This project deals with the design and realisation of a set that will work as a power supply point with electricity generated from renewable energy sources. The theoretical part deals with information about renewable energy sources and energy storage options. In the practical part, a mobile kit for powering variable message traffic signs is designed. It uses photovoltaic panels and stores energy in a lead-acid battery. A methanol fuel cell is used for backup power. The device is adapted for use in road traffic and meets the requirements of the relevant authorities. To verify the stability of the structure, there were performed static calculations, which proved the ability of the device to withstand wind stress. Part of the work was to draw a complete production documentation, which was used to create a test sample. Long-term measurements of energy flows in the system were performed on that sample. These measurements confirmed the ability of the device to operate autonomously and the possibility of using it for the required purpose.

Cancer has been a pervasive and deadly problem for many years. No treatments have been developed that effectively destroy cancer cells while also keeping healthy cells safe. In this work, the knob-socket construct is used to analyze two systems involved in cancer pathways, the PDZ domain and the Bcl-BH3 complex. Application of the knob-socket model in mapping the packing surface topology (PST) allows a direct analysis of the residue groups important for peptide specificity and affinity in both of these systems. PDZ domains are regulatory proteins that bind the C-terminus of peptides involved in the signaling pathway of cancer progression. The domain includes five -strands, two -helices, and six coils/turns. In this study, the PST of all eight solved crystal structures of T-cell lymphoma invasion and metastasis 1 (Tiam1) PDZ domains are mapped to reveal details of ligand-domain binding pockets and packing interactions. Four main interactions were identified in the comparison of the PST maps and a consensus sequence was calculated using knob-socket interaction data. In the case of the Bcl-BH3 complex, binding of these two proteins prevents an unhealthy cell from undergoing apoptosis. In the knob-socket mapped protein-ligand interactions, the helical ligand consists of 8 to 10 residues that specifically interact with four helices on the binding protein: the N-terminus of Helix2, the main bodies of Helix3 and Helix4 and the C-terminus of Helix5. Among all of the interactions that were analyzed, there were three amino acids from the ligand, glycine, leucine, and isoleucine, that always packed into the hydrophobic groove that is key for ligand recognition. By using knob-socket analysis to map quaternary packing structure, it was possible to identify the quaternary-level protein interactions that define ligand specificity and binding strength. From this analysis, possible protein mimetics can be developed that could be used as cancer treatments.

No description available.

No description available.

Die tight junction schränken die Diffusion durch den parazellulären Raum in Epithel- und Endothelzellschichten für viele Moleküle stark ein. Dadurch behindern sie die Aufnahme von wasserlöslichen Medikamenten in das dahinterliegende Gewebe. Zwei Proteine, die am tight junction Aufbau mitwirken, sind Zonula Occludens Protein 1 (ZO-1) und Occludin. Eine Öffnung der tight junctions stellt eine Möglichkeit für die Verabreichung von Medikamenten dar. Deshalb wurden die tight junction Proteine ZO-1 und Occludin auf ihre Funktion, Struktur und Regulation untersucht. Für die Interaktion beider Proteine gab es ein Modell, welches eine Oligomerisierung der Bindungspartner als Voraussetzung ihrer Interaktion über helikale Wechselwirkungen vorhersagte. Die Annahmen aus dem Modell der Interaktion von ZO-1 und Occludin konnten experimentell bestätigt werden. Für den C-Terminus von Occludin wurde darüber hinaus eine Interaktion über Disulfidbrücken nachgewiesen. Diese Interaktion könnte in der Zelle von pathologischer Bedeutung bei Schlaganfall und Ischchämie sein. Beide Erkrankungen verursachen eine Öffnung der tight junction im Zusammenhang mit oxidativem Stress. ZO-1 bindet über PDZ Domänen eine Vielzahl von tight junction Proteinen, die an der Abdichtung des parazellulären Raums beteiligt sind. Deshalb wurde die Interaktion und Regulation der PDZ-Domänen aus ZO-1 untersucht. Eine Phosphorylierung der PDZ durch die Proteinkinase C alpha sowie eine Interaktion mit den Phosphatasen 2A und 4 konnte nachgewiesen werden. In vitro konnte gezeigt werden, dass die Phosphorylierung der PDZ-Domänen die Bindung an Membranproteine der tight junction beeinflusst. Diese Arbeit leistet einen Beitrag, die Mechanismen, die zum Verschluss des parazellulären Spaltes führen, aufzuklären. Damit zeigt sie Ansatzpunkte für eine pharmakologische Beeinflussung der Permeabilität der tight junction auf. / Tight junctions restrict diffusion through the paracellular gap in endothelia and epithelia. Thereby they constrain the uptake of water soluble drugs to the tissue. Zonula occludens protein 1 (ZO-1) and occludin are some of proteins involved in tight junction assembly. The opening of tight junctions is a possibility to apply drugs. Therefore the structure, function and regulation of ZO-1 and occludin is characterised. In previous studies, a model predicted the interaction of occludin and ZO-1 through helices. It was proposed that the interaction is mediated by oligomers of ZO-1 and Occludin. This author´s experimental research supports these hypotheses. Furthermore, occludin is shown to self assemble via disulfide bridges. This interaction could be of importance during stroke and ischemia. Both diseases cause the opening of tight junctions in combination with oxidative stress. In addition, this author investigated the interaction and regulation of the PDZ domains of ZO-1. It was shown that the PDZ domains are phosphorylated by protein kinase C alpha and interact with protein phosphatases 2A and 4. Phosphorylation led to a reduction in affinity of PDZ to membrane proteins in vitro. This thesis contributes to the understanding of the mechanisms which are involved in the sealing of the paracellular gap.

Les papillomavirus humains (HPV) constituent l’archétype des virus à ADN oncogènes. Les HPV muqueux à haut risque (principalement HPV16) sont les principaux agents étiologiques du cancer du col utérin. Les protéines virales E6 et E7 sont des acteurs cruciaux de la cancérogenèse induite par HPV. Nous avons construit une ressource composée de 600 ADNc codant les effecteurs humains du système ubiquitine-protéasome (UPS) et identifié de nouvelles cibles potentielles des protéines E6 et E7 en utilisant une méthode basée sur la complémentation protéique de la Gaussia princeps luciférase (GPCA). HPV16 E6 lie les motifs LxxLL présents dans E6AP et IRF3. Nous avons résolu la structure cristallographique des complexes E6/LxxLL de E6AP/p53 et E6/LxxLL de IRF3. Par ailleurs, nous avons montré que les HPV ciblent une nouvelle voie suppresseur de tumeurs, la voie Hippo, avec ses deux médiateurs clef YAP et TAZ. Nous avons généré une banque d’ADNc codant 265 domaines PDZ humains et identifié de nouveaux partenaires potentiels des protéines YAP/TAZ en utilisant la méthode GPCA. Les résultats obtenus permettent de mieux comprendre la biologie des HPV et leur pouvoir oncogène. / The human papillomavirus (HPVs) are the archetype of DNA oncogenic viruses. High-risk mucosal HPVs (mainly HPV16) are the main causative agents of cervical cancer and are also involved in other cancers. HPV oncogenic properties are mainly due to the expression of E6 and E7 proteins. We built a resource composed of 600 cDNA encoding the human ubiquitin-proteasome system (UPS) effectors and identified novel E6 and E7 potential targets by using a method based on the complementation of the Gaussia princeps luciferase (GPCA). HPV16 E6 binds to specific LxxLL motifs present in E6AP and IRF3. We have solved the crystallographic structure of the E6/E6AP LxxLL/p53 and E6/IRF3 LxxLL complexes. Furthermore, HPV may target a novel tumour suppressor pathway, the Hippo signalling pathway with its two main mediators YAP and TAZ. We have built a cDNA library dedicated to the 265 human PDZ domains and identified news potential partners of YAP and TAZ proteins by using the GPCA. The results provide novel insights on HPV biology and their oncogenic property.

