La plus grande famille de récepteurs membranaires est constituée par des récepteurs à sept domaines transmembranaires couplés aux protéines G (RCPG). Ces récepteurs sont impliqués dans un grand nombre de réponses cellulaires physiologiques et pathologiques et représentent la ciblé de une grande majorité des produits thérapeutiques. La fonction d’un récepteur est déterminée par la quantité de récepteur fonctionnel à la surface cellulaire, qui dépend de différents paramètres comme le niveau de biosynthèse, l’export vers la surface cellulaire à partir de stocks intracellulaires, l’endocytose et les modifications post-transcriptionelles (ex. phosphorylation). Le nouveau concept d’export régulé pour les RCPG présent l’importance physiologique de la rétention de récepteurs, leur relargage, leur interaction avec les partenaires chaperonnes et les escortes. Les études présentées ici concernent les mécanismes d’export régulé de deux RCPG, le récepteur métabotropique de l’acide γ-amino butyrique (GABAB) et le récepteur de chimiokines CC 5 (CCR5). GABAB est un récepteur constitué de deux sous-unités GB1 et GB2 et CCR5 est probablement un homo-dimer. GB1 ainsi que CCR sont retenus dans des compartiments intracellulaire (RE et appareil Golgi) d’où ils sont relâchés en réponse à un signal extern (CCR5) ou/et en interagissant avec protéines d’escorte (comme CD4 pour CCR5 et GB2 pour GB1). L’objectif de ces études était de comprendre le mécanisme de rétention de ces récepteurs et leur régulation. Dans ce contexte, nous avons déterminé en utilisant des approches biophysiques et biochimiques que ces récepteurs interagissent de façon spécifique avec les membres de Prenylated Rab Acceptors Family (PRAF). Ces protéines sont résidentes dans le RE (PRAF2 et PRAF3) et dans le appareil Golgi (PRAF1) où elles fonctionnent comme de gatekeepers pour les récepteurs. Nous avons pu démontrer que PRAF2 interagie de manière spécifique avec des motifs de rétention connus pour leur implication dans la rétention de récepteurs. Cette interaction détermine une rétention au niveau de RE donc régule de façon négatif l’export vers la membrane cellulaire. Dans le cas de récepteur GABAB, l’interaction de GB2 avec GB1 permet la libération de GB1 de sa rétention par PRAF2 par simple compétition. La modification de l’équilibre stoichiométrique entre les gatekeepers PRAF et les protéines d’escorte pour les récepteurs induit des modifications de la fonction du récepteur in vitro et in vivo. Les PRAFs sont ubiquitaires et peuvent interagir avec plusieurs RCPG représentant dans ce cas des régulateurs majors de la fonction de RCPG dans des conditions physiologiques et pathologiques. / The largest family of membrane receptors is constituted by conserved seven-membrane domain spanning receptors, the G-protein coupled receptors (GPCRs). They are involved in numerous cell responses and diseases thus being a major drug target. Receptor function is determined by the amount of active receptors at the cell surface, which depends on various parameters, such as the biosynthetic rate, the export to the cell surface from internal stores, the endocytosis and post-transcriptional modifications (i.e. phosphorylation). Only recently, the importance of the regulated export has emerged, shedding new light on the physiological role of receptor retention, release, chaperoning and escorting. This work concerns the regulated export mechanisms of two members of the GPCRs family, the chemokine receptor 5 (CCR5) and the metabotropic receptor of the g amino butyric acid (GABAB). Whereas CCR5 is likely a homo-dimer of 2 identical protomers, GABAB is an obligatory hetero-dimer of 2 distinct subunit known as GB1 and GB2. Both CCR5 and GB1 are retained in intracellular compartments (the ER and the Golgi) from which they are released in response to external signals (CCR5) and/or interaction with “private escort proteins” (CD4 for CCR5 and GB2 for GB1). The main goal of our work was to understand the mechanism of retention of these receptors and its regulation. In this context, we determined using biochemical and biophysical approaches that these GPCRs specifically interact with the members of the Prenylated Rab Acceptor Family (PRAF). These proteins are resident either in the ER (PRAF2 and PRAF3) or in the Golgi apparatus (PRAF1) where they function as receptor gatekeepers. Indeed, we could document for PRAF2 that this protein likely interacts directly with previously identified receptor retention motifs and inhibits receptor egress from the ER and subsequent trafficking to the plasma membrane. In the context of the GABAB receptor, PRAF2-dependent retention of GB1 can be overridden by GB2 via simple competition. Perturbing the stoichiometry of PRAF gatekeepers respective to that of receptors significantly perturbs receptor function both in vitro and in vivo. Because PRAFs are ubiquitous and seem to interact with many other GPCRs, they might represent major regulators of receptor function both in physiological and pathological conditions.

