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Item Open Access Catalytic enantioselective total synthesis of picrotoxane alkaloids and guaiane sesquiterpene englerins A and B(2019) Guo, Lei; Plietker, Bernd (Prof.Dr.)Alkaloids from the picrotoxane family are biologically potent natural products that show hypertensive, antipyretic, analgesic and anti-influenza A virus activities. Herein a concise catalytic, enantioselective total synthesis of (-)-dendrobine, (-)-mubironine B and (-)-dendroxine is described with an overall yield of 6.7%, 7.8% and 7.4%, respectively. This represents a significantly improved yield as compared to synthetic approaches reported in the past, and it is the first report on the total synthesis of (-)-dendroxine. Importantly, the asymmetric Yb-catalyzed Diels-Alder reaction between Danishefsky’s diene and an oxazolidinone moiety allowed for an enantioselective synthesis of the natural products in the enantioselective way, while the Fe-catalyzed aerobic oxidation, Cu- or Au-catalyzed cycloisomerization and hydroazidation underlined the strength of modern synthetic sequences in total synthesis. Englerin A is a guaiane sesquiterpene natural product that shows antitumor activity when binding to the TRPC4/5 target (a new target for antitumor compounds) in vitro. In this part a bio-inspired, catalytic enantioselective strategy towards the total synthesis of (-)-englerins A and B in 12 or 13 steps with 6.7% or 4.8% yield, respectively, is described. The success was initialized by a biomimetic catalytic enantioselective decarboxylative aldol reaction for chirality introduction. A [4+3] cycloaddition with neighboring group participation was used for the construction of the central core structure, which was inspired by the biogenesis of tropinone. A late stage one-pot Heck coupling-regioselective hydrosilylation-Fleming oxidation cascade sequence afforded the cyclopentane core while a kinetic CBS reduction enriched enantiopurity and eventually delivered the natural products.Item Open Access Biochemical characterization and identification of novel substrates of protein lysine methyltransferases(2019) Schuhmacher, Maren Kirstin; Jeltsch, Albert (Prof. Dr.)The methylation of lysine side chains is a prevalent post-translational modification (PTM) of proteins, which is introduced by protein lysine methyltransferases (PKMTs). Histone methylation can have different effects on chromatin structure, lysine methylation of non-histone proteins can regulate protein/protein interactions and protein stability. For most PKMTs currently not all methylation sites are known which limits our understanding of the regulatory role of these enzymes in cells. Therefore, it is an important research aim to gain more information about the substrate spectrum of PKMTs. The identification of the substrate specificity of a PKMT is a very important step on the way to identify new PKMT methylation sites. The focus of this study was the analysis of the substrate specificity of different PKMTs by SPOT peptide arrays and based on this on the identification and validation of possible new methylation substrates. The analysis of the substrate specificity of human SUV39H2 revealed significant differences to its human homolog SUV39H1, although both enzymes methylate the same histone substrate (H3K9). SUV39H2 is more stringent than the SUV39H1, which could be demonstrated by the lack of methylation of SUV39H1 non-histone targets by SUV39H2 and by the fact that it was not possible in this study to identify non-histone substrates for SUV39H2. Kinetic studies showed that SUV39H2 prefers the unmethylated H3K9 as substrate. Moreover, it was shown that the N324K mutation of SUV39H2 which leads to a genetic disease in Labrador retrievers causes a change in folding finally leading to the inactivation of the enzyme. It had been reported by another group that the histone variant H2AX is methylated by SUV39H2. However, the sequence of H2AX K134 does not fit to the substrate specificity profile of SUV39H2 determined in the present work. Follow-up in vitro peptide and protein methylation studies indeed showed that H2AX K134 is not methylated by SUV39H2. This indicates that H2AX methylation by SUV39H2 is most probably a wrong assignment of a substrate to a PKMT. Based on already available specificity data for the SUV39H1 PKMT, the SET8 protein was validated as novel substrate in cellular studies. SET8 is a PKMT itself and it could be shown in this thesis that methylation of SET8 at residue K210 by SUV39H1 stimulated the SET8 activity. In humans, there exist different PKMTs, which methylate H3K36. For example, NSD1, NSD2 and SETD2 which were investigated in this thesis. In literature, it was shown that the oncohistone mutation K36M inactivates NSD2 and SETD2. Steady-state methylation kinetics using a peptide substrate and a K36M peptide as inhibitor revealed that NSD1 is inhibited by this histone oncomutation as well. The steady-state inhibition parameters for all enzymes showed a better binding of the PKMTs to the inhibitor peptide than to the substrate, suggesting some mechanistic similarities in target peptide interaction. The SETD2 is a methyltransferase, which is able to introduce trimethylation of H3K36. During this thesis two substrate specificity motifs of SETD2 were determined using peptide array methylation experiments. Additionally, based on the substrate specificity investigations a super-substrate at peptide and protein level was determined. Furthermore, one novel substrate (FBN1) for SETD2 was discovered and validated. The Legionella pneumophila RomA PKMT was shown previously by our collaborators to methylate H3 at K14. Based on the specificity profile of RomA determined in this study it could be shown that this enzyme methylates seven additional human non-histone proteins. Collaborators tested the methylation of one of the non-histone targets (AROS) and could demonstrate its methylation during the infection of human cells with L. pneumophila. The role of these methylation events in the infection process must be studied in future experiments.Item Open Access Mechanistic study on the DNA methyltransferase DNMT3A(2019) Emperle, Max; Jeltsch, Albert (Prof. Dr.)The phenotypical and functional diversity of mammalian cell types can be attributed to a large extent to epigenetic signals that determine and stabilize gene expression profiles. One of the most