<p>Stabilization of proteins is of great interest for the biotechnological society, industrial as well as research areas. Proteins with high stability are more suitable as reagents, easier to handle, store, transport and use in industrial processes. One way to stabilize a protein is to introduce a disulfide bridge into the structure by protein engineering. In this report the formation of a disulfide bridge between engineered cysteines in non ideal conformations in human carbonic anhydrase has been investigated. The disulfide bridge is not formed when the protein is in its native state. It is shown that when the protein is exposed to mild concentrations of urea in the presence of DTTox the disulfide bridge is formed. Also upon refolding in vitro, in a non oxidative environment, disulfide bridges are formed. This observation is worth to notice, since the disulfide bridge does not form to any appreciable extent when the protein is expressed and folded in vivo in Escherichia coli.</p>

Stabilization of proteins is of great interest for the biotechnological society, industrial as well as research areas. Proteins with high stability are more suitable as reagents, easier to handle, store, transport and use in industrial processes. One way to stabilize a protein is to introduce a disulfide bridge into the structure by protein engineering. In this report the formation of a disulfide bridge between engineered cysteines in non ideal conformations in human carbonic anhydrase has been investigated. The disulfide bridge is not formed when the protein is in its native state. It is shown that when the protein is exposed to mild concentrations of urea in the presence of DTTox the disulfide bridge is formed. Also upon refolding in vitro, in a non oxidative environment, disulfide bridges are formed. This observation is worth to notice, since the disulfide bridge does not form to any appreciable extent when the protein is expressed and folded in vivo in Escherichia coli.

Proteins are substances with great usage. For industrial usage, proteins are often taken from their natural enviroment. In foreign environment, it proteins can unfold and their function can be compromised. This is the reason for stabilization of proteins and one of ways to stabilization is using disulphide bonds. This work describes basic terms related to protein stabilization - proteins, their structure and interactions within them, basic terms from thermodynamics. Problem of protein stability is discussed and the factors which stabilize or destabilize protein are enumerated with the emphasis on disulphide bonds. Existing approaches to disulphide bonds design, dataset for testing own tool are described. Implementation of the tool using geometrical properties of the bonds and fl exibility of places in protein is described. The tool was tested on proteins with native disulfide bonds and compared to existing tools, also metrics FRO (fractional rank order) was used. Native disulfide bond was found in 64 % of cases, in 60 % of cases this native disulfi de bond was in the first quarter of ordered found disulfi de bonds.

