Regulation of the AKAP-LBC signaling complex : molecular characterization and functional implications

RÉSUMÉ Les protéines d'ancrage de la protéine kinase A (AKAPs) constituent une grande famille de protéines qui ciblent la protéine kinase A (PKA) à proximité de ses substrats physiologiques pour assurer leur régulation. Une nouvelle protéine de cette famille, appelée AKAP-Lbc, a été récemment caractérisée et fonctionne comme un facteur d'échange de nucléotides guanine (GEF) pour la petite GTPase Rho. AKAP-Lbc est régulée par différents signaux qui activent et désactivent son activité Rho-GEF. Son activation est assurée par la sous-unité alpha de la protéine G hétérotrimérique G12, tandis que son inhibition dépend de son interaction avec la PKA et 14-3-3. AKAP-Lbc est principalement exprimée dans le coeur et pourrait réguler des processus importants tels que l'hypertrophie et la différenciation des cardiomyocytes. Ainsi, il est crucial d'élucider les mécanismes moléculaires impliqués dans la régulation de son activité Rho-GEF. Le but général de ce travail de thèse est la caractérisation de deux nouveaux mécanismes impliqués dans la régulation de l'activité de AKAP-Lbc. Le premier mécanisme consiste en la régulation de l'activité de AKAP-Lbc par son homo-oligomérisation. Mes travaux montrent que l'homo-oligomérisation maintient AKAP-Lbc inactive, dans une conformation permettant à la PKA ancrée et à 14-3-3 d'exercer leur effet inhibiteur sur l'activité de AKAP-Lbc. Le second mécanisme concerne la régulation de l'activité de AKAP-Lbc via une nouvelle interaction entre AKAP-Lbc et la protéine LC3. LC3 joue un rôle crucial dans l'autophagie, un processus cellulaire qui adresse les protéines cytoplasmiques au lysosome pour leur dégradation. Ce mécanisme est particulièrement important pour le survie des cardiomyocytes durant les périodes d'absence de nutriments. Mes travaux mettent en évidence que LC3 inhibe l'activité Rho-GEF de AKAP-Lbc, ce qui suggère que, au-delà son rôle bien établi dans l'autophagie, LC3 participerait à la régulation de la signalisation de Rho. Prises ensembles, ces études contribuent à comprendre comment le complexe de signalisation formé par AKAP-Lbc régule la signalisation de Rho dans les cellules. Au-delà de leur intérêt au niveau biochimique, ces travaux pourraient aussi contribuer à élucider les réseaux de signalisation qui régulent des phénomènes physiologiques dans le coeur. ABSTRACT A-kinase anchoring proteins (AKAPs) are a group of functionally related proteins, which target the cAMP dependent protein kinase A (PKA) in close proximity to its physiological substrates for ensuring their regulation. A novel PKA anchoring protein, termed AKAP-Lbc, has been recently characterized, which also functions as a guanine nucleotide exchange factor (GEF) for the small GTPase Rho. AKAP-Lbc is regulated in a bi-directional manner by signals which activate or deactivate its Rho-GEF activity. Activation is mediated by the alpha subunit of the heterotrimeric G protein G12, whereas inhibition occurs following its interaction with PKA and 14-3-3. AKAP-Lbc is predominantly expressed in the heart and might regulate important processes such as hypertrophy and differentiation of cardiomyocytes. Therefore ít is crucial to elucidate the molecular mechanisms involved in the regulation of the Rho-GEF activity of AKAP-Lbc. The general aim of the present thesis work is the characterization of two novel molecular mechanisms involved in the regulation of the Rho-GEF activity of AKAP-Lbc. The first mechanism consists of the. regulation of AKAP-Lbc activity through its homooligomerization. I report here that homo-oligomerization maintains AKAP-Lbc inactive, under a conformation suitable for ensuring the inhibitory effect of anchored PKA and 14-33 on AKAP-Lbc activity. The second mechanism concerns the regulation of AKAP-Lbc activity through a novel interaction between AKAP-Lbc and ubiquitin-like protein LC3. LC3 is a key mediator of autophagy, which is a cellular process that targets cytosolic proteins to the lysosome for degradation. This process is particularly important for cardiomyocyte survival during conditions of nutrient starvation. Here, I show that LC3 is a negative regulator of the Rho-GEF activity of AKAP-Lbc, which suggests that, beyond its well established role in autophagy, LC3 can participate in the regulation of Rho signaling in cells. Overall, these findings contribute to understand how the AKAP-Lbc signaling complex can regulate the Rho signaling in cells. Beyond its interest at the biochemical level, this work might also contribute to elucidate the signaling network that regulate physiological events in the heart.