important types of epigenetic signals is DNA methylation. This modification is set early in development by the de novo DNA methyltransferases DNMT3A and DNMT3B, and is found predominantly at the C5 position of cytosine bases in a CpG dinucleotide context. The accurate setting of DNA methylation patterns is critical for normal development and is determined by the precise recruitment and control of DNMT activity on chromatin. In this work, four main directions of research were undertaken, with the ultimate goal of shedding novel mechanistic insights into the mechanism of DNMT3A, its regulation by chromatin signals and interaction partners, as well as the dysregulation of this enzyme in cancer. Furthermore, the potential of DNMT3A to generate 3-methylcytosine as a side reaction was explored. The DNA methyltransferase DNMT3A has been shown to multimerize on DNA and to form large multimeric protein/DNA fibers. However, it has also been postulated that this enzyme can methylate DNA in a processive manner, a property incompatible with fiber formation. By using a dedicated set of biochemical experiments, I was able to show that the DNA methylation rate of DNMT3A increases more than linearly with increasing enzyme concentration on a long DNA substrate, but not on a short 30-mer oligonucleotide, which cannot accommodate DNMT3A polymers. Methylation experiments over a range of enzyme concentrations and with substrates containing one or two CpG sites did not provide evidence for a processive mechanism. The addition of a catalytically inactive DNMT3A mutant was found to increase the DNA methylation rate by DNMT3A on the long substrate but not on the short one. Together, these data clearly indicate that DNMT3A binds to DNA in a cooperative reaction and the formation of protein/DNA fibers increases the DNA methylation rate. These results contribute mechanistic insights into the mode by which DNA methylation patterns are established during development. The second project dealt with characterizing the effects of the R882H exchange on DNMT3A. The R882H mutation is found in the DNA binding interface of DNMT3A and is frequently observed in acute myeloid leukemia (AML). By establishing a double-tag affinity purification system, I was able to show that the mutation only leads to a minor reduction in overall DNA methylation activity in mixed R882H/wildtype DNMT3A complexes. However, a pronounced change in flanking sequence preference of the DNMT3A-R882H mutant was found. Accordingly, a substrate designed to contain the target CpG site flanked by sequences preferred by R882H was better methylated by the variant than by the wildtype enzyme. Together, these data strongly argue against a dominant-negative effect of the R882H mutation and rather propose a site-specific gain-of-activity effect. These findings are in agreement with a recently determined structure of DNMT3A in complex with DNA and they might explain the high prevalence of this specific point mutation in AML. The third project was built on previous data from the lab, documenting a strong and direct interaction between the ADD domain of DNMT3A and the TRD domain of the 5mC reading protein MECP2. These experiments revealed that through its binding, MECP2 allosterically stabilizes the autoinhibitory conformation of DNMT3A, resulting in a strong inhibition of enzymatic activity in vitro. The interaction between these two proteins and its associated inhibition could be disrupted by unmodified histone H3. In my work, I further validated the interaction between the ADD and the TRD domains by size exclusion chromatography. Also, by generating cell lines with stable over-expression of MECP2, I could show that MECP2 inhibits DNMT3A activity in cells. Together, the data from this study offer unprecedented insights into the regulation of DNMT3A by the combined action of chromatin modifications and interaction partners. Accordingly, depending on the modification status of the H3 tail at the target site, MECP2 can act as either a repressor or activator of DNA methylation. The last project dealt with the coevolution between DNA methylation and DNA repair systems, a very exciting topic that was addressed in close collaboration with the laboratory of Dr. Peter Sarkies (MRC London). By performing in vitro methylation experiments with the catalytic domain of DNMT3A, I could show that, in addition to 5mC, DNMT3A can also introduce 3mC, a modification which represents an alkylation damage of DNA. This study provides a new evolutionary perspective on the loss of DNA methylation that is observed in many species.Item Open Access Novel X-ray lenses for direct and coherent imaging(2019) Sanli, Umut Tunca; Schütz, Gisela (Prof. Dr.)Item Open Access Chirality effects in thermotropic and lyotropic nematic liquid crystals under confined geometries(2019) Dietrich, Clarissa; Giesselmann, Frank (Prof. Dr.)Chirality is a phenomenon in nature that appears across all disciplines of natural science, from biology to mathematics. The spontaneous formation of chiral structures in a system of achiral components is known as spontaneous mirror symmetry breaking and is by itself of fundamental interest leading also towards the question of the origin of homochirality in nature in general. In this work, we show that by means of the topology imposed by the confining geometry and by interfacial boundary conditions - in combination with the physical properties of a liquid crystal - spontaneous mirror symmetry broken structures can be obtained. They are analyzed, inter alia, with respect to the types of geometrical confinements used, e.g. how the confinement amplifies, induces, and influences the detection of chirality effects in order to facilitate the measurement of tiny amounts of chiral additives qualitatively and quantitatively.Item Open Access Chirale lyotrop-lamellare Flüssigkristalle : Phasenverhalten neuer chiraler Amphiphile und Nachweis des elektroklinen Effektes(2019) Harjung, Marc D.; Gießelmann, Frank (Prof. Dr.)Ziel dieser Arbeit ist es, neue Erkenntnisse zur Bildung lyotroper SmC*-Phasen zu gewinnen und einen elektroklinen Effekt in chiral lamellaren Phasen nachzuweisen.Item Open Access Generierung von gesättigten N-Heterozyklen mit Iminreduktasen(2019) Borlinghaus, Niels; Hauer, Bernhard (Prof. Dr.)Item Open Access Defect chemistry of bulk and thin film lithium chalcogenides(2019) Lorger, Simon; Maier, Joachim (Prof. Dr.)Item