Domain swapping is a wide spread phenomenon which involves the association between two or more protein subunits such that intra-molecular interactions between domains in each subunit are replaced by equivalent inter-molecular interactions between the same domains in different subunits. This thesis is devoted to the analysis of the factors that drive proteins to undergo such association modes. The specific system analyzed is the monomer to swapped dimer formation of the B1 domain of the immunoglobulin G binding protein (GB1). The formation of this dimer was shown to be fostered by 4 amino acid substitutions (L5V, F30V, Y33F, A34F) (Byeon et al., 2003). In this work, computational protein design and molecular dynamics simulations, both with detailed atomic models, were used to gain insight into how these 4 mutations may promote the domain swapping reaction. The stability of the wt and quadruple mutant GB1 monomers was assessed using the software DESIGNER, a fully automatic procedure that selects amino acid sequences likely to stabilize a given backbone structure (Wernisch et al., 2000). Results suggest that 3 of the mutations (L5V, F30V, A34F) have a destabilizing effect. The first mutation (L5V) forms destabilizing interactions with surrounding residues, while the second (F30V) is engaged in unfavorable interactions with the protein backbone, consequently causing local strain. Although the A34F substitution itself is found to contribute favorably to the stability of the monomer, this is achieved only at the expense of forcing the wild type W43 into a highly strained conformation concomitant with the formation of unfavorable interactions with both W43 and V54. Finally, we also provide evidence that A34F mutation stabilizes the swapped dimer structure. Although we were unable to perform detailed protein design calculations on the dimer, due to the lower accuracy of the model, inspection of its 3D structure reveals that the 34F side chains pack against one another in the core of the swapped structure, thereby forming extensive non-native interactions that have no counterparts in the individual monomers. Their replacement by the much smaller Ala residue is suggested to be significantly destabilizing by creating a large internal cavity, a phenomenon, well known to be destabilizing in other proteins. Our analysis hence proposes that the A34F mutation plays a dual role, that of destabilizing the GB1 monomer structure while stabilizing the swapped dimer conformation. In addition to the above study, molecular dynamics simulations of the wild type and modeled quadruple mutant GB1 structures were carried out at room and elevated temperatures (450 K) in order to sample the conformational landscape of the protein near its native monomeric state, and to characterize the deformations that occur during early unfolding. This part of the study was aimed at investigating the influence of the amino acid sequence on the conformational properties of the GB1 monomer and the possible link between these properties and the swapping process. Analysis of the room temperature simulations indicates that the mutant GB1 monomer fluctuates more than its wild type counter part. In addition, we find that the C-terminal beta-hairpin is pushed away from the remainder of the structure, in agreement with the fact that this hairpin is the structural element that is exchanged upon domain swapping. The simulations at 450 K reveal that the mutant protein unfolds more readily than the wt, in agreement with its decreased stability. Also, among the regions that unfold early is the alpha-helix C-terminus, where 2 out of the 4 mutations reside. NMR experiments by our collaborators have shown this region to display increased flexibility in the monomeric state of the quadruple mutant. Our atomic scale investigation has thus provided insights into how sequence modifications can foster domain swapping of GB1. Our findings indicate that the role of the amino acid substitutions is to decrease the stability of individual monomers while at the same time increase the stability of the swapped dimer, through the formation of non-native interactions. Both roles cooperate to foster swapping.

