The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K+ channel KcsA are discussed.

This thesis is focused on synthesis and polymerization of caprolactone and its derivatives by living ring opening polymerization (LROP), Self-assembly in aqueous solutions produced nanoaggregates comprised of amphiphilic block copolymers or telechelic polymers with incorporated boron compounds (phenyl boronic acids and boron clusters). Incorporation of boron compounds was facilitated either by covalent or non-covalent bonding. Obtained complex nanoparticle structures manifested stimuli-responsive behaviour and were investigated under varying conditions by combination of light scattering, fluorescence spectroscopy and electron microscopy. The obtained results on solution behaviour of polymers in combination with added value of boron compounds, yield general aspects of nano aggregate morphology, responsive character tuning and practical aspects of synthesis and self-assembly overcame in the preparation process. The publications wrote during this thesis are therefore adding valuable information to researchers engaged in biomedical utilization of such nano assemblies.

The development of synthetic molecular receptors that can selectively bind anions, translocate them through a lipidic bilayer membrane and release them on the other side is a very topical and emerging field of supramolecular chemistry, warranted by the biological importance of transmembrane anion transport.The first part of this thesis is devoted to the study of the transmembrane transport of chloride and of the organic ion pair propylammonium chloride with calix[6]arene receptors functionalized with three (thio)urea arms on their small rim. The transport of chloride across the lipid bilayer of liposomes was monitored by fluorescence spectroscopy using the lucigenin assay. We report the first example of calix[6]arenes able to act as mobile carrier for the transport of chloride via a Cl-/NO3- antiport. We furthermore show that our calixarene systems are able to perform the cotransport of propylammonium chloride, with the chloride bound at the level of the (thio)urea groups and the ammonium included in the calixarene cavity. To provide direct proof of cotransport, we developed a 1H NMR methodology involving a thulium- complex shift reagent with which we were able to distinguish the signals of the ammonium transported inside the liposomes from those of the external ammonium. We also highlight the role of the complexing calixarene cavity for the cotransport by comparing the calixarenes to known transporters deprived of a cavity. The transmembrane transport organic ion pairs could find applications in the transport of biologically relevant ammonium compounds such as catecholamines and amino acids. Our results are reported in the publication “Repositioning Chloride Transmembrane Transporters: Transport of Organic Ion Pairs” Grauwels, G. Valkenier, H. Davis, A. P. Jabin, I. Bartik, K. Angew. Chemie - Int. Ed. 2019, 58, 6921–6925.The second part of this thesis is devoted to the study of binding of chloride to receptors embedded in a lipid membrane, the first step of the transmembrane transport process. Both 1H and 31P NMR spectroscopy proved to be inadequate to study the binding using liposomes or micelles as model membranes. With liposomes, the NMR signals are too broad to be exploited and in the case of micelles, the competition between the lipid headgroups and chloride made it impossible to obtain a NMR signature which unambiguously characterizes chloride binding. The 35Cl NMR signal is on the other hand strongly affected by the presence of anion receptors, both in organic solvents and when incorporated lipid bilayers. We developed a methodology to evaluate the binding of chloride, based on the monitoring of the chloride linewidth during titration experiments. A linear relationship between the linewidth and the concentration of receptors is observed and the slopes can be exploited to compare the binding strengths of different structurally related receptors. We show that 35/37Cl NMR is a versatile tool which can help in the understanding and development of new transporters by providing new insights of the physicochemical understanding of the transport process. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

Les interactions ARN/ARN de type kissing-loop sont des éléments de structure tertiaire qui jouent souvent des rôles clés chez les ARN, tant au niveau fonctionnel que structural. En effet, ce type d’interaction est crucial pour plusieurs processus dépendant des ARN, notamment pour l’initiation de la traduction, la reconnaissance des ARN antisens et la dimérisation de génome rétroviral. Les interactions kissing-loop sont également importantes pour le repliement des ARN, puisqu’elles permettent d’établir des contacts à longue distance entre différents ARN ou encore entre les domaines éloignés d’un même ARN. Ce type d’interaction stabilise aussi les structures complexes des ARN fonctionnels tels que les ARNt, les riborégulateurs et les ribozymes. Comme d’autres ARN fonctionnels, le ribozyme VS de Neurospora contient une interaction kissing-loop importante. Celle-ci est impliquée dans la reconnaissance du substrat et se forme entre la tige-boucle I (stem-loop I, SLI) du substrat et la tige-boucle V (stem-loop V, SLV) du domaine catalytique. Des études biochimiques ont démontré que l’interaction kissing-loop I/V, dépendante du magnésium, implique trois paires de bases Watson-Crick (W-C). De plus, cette interaction est associée à un réarrangement de la structure du