophysiques, structuraux etin vivo offre des aperçus inattendus quant au mode de fonctionnement des moteurs moléculaires.

Noise is pervasive in cellular biology and inevitably affects the dynamics of cellular processes. Biological systems have developed regulatory mechanisms to ensure robustness with respect to noise or to take advantage of stochasticity. We review here, through a couple of selected examples, some insights on possible robustness factors and constructive roles of noise provided by computational modeling. In particular, we focus on (1) factors that likely contribute to the robustness of oscillatory processes such as the circadian clocks and the cell cycle, (2) how reliable coding/decoding of calcium-mediated signaling could be achieved in presence of noise and, in some cases, enhanced through stochastic resonance, and (3) how embryonic cell differentiation processes can exploit stochasticity to create heterogeneity in a population of identical cells., SCOPUS: re.j, info:eu-repo/semantics/published

The impact of fluctuations on the dynamical behaviour of complex biological systems is a longstanding issue, whose understanding would elucidate how evolutionary pressure tends to modulate intrinsic noise. Using the Itō stochastic differential equation formalism, we performed analytic and numerical analyses of model systems containing different molecular species in contact with the environment and interacting with each other through mass-action kinetics. For networks of zero deficiency, which admit a detailed- or complex-balanced steady state, all molecular species are uncorrelated and their Fano factors are Poissonian. Systems of higher deficiency have non-equilibrium steady states and non-zero reaction fluxes flowing between the complexes. When they model homo-oligomerization, the noise on each species is reduced when the flux flows from the oligomers of lowest to highest degree, and amplified otherwise. In the case of hetero-oligomerization systems, only the noise on the highest-degree species shows this behaviour., SCOPUS: ar.j, info:eu-repo/semantics/published

During the cell life many endo or exogenous genotoxic agents lead to the formation of DNA double strand breaks (DSBs). These lesions are extremely toxic and must be repaired in order to maintain the integrity of the genome and the survival of the cell. In mammalian, most DSBs are repaired by the Non Homologous End Joining (NHEJ) pathway. The recognition step of NHEJ is mediated by the ring-shape Ku70-Ku80 (Ku) heterodimer that protects the DNA extremities from resection and can recruit several core NHEJ factors (DNA-PKcs, ligase complex Ligase4-XRCC4 and ligation co-factor XLF) as well as several accessory NHEJ factors (PAXX, APLF and WRN). Beyond its DNA ends binding activity, Ku appears more and more as the central coordinator of the NHEJ pathway. How do all the NHEJ factors interact with Ku and are involved in the repair of all DNA ends (clean or dirty, accidental or programmed) are questions not well elucidated. Our laboratory is interested in the recruitment of XLF and XRCC4 by Ku, either as individual factors or as filaments as the one we described previously1,2.During my thesis, I characterized the crystal structures between Ku70/Ku80/DNA and peptides containing the Ku Binding Motif (KBM) of two NHEJ factors, XLF and APLF (the Aprataxin like-factor nuclease). The KBM of APLF binds to Ku with a tight affinity (Kd of 33nM) and it interacts within a conserved pocket of Ku80. The KBM of APLF is located in a position remote from the DNA binding site, at the periphery of the Ku ring. The crystal structure rationalizes the role of the conserved basic and hydrophobic parts of the APLF KBM motif. The KBM of XLF has a moderate affinity (Kd of 4 µM) and a sequence with a similar basic and hydrophobic parts. Interestingly, the crystal structure of a Ku70/Ku80/ADN complex with a XLF KBM shows that this motif occupies a different site from the KBM of APLF. The XLF motif induces a large conformational change of Ku80 and occupies a cleft that does not exist in the original Ku70/Ku80/DNA complex.I then characterized two mutants of XLF in the KBM motif, (L297E and L297W) that respectively disrupt the binding of the KBM with Ku or redirect the XLF KBM to the APLF site.All together those results help us to better understand the coordination of several NHEJ factors by Ku. This support our idea that Ku acts as a coordinator of the NHEJ pathway.; Au cours du cycle cellulaire, de nombreux agents génotoxiques conduisent à la formation de cassures double brins (CDB) de d’ADN. Ces lésions extrêmement dangereuses doivent être réparées afin de ne pas altérer l’intégrité du génome et la survie cellulaire. Chez les mammifères, la plupart de ces CDB sont prise en charge par la voie de réparation NHEJ (pour Non Homologous End Joining, recombinaison non homologue en français). La première étape de cette voie, la reconnaissance des extrémités d’ADN, est assurée par l’hétérodimère Ku70-Ku80. Ce complexe protège les extrémités d’ADN des activités de résection et recrute les facteurs impliqués dans la poursuite de la voie de réparation (la DNA-PKcs, XLF et le complexe de ligation XRCC4-LigIV) ainsi que des facteurs accessoires (PAXX, WRN et APLF). De cette observation, une vision plus générale de la fonction de Ku a émergé, une fonction de coordination de la voie NHEJ. La manière dont Ku interagit avec tous les facteurs du NHEJ, pour la réparation de toutes les CDB (propres ou non, accidentelles ou programmées) reste une question ouverte. Notre équipe travaillait précédemment sur l’étude des facteurs XRCC4 et XLF, dont ils ont pu mettre en évidence l’association en filaments dans un cristal.Au cours de ma thèse, j’ai caractérisé les structures cristallines de complexes comprenant Ku70-Ku80, un ADN et des peptides portant un motif de liaison à Ku (KBM) issus des protéines APLF et XLF. Le motif KBM de APLF se fixe de manière très forte à Ku (avec une affinité de 33 nM) et interagit avec une surface conservée sur Ku80. Cette interaction se déroule loin du site de fixation de Ku à l’ADN, à la périphérie du complexe. La connaissance des détails moléculaires de cette interaction a permis de comprendre et de rationnaliser la présence de résidus très conservés à la surface de Ku80 et dans la séquence d’APLF.Le motif KBM présent chez XLF, présentent une affinité plus modérée (un Kd de quelques μM) malgré une similarité de séquence importante avec le KBM de APLF (une région basique suivi d’une région hydrophobe). La structure du complexe Ku70-Ku80-ADN et du KBM de XLF montre que ce peptide se fixe sur un site différent de celui d’APLF. En effet ce peptide induit un large changement de conformation de Ku80 et vient se loger dans le sillon ainsi découvert. Par la suite, j’ai caractérisé deux mutants du KBM de XLF (L297E et L297W) qui respectivement abroge et renforce l’interaction de ce motif KBM avec Ku.Ensemble ces résultats confortent notre idée que Ku joue le rôle de chef d’orchestre de la voie de réparation NHEJ chez l’humain.