Les interactions protéine-protéine (IPPs) médient la signalisation cellulaire. Leur ingénierie peut fournir des informations et conduire au développement de molécules thérapeutiques. Les domaines PDZ sont des médiateurs importants de IPPs. Elles lient les 4--10 résidus C-terminaux de protéines cibles. Elles lient aussi les peptides correspondants, qui peuvent servir de systèmes modèles ou d'inhibiteurs. Nous avons développé deux approches computationnelles et les avons appliquées au domaine PDZ de la protéine Tiam1, un facteur d'échange pour la protéine Rac, impliqué dans la protrusion neuronale. Sa cible est la protéine Syndecan1. Des affinités expérimentales sont connues pour le peptide C-terminal, noté Sdc1, et plusieurs mutants; elles ont servi pour tester les calculs. Nous avons d'abord développé une méthode de dessin computationnel haut débit. Une simulation Monte Carlo est faite où les chaines latérales de la protéine et du peptide peuvent changer de conformères et certaines positions peuvent muter. Le solvant est implicite. Le paysage énergétique est aplati par la méthode adaptative de Wang-Landau, de sorte qu'un vaste ensemble de variantes est échantillonné. Effectuant des simulations distinctes du complexe et du peptide seul nous avons obtenu les énergies libres relatives d'association de 75,000 variantes en heure CPU sur une machine de bureau. Les valeurs sont compatibles avec les quelques données expérimentales disponibles. Ensuite, nous avons développé une approche beaucoup plus détaillée et réaliste. Soluté et solvant sont décrits par un champ de force atomique, qui représente explicitement la polarisation électronique: le champ de force Drude de Charmm. La polarisabilité peut être importante car les résidus de l'interface PDZ:peptide passent, lors de l'association, d'un environnement riche en solvant à un autre pauvre en solvant. Nous avons fait des simulations alchimiques d'énergie libre pour comparer quatre variantes du peptide qui diffèrent par une ou deux chaines latérales ioniques. Les résultats sont en bon accord avec l'expérience. Les champs de force additifs Charmm et Amber, qui représentent la polarisabilité implicitement, donnent un moins bon accord. Ces calculs sont le premier exemple de simulations alchimiques d'énergies libre d'association relatives protéine: ligand avec un champ de force polarisable. Enfin, pour une modélisation future de peptides phosphorylés, nous avons étendu le champ de force Drude pour inclure le méthyl phosphate et la phospho tyrosine. Il en résulte un excellent accord avec les affinités expérimentales phosphate: magnésium. / Protein-protein interactions (PPIs) regulate complex signaling networks in eukaryotic cells. Many binding events between several protein domains transfer information through communication pathways. Disrupting or altering the equilibrium between PPIs plays an important role inseveral diseases and the inibition of targeted PPIs is a recognized strategy for computational drug design. In the present thesis we focused on PDZ domains, which are among the most widespread signaling domains. PDZs recognize the 4-10 C-terminal amino acids of their target proteins as well as the corresponding peptides in isolation. We studied PDZ:peptide binding for the Tiam1 protein, which is a Rac GTP exchange factor involved in neuronal protrusion and axon guidance. Tiam1 activity modulates signaling for cell proliferation and migration, whose dysregulation increases growth of metastatic cancers. Its natural binder peptide is Syndecan1 (Sdc1), composed of 8 amino acids. Its last 5 Cter residues drive interactions in the binding pocket. Experimental affinities for several mutants of Sdc1 and in the protein domain constitute a complete dataset to study many ionic interactions with molecular simulations. These calculations are still challenging, despite the dramatic improvement of biomolecular modelling in the 1990's and 2000's. Upon binding, residues are transferred from a solvent-exposed environment to a solvent-poor one. This is expected to change the electron distribution within residues and nearby solvent molecules. Comparing ligands that differ by one