This thesis describes NMR studies which probe weak interactions between amino acid side chains in folded peptide structures. Aromatic/aromatic interactions between facing phenylalanine residues have been probed in antiparallel β-sheets, while aromatic/proline interactions have been examined using cyclic peptide disulfides that occur in the venom of marine cone snails. Novel intramolecular hydrogen bonded structures in hybrid peptides containing backbone homologated residues, specifically γ-amino acids, are also described. Chapter 1 provides a brief background to the principles involved in the design of antiparallel β-sheet structures and an introduction to previous studies on aromatic/aromatic and aromatic/proline interactions in influencing peptide conformations. A summary of the NMR methods used is also presented. Chapter 2 discusses the structural characterisation of a designed 14 residue, three stranded β-sheet peptide, Boc-LFVDP-PLFVADP-PLFV-OMe (LFV14). The results described in this Chapter support the presence of multiple conformational states about the χ1 (Cα-Cβ) torsional degree of freedom for the interacting aromatic pairs in solution. Chapter 3 presents the structural characterisation of a designed 19 residue three stranded hybrid β-sheet peptide, Boc-LVβFVDPGLβFVVLDPGLVLβFVV-OMe (BBH19). β-amino acid residues (β-phenylalanine, βPhe) were incorporated at facing positions on antiparallel β-sheets. The BBH19 structure provides an example of interaction between the N and C-terminal strands in a three stranded structure with an α/β hybrid backbone. Chapter 4 focuses on studies of the conformations of the contryphan In936 (GCVDLYPWC*) from Conus inscriptus and the related peptide Lo959 (GCPDWDPWC*) from Conus loroissi. Both peptides possess a macrocyclic 23 membered ring, with multiple accessible conformational states. Chapter 5 describes conformational analysis of a novel 20 membered cyclic peptide disulfide, CIWPWC (Vi804), from Conus virgo. NMR structures were calculated for Vi804 and an analog peptide, CIDWPWC, DW3-Vi804. Chapter 6 explores the solution conformation of hybrid sequences containing α and γ residues. Oligopeptides of the type (αγ)n and (αγγ)n have been studied in solution by NMR methods. Chapter 7 provides a summary of the results described in this thesis and highlights the major conclusions.

Molecular Biology has allowed the characterization and manipulation of the molecules of life in the wet lab. Also the structures of those macromolecules are being continuously elucidated. During the last decades of the past century, there was an increasing interest to study how the different genes are organized into different organisms (‘genomes’) and how those genes are expressed into proteins to achieve their functions. Currently the sequences for many genes over several genomes have been determined. In parallel, the efforts to have the structure of the proteins coded by those genes go on. However it is experimentally much harder to obtain the structure of a protein, rather than just its sequence. For this reason, the number of protein structures available in databases is an order of magnitude or so lower than protein sequences. Furthermore, in order to understand how living organisms work at molecular level we need the information about the interaction of those proteins. Elucidating the structure of protein macromolecular assemblies is still more difficult. To that end, the use of computers to predict the structure of these complexes has gained interest over the last decades.<p>The main subject of this thesis is the evaluation of current available computational methods to predict protein – protein interactions and build an atomic model of the complex. The core of the thesis is the evaluation protocol I have developed at Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, and its computer implementation. This method has been massively used to evaluate the results on blind protein – protein interaction prediction in the context of the world-wide experiment CAPRI, which have been thoroughly reviewed in several publications [1-3]. In this experiment the structure of a protein complex (‘the target’) had to be modeled starting from the coordinates of the isolated molecules, prior to the release of the structure of the complex (this is commonly referred as ‘docking’).<p>The assessment protocol let us compute some parameters to rank docking models according to their quality, into 3 main categories: ‘Highly Accurate’, ‘Medium Accurate’, ‘Acceptable’ and ‘Incorrect’. The efficiency of our evaluation and ranking is clearly shown, even for borderline cases between categories. The correlation of the ranking parameters is analyzed further. In the same section where the evaluation protocol is presented, the ranking participants give to their predictions is also studied, since often, good solutions are not easily recognized among the pool of computer generated decoys.<p>An overview of the CAPRI results made per target structure and per participant regarding the computational method they used and the difficulty of the complex. Also in CAPRI there is a new ongoing experiment about scoring previously and anonymously generated models by other participants (the ‘Scoring’ experiment). Its promising results are also analyzed, in respect of the original CAPRI experiment. The Scoring experiment was a step towards the use of combine methods to predict the structure of protein – protein complexes. We discuss here its possible application to predict the structure of protein complexes, from a clustering study on the different results.