The use of detergents is often unavoidable in the structural studies of membrane proteins. Dodecylphosphocholine (DPC) is one of the most commonly used detergents for such studies in solution state NMR spectroscopy. The effect of detergent on structure and dynamics remains an important and poorly understood question. In this study we have investigated millisecond dynamics, substrate binding and structural features of three different yeast proteins from mitochondrial carrier family (GGC1, ORC1 and AAC3) in DPC micelles. We have detected millisecond dynamics, which are asymmetrically distributed across the structure. Contrary to previous claims, we show that these dynamics are unrelated to function, as they are not affected by the substitutions which abolish mitochondrial carrier transport in proteoliposomes. Furthermore, we could show that the very well-defined substrate specificity of these proteins in membranes is abolished when they are reconstituted in DPC, questioning their functionality. Structural investigations have revealed that both tertiary and secondary structures of these carriers are perturbed in DPC micelles, with some TM helices showing substantial solvent exposure. We have concluded from these observations that DPC detergent strongly perturbs these, and likely other mitochondrial carriers by rendering them very flexible. Our findings point to a possibly general effect of this detergent on membrane proteins, as we discuss with examples of previously studied membrane proteins. In the second part we have addressed a fundamental question of protein dynamics: how do proteins move inside crystals? We have investigated ms dynamics in a crystalline ubiquitin to gain the insight on the impact of the crystalline lattice on such motions, using solid-state NMR and ms long MD simulations of explicit crystal arrangements. Interestingly a local dynamic exchange process on a ms time scale is still present in crystals. However, by comparing different crystal forms we establish that the thermodynamics of the exchanging states and their interconversion rate constants are significantly altered by the crystal contacts. Furthermore, we detect overall "rocking" motion of molecules in the crystal, occurring on a tens-of-ms time scale, and provide evidence that overall and local motion are coupled. We discuss the implications of ms dynamics on the data quality in X-ray diffraction experiments., L’utilisation de détergents est inévitable pour les études structurales des protéines membranaires. Dodecylphosphocholine (DPC) est un des détergents les plus utilisés pour ce type d’études employant la spectroscopie de résonance magnétique nucléaire (RMN) en solution. L’effet des détergents sur la structure et la dynamique des macromolécules est une problématique importante, mais peu étudiée à ce jour. Dans cette étude nous avons caractérisé la dynamique à l’échelle de la milliseconde, la liaison des substrats ainsi que des propriétés structurales de trois protéines membranaires différentes solubilisées dans des micelles de DPC. Ces protéines font partie de la famille des transporteurs mitochondriaux et nous avons choisi les séquences de la levure (ORC1, GGC1, AAC3). Nous avons détecté de la dynamique à l’échelle de la milliseconde qui est distribuée d’une manière asymétrique à travers la structure. En contradiction avec des propos de la littérature, nous montrons que cette dynamique n’est pas corrélée à la fonction, puisqu’elle n’est pas modifiée par des mutations qui inhibent le transport effectué par ces protéines quand elles sont reconstituées dans des liposomes. En plus, nous avons pu montrer que leur spécificité par rapport aux substrats, n’est pas conservée quand ces transporteurs sont reconstitués dans du DPC, mettant en question leur fonctionnalité dans ce détergent. La RMN a aussi permis de démontrer que les structures tertiaire et secondaire sont perturbées dans les micelles avec quelques hélices transmembranaires apparaissant exposées au solvant. Nous avons donc conclu que la présence du détergent a un effet fort sur les trois transporteurs mitochondriaux de notre étude et probablement d’autres protéines similaires, en les rendant très flexible. Nos résultats indiquent un probable effet général de ce détergent sur les protéines membranaires, comme nous le discutons dans une analyse détaillée de quelques études de protéines membranaires décrites dans la littérature. Dans la seconde partie de ce travail, nous avons adressé une question fondamentale de la dynamique des protéines: comment se comportent les protéines dans des cristaux ? Nous avons étudié la dynamique de l’ubiquitine cristalline à l’échelle de la milliseconde afin de comprendre l’influence de la maille cristalline sur ce type de mouvement. Pour ce faire, nous avons employé la RMN à l’état solide et des simulations de dynamique moléculaire de la protéine dans différents réseaux cristallins distincts. Il est intéressant à noter que dans ces cristaux on détecte toujours des processus locaux d’échange dynamique sur une échelle de temps de la milliseconde. Cependant, en comparant les résultats obtenus avec différentes formes cristallines, nous constatons que les paramètres thermodynamiques des différents états en échange et les vitesses d’interconversion entre ces dernières sont significativement modifiés par les contacts cristallins. De plus, nous avons détecté des mouvements globaux de type «rocking» des ces molécules à l’état cristallin qui surviennent également à l’échelle de la milliseconde. Ceci suggère que les mouvements globaux et locaux sont corrélés. Cette observation ouvre la discussion de l’importance de ce type de mouvements pour la qualité et l’interprétation des données des expériences de diffraction des rayons-X.