or more ionic side-chain mutations, more sophisticated force fields where electronic polarizability is treated explicitly may be required. We developed and tested both Computational Protein Design (CPD) models and more precise free energy calculation methods based on polarizable molecular dynamics. We developed a general, high-througtput CPD protocol to optimize protein:peptide binding. The model has been implemented in on our in-house CPD package Proteus ( Simonson et al, 2014) and has been tested computing relative binding affinities for many variants of the Tiam1:Sdc1 complex. Monte Carlo sampling of equilibrium distributions of protein sequences is performed using an adaptive bias potential which flattens the energy landscape in sequence space and allows to estimate binding affinities for thousands of protein variants in limited CPU time (~1hour). We also improved our CPD implicit solvent model, implementing a more realistic description of the solute-solvent dielectric boundary. The new method, called Fluctuating Dielectric Boundary (FDB) showed a systematic improvement in the prediction of acid:base constants of several proteins. Promising results were also obtained for the complete sequence redesign of three PDZ domains. In the second part of this work we studied Tiam1:peptide affinities with more sophisticated models, based on free energy simulations with the Drude Polarizable Force field (DrudeFF). We first computed relative binding free energies for charge mutations in the Tiam1:Sdc1 complex, obtaining a clear improvement respect to equivalent calculations performed using two additive force fields. We applied the well-enstablished Dual Topology Approach: to our knowledge, this was the first example of such a calculation for a protein:peptide complex with uses the DrudeFF. Then we went on, developing the Drude polarizable models for methyl phosphate (MP) and phospho tyrosine (pTyr). We were interested in the change in binding affinity associated with phosphorylation of a Tyrosine residue of Sdc1, but Drude pTyr parameters were not yet developed. We tested our new phosphate parameters studying standard binding free energies between MP and magnesium (Mg2+) in water solution. Results showed a good agreement with experiment, improving previous calculations performed using additive force field

The chloride/proton antiporter ClC-5 is primarily expressed in the kidney where it aids in re-absorption of proteins from the glomerular filtrate. Functional disruption of ClC-5 causes Dent’s Disease – a renal condition characterized by proteinuria and kidney failure in a third of all cases. The majority of disease-causing mutations translate into premature truncations of the carboxy-terminal (Ct) region of ClC-5 and are predicted to disrupt the protein-protein interactions mediated by this domain. In this thesis, direct ATP binding to the two cystathionine β-synthase (CBS) domains of ClC-5 was demonstrated. ATP binding enhanced the global compactness of the ClC-5 Ct region likely through a clamping motion of the CBS domains around the nucleotide. Along with ATP, the sodium proton exchange regulatory factor 2 (NHERF2) also binds ClC-5; however, the molecular mechanism behind this interaction was unknown as ClC-5 lacked the PDZ binding motif traditionally localized at the Ct end of bait proteins. Here, we also identified a class I PDZ binding motif (657-660; TSII) within the internal sequence of ClC-5. Despite the buried position of this motif in the Ct peptide’s X-ray crystal structure (PDB: 2J9L), the high propensity of this region for dynamic flexibility prompted us to test whether it could mediate NHERF2 interactions. In support of this hypothesis, we demonstrated that the motif is transiently available to interact directly with NHERF2 in vivo and to enable an enhancement in receptor-mediated endocytosis in mammalian cells. Collectively, these results gave further evidence that the intracellular Ct region of ClC-5 serves as a hub to mediate interactions essential for its maturation, stability, and trafficking in renal epithelium, as well as providing further insights into the molecular basis of Dent’s Disease.