<p>In the last chapter of the thesis, I present the preliminary results of an ongoing study on the conformational changes in protein structures upon complexation, as those rearrangements pose serious limitations to current computational methods predicting the structure protein complexes. Protein structures are classified according to the magnitude of its conformational re-arrangement and the involvement of interfaces and particular secondary structure elements is discussed. At the end of the chapter, some guidelines and future work is proposed to complete the survey. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The involvement of dynamical fluctuations in driving enzymatic processes is widely accepted. With respect to NQM tunnelling enzymes, the role of promoting motions in facilitating hydrogenic transfers is well studied. Few studies have however, specifically attributed, dedicated dynamical fluctuations characterised by their timescales and magnitudes, as a function of a reaction coordinate, to specific groups in a protein system. An effectively full suite of backbone resonance assignments were obtained for PETNR and on relevant ligand complexes. This provided an essential platform on which residue specific, backbone amide fluctuations were assessed. This thesis documents the application of pressure up to 1500 bar, in tandem with high resolution TROSY based NMR analysis, as a means of studying residue specific, conformer exchange perturbations. Residue specific amide compression profiles of the PETNR:FMN free enzyme system, and complexes with progesterone and tetrahydropyridine dinucleotides have been obtained. The binding of progesterone appears to induce conformational tightening of residues within the active site vicinity. The complexation of PETNR:FMN with tetrahydropyridine dinucleotides, appears to stimulate conformational shifts towards intermediate, and in some cases, slow exchange regimes in multiple residues about the active site vicinity. This is evidenced by extensive intensity attenuation of 1H-15N TROSY resonances, on the binding of tetrahydropyridine dinucleotides at 1 bar pressure, and on going from 1 bar to 1500 bar pressure. Multiple regions of sequence, spatially clustering about the active site vicinity within a 10 Å sphere of the FMN binding pocket, display appreciable sensitivity to ligand binding. Differential responses of residues to the application of high pressure between complexes was noted within segments of these regions. A region of sequence, named the β-hairpin flap displays significant differential compression profiles between the PETNR:FMN free enzyme system, and associated progesterone and tetrahydropyridine dinucleotide complexes. A role in mediating ligand engagement is proposed for R130 and R142 in the β-hairpin flap. A central hydrogen bonding network, perhaps constituting a putative proton wire in the active site of the PETNR:FMN:Progesterone complex, has been identified that could enable the shuttling of protons following catalytic protonation of oxidative substrate. The resonance response behaviour of G185 acts as a sensitive reporter on the formation of these interactions, revealed by an interrogation of the differences in chemical shift changes on progesterone binding, and in response to high pressure. The recruitment of high resolution crystallographic data sets readily supported a structural and dynamical interpretation of the observed chemical shift responses to ligand binding at 1 bar pressure, and on the application high pressure. A definitive atomistic identification of fast motion contribution to activation barrier compression was not obtained. Nevertheless, detailed, residue specific amide compression profiles, and shifts in backbone amide conformational exchange regimes in response to ground state ligand binding, and at high pressure, have been catalogued in the PETNR:FMN free enzyme system. These dynamical profiles in the free enzyme are contrasted against comparative, residue specific observations in analogue complexes of the oxidative and reductive half reactions of PETNR.

Here, we report on a new temperature responsive polymer brush system with a terminal “click” functionality. Bifunctionalized poly(N-isopropylacrylamide) (PNiPAAm) with distinct functional end groups was synthesized by atom transfer radical polymerization (ATRP) and grafted to a modified silicon substrate. The presence of the active terminal alkyne functionality is validated using an azide-modified rhodamine B (N3-RhB) via copper(I) catalyzed alkyne–azide cycloaddition (CuAAC). The optical properties and swelling dynamics of an N3-RhB modified PNiPAAm brush are analyzed in dry state and in situ by VIS-spectroscopic ellipsometry (SE). The best-fit results are obtained using a Gaussian oscillator model and are confirmed by UV/VIS-spectroscopy. We observed evidence of interactions between the aromatic residues of the dye and the PNiPAAm amide groups, which significantly affect the swelling behavior of the modified polymer brush. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

No description available.