The cell cycle and the circadian clock represent major cellular rhythms, which appear to be coupled. Thus the circadian factor BMAL1 controls the level of cell cycle proteins such as Cyclin E and WEE1, the latter of which inhibits the kinase CDK1 that governs the G2/M transition. In reverse the cell cycle impinges on the circadian clock through direct control by CDK1 of REV-ERBα, which negatively regulates BMAL1. These observations provide evidence for bidirectional coupling of the cell cycle and the circadian clock. By merging detailed models for the two networks in mammalian cells, we previously showed that unidirectional coupling to the circadian clock can entrain the cell cycle to 24 or 48 h, depending on the cell cycle autonomous period, while complex oscillations occur when entrainment fails. Here we show that the reverse unidirectional coupling via phosphorylation of REV-ERBα or via mitotic inhibition of transcription, both controlled by CDK1, can elicit entrainment of the circadian clock by the cell cycle. We then determine the effect of bidirectional coupling of the cell cycle and circadian clock as a function of their relative coupling strengths. In contrast to unidirectional coupling, bidirectional coupling markedly reduces the likelihood of complex oscillations. While the two rhythms oscillate independently as long as both couplings are weak, one rhythm entrains the other if one of the couplings dominates. If the couplings in both directions become stronger and of comparable magnitude, the two rhythms synchronize, generally at an intermediate period within the range defined by the two autonomous periods prior to coupling. More surprisingly, synchronization may also occur at a period slightly below or above this range, while in some conditions the synchronization period can even be much longer. Two or even three modes of synchronization may sometimes coexist, yielding examples of birhythmicity or trirhythmicity. Because synchronization readily occurs in the form of simple periodic oscillations over a wide range of coupling strengths and in the presence of multiple connections between the two oscillatory networks, the results indicate that bidirectional coupling favours the robust synchronization of the cell cycle and the circadian clock., SCOPUS: ar.j, info:eu-repo/semantics/published