Les ARNs sont impliqués dans de nombreux processus biologiques et peuvent adopter des structures secondaires différentes. Par leurs propriétés, ils constituent des outils biologiques puissants pour des applications diverses, tels les ARNs interférents (siARN) qui permettent l’extinction de l’expression des gènes par exemple. L’introduction de modifications sur des ARNs s’est avérée essentielle pour améliorer leurs propriétés et faciliter l’étude de leurs rôles biologiques et leurs applications thérapeutiques.Ce manuscrit rapporte la synthèse et les propriétés d’ARNs modifiés en position 2’ du ribose par des groupements contenant des ponts disulfures, sensibles à un environnement réducteur.Dans la première partie, la synthèse de prodrogues de siARNs partiellement modifiés par des groupements benzyldithiométhyles est décrite. Leurs stabilités thermiques et enzymatiques, ainsi que leur démasquage en milieu réducteur, sont montrés. Les résultats prometteurs d’activité inhibitrice et de pénétration cellulaire, sur une lignée cellulaire du sarcome d’Ewing, permettent d'envisager une application potentielle de ces siARNs modifiés comme outils thérapeutiques.La deuxième partie décrit une approche de co-délivrance par des siARNs couplés avec une drogue anticancéreuse, la doxorubicine, via un lien auto-immolable contenant des ponts disulfures. Les propriétés physico-chimiques des conjugués sont déterminées, et la libération du siARN et de la drogue en milieu réducteur est mise en évidence.La troisième partie présente une autre méthode de conjugaison en solution entre la position 2’ d’un ARN et des petites molécules (sucres, coumarine, biotine, acide désoxycholique, glutathion) via un pont disulfure. La synthèse des ARNs conjugués et leur devenir en milieu réducteur sont décrits.Dans la dernière partie, l’impact d’un lien avec un pont disulfure intrabrin entre les positions 2’ de deux nucléotides adjacents est étudié dans un duplex ou la partie boucle d’hairpins. L’influence du pont disulfure sur l’équilibre des conformations duplex et hairpin d’un ARN d’intérêt biologique est évaluée, en absence et en présence d’agents réducteurs. Une application en fluorescence d’une hairpin contrainte en tant que « molecular beacon » montre des utilisations potentielles de ce lien dans des outils pour étudier la conformation de structures secondaires d’ARNs ou dans des sondes pour détecter les agents réducteurs. / RNAs are involved in numerous biological processes and can adopt different secondary structures. Thanks to their properties, they are powerful biological tools for diverse applications, such as small interfering RNA (siRNA) for gene silencing. Modified RNAs have proven to be essential to improve their properties, and to facilitate the study of their biological and therapeutic functions.This manuscript reports the synthesis and properties of 2’-O-modified RNAs bearing disulfide-containing groups, sensitive to reductive environment.The first part describes the synthesis of siRNAs prodrugs bearing lipophilic benzyldithiomethyl groups. The thermal stability, the serum stability and the response to glutathione treatment of modified siRNAs are thoroughly investigated. The gene silencing and the gymnotic delivery of several siRNAs are assessed, and demonstrates promising results on Ewing’s sarcoma cell line.A second part concerns the co-delivery of siRNAs and a hydrophobic anti-cancer drug (doxorubicin) using a self-immolative spacer bearing disulfide bonds. The chemico-physical properties of these conjugates are determined and the recovery of native siRNA and doxorubicin in response to reductive treatment is highlighted.A third part presents the conjugation of RNAs to small molecules (sugars, coumarin, biotin, deoxycholic acid, glutathione) using disulfide linkages. The synthesis of the RNA conjugates and their release in reducing conditions are also demonstrated.The last part reports the synthesis and the impact of an intrastrand dimethylene disulfide bridge between 2’-O-positions of two adjacent nucleotides in an RNA duplex and in the loop of RNA hairpins. Then, the influence of this linkage on the folding of a biologically relevant RNA structure is reported. Finally, an application of a constrained hairpin as a fluorescent molecular beacon highlights its potential use in tools for understanding RNA folding and in probes for the detection of reducing reagents

Elevated reaction temperatures are crucial for the efficient enzymatic degradation of polyethylene terephthalate (PET). A disulfide bridge was introduced to the polyester hydrolase TfCut2 to substitute its calcium binding site. The melting point of the resulting variant increased to 94.7°C (wild-type TfCut2: 69.8 °C) and its half-inactivation temperature to 84.6 °C (TfCut2: 67.3 °C). The variant D204C-E253C-D174R obtained by introducing further mutations at vicinal residues showed a temperature optimum between 75 and 80 °C compared to 65 and 70 °C of the wild-type enzyme. The variant caused a weight loss of PET films of 25.0 +/- 0.8% (TfCut2: 0.3 +/-0.1%) at 70 °C after a reaction time of 48 h. The results demonstrate that a highly efficient and calcium-independent thermostable polyester hydrolase can be obtained by replacing its calcium binding site with a disulfide bridge.

L’albumine sérique humaine (HSA) est une protéine connue pour ses propriétés de transport exceptionnelles et son contenu élevé en ponts disulfure. L’étude de sa dynamique conformationnelle représente un défi important dans la compréhension de ses fonctions physiologiques. Le but de notre travail a été d’étudier cette dynamique conformationnelle et de comprendre le rôle des ponts disulfure dans le maintien de la structure native de la protéine. Notre analyse est basée sur des simulations de dynamique moléculaire couplées à des analyses par composantes principales. Outre la validation de la méthode de simulation les résultats fournissent de nouveaux éclairages sur les principaux effets de la réduction des ponts disulfure dans les albumines sériques. Les processus de dépliement/repliement protéique ont été détaillés. La prédiction de la structure réduite d’équilibre a également fait l’objet d’une attention particulière. Une étude détaillée de la dynamique conformationnelle globale de la protéine ainsi que celle des deux sites principaux de complexation a été effectuée. D’éventuels effets allostériques entre ces deux sites ont été recherchés. Les résultats théoriques obtenus ont été discutés avec les données expérimentales disponibles / Human serum albumin (HSA) is a protein known for its exceptional transport properties and its high content of disulfide bridges. The study of the conformational dynamics represents a major challenge in the comprehension of its physiological functions. The aim of our work was to study the conformational dynamics and to understand the roleof disulfide bonds in the stability of the native protein structure. Our analysis is based on simulations of molecular dynamics coupled with principal component analysis. Beyond the validation of the simulation method, the results provide new insights on the main effects of the disulfide bonds reduction in serum albumins. Protein unfolding/refolding processes were detailed. A special attention is paid to the prediction of the reduced structure at the equilibrium. A detailed study of the global protein conformational dynamics as well as the two main binding sites were performed. Possible allosteric effects between these two sites were researched. The theoretical results have been discussed with the available experimental data