Le travail de thèse consistera à explorer et caractériser l'ensemble conformationnel de protéines intrinsèquement désordonnées (IDPs) en utilisant plusieurs techniques complémentaires, notamment des simulations avancées de dynamique moléculaire et la diffusion des rayons X aux petits angles (SAXS). Les IDPs sont des protéines possédant une ou plusieurs régions n'ayant pas de structures secondaires stables lorsqu'elles sont isolées, mais pouvant en adopter lors de leur association avec de multiples autres protéines. La question, à laquelle ce travail souhaite répondre dans le cas de trois IDPs, est de savoir si ces éléments de structures secondaires, formés à l'interfaces des complexes protéine-protéine, pré-existent de façon transitoire, ou non, à l'état non-lié des IDPs en solution. S'il est possible d'identifier et de caractériser ces éléments de reconnaissance moléculaire dans les IDPs isolées, alors les résultats de ce travail permettront de guider par la suite la détermination des structures de complexes protéiques impliquant des IDPs. / The PhD work will consist in exploring and characterizing the conformational ensemble of intrinsically disordered proteins (IDPs), by using several complementary methods, including enhanced molecular dynamics simulations and small angle X-ray scattering (SAXS). IDPs are proteins having one or several regions that lack stable secondary structures in the unbound state, but which can adopt various structured conformations to bind other proteins. In the case of three IDPs, the project aims to answer the question of whether these secondary structures formed at the protein-protein interfaces transiently pre-exist or not in the unbound state of solvated IDPs. If it is possible to identify and characterize these molecular recognition features (MoRFs) in the IDP unbound state, then the results of this work will subsequently help to determine the structures of protein complexes involving IDPs.

Les récepteurs couplés aux protéines G (RCPGs) forment la plus grande et la plus diversifiée des familles de protéines localisées à la surface cellulaire et responsables de la transmission de signaux à l’intérieur des cellules. D’intenses recherches effectuées au cours des trente dernières années ont mené à l’identification de dizaines de protéines interagissant avec les RCPGs et contrôlant la signalisation, la désensibilisation, l’internalisation et la dégradation de ces importantes cibles pharmacologiques. Contrairement aux processus régulant l’activité des récepteurs à partir de la membrane plasmique, les mécanismes moléculaires contrôlant la biosynthèse des RCPGs dans le reticulum endoplasmique (RE) et leur transport jusqu’à la surface cellulaire sont très peu caractérisés. Une meilleure compréhension de ces processus nécessite l’identification de la machinerie protéique responsable de la maturation des RCPGs. Un crible protéomique basé sur le transfert d’énergie de résonance de bioluminescence (BRET), qui permet la mesure d’interactions protéiques dans les cellules vivantes, a mené à l’identification de plusieurs nouvelles protéines localisées dans la voie de sécrétion et interagissant potentiellement avec les RCPGs. Ces protéines étant localisées dans les compartiments cellulaires (reticulum endoplasmique et appareil de Golgi) responsables de la synthèse, du repliement adéquat et du transport à la membrane plasmique des récepteurs, il est très probable qu’elles soient impliquées dans le contrôle de l’expression des RCPGs à la surface cellulaire. La caractérisation de l’homologue humain de cornichon 4 (CNIH4), un nouvel intéracteur des RCPGs identifié dans le crible, a démontré que cette protéine localisée dans les compartiments précoces de la voie de sécrétion (RE et ERGIC) interagit de façon sélective avec les RCPGs. De plus, la suppression de l’expression endogène de cette protéine préalablement non-caractérisée, diminue le transport à la membrane plasmique d’un récepteur, indiquant que CNIH4 influence positivement l’export des RCPGs du RE. Ceci est supporté par l’observation que la surexpression de CNIH4 à de faibles niveaux favorise la maturation d’un récepteur mutant normalement retenu dans le RE. Nous avons également pu démontrer que CNIH4 est associée à la protéine Sec23, une des composantes de l’enveloppe des vésicules COPII qui