The cell cycle and the circadian clock represent two major cellular rhythms, which are coupled because the circadian clock governs the synthesis of several proteins of the network that drives the mammalian cell cycle. Analysis of a detailed model for these coupled cellular rhythms previously showed that the cell cycle can be entrained at the circadian period of 24 h, or at a period of 48 h, depending on the autonomous period of the cell cycle and on the coupling strength. We show by means of numerical simulations that multiple stable periodic regimes, i.e. multi-rhythmicity, may originate from the coupling of the two cellular rhythms. In these conditions, the cell cycle can evolve to any one of two (birhythmicity) or three stable periodic regimes (trirhythmicity). When applied at the right phase, transient perturbations of appropriate duration and magnitude can induce the switch between the different oscillatory states. Such switching is characterized by final state sensitivity, which originates from the complex structure of the attraction basins. By providing a novel instance of multi-rhythmicity in a realistic model for the coupling of two major cellular rhythms, the results throw light on the conditions in which multiple stable periodic regimes may coexist in biological systems., SCOPUS: ar.j, info:eu-repo/semantics/published

Dietary fat composition can interfere in the development of obesity due to the specific roles of some fatty acids that have different metabolic activities, which can alter both fat oxidation and deposition rates, resulting in changes in body weight and/or composition. High-fat diets in general are associated with hyperphagia, but the type of dietary fat seems to be more important since saturated fats are linked to a positive fat balance and omental adipose tissue accumulation when compared to other types of fat, while polyunsaturated fats, omega-3 and omega-6, seem to increase energy expenditure and decrease energy intake by specific mechanisms involving hormone-sensitive lipase, activation of peroxisome proliferator-activated receptor α (PPARα) and others. Saturated fat intake can also impair insulin sensitivity compared to omega-3 fat, which has the opposite effect due to alterations in cell membranes. Obesity is also associated with impaired mitochondrial function. Fat excess favors the production of malonyl-CoA, which reduces GLUT4 efficiency. The tricarboxylic acid cycle and beta-oxidation are temporarily uncoupled, forming metabolite byproducts that augment reactive oxygen species production. Exercise can restore mitochondrial function and insulin sensitivity, which may be crucial for a better prognosis in treating or preventing obesity., SCOPUS: ar.j, info:eu-repo/semantics/published

Wild-type and variant forms of transthyretin (TTR), a normal plasma protein, are amyloidogenic and can be deposited in the tissues as amyloid fibrils causing acquired and hereditary systemic TTR amyloidosis, a debilitating and usually fatal disease. Reduction in the abundance of amyloid fibril precursor proteins arrests amyloid deposition and halts disease progression in all forms of amyloidosis including TTR type. Our previous demonstration that circulating serum amyloid P component (SAP) is efficiently depleted by administration of a specific small molecule ligand compound, that non-covalently crosslinks pairs of SAP molecules, suggested that TTR may be also amenable to this approach. We first confirmed that chemically crosslinked human TTR is rapidly cleared from the circulation in mice. In order to crosslink pairs of TTR molecules, promote their accelerated clearance and thus therapeutically deplete plasma TTR, we prepared a range of bivalent specific ligands for the thyroxine binding sites of TTR. Non-covalently bound human TTR-ligand complexes were formed that were stable in vitro and in vivo, but they were not cleared from the plasma of mice in vivo more rapidly than native uncomplexed TTR. Therapeutic depletion of circulating TTR will require additional mechanisms., SCOPUS: ar.j, info:eu-repo/semantics/published

To understand the dynamics of the cell cycle, we need to characterize the balance between cell cycle arrest and cell proliferation, which is often deregulated in cancers. We address this issue by means of a detailed computational model for the network of cyclin-dependent kinases (Cdks) driving the mammalian cell cycle. Previous analysis of the model focused on how this balance is controlled by growth factors (GFs) or the levels of activators (oncogenes) and inhibitors (tumour suppressors) of cell cycle progression. Supra-threshold changesin the level of anyofthese factors can trigger a switch in the dynamical behaviour of the Cdk network corresponding to a bifurcation between a stable steady state, associated with cell cycle arrest, and sustained oscillations of the various cyclin/Cdk complexes, corresponding to cell proliferation. Here, we focus on the regulation of cell proliferation by cellular environmental factors external to the Cdk network, such as the extracellular matrix (ECM), and contact inhibition, which increases with cell density. We extend the model for the Cdk network by including the phenomenological effect of both the ECM, which controls the activation of the focal adhesion kinase (FAK) that promotes cell cycle progression, and cell density, which inhibits cell proliferation via the Hippo/YAP pathway. The model shows that GFs and FAK activation are capable of triggering in a similar dynamical manner the transition to cell proliferation, while the Hippo/YAP pathway can arrest proliferation once cell density passes a critical threshold. The results account for the dependence or independence of cell proliferation on serum and/or cell anchorage to ECM. Whether the balance in the Cdk network is tilted towards cell cycle arrest or proliferation depends on the direction in which the threshold associated with the bifurcation is passed once the cell integrates the multiple, internal or external signals that promote or impede progression in the cell cycle. © 2014 The Authors., SCOPUS: ar.j, info:eu-repo/semantics/published