Moléculas de L-cisteína (CSH) e L-glutationa (GSH) foram ancoradas na superfície de eletrodos de ouro, previamente modificados com uma camada autoarranjada de ácido 3-mercaptopropiônico (MPA). Esta arquitetura molecular foi importante para preservar a atividade redox dos grupos tiólicos da CSH e GSH na interface eletrodo/solução. A identificação do par redox R-S-S-R/R-SH, bem como a determinação do pKa dos grupos -SH superficiais, foram efetuadas usando voltametria cíclica em soluções de eletrólito em diferentes pH contedo ferricianeto de potássio. A presença dos grupos -SH e -S-S- na superfície dos eletrodos modificados foi ainda confirmada por Espectroscopia Raman de Superfície. Determinaram-se as constantes de velocidade de transferência de carga do processo quase reversível R-S-S-R / R-SH. Estes eletrodos modificados apresentaram resposta eletrocatalítica para a redução de espécies reativas de oxigênio (ROS), como peróxido de hidrogênio e para a oxidação de compostos com atividade antioxidante como a quercetina. Demonstrou-se que a presença de íons Cu2+ na superfície destes eletrodos é capaz de deslocar o equilíbrio do par R-SS-R/R-SH, no sentido oxidativo. Métodos de quantificação para estes compostos foram desenvolvidos por amperometria hidrodinâmica e voltametria cíclica. / L-cysteine molecules (CSH) and L-glutathione (GSH) were anchored on the surface of gold electrodes, previously modified with a self assembled monolayer of 3-mercaptopropionic acid (MPA). This molecular architecture was important to preserve the redox properties of the thiol groups of CSH and GSH in the interface electrode / solution. The identification of the redox couple RSSR / R-SH and the determination of the pKa of -SH groups surface were made using cyclic voltammetry in electrolyte solutions at different pH contents potassium ferricyanide. The presence of the -SH and -SS- modified electrode surface was further confirmed by Raman spectroscopy of surface. It was determined the rate constants of direct electron transfer of quasi-reversible coupled R-SS-R/R-SH. The modified electrodes showed electrocatalytic response to the reduction of reactive oxygen species (ROS) such as hydrogen peroxide and the oxidation of compounds with antioxidant activity such as quercetin. It was demonstrated that presence of Cu2+ ions on the electrode surface can shift the equilibrium of the RSSR/R-SH redox coupled into oxidative direction. Hydrogen peroxide and Quercetin were detected at these modified electrodes using amperometry and hydrodynamic cyclic voltammetry.