Membrane insertion and antibody recognition of a glycosylphosphatidylinositol-anchored protein: an optical study.

The kinetics of binding of a glycolipid-anchored protein (the promastigote surface protease, PSP) to planar lecithin bilayers is studied by an integrated optics technique, in which the bilayer membrane is supported on an optical wave guide and the phase velocities of guided light modes in the wave guide are measured. From these velocities, the optical parameters of the membrane and PSP layers deposited on the waveguide are determined, yielding in particular the mass of PSP bound to the membrane, which is followed in real time. From a comparison of the binding rates of PSP and PSP from which the lipid moiety has been removed, it is shown that the lipid moiety plays a key role in anchoring the protein to the membrane. Specific and nonspecific binding of antibodies to membrane-anchored PSP is also investigated. As little as a fifth of a monolayer of PSP is sufficient to suppress the appreciable nonspecific binding of antibodies to the membrane.

Local optima networks of hard combinatorial landscapes

Combinatorial optimization involves finding an optimal solution in a finite set of options; many everyday life problems are of this kind. However, the number of options grows exponentially with the size of the problem, such that an exhaustive search for the best solution is practically infeasible beyond a certain problem size. When efficient algorithms are not available, a practical approach to obtain an approximate solution to the problem at hand, is to start with an educated guess and gradually refine it until we have a good-enough solution. Roughly speaking, this is how local search heuristics work. These stochastic algorithms navigate the problem search space by iteratively turning the current solution into new candidate solutions, guiding the search towards better solutions. The search performance, therefore, depends on structural aspects of the search space, which in turn depend on the move operator being used to modify solutions. A common way to characterize the search space of a problem is through the study of its fitness landscape, a mathematical object comprising the space of all possible solutions, their value with respect to the optimization objective, and a relationship of neighborhood defined by the move operator. The landscape metaphor is used to explain the search dynamics as a sort of potential function. The concept is indeed similar to that of potential energy surfaces in physical chemistry. Borrowing ideas from that field, we propose to extend to combinatorial landscapes the notion of the inherent network formed by energy minima in energy landscapes. In our case, energy minima are the local optima of the combinatorial problem, and we explore several definitions for the network edges. At first, we perform an exhaustive sampling of local optima basins of attraction, and define weighted transitions between basins by accounting for all the possible ways of crossing the basins frontier via one random move. Then, we reduce the computational burden by only counting the chances of escaping a given basin via random kick moves that start at the local optimum. Finally, we approximate network edges from the search trajectory of simple search heuristics, mining the frequency and inter-arrival time with which the heuristic visits local optima. Through these methodologies, we build a weighted directed graph that provides a synthetic view of the whole landscape, and that we can characterize using the tools of complex networks science. We argue that the network characterization can advance our understanding of the structural and dynamical properties of hard combinatorial landscapes. We apply our approach to prototypical problems such as the Quadratic Assignment Problem, the NK model of rugged landscapes, and the Permutation Flow-shop Scheduling Problem. We show that some network metrics can differentiate problem classes, correlate with problem non-linearity, and predict problem hardness as measured from the performances of trajectory-based local search heuristics.