sont responsables du transport des protéines du RE vers le Golgi, suggérant que CNIH4 pourrait favoriser le recrutement des récepteurs dans ces vésicules. La surexpression de CNIH4 à de très hauts niveaux provoque également la rétention intracellulaire des récepteurs. Cet effet dominant négatif pourrait être causé par la titration d’un autre facteur d’export des RCPGs. Une deuxième étude a permis de révéler que la protéine transmembranaire 9 (TMEM9), un nouvel intéracteur des RCPGs également identifié dans le crible, interagit sélectivement avec les récepteurs et avec CNIH4. La surexpression de cette protéine aux fonctions précédemment inconnues, rétablit le transport normal d’un récepteur en présence de CNIH4 surexprimée. De plus, la co-expression de TMEM9 potentialise la capacité de CNIH4 à augmenter la maturation d’un récepteur mutant normalement retenu dans le RE, suggérant que ces deux protéines forment un complexe régulant la maturation des RCPGs. Au cours de cette thèse, de nouvelles protéines interagissant avec les RCPGs et contrôlant leur expression à la membrane plasmique ont donc été identifiées, permettant une meilleure compréhension des mécanismes régulant le transport des récepteurs du RE à la surface cellulaire. / G protein coupled receptors (GPCR) form the largest and most diversified family of cell-surface receptors responsible for signal transduction inside the cells. Extensive research over the last thirty years have led to the identification of multiple proteins interacting with GPCRs and controlling the signalisation, desensitization, internalization and degradation of these important pharmaceutical targets. In contrast to the processes regulating GPCR activity at the plasma membrane, the molecular mechanisms controlling GPCR biogenesis in the endoplasmic reticulum (ER) and their transport to the cell-surface are poorly characterized. The identification of the proteins regulating GPCR maturation is essential in order to understand how receptors are expressed at the plasma membrane. A proteomic screen based on bioluminescence resonance energy transfer (BRET), which allows for the detection of protein-protein interaction in living cells, led to the identification of several potential novel GPCR interactors localized in the secretory pathway. Since the cellular compartments where these proteins are localized are responsible for the synthesis, proper folding and transport to the plasma membrane of the receptors, it is highly probable that they are involve in regulating GPCR cell-surface expression. The characterization of the human cornichon homolog 4 (CNIH4), a novel GPCR interactor identified in the screen, showed that this protein localized in the early secretory pathway (ER and ERGIC), selectively interacts with GPCRs. Knockdown of the endogenous expression of this previously uncharacterized protein led to a decrease in the cell-surface expression of a receptor indicating that CNIH4 has a positive function in the ER export of GPCR. Supporting this, over-expression of CNIH4 at low levels increased the maturation of a mutant receptor normally retained in the ER. Moreover, CNIH4 interacts with Sec23, a component of the inner coat of COPII vesicles which transport proteins from the ER to the Golgi apparatus, suggesting that CNIH4 could recruit GPCRs in these vesicles. CNIH4 over-expression at very high levels also resulted in the intracellular trapping of the receptors. This dominant negative effet could be caused by the titration of another component of the GPCR export process. Another study showed that the transmembrane protein 9 (TMEM9), a novel GPCR interactor also identified in the screen, selectively interacts with GPCRs and CNIH4. Over-expression of this protein of previously unknown function restored normal receptor trafficking in presence of over-expressed CNIH4. Morevover, co-expression of TMEM9 potentialized CNIH4 ability to increase the maturation of a mutant receptor normally retained in the ER, suggesting that these proteins form a complex regulating GPCR maturation. During this thesis, novel GPCR interacting proteins controlling receptor expression at the plasma membrane were identified, allowing for a better understanding of the mechanisms controlling receptor trafficking from the ER to the cell-surface.

No description available.