Wachstumshormon (GH) besteht aus 191 Aminosäuren, hat eine Molekülmasse von 22kD und ist essentiell für postnatales Wachstum. Es wird aus der Adenohypophyse freigesetzt. GH bindet an einen GH-Rezeptor (GHR) und aktiviert somit über intrazelluläre Signalvorgänge Zielgene, insbesondere das, welches für die Kodierung von insulin-like growth factor (IGF-1) zuständig ist. IGF-1 vermittelt den Großteil aller GH-Signale. Zusammen mit den bereits bekannten GH Mutanten R77C und D112G ist in dieser Studie der neue GH Mutant d188-190 charakterisiert worden. Alle drei Mutanten wurden in heterozygoter Form in kleinwüchsigen Patienten identifiziert. Diesen Patientendaten zu Folge schien es möglich, dass d188-190 eine GH-antagonistische Wirkung besitzt. Zusätzlich wurde die extrem konservierte C-terminale Disulfidbrücke des GH im Mutanten d188-190 unterbrochen vorgefunden. Die Auswirkung der Unterbrechung wurde durch Substitution einer oder beider involvierter Cysteine durch Alanine untersucht. Alle Mutanten und Wildtypen des GH wurden in menschlichen embryonalen Nierenzellen (HEK-293) angezüchtet und eine Reihe von in vitro Experimenten sind für deren Charakterisierung etabliert worden. Es zeigte sich, dass d188-190 keine GH-antagonistische Wirkung besitzt. Im Vergleich zum Wildtyp weist der Mutant eine verminderte Bindungsaffinität zu GH, schwächere biologische Aktivität und höhere Stabilität auf. R77C und D112G sind dem Wildtyp GH sehr ähnlich. Die Disulfidbrücke ist wichtig für die Rezeptorbindung und für die biologische Aktivität von GH. Wenn ein Cystein entfernt wird vermindert sich die Stabilität des Moleküls. Dieser Effekt kann durch Entfernen des zweiten Cysteins wieder rückgängig gemacht werden. Die in dieser Studie etablierten Experimente können Verwendung finden in der Charakterisierung bislang nicht bekannter GH Mutanten und können darüber hinaus zur Behandlung von Patienten eingesetzt werden. / Growth hormone (GH) is a 22 kD, 191-aa, pituitary-derived peptide hormone that is essential for postnatal growth. GH signals via binding to GH receptor (GHR), which initiates intracellular signal transduction pathways. This leads to activation of target genes, most importantly the one encoding insulin-like growth factor (IGF)-1, which mediates most GH action. In this study a novel GH mutant, d188-190, was characterized along with previously reported GH mutants R77C and D112G. All of these mutants had been identified in heterozygous form in patients with retarded growth. Based on patient data, d188-190 was thought to be a GHR antagonist. Moreover, the extremely conserved C-terminal disulfide bridge of GH was disrupted in mutant d188-190 and its role was studied by substituting one or both of the involved cysteines with alanines. All mutants and wild type (wt) GH were produced in human embryonic kidney (HEK)-293 cells and an array of in vitro experiments was established for their characterization. It turned out that the novel d188-190 mutant is not a GHR antagonist after all. It has a diminished binding affinity to GHR, low biological activity and high stability compared to wt GH. R77C and D112G are rather similar to wt GH. The disulfide bridge is important for receptor binding and biological activity of GH. If one of the cysteines is removed the stability of the molecule drops but this can be reversed by removing both cysteines. If further GH mutants are to be identified, the established array of experiments will be useful for their fast characterization and could even contribute to correct treatment of patients.

Moléculas de L-cisteína (CSH) e L-glutationa (GSH) foram ancoradas na superfície de eletrodos de ouro, previamente modificados com uma camada autoarranjada de ácido 3-mercaptopropiônico (MPA). Esta arquitetura molecular foi importante para preservar a atividade redox dos grupos tiólicos da CSH e GSH na interface eletrodo/solução. A identificação do par redox R-S-S-R/R-SH, bem como a determinação do pKa dos grupos -SH superficiais, foram efetuadas usando voltametria cíclica em soluções de eletrólito em diferentes pH contedo ferricianeto de potássio. A presença dos grupos -SH e -S-S- na superfície dos eletrodos modificados foi ainda confirmada por Espectroscopia Raman de Superfície. Determinaram-se as constantes de velocidade de transferência de carga do processo quase reversível R-S-S-R / R-SH. Estes eletrodos modificados apresentaram resposta eletrocatalítica para a redução de espécies reativas de oxigênio (ROS), como peróxido de hidrogênio e para a oxidação de compostos com atividade antioxidante como a quercetina. Demonstrou-se que a presença de íons Cu2+ na superfície destes eletrodos é capaz de deslocar o equilíbrio do par R-SS-R/R-SH, no sentido oxidativo. Métodos de quantificação para estes compostos foram desenvolvidos por amperometria hidrodinâmica e voltametria cíclica. / L-cysteine molecules (CSH) and L-glutathione (GSH) were anchored on the surface of gold electrodes, previously modified with a self assembled monolayer of 3-mercaptopropionic acid (MPA). This molecular architecture was important to preserve the redox properties of the thiol groups of CSH and GSH in the interface electrode / solution. The identification of the redox couple RSSR / R-SH and the determination of the pKa of -SH groups surface were made using cyclic voltammetry in electrolyte solutions at different pH contents potassium ferricyanide. The presence of the -SH and -SS- modified electrode surface was further confirmed by Raman spectroscopy of surface. It was determined the rate constants of direct electron transfer of quasi-reversible coupled R-SS-R/R-SH. The modified electrodes showed electrocatalytic response to the reduction of reactive oxygen species (ROS) such as hydrogen peroxide and the oxidation of compounds with antioxidant activity such as quercetin. It was demonstrated that presence of Cu2+ ions on the electrode surface can shift the equilibrium of the RSSR/R-SH redox coupled into oxidative direction. Hydrogen peroxide and Quercetin were detected at these modified electrodes using amperometry and hydrodynamic cyclic voltammetry.