substrat, le faisant passer d’une conformation inactive dite unshifted à une conformation active dite shifted. Les travaux présentés dans cette thèse consistent en une caractérisation structurale et thermodynamique de l’interaction kissing-loop I/V du ribozyme VS, laquelle est formée de fragments d’ARN représentant les tige-boucles I et V dérivées du ribozyme VS (SLI et SLV). Cette caractérisation a été réalisée principalement par spectroscopie de résonance magnétique nucléaire (RMN) et par titrage calorimétrique isotherme (isothermal titration calorimetry, ITC) en utilisant différents complexes SLI/SLV dans lesquels l’ARN SLV est commun à tous les complexes, alors que différentes variations de l’ARN SLI ont été utilisées, soit en conformation shiftable ou preshifted. Les données d’ITC ont permis de démontrer qu’en présence d’une concentration saturante de magnésium, l’affinité d’un substrat SLI preshifted pour SLV est extrêmement élevée, rendant cette interaction plus stable que ce qui est prédit pour un duplexe d’ARN équivalent. De plus, l’étude effectuée par ITC montre que des ARN SLI preshifted présentent une meilleure affinité pour SLV que des ARN SLI shiftable, ce qui a permis de calculer le coût énergétique associé au réarrangement de structure du substrat. En plus de confirmer la formation des trois paires de bases W-C prédites à la jonction I/V, les études de RMN ont permis d’obtenir une preuve structurale directe du réarrangement structural des substrats SLI shiftable en présence de magnésium et de l’ARN SLV. La structure RMN d’un complexe SLI/SLV de grande affinité démontre que les boucles terminales de SLI et SLV forment chacune un motif U-turn, ce qui facilite l’appariement W-C intermoléculaire. Plusieurs autres interactions ont été définies à l’interface I/V, notamment des triplets de bases, ainsi que des empilements de bases. Ces interactions contribuent d’ailleurs à la création d’une structure présentant un empilement continu, c’est-à-dire qui se propage du centre de l’interaction jusqu’aux bouts des tiges de SLI et SLV. Ces études de RMN permettent donc de mieux comprendre la stabilité exceptionnelle de l’interaction kissing-loop I/V au niveau structural et mènent à l’élaboration d’un modèle cinétique de l’activation du substrat par le ribozyme VS. En considérant l’ensemble des données d’ITC et de RMN, l’étonnante stabilité de l’interaction I/V s’explique probablement par une combinaison de facteurs, dont les motifs U-turn, la présence d’un nucléotide exclu de la boucle de SLV (U700), la liaison de cations magnésium et l’empilement de bases continu à la jonction I/V. / Kissing loops are tertiary structure elements that often play key roles in functional RNAs. Their formation is central to many RNA-mediated processes, such as translation initiation, antisense recognition and retroviral dimerization. Kissing loops are also involved in RNA folding as they form long-range interactions between different RNAs or remote domains within the same RNA and stabilize the complex architecture of functional RNA, such as tRNA, riboswitch aptamers and ribozymes. Like several other functional RNAs, the Neurospora VS ribozyme contains an important kissing-loop interaction. The substrate recognition by the VS ribozyme depends largely on the formation of a magnesium-dependent kissing-loop interaction between stem-loop V (SLV) of the catalytic domain and stem-loop I (SLI) that defines the substrate domain. It has been shown from biochemical studies that the I/V kissing-loop interaction involves three Watson-Crick base pairs and is associated with a structural rearrangement of the SLI substrate from an unshifted and inactive to a shifted and active conformation. Here, we present a thermodynamic and structural characterization of the VS ribozyme I/V kissing-loop interaction using isolated stem-loop fragments (SLI and SLV). Both isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR) spectroscopy studies were conducted with several SLI/SLV complexes using a common SLV, but either shiftable or preshifted SLI variants. From the ITC studies, we show that, under saturating amount of magnesium ions, the affinity of the preshifted SLI variants for SLV is remarkably high, the interaction being more stable than predicted for a comparable duplex. In addition, these ITC studies demonstrate that preshifted SLI variants have higher affinity for SLV than shiftable SLI variants, and these results allow us to evaluate the energetic cost of the conformational shift in SLI. From the NMR studies, we confirm formation of three Watson-Crick base pairs at the kissing-loop junction and provide direct evidence on the structural rearrangement of shiftable SLI variants in the presence of magnesium and SLV. The NMR structure of a high-affinity SLI/SLV complex demonstrates that both the SLI and SLV loops adopt U-turn structures, which facilitate intermolecular Watson-Crick base pairing. Several other interactions at the I/V interface, including base triples and base stacking help create a continuously stacked structure. These NMR studies provide a structural basis for the high stability of the kissing-loop interaction and lead us to propose a kinetic model for substrate activation by the VS ribozyme. Taken together, our ITC and NMR data suggest that the remarkable stability of the I/V interaction is likely provided by a combination of several elements, especially the presence of the U-turn motif, the presence of an extruded nucleotide in SLV (U700), the binding of magnesium ions and the extensive base stacking interactions at the junction.