Le récepteur mélanocortine de type 4 (MC4R) est un récepteur couplé aux protéines G impliqué dans la régulation de la prise alimentaire et de l’homéostasie énergétique. Quatre-vingt pour cent des mutants du MC4R reliés à l’obésité morbide précoce (OMP) sont retenus à l’intérieur de la cellule. Le système de contrôle de qualité (SCQ) est probablement responsable de cette rétention, par la reconnaissance d’une conformation inadéquate des mutants. Le rétablissement de l’expression à la surface cellulaire et de la fonctionnalité de ces mutants est donc d’intérêt thérapeutique. Dans cette optique, des composés lipophiles spécifiques pour le MC4R ont été sélectionnés sur la base de leur sélectivité. Nous avons démontré qu’ils agissent à titre de chaperone pharmacologique (CP) en rétablissant l’expression à la surface cellulaire et la fonctionnalité des récepteurs mutants S58C et R165W, et qu’ils favorisent leur N-glycosylation complexe (maturation). Le suivi par BRET du site d’action des CP du MC4R suggère une action en aval de l’interaction calnexine-MC4R. De manière générale, une CP peut avoir un effet différent selon le mutant traité en induisant des conformations distinctes du récepteur plus ou moins aptes à se dissocier du SCQ et à activer la voie de signalisation, et un mutant peut répondre différemment selon la CP utilisée par des différences d’affinité pour le ligand, la CP et les effecteurs. Une meilleure compréhension du mode d’action des CP pourrait aider au développement de nouvelles approches thérapeutiques non seulement pour l’OMP, mais aussi pour d’autres maladies conformationnelles causées par le mauvais repliement de protéines. / The MC4R is a G-protein coupled receptor involved in the central regulation of food intake and energy homeostasis. Eighty percent of childhood obesity-related MC4R mutants are retained intracellularly, probably via the quality control system acting on misfolded receptors. Thus, rescuing cell surface targeting and functionality of these mutant receptors could be of therapeutic value. Cell permeable MC4R selective ligands have been tested and were able to restore cell surface expression and signalling activity of S58C and R165W MC4R mutants. Those compounds, according to their mode of action, are described as pharmacological chaperones (PC). The MC4R-PCs also helps to rescue the glycosylation pattern (maturation) of the MC4R mutants. The site of action of MC4R-PCs of the MC4R mutants monitored by BRET suggests an action downstream of the calnexin-MC4R interaction, most likely at the level of the Golgi apparatus. Generally, a CP can have different effects according to the mutant by stabilizing distinct conformations of the receptor that are more or less able to exit the quality control system and to activate the signaling pathway, and a mutant can respond differently according to the CP used by its distinct affinity to the ligand, the CP itself and the effectors. A better understanding of PCs’ mode of action could help in the design of novel therapeutic approaches not only for early-onset morbid obesity (EOMO) but also for other conformational diseases resulting from protein misfolding.

Les récepteurs couplés aux protéines G (RCPGs) forment la plus grande et la plus diversifiée des familles de protéines localisées à la surface cellulaire et responsables de la transmission de signaux à l’intérieur des cellules. D’intenses recherches effectuées au cours des trente dernières années ont mené à l’identification de dizaines de protéines interagissant avec les RCPGs et contrôlant la signalisation, la désensibilisation, l’internalisation et la dégradation de ces importantes cibles pharmacologiques. Contrairement aux processus régulant l’activité des récepteurs à partir de la membrane plasmique, les mécanismes moléculaires contrôlant la biosynthèse des RCPGs dans le reticulum endoplasmique (RE) et leur transport jusqu’à la surface cellulaire sont très peu caractérisés. Une meilleure compréhension de ces processus nécessite l’identification de la machinerie protéique responsable de la maturation des RCPGs. Un crible protéomique basé sur le transfert d’énergie de résonance de bioluminescence (BRET), qui permet la mesure d’interactions protéiques dans les cellules vivantes, a mené à l’identification de plusieurs nouvelles protéines localisées dans la voie de sécrétion et interagissant potentiellement avec les RCPGs. Ces protéines étant localisées dans les compartiments cellulaires (reticulum endoplasmique et appareil de Golgi) responsables de la synthèse, du repliement adéquat et du transport à la membrane plasmique des récepteurs, il est très probable qu’elles soient impliquées dans le contrôle de l’expression des RCPGs à la surface cellulaire. La caractérisation de l’homologue humain de cornichon 4 (CNIH4), un nouvel intéracteur des RCPGs identifié dans le crible, a démontré que cette protéine localisée dans les compartiments