Nanomaterials raise new questions in environmental and human toxicology and represent a novel interface with specific properties with the biological medium. Several unknown remain to explain all the mechanisms of toxicity, especially at the molecular lever. When they enter the biological medium, nanoparticles get covered by a protein corona. This corona yields to a new “biological identity” that controls the cellular response to nanoparticles and their fate in the organism. We studied the adsorption of model proteins on nanostructured silica. The first part is dedicated to the characterization of nanoporous silica and silica nanoparticles that we used. Then the adsorption of myoglobin, hemoglobin and protein mixture from yeast cells was studied to determine the thermodynamic and physical-chemical parameters of protein adsorption on silica. The enrichment of basic residues, gathered in charge clusters, favors the adsorption of proteins by the formation of electrostatic interactions with the charged surface of silica, independently of the global charge of the protein. On the contrary, the enrichment in aromatic residues is unfavorable to protein adsorption because they form π-π interactions that rigidify the protein structure. The identification of adsorbed and non-adsorbed proteins from a complex medium could also be used for cellular toxicity studies. From the study of the structure, the dynamics and the activity of myoglobin and hemoglobin adsorbed on silica nanoparticles, we tried to define the state of an adsorbed protein. The structural study, based on circular dichroism, fluorescence, infrared, X-ray and UV-visible spectroscopy and microcalorimetry, shows a substantial partial structure loss of adsorbed proteins together with a high conformational heterogeneity, without major modifications of the heme structure. Two potential interaction sites of myoglobin with silica nanoparticles have been identified by a footprinting technique. The study of adsorbed myoglobin dynamics by elastic and inelastic neutron scattering highlighted the important decrease of protein dynamics that occurs upon adsorption. However, despite the structure loss, adsorbed metmyoglobin retains almost all of its activity of ligand binding. Unexpectedly, adsorbed hemoglobin shows an increase of its oxygen affinity and a decrease of its cooperativity, without any dissociation of the tetramer. This effect can be reproduced on human hemoglobin, cross-linked DCL hemoglobin and variant S hemoglobin. Besides, two effectors allow modulating the affinity of adsorbed hemoglobin. Despite the extent of structural and activity changes, all these modifications are entirely reversible upon desorption in soft conditions. The adsorption of hemoproteins on silica nanoparticles depicts a new sort of stress with resilience for proteins in terms of structure, dynamics and activity relationship., Les nanomatériaux posent de nouvelles questions en termes de toxicologie humaine et environnementale et représentent une nouvelle interface avec le milieu biologique aux propriétés spécifiques. De nombreuses inconnues demeurent, en particulier à l’échelle moléculaire, pour permettre d’expliquer certains mécanismes de toxicité. Lorsqu’elles entrent en contact avec le milieu biologique, les nanoparticules se couvrent d’une couche de protéines adsorbées. Celle-ci leur confère une nouvelle « identité biologique » qui contrôle la réponse cellulaire et leur devenir au sein de l’organisme. Nous avons étudié l’adsorption de protéines modèles sur la silice nanostructurée. Après avoir caractérisé la silice nanoporeuse et les nanoparticules de silice utilisées, l’adsorption de la myoglobine, de l’hémoglobine et des protéines d’un extrait cellulaire de levure a été étudiée afin de déterminer les paramètres physico-chimiques et thermodynamiques de l’adsorption des protéines sur la silice. Un enrichissement en résidus basiques, regroupés en clusters de charge, favorise l’adsorption des protéines grâce à la formation d’interactions électrostatiques avec la surface chargée de la silice, indépendamment de la charge globale de la protéine. A l’inverse, un enrichissement en résidus aromatiques est défavorable à l’adsorption car ces résidus forment des interactions π-π qui rigidifient la structure de la protéine. L’identification des protéines adsorbées et non adsorbées à partir d’un milieu complexe pourrait également être utilisée pour les études de toxicité cellulaire. A partir de l’étude de la structure, de la dynamique et de l’activité de la myoglobine et de l’hémoglobine adsorbées sur les nanoparticules de silice, nous avons cherché à définir l’état d’une protéine adsorbée. L’étude de la structure, réalisée par dichroïsme circulaire, spectroscopie UV-visible, d’absorption X, infrarouge, fluorescence et microcalorimétrie, montre une perte partielle de structure importante des protéines adsorbées associée à une grande hétérogénéité de conformations, sans modification majeure de la structure de l’hème. Deux sites potentiels d’interaction entre myoglobine et nanoparticules de silice ont été identifiés à l’aide d’une technique de cartographie de surface par irradiation. L’étude de la dynamique de la myoglobine adsorbée par diffusion élastique et inélastique de neutrons a permis de montrer que l’adsorption s’accompagnait d’une diminution importante de la flexibilité de la protéine. Malgré la perte de structure, la metmyoglobine adsorbée conserve une activité de fixation de ligands très proche de celle de la protéine libre. L’hémoglobine adsorbée présente de façon inattendue une augmentation de son affinité pour l’oxygène et une diminution de sa coopérativité, sans dissociation du tétramère. Cet effet est reproductible lors de l’adsorption de l’hémoglobine humaine, de l’hémoglobine pontée DCL et de l’hémoglobine mutée S. Deux effecteurs permettent par ailleurs de moduler l’affinité de l’hémoglobine adsorbée. Aussi importantes soient-elles, les modifications de structure et d’activité observées sont entièrement réversibles après désorption dans des conditions douces. L’adsorption des hémoprotéines sur les nanoparticules de silice représente véritablement un nouveau type de stress avec résilience pour les protéines en termes de relations entre structure, dynamique et activité.