Le ribozyme VS de Neurospora catalyse des réactions de clivage et de ligation d’un lien phosphodiester spécifique essentielles à son cycle de réplication. Il est formé de six régions hélicales (I à VI), qui se divisent en deux domaines, soit le substrat (SLI) et le domaine catalytique (tiges II à VI). Ce dernier comprend deux jonctions à trois voies qui permettent de reconnaître le substrat en tige-boucle de façon spécifique. Ce mode de reconnaissance unique pourrait être exploité pour cibler des ARN repliés pour diverses applications. Bien que le ribozyme VS ait été caractérisé biochimiquement de façon exhaustive, aucune structure à haute résolution du ribozyme complet n’a encore été publiée, ce qui limite la compréhension des mécanismes inhérents à son fonctionnement. Précédemment, une approche de divide-and-conquer a été initiée afin d’étudier la structure des sous-domaines importants du ribozyme VS par spectroscopie de résonance magnétique nucléaire (RMN) mais doit être complétée. Dans le cadre de cette thèse, les structures de la boucle A730 et des jonctions III-IV-V et II-III-VI ont été déterminées par spectroscopie RMN hétéronucléaire. De plus, une approche de spectroscopie RMN a été développée pour la localisation des ions divalents, tandis que diverses approches de marquage isotopique ont été implémentées pour l’étude d’ARN de plus grandes tailles. Les structures RMN de la boucle A730 et des deux jonctions à trois voies révèlent que ces sous-domaines sont bien définis, qu’ils sont formés de plusieurs éléments structuraux récurrents (U-turn, S-turn, triplets de bases et empilement coaxial) et qu’ils contiennent plusieurs sites de liaison de métaux. En outre, un modèle du site actif du ribozyme VS a été construit sur la base des similarités identifiées entre les sites actifs des ribozymes VS et hairpin. Dans l’ensemble, ces études contribuent de façon significative à la compréhension de l’architecture globale du ribozyme VS. De plus, elles permettront de construire un modèle à haute résolution du ribozyme VS tout en favorisant de futures études d’ingénierie. / The Neurospora VS ribozyme catalyzes the cleavage and the ligation of a specific phosphodiester bond, which is essential for its replication cycle. It is formed of six helical regions (I to VI) that are divided in two domains: the substrate (SLI) and the catalytic domain (stems II-VI). The latter contains two three-way junctions that allow recognition of the stem-loop substrate in a specific manner. This unique mode of substrate recognition could be exploited to target folded RNAs for diverse applications. Even though the VS ribozyme has been extensively characterized biochemically, no high-resolution structure of the complete ribozyme has been published yet and this limits our mechanistic understanding. A divide-and-conquer approach was previously initiated to study the structure of the important subdomains of the VS ribozyme by nuclear magnetic resonance (NMR), but this approach needs to be completed. In this thesis, the structures of the A730 loop, the III-IV-V junction and the II-III-VI junction were determined by heteronuclear NMR spectroscopy. Moreover, a unique NMR approach was developed for localizing divalent metal ions, whereas several isotope-labeling strategies were implemented to facilitate the study or large RNA molecules. The NMR structures of the A730 loop and the two three-way junctions reveal that these subdomains are well defined, that they are formed by several recurrent structural elements (U-turn and S-turn motifs, base triples and coaxial stacking) and that they contain several metal-binding sites. Interestingly, structural similarities were identified between the VS and hairpin ribozymes, which allowed the modeling of the VS ribozyme active site. In summary, these studies significantly contribute to a better understanding of the global architecture of the VS ribozyme. In addition, they will allow the construction of a high-resolution model of the complete VS ribozyme and facilitate future engineering studies.