Justification du système économique et perception du travail en groupe

L'étude classique des attributions de responsabilité instiguée par Heider en psychologie sociale s'est principalement bornée à aborder ce processus psychosocial dans une perspective individualiste qui se cantonne aux niveaux intra-individuel et interpersonnel (selon la distinction opérée par Doise). Les réflexions et les travaux empiriques présentés dans cette thèse ont deux objectifs. Dans un premier temps, il s?agit d'élargir cette perspective aux autres niveaux sociologique et idéologique (en faisant notamment recours à l'approche des attributions sociales et aux propositions de Fauconnet sur les règles de responsabilité). Deuxièmement, il s?agit d'éprouver la pertinence d'une telle approche dans un contexte particulier : celui du travail en groupe dont la nature des rapports sociaux qui y étaient présentés ont été manipulés à l'aide de scénarii chez des étudiant-e-s de l?Université de Lausanne. L?objectif principal de cette thèse est donc de tester un modèle d?ancrage des attributions de responsabilité qui permette de souligner les dynamiques représentationnelles sous-jacentes en termes de légitimation ou de remise en cause de l?organisation des groupes. Dans l?ensemble les résultats indiquent que si la nature des rapports sociaux (re)présentés dans un groupe sont de puissants déterminants de la manière de légitimer ou de remettre en cause l?organisation des groupes, le niveau individuel d'adhésion à des croyances idéologiques dominantes, comme la justification du système économique, représente un modérateur des prises de position des répondant-e-s interrogé-e-s. De plus, il semble que ces processus évoluent dans le temps, faisant ainsi apparaître l'existence de phénomènes de socialisation relativement plus complexes que ne le laissent entendre les recherches actuellement effectuées dans ce domaine. En effet, si des connaissances idéologiques sur le monde sont acquises dans les filières universitaires et n?interviennent pas toujours dans les processus de formation des représentations du travail en groupe, des connaissances spécifiques aux disciplines et à la politique de sélection universitaire semblent intervenir dans le processus de légitimation des rapports sociaux dans les groupes au niveau des attributions. En tentant une articulation entre les concepts d?ancrage des représentations sociales, d?attribution et de socialisation, cette thèse permet ainsi de souligner la pertinence qu?il y a à insérer une problématique en termes de croyances idéologiques dans l?étude des groupes sociaux.<br/><br/>Heider?s approach of responsibility attributions almost exclusively emphasized on an individualistic point of view ; i.e. focusing at an intraindividual and interpersonnal level of analysis according to Doise?s distinction. The reflexions and empirical studies presented here firstly aim at broaden this perspective by taking socio-structural as well as societal levels of analysis into account. Secondly, it is to test this approach in the particular domain of organized groups. Manipulation of the structure of social relations in work groups on screenplays were undertaken (in a population of students from the Lausanne University). Hence, the main goal of these studies is to test the impact of the social ancoring of social representations in the responsibility processes in terms of legitimation or opposition to the group organization. All in all, the results show that social structures are powerfull predictors of the formation of social representations of a work situation and so forth of the attribution process. Nevertheless hegemonic ideological beliefs, such as Economical System Justification, do play a substantial moderating role in this process. It also proves to be evolving through time. The present findings show that a complexe process of socialization is occuring during the student?s university life. Indeed, the results let us believe that ideological beliefs may not interact anytime in the group?s perception and in the construction of the representation of the situation. In the same time, it seems that more discipline specific oriented knowledge and the impact of selection policy at the Lausanne University also predict the groupe legimation process and interfer with the ideological beliefs. Trying to articulate concepts of fields of research like social representations, attribution and socialization, the present thesis allows to underline the heuristic potential of reabilitating ideological beliefs at a dispositional level in the study of group process.

Surface functionalization of alumina ceramic foams with organic ligands.

Different anchoring groups have been studied with the aim of covalently binding organic linkers to the surface of alumina ceramic foams. The results suggested that a higher degree of functionalization was achieved with a pyrogallol derivative - as compared to its catechol analogue - based on the XPS analysis of the ceramic surface. The conjugation of organic ligands to the surface of these alumina materials was corroborated by DNP-MAS NMR measurements.

Vacuolar SNARE Protein Transmembrane Domains Serve as Nonspecific Membrane Anchors with Unequal Roles in Lipid Mixing.

Membrane fusion is induced by SNARE complexes that are anchored in both fusion partners. SNAREs zipper up from the N to C terminus bringing the two membranes into close apposition. Their transmembrane domains (TMDs) might be mere anchoring devices, deforming bilayers by mechanical force. Structural studies suggested that TMDs might also perturb lipid structure by undergoing conformational transitions or by zipping up into the bilayer. Here, we tested this latter hypothesis, which predicts that the activity of SNAREs should depend on the primary sequence of their TMDs. We replaced the TMDs of all vacuolar SNAREs (Nyv1, Vam3, and Vti1) by a lipid anchor, by a TMD from a protein unrelated to the membrane fusion machinery, or by artificial leucine-valine sequences. Individual exchange of the native SNARE TMDs against an unrelated transmembrane anchor or an artificial leucine-valine sequence yielded normal fusion activities. Fusion activity was also preserved upon pairwise exchange of the TMDs against unrelated peptides, which eliminates the possibility for specific TMD-TMD interactions. Thus, a specific primary sequence or zippering beyond the SNARE domains is not a prerequisite for fusion. Lipid-anchored Vti1 was fully active, and lipid-anchored Nyv1 permitted the reaction to proceed up to hemifusion, and lipid-anchored Vam3 interfered already before hemifusion. The unequal contribution of proteinaceous TMDs on Vam3 and Nyv1 suggests that Q- and R-SNAREs might make different contributions to the hemifusion intermediate and the opening of the fusion pore. Furthermore, our data support the view that SNARE TMDs serve as nonspecific membrane anchors in vacuole fusion.

Introduction à la visualisation de données: l'analyse de réseau en histoire

The use of data visualization in history leads to contradictory reactions: some are fascinated by its heuristic potential and forget their critical faculties while others reject this practice, suspecting it of hiding explanatory weaknesses. This paper proposes a distinction between demonstration visualization and research visualization, reminding that scholars should not only use data visualization for communication purposes, but also for the research itself. It is particularly in its more complex form that this research visualization category will be approached here: network analysis.