Rhythms abound in biological systems, particularly at the cellular level where they originate from the feedback loops present in regulatory networks. Cellular rhythms can be investigated both by experimental and modeling approaches, and thus represent a prototypic field of research for systems biology. They have also become a major topic in synthetic biology. We review advances in the study of cellular rhythms of biochemical rather than electrical origin by considering a variety of oscillatory processes such as Ca++ oscillations, circadian rhythms, the segmentation clock, oscillations in p53 and NF-κB, synthetic oscillators, and the oscillatory dynamics of cyclin-dependent kinases driving the cell cycle. Finally we discuss the coupling between cellular rhythms and their robustness with respect to molecular noise., Journal Article, Research Support, Non-U.S. Gov't, Review, SCOPUS: cp.j, info:eu-repo/semantics/published

Aggregated forms of the amyloid-β peptide are hypothesized to act as the prime toxic agents in Alzheimer disease (AD). The in vivo amyloid-β peptide pool consists of both C- and N-terminally truncated or mutated peptides, and the composition thereof significantly determines AD risk. Other variations, such as biotinylation, are introduced as molecular tools to aid the understanding of disease mechanisms. Since these modifications have the potential to alter key aggregation properties of the amyloid-β peptide, we present a comparative study of the aggregation of a substantial set of the most common in vivo identified and in vitro produced amyloid-β peptides. STRUCTURED SUMMARY OF PROTEIN INTERACTIONS: Amyloid beta and Amyloid betabind by fluorescence technology (View Interaction: 1, 2, 3, 4, 5) Amyloid beta and Amyloid betabind by transmission electron microscopy (View Interaction: 1, 2) Amyloid beta and Amyloid betabind by filter binding (View Interaction: 1, 2, 3)., Journal Article, SCOPUS: ar.j, info:eu-repo/semantics/published

ATP-binding cassette (ABC) transporters constitute a large class of molecular pumps whose central role in chemotherapy resistance has highlighted their clinical relevance. We investigated whether the lipid composition of the membrane affects the function and structure of HorA, a bacterial ABC multidrug transporter. When the transporter was reconstituted in a bilayer where phosphatidylethanolamine (PE), the main lipid of the bacterial membrane, was replaced with phosphatidylcholine (PC), ATP hydrolysis and substrate transport became uncoupled. Although ATPase activity was maintained, HorA lost its ability to extrude the prototypical substrate Hoechst33342. Attenuated Total Reflection-Fourier Transform Infrared spectroscopy (ATR-FTIR) revealed that, although the secondary structure of the protein was unaffected, the orientation of the transmembrane helices (TM) was modified by the change in lipid composition. The orientation of the backbone carbonyls indicated that the helices opened wider in PE versus PC-containing liposomes, with 10 degrees difference. This was supported by hydrogen/deuterium exchange studies showing increased protection of the backbone from the solvent in PC-containing liposomes. Electron Paramagnetic Resonance was used to further probe the structural change. In the PC-containing liposomes we observed increased mobility of the spin label in TM4, along with increased exposure to molecular oxygen, used as a hydrophobic quencher. This indicates that the lipid change induced modification of the orientation of TM4, exposing Cys-180 to the lipid phase. The lipid composition of the bilayer thus modulates the structure of HorA, and in turn its ability to extrude its substrates., Journal Article, SCOPUS: ar.j, info:eu-repo/semantics/published

Protein-lipid interactions are increasingly recognized as central to the structure and function of membrane proteins. However, with the exception of simplified models, specific protein-lipid interactions are particularly difficult to highlight experimentally. Here, we used molecular dynamics simulations to identify a specific protein-lipid interaction in lactose permease, a prototypical model for transmembrane proteins. The interactions can be correlated with the functional dependence of the protein to specific lipid species. The technique is simple and widely applicable to other membrane proteins, and a variety of lipid matrices can be used., Journal Article, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