Protein dynamics are critical to the structure and function of proteins. However, due to the complexity they inherently bring to the protein design problem, dynamics historically have not been considered in computational protein design (CPD). Herein, we present meta-MSD, a new CPD methodology for the design of protein dynamics. We applied our methodology to the design of a novel mode of conformational exchange in Streptococcal protein G domain B1, producing dynamic variants we termed DANCERs. Predictions were validated by NMR characterization of selected DANCERs, confirming that our meta-MSD framework is suitable for the computational design of protein dynamics. We then performed a thorough NMR characterization of the sequence determinants of dynamics in one DANCER, isolating two mutations responsible for the novel dynamics this protein exhibits. The first, A34F, is responsible for destabilizing the highly stable native Gβ1 conformation, allowing the protein to sample other conformational states. The second, V39L mediates subtle interactions that stabilize the designed conformational trajectory in the context of the A34F mutation. Together, these results highlight the role of protein plasticity in the development of dynamics and the need for highly accurate computational tools to approach similar design problems. Finally, we present an NMR-based characterization of structural dynamics in a family of related red fluorescent proteins (RFPs) and pinpoint regions of the RFP structure where dynamics correlate to RFP brightness. This overview of the RFP dynamics-function relationship will be used in future projects to perform a computation design of functional dynamics in RFPs.

No description available.

Domain swapping is a wide spread phenomenon which involves the association between two or more protein subunits such that intra-molecular interactions between domains in each subunit are replaced by equivalent inter-molecular interactions between the same domains in different subunits. This thesis is devoted to the analysis of the factors that drive proteins to undergo such association modes. The specific system analyzed is the monomer to swapped dimer formation of the B1 domain of the immunoglobulin G binding protein (GB1). The formation of this dimer was shown to be fostered by 4 amino acid substitutions (L5V, F30V, Y33F, A34F) (Byeon et al. 2003). In this work, computational protein design and molecular dynamics simulations, both with detailed atomic models, were used to gain insight into how these 4 mutations may promote the domain swapping reaction.<p>The stability of the wt and quadruple mutant GB1 monomers was assessed using the software DESIGNER, a fully automatic procedure that selects amino acid sequences likely to stabilize a given backbone structure (Wernisch et al. 2000). Results suggest that 3 of the mutations (L5V, F30V, A34F) have a destabilizing effect. The first mutation (L5V) forms destabilizing interactions with surrounding residues, while the second (F30V) is engaged in unfavorable interactions with the protein backbone, consequently causing local strain. Although the A34F substitution itself is found to contribute favorably to the stability of the monomer, this is achieved only at the expense of forcing the wild type W43 into a highly strained conformation concomitant with the formation of unfavorable interactions with both W43 and V54.<p>Finally, we also provide evidence that A34F mutation stabilizes the swapped dimer structure. Although we were unable to perform detailed protein design calculations on the dimer, due to the lower accuracy of the model, inspection of its 3D structure reveals that the 34F side chains pack against one another in the core of the swapped structure, thereby forming extensive non-native interactions that have no counterparts in the individual monomers. Their replacement by the much smaller Ala residue is suggested to be significantly destabilizing by creating a large internal cavity, a phenomenon, well known to be destabilizing in other proteins. Our analysis hence proposes that the A34F mutation plays a dual role, that of destabilizing the GB1 monomer structure while stabilizing the swapped dimer conformation.<p>In addition to the above study, molecular dynamics simulations of the wild type and modeled quadruple mutant GB1 structures were carried out at room and elevated temperatures (450 K) in order to sample the conformational landscape of the protein near its native monomeric state, and to characterize the deformations that occur during early unfolding. This part of the study was aimed at investigating the influence of the amino acid sequence on the conformational properties of the GB1 monomer and the possible link between these properties and the swapping process. Analysis of the room temperature simulations indicates that the mutant GB1 monomer fluctuates more than its wild type counter part. In addition, we find that the C-terminal beta-hairpin is pushed away from the remainder of the structure, in agreement with the fact that this hairpin is the structural element that is exchanged upon domain swapping. The simulations at 450 K reveal that the mutant protein unfolds more readily than the wt, in agreement with its decreased stability. Also, among the regions that unfold early is the alpha-helix C-terminus, where 2 out of the 4 mutations reside. NMR experiments by our collaborators have shown this region to display increased flexibility in the monomeric state of the quadruple mutant.<p>Our atomic scale investigation has thus provided insights into how sequence modifications can foster domain swapping of GB1. Our findings indicate that the role of the amino acid substitutions is to decrease the stability of individual monomers while at the same time increase the stability of the swapped dimer, through the formation of non-native interactions. Both roles cooperate to foster swapping. / Doctorat en sciences, Spécialisation biologie moléculaire / info:eu-repo/semantics/nonPublished