Fetal pancreatic tissues can be a promising source for pancreatic progenitor cells (PPCs). In this regard, we have successfully isolated and characterized a population of fetal PPCs from first trimester human fetal pancreas using a previously established basic protocol. Upon exposure to a cocktail of conventional growth factors, these PPCs are amenable to differentiate into insulin-secreting islet-like cell clusters (ICCs); however, these ICCs have yet to exert additional efforts to direct to glucose-responsive cells. To address this issue, we have proposed two novel morphogenic factors in the present study, namely PDZ-domain-containing 2 (PDZD2) and angiotensin II (Ang II), a physiologically active peptide of the renin-angiotensin system (RAS), that potentially promote the differentiation and maturation of PPCs/ICCs. / In light of these findings, we conclude that we have discovered two novel mechanisms, the PDZD2 and Ang II/AT2 receptor signaling pathways, in the regulation of the development of PPCs/ICCs, thus implying their novel roles during islet development in vivo. The present study provides a "proof-of-principle" that a local RAS is critically involved in governing islet cell development. This work may contribute to devising protocols for maturation of pancreatic progenitors for clinical islet transplantation. / Local RASs have been reported to regulate the differentiation of tissue progenitor cells. It has yet to be confirmed whether such systems exist and govern the PPC development. To address this issue, we herein provided evidence that expression of RAS components was highly regulated throughout PPC differentiation. Locally generated Ang II was found to maintain PPC growth and differentiation via mediation of the Ang II type 1 and type 2 (AT1 and AT 2) receptors. We found that the AT2, but not AT1, receptor was a key mediator of Ang II-induced upregulation of beta-cell transcription factors. Transplantation of AT2 receptor-depleted ICCs into immune-privileged diabetic mice failed to ameliorate hyperglycemia, implying that AT2 receptors are indispensable during ICC maturation in vivo. / PDZD2 and its secreted form (sPDZD2) have been found to express in our fetal PPCs. We first evaluated the potential role of sPDZD2 in stimulating PPC differentiation and established an optimal concentration for such stimulation. We found that 10-9 M sPDZD2 promoted PPC differentiation, as evidenced by the up-regulation of the pancreatic endocrine markers and C-peptide content in the ICCs. It enhanced their expression of the L-type voltage-gated calcium ion channel (Cav1.2) and conferred an ability to secrete insulin in response to membrane depolarization. Yet these ICCs remained glucose-unresponsive because of the minimal expression of GLUT-2. We thus attempted to study another potential morphogenic candidate, Ang II. / To further test whether a functional RAS is present and if so, whether it regulates islet development in vivo, we employed a mouse embryo model at different embryonic days and reported a stronger AT2 receptor expression during the 2nd developmental transition of pancreas development. AT2 receptor blockade from e8.0 resulted in abnormalities in fetal pancreatic development. Neonates from these mother mice displayed destructed pancreas/islet architecture, a hampered ability in glucose-stimulated insulin-secretion possibly attributed to a decreased ratio of beta-cell to alpha-cell, and an impaired glucose tolerance at 4-wk old. / Leung, Kwan Keung. / Adviser: Po Sing Leung. / Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 254-284). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Même si le docking protéine-protéine devient un outil incontournable pour répondre aux problématiques biologiques actuelles, il reste cependant deux difficultés inhérentes aux méthodes actuelles: 1) la majorité de ces méthodes ne considère pas les possibles déformations internes des protéines durant leur association. 2) Il n'est pas toujours simple de traduire les informations issues de la littérature ou d'expérimentations en contraintes intégrables aux programmes de docking. Nous avons donc tenté de développer une approche permettant d'améliorer les programmes de docking existants. Pour cela nous nous sommes inspirés des méthodologies mises en place sur des cas concrets traités durant cette thèse. D'abord, à travers la création du complexe ERBIN PDZ/Smad3 MH2, nous avons pu tester l'utilité de la Dynamique Moléculaire en Solvant Explicite (DMSE) pour mettre en évidence des résidus importants pour l'interaction. Puis, nous avons étendu cette recherche en utilisant divers serveurs de docking puis la DMSE pour cibler un résultat consensus. Enfin, nous avons essayé le raffinage par DMSE sur une cible du challenge CAPRI et comparé les résultats avec des simulations courtes de Monte-Carlo. La dernière partie de cette thèse portait sur le développement d'un nouvel outil de visualisation de la surface moléculaire. Ce programme, nommé MetaMol, permet de visualiser un nouveau type de surface moléculaire: la Skin Surface Moléculaire. La distribution des calculs à la fois sur le processeur de l'ordinateur (CPU) et sur ceux de la carte graphique (GPU) entraine une diminution des temps de calcul autorisant la visualisation, en temps réel, des déformations de la surface moléculaire.