Doppel protein (Dpl) is a paralog of the cellular form of the prion protein (PrP(C)), together sharing common structural and biochemical properties. Unlike PrP(C), which is abundantly expressed throughout the central nervous system (CNS), Dpl protein expression is not detectable in the CNS. Interestingly, its ectopic expression in the brain elicits neurodegeneration in transgenic mice. Here, by combining native isoelectric focusing plus non-denaturing polyacrylamide gel electrophoresis and mass spectrometry analysis, we identified two Dpl binding partners: rat alpha-1-inhibitor-3 (alpha(1)I(3)) and, by sequence homology, alpha-2-macroglobulin (alpha(2)M), two known plasma metalloproteinase inhibitors. Biochemical investigations excluded the direct interaction of PrP(C) with either alpha(1)I(3) or alpha(2)M. Nevertheless, enzyme-linked immunosorbent assays and surface plasmon resonance experiments revealed a high affinity binding occurring between PrP(C) and Dpl. In light of these findings, we suggest a mechanism for Dpl-induced neurodegeneration in mice expressing Dpl ectopically in the brain, linked to a withdrawal of natural inhibitors of metalloproteinase such as alpha(2)M. Interestingly, alpha(2)M has been proven to be a susceptibility factor in Alzheimer's disease, and as our findings imply, it may also play a relevant role in other neurodegenerative disorders, including prion diseases., Journal Article, Research Support, N.I.H. Extramural, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

International audience; Cell-surface proteins are important in cell-cell communication. They assemble into heterocomplexes that include different receptors and effectors. Elucidation and manipulation of such protein complexes offers new therapeutic possibilities. We describe a methodology combining time-resolved fluorescence resonance energy transfer (FRET) with snap-tag technology to quantitatively analyze protein-protein interactions at the surface of living cells, in a high throughput-compatible format. Using this approach, we examined whether G protein-coupled receptors (GPCRs) are monomers or assemble into dimers or larger oligomers--a matter of intense debate. We obtained evidence for the oligomeric state of both class A and class C GPCRs. We also observed different quaternary structure of GPCRs for the neurotransmitters glutamate and gamma-aminobutyric acid (GABA): whereas metabotropic glutamate receptors assembled into strict dimers, the GABA(B) receptors spontaneously formed dimers of heterodimers, offering a way to modulate G-protein coupling efficacy. This approach will be useful in systematic analysis of cell-surface protein interaction in living cells.

We derive asymptotically an order parameter equation in the limit where nascent bistability and long-wavelength modulation instabilities coalesce. This equation is a variant of the Swift-Hohenberg equation that generally contains nonvariational terms of the form ψ ∇2 ψ and ∫∇ψ ∫2. We briefly review some of the properties already derived for this equation and derive it on three examples taken from chemical, biological, and optical contexts. Finally, we derive the equation on a general class of partial differential systems. © 2007 American Institute of Physics., info:eu-repo/semantics/published

Omeprazole is a benzimidazole derivative which induces both P450 1A1 and 1A2 in human liver in vitro and in vivo. Northern blot analysis of polyA RNA prepared from primary cultures of human hepatocytes indicates that both 1A1 and 1A2 messages are induced by beta-naphthoflavone and omeprazole. Co-treatment of cells with these inducers and with actinomycin D or cycloheximide results in no accumulation of both mRNA or superinduction of 1A1 mRNA, respectively. 9S enriched fraction of cytosol was prepared either from human hepatocytes in culture or from human liver tissue and analyzed by sucrose density gradient sedimentation for its capacity to bind 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), omeprazole or omeprazole sulfone (a metabolite of omeprazole in man). Whereas 2 microM TCDD displaced almost totally [3H]TCDD from the Ah receptor, both omeprazole and omeprazole sulfone did not, even at 5000-fold molar excess. In addition, when [14C] omeprazole was incubated with 9S enriched fraction of human liver or hepatocyte cytosol, no interaction could be detected in sucrose density gradient. These experiments suggest that omeprazole is not a ligand for the human liver Ah receptor.