précoces de la voie de sécrétion (RE et ERGIC) interagit de façon sélective avec les RCPGs. De plus, la suppression de l’expression endogène de cette protéine préalablement non-caractérisée, diminue le transport à la membrane plasmique d’un récepteur, indiquant que CNIH4 influence positivement l’export des RCPGs du RE. Ceci est supporté par l’observation que la surexpression de CNIH4 à de faibles niveaux favorise la maturation d’un récepteur mutant normalement retenu dans le RE. Nous avons également pu démontrer que CNIH4 est associée à la protéine Sec23, une des composantes de l’enveloppe des vésicules COPII qui sont responsables du transport des protéines du RE vers le Golgi, suggérant que CNIH4 pourrait favoriser le recrutement des récepteurs dans ces vésicules. La surexpression de CNIH4 à de très hauts niveaux provoque également la rétention intracellulaire des récepteurs. Cet effet dominant négatif pourrait être causé par la titration d’un autre facteur d’export des RCPGs. Une deuxième étude a permis de révéler que la protéine transmembranaire 9 (TMEM9), un nouvel intéracteur des RCPGs également identifié dans le crible, interagit sélectivement avec les récepteurs et avec CNIH4. La surexpression de cette protéine aux fonctions précédemment inconnues, rétablit le transport normal d’un récepteur en présence de CNIH4 surexprimée. De plus, la co-expression de TMEM9 potentialise la capacité de CNIH4 à augmenter la maturation d’un récepteur mutant normalement retenu dans le RE, suggérant que ces deux protéines forment un complexe régulant la maturation des RCPGs. Au cours de cette thèse, de nouvelles protéines interagissant avec les RCPGs et contrôlant leur expression à la membrane plasmique ont donc été identifiées, permettant une meilleure compréhension des mécanismes régulant le transport des récepteurs du RE à la surface cellulaire. / G protein coupled receptors (GPCR) form the largest and most diversified family of cell-surface receptors responsible for signal transduction inside the cells. Extensive research over the last thirty years have led to the identification of multiple proteins interacting with GPCRs and controlling the signalisation, desensitization, internalization and degradation of these important pharmaceutical targets. In contrast to the processes regulating GPCR activity at the plasma membrane, the molecular mechanisms controlling GPCR biogenesis in the endoplasmic reticulum (ER) and their transport to the cell-surface are poorly characterized. The identification of the proteins regulating GPCR maturation is essential in order to understand how receptors are expressed at the plasma membrane. A proteomic screen based on bioluminescence resonance energy transfer (BRET), which allows for the detection of protein-protein interaction in living cells, led to the identification of several potential novel GPCR interactors localized in the secretory pathway. Since the cellular compartments where these proteins are localized are responsible for the synthesis, proper folding and transport to the plasma membrane of the receptors, it is highly probable that they are involve in regulating GPCR cell-surface expression. The characterization of the human cornichon homolog 4 (CNIH4), a novel GPCR interactor identified in the screen, showed that this protein localized in the early secretory pathway (ER and ERGIC), selectively interacts with GPCRs. Knockdown of the endogenous expression of this previously uncharacterized protein led to a decrease in the cell-surface expression of a receptor indicating that CNIH4 has a positive function in the ER export of GPCR. Supporting this, over-expression of CNIH4 at low levels increased the maturation of a mutant receptor normally retained in the ER. Moreover, CNIH4 interacts with Sec23, a component of the inner coat of COPII vesicles which transport proteins from the ER to the Golgi apparatus, suggesting that CNIH4 could recruit GPCRs in these vesicles. CNIH4 over-expression at very high levels also resulted in the intracellular trapping of the receptors. This dominant negative effet could be caused by the titration of another component of the GPCR export process. Another study showed that the transmembrane protein 9 (TMEM9), a novel GPCR interactor also identified in the screen, selectively interacts with GPCRs and CNIH4. Over-expression of this protein of previously unknown function restored normal receptor trafficking in presence of over-expressed CNIH4. Morevover, co-expression of TMEM9 potentialized CNIH4 ability to increase the maturation of a mutant receptor normally retained in the ER, suggesting that these proteins form a complex regulating GPCR maturation. During this thesis, novel GPCR interacting proteins controlling receptor expression at the plasma membrane were identified, allowing for a better understanding of the mechanisms controlling receptor trafficking from the ER to the cell-surface.