Die Fortschritte bei synthetischen Polymeren konzentrieren sich in erster Linie auf die Bemühungen, Kunststoffe auf molekularer Ebene zu entwickeln, um vielversprechende Eigenschaften und Funktionen auf makroskopischer Ebene zu erreichen. Daher sind die Verbesserung der Materialsynthese sowie die Zunahme der Komplexität des makromolekularen Designs zu einem wichtigen Forschungsschwerpunkt geworden. Es wurden bemerkenswerte synthetische Strategien zur Entwicklung von sequenzgesteuerten Oligomeren entwickelt, die durch eine präzise Mikrostruktur eine anschließende Faltung zu kontrollierten multizyklischen Origamis ermöglichten. Allerdings bleiben die derzeitigen synthetischen Methoden für die Herstellung von Präzisionspolymeren mit hohem Molekulargewicht bis zu einem gewissen Grad statistisch. Daher ist es nach wie vor schwierig, große synthetische Makromoleküle zu entwerfen, die sich zu präzisen und einheitlichen zyklischen Strukturen zusammenfügen können. Sind parallele Fortschritte bei der Charakterisierung von großen multizyklischen makromolekularen Strukturen sehr gefragt, da die meisten der derzeitigen Techniken nur in der Lage sind, Indizien für die Strukturorganisation zu liefern. Die vorliegende Arbeit untersucht dabei die Synthese und die Morphologie von dynamischen und kontrollierten zyklischen Polymeren. Das synthetische Konzept basiert auf der Herstellung von sequenzgesteuerten Makromolekülen mittels regulierten Einbaus von reaktiven Selenol- oder Thiolgruppen an gewünschten Positionen innerhalb einer Polymerkette. Die kontrollierte oxidative Dimerisierung der funktionellen Gruppen führt zu Diselenid- bzw. Disulfidbrücken und bewirkt eine intramolekulare Vernetzung zur Erzeugung einer dynamischen einkettigen Zyklisierung. Um Einblicke auf molekularer Ebene zu gewinnen und den Grad an struktureller Kontrolle aufzuzeigen, wird eine synthetische Strategie entwickelt, die eine direkte Visualisierung der erhaltenen Polymerkonformation ermöglicht. / The field of material science has evolved drastically in the last decades. Progress in synthetic polymers primarily focuses on efforts to design materials at a molecular level to reach promising properties and functions. Improving material synthesis and increasing the complexity of macromolecular design have become a major research focus. Remarkable synthetic strategies have been developed toward the elaboration of sequence-defined oligomers, in which the precise microstructure can allow subsequent folding into controlled and precise multi-cyclic origamis. However, current synthetic routes toward precision polymers with high molecular weight remain statistical to some degree, which reflects a loss of structural control. Thus, designing large synthetic macromolecules that can fold into precise and uniform cyclic-shape structures remains difficult to reach. Parallel progress in characterization of large multi-cyclic macromolecular designs are highly demanded since most of the current techniques are only capable of providing circumstantial evidence of structural organization. Macromolecules with dynamic intramolecular crosslinks have become relevant due to their ability to potentially reach equilibrium structures in response to external stimuli. In this study, controlled synthetic route and morphology characterization of dynamic cyclic polymers are investigated. The synthetic concept is based on the preparation of sequence-controlled macromolecules to guide the insertion of reactive selenol or thiol groups at desired positions within a polymer chain. Controlled oxidative dimerization of the functional groups leads to diselenide or disulfide bridges respectively and induces intramolecular crosslinking to generate dynamic cyclization. To gain insight into the molecular level to reveal the degree of structural control, a synthetic strategy is developed to access an additional analytic tool and enable direct visualization of the obtained polymer conformations.