Photoaffinity labeling with [α-32P]GTP allowed to detect a 54 kDa GTP-binding protein in rat pancreatic plasma membranes and in pancreatic AR 4-2J cell membranes. Like the 42 and 48 kDa G(s)α subunits and the 41 kDa G(i)α subunit, this protein was absent from zymogen granule membranes. Contrastingly, a new 28 kDa GTP-binding protein (detected by [α-32P]GTP binding on immobilized proteins) and a 25 kDa protein (ADP-ribosylated by botulinum toxin D) were found in all three membrane preparations. This is to our knowledge the first report on GTP-binding proteins in zymogen granule membranes., SCOPUS: ar.j, info:eu-repo/semantics/published

SCOPUS: ar.j, info:eu-repo/semantics/published

The concentration of carbamylcholine, bombesin, pancreozymin, pentagastrin and secretin evoking a similar 4-5 fold maximal increase in amylase secretion from rat pancreatic fragments were 3x10-6, 10-7, 10-8, 3x10-6, and 3x10-6M, respectively. The maximal concentration of vasoactive intestinal peptide tested, (3x10-6M) increased amylase secretion by 250%. The six secretagogues could be separated into two groups according to their effects on lipid metabolism and ATP levels. When used at their optimal concentrations, carbamylcholine, bombesin, pancreozymin, and pentagastrin lowered pancreatic ATP levels by 18-26% and increased net release of free fatty acids by 68-105%. The effects of 3x10-6M carbamylcholine and 10-8M pancreozymin on the metabolism of 3H2O, D-[U-14C]glucose and [1-14C]acetate were similar; the incorporation of radioactivity in the fatty acid moiety of glycerolipids decreased by 20-50% whereas the incorporation of 3H from 3H2O and of 14C from [U-14C]glucose increased by 20-35% in the glycerol moiety. In addition, the oxidation of [U-14C]glucose, [1-14C]acetate and [1-14C]palmitate to 14CO2 increased by 15-32% while the esterification of [1-14C]palmitate, [1-14C]-linoleate, and [1-14C]arachidonate was inhibited by 14-23%. The spectrum of fatty acids labeled with [1-14C]acetate indicated an inhibition of the malonic acid pathway whereas the elongation of polyenoic fatty acids was unaltered. The effects of carbamylcholine and pancreozymin on amylase secretion and lipid metabolism were markedly reduced in a Ca2+-free medium or in the presence of heavy water. Secretin and vasoactive intestinal peptide provoked none of the preceding effects even when tested at concentrations inducing a comparable rate of secretion., SCOPUS: ar.j, info:eu-repo/semantics/published

1. 1. The rate of incorporation of 14C-glycine into the proteins of reticulocytes and their RNA content have been determined as a function of the development and disappearance of a phenyl-hydrazine induced reticulocytosis in rabbits. 2. 2. The peak of labelled amino acid incorporation occurred 1 to 2 days before the RNA peak. 3. 3. The formation of carbonic anhydrase, hemoglobin and peptidase corresponds quite closely with the RNA curve rather than with the 14C glycine incorporation curve. 4. 4. These results are interpreted to indicate that RNA is not involved in the initial incorporation of amino acids into proteins but rather mediates the differentiation of a "primary" protein into its final stereospecific, biologically active form. © 1954., SCOPUS: ar.j, info:eu-repo/semantics/published

Addition of 200 mm of a polyol to anthocyanin containing carrot (Daucus carota L.) cells in suspension culture decreased turgor pressure to zero and induced hyperpolarization of the membrane potential and acidification of the medium due to H+ extrusion. These changes were shown to be slightly affected by vanadate. In parallel, a decrease in intracellular ATP and total adenylate concentrations were observed. However, when the osmoticum was NaCl acidification of the medium occurred in the absence of considerable changes in intracellular ATP concentration. These results are interpreted as indicating that a drop of turgor, by addition of a polyol, triggers a proton extrusion activity which is only slightly inhibited by vanadate but apparently ATP utilizing. The observed decrease in ATP level occurs without a change in respiration rate and is accompanied by a drop in total adenylate pool. However when NaCl is the osmoticum it is assumed that ΔμH+ is enhanced through a Na+/H+ antiporter. The difference between the two types of osmotica as related to their ability to penetrate through the cellular membrane is discussed.

The complete amino acid sequence of helodermin isolated from the venom of Gila monster was elucidated. The peptide was shown to be a basic pentatriacontapeptide amide: His-Ser-Asp-Ala-Ile-Phe-Thr-Gln-Gln- Tyr-Ser-Lys-Leu-Leu-Ala-Lys-Leu-Ala-Leu-Gln-Lys-Tyr-Leu-Ala-Ser-Ile-Leu-Gly-Ser-Arg-Thr-Ser-Pro-Pro-Pro-NH2. A high degree of sequence similarities to secretin/VIP/PHI/(PHM)/GRF from mammal and bird was observed over the entire N-terminal 1-27 sequence. In particular, the amino acid residues in positions 3, 6 and 7 were found to be common to 9 peptides of the family. Another interesting feature of the structure of helodermin was its C-terminal -Pro-Pro-Pro-NH2 sequence. Isolation of helodermin was the first demonstration of the existence of a secretin/VIP-related peptide in an animal that is neither mammal nor bird. © 1984., SCOPUS: ar.j, info:eu-repo/semantics/published