Rapid development of bacterial resistance and multiresitance to conventional antibiotics has resulted in an intensive search for alternative antimicrobial agents. Antimicrobial peptides (AMPs) belong to promising anti-infective candidates since they do not development bacterial resistance. They kill microbes by disturbing or permeabilizing the cytoplasmic membrane, or may target putative key intracellular compartments. Their advantages include fast action and selectivity between prokaryotic and eukaryotic cells. We have isolated several novel AMPs from the venom of wild bees: halictines (HAL-1 and HAL-2) from Halictus sexcinctus, lasiocepsin (Las) from Lasioglossum laticeps and macropin (MAC-1) from Macropis fulvipes. They are active against Gram-positive and Gram- negative bacteria and against yeast Candida albicans. While halictines and macropin have moderate hemolytic activity, Las shows no hemolytic activity. A novel AMP was isolated also from the mucus of Xiphydria camelus. This AMP belongs to the category of insect defensins. It contains 55 amino acid residues, three disulphide bridges and its C-terminus is amidated. CD and NMR studies of HAL-1, HAL-2 and MAC-1 revealed propensity to form amphipathic α-helical structure in the presence of sodium dodecyl sulfate or trifluoroethanol. For the...

All life on earth depends mainly on the presence of oxygen. Largest producers of oxygen are green plants, cyanobacteria and algae. Oxygen is released from the oxygenevolving complex of photosystem II during photosynthesis and it is used in cellular respiration of all life complexes. The oxygen-evolving complex of photosystem II has the same function in each photosynthetic organism, but it has a different composition and organization of extrinsic proteins; only PsbO protein is ubiquitous in all known oxyphototrophs. Until now only low resolution electron microscopy structural models of plant PSII and crystal structures of cyanobacterial PSII are available. Higher plant extrinsic proteins (PsbP, PsbQ and PsbR) are structurally unrelated, non-homologues to the cyanobacterial extrinsic proteins (PsbO, PsbU and PsbV) and this is the reason why it is not possible to predict arrangement of these proteins on the lumenal site of higher plant PSII. Recently, models differ mainly in the structure of the oxygen-evolving complex, which could be resolved by determination of the exact binding sites for extrinsic proteins. An other question evolves: if the difference in the oxygen-evolving complex composition is the result of evolution or adaptation of photosynthetic organisms to their environment. Structural knowledge of extrinsic proteins that could help to resolve the location and subsequently the function of extrinsic proteins is still incomplete. From this case,structural analysis, interactions and probably arrangement of proteins PsbP and PsbQ was studied and is described in detail in this thesis.

For the first time, successful synthesis of an unknown class of compounds, 3-azido-2H-azirines, which are implicated as highly reactive intermediates in the thermolysis of the corresponding 1,1-diazidoethenes, has been performed. These elusive heterocycles have been detected and characterised by low-temperature NMR and in situ IR spectroscopy. Even the parent compound, 3-azido-2H-azirine, has been observed via low-temperature photolysis of 1,1-diazidoethene, as a highly reactive species with a half-life period of only 12 min at −40 °C. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Motiviert durch die Zunahme der weltweiten Nachfrage nach hochwertigen Humusstoffen wurde am Institut für Holz- und Pflanzenchemie ein neuartiger Humusersatzstoff entwickelt. Dieses N-modifizierte Produkt wird auf Basis eines patentierten Normaldruckverfahrens der oxidativen Ammonolyse (OA) aus ligninhaltigen Ausgangssubstanzen, im vorliegenden Fall Lausitzer Braunkohle, hergestellt. Ziel war, die bisher vorliegenden Erkenntnisse der strukturellen Eigenschaften solcher Humusstoffe zu erweitern. Im Fokus standen die Gehalte und Charakteristik der Huminstofffraktionen (Humine, Humin- und Fulvosäuren). Der Stickstoff und die Art seines Einbaus in die organische Substanz spielt hierbei eine besondere Rolle. Für die Huminstoffisolierung kam die hinsichtlich der Ausbeuten und des Zeitaufwandes optimierte IHSS-Methode zum Einsatz. Wesentliche Merkmale N-modifizierter Substanzen sind erhöhte Huminsäurengehalte, zeitlich differenziert wirksame N-Bindungsformen und damit eine Diversifizierung der Funktionalität. Zusätzlich mit dem geringen Aschegehalt unterscheidet dies N-modifizierte Lausitzer Braunkohle von anderen auf Braunkohlebasis erzeugten Bodenverbesserungsmitteln des Marktes. Es konnte gezeigt werden, dass Huminsäuren hinsichtlich der Bereitstellung von Stickstoff und Funktionalität (z.B. Austauscherplätze) eine Schlüsselrolle einnehmen. Die Veränderungen durch die OA basieren stofflich auf der Bildung regenerierter Huminsäuren und chemisch u.a. auf der oxidativen Ringspaltung von Aromaten an nicht veretherten phenolischer OH-Gruppen von Methoxyphenolstrukturen. Dabei ist diese Reaktion entgegen früherer Annahmen nicht an eine Demethoxylierung gebunden und erfordert auch keine verschärften Reaktionsbedingungen (z.B. erhöhter Druck). Diese und weitere Reaktionsmechanismen führen zu ammoniumartig, amidartig und fest organisch gebundenen N-Bindungsformen. 15N-NMR-Spektroskopische Untersuchungen an einem 15N-angereicherten Produkt, Py-GC/MS-Untersuchungen und nasschemische Experimente zeigen, dass in der Vergangenheit die Bedeutung heterocyclischer, insbesondere heteroaromatischer N-Bindungsformen überschätzt wurde. Amidartiger Stickstoff präsentiert sich dabei als außerordentlich heterogen hinsichtlich seiner Hydrolysestabilität bzw. Pflanzenverfügbarkeit. Für die effektive Beurteilung möglicher Ausgangssubstanzen hinsichtlich ihrer Eignung für die Herstellung von Humusdüngestoffen nach dem Prinzip der OA kann der Huminsäurengehalt herangezogen werden. Er wird mit Hilfe eines degradativen Verfahrens ermittelt. Die mit dem Huminsäurengehalt in Verbindung stehenden Stoffeigenschaften von Kohlen korrelieren gut mit dem N-Einbau. Aus Sicht der Verfahrensführung hängt die Intensität des N-Einbaus eng mit dem Oxidationsregime zusammen. Durch Anwendung von reinem Sauerstoff anstelle von Luft als sehr einfach und günstig zu realisierende Maßnahme kann die Reaktionszeit halbiert werden. / The development of a novel artificial humus material at the Institute of Wood- and Plant Chemistry was accounted by the increasing demand for high grade humic matter. This N-modified product base on a patented ambient pressure technology of the oxidative ammonolysis. of lignin containing substances, in particular Lusitian lignite. Objective of the work was to broadening the current knowledge of structural properties with focus on the contents and characteristics of humic substances fractions (humins, humic acids, fulvic acids). Especially attention was given to nitrogen and its way of incorporation into organic matter. For isolating humic substances the IHSS method was used. The procedure was adapted in order to increase the yield of humic acids and decrease time needed. Main characteristics of N-modified substances are higher contents of humic acids and subtly differenciateted effective N-binding forms with leads to higher diversity of the chemical functionality. This and the low ash content makes the differences to other brown coal based soil improving agents available on the marked. It has been shown that humic acids give the main part providing nitrogen and functionality (e.g. cation exchange capacity). The oxidative ammonolysis leads to regenerated humic acids as well as e.g. the clevage of aromatic structures by reactions of free phenolic groups. In contrast to former assumptions the cleavage is not strongly related to demethoxylation or strong reaction conditions like high pressure. This and other reactions lead to short, middle, and long lasting N-binding forms. 15N-NMR-spectroscopic investigations on a 15N-enriched product, Py-GC/MS-investigations and conventional investigations show an overestimation of heterocyclic, in particular heteroaromatic N-binding forms up to now. Consequently amide like nitrogen reveals as extraordinary according to its persistent behaviour to hydrolysis and plant availability respectively. Corresponding the correlation of the N-incorporation and humic acid content of raw materials the latter can be used for evaluating possible raw material for its usage for N-modification. It can be easy obtained in a degratadive way. From the process engineering point of view the success of N-incorporating is strongly correlated to the oxidation conditions during processing. Using pure oxygen instead of air shorts the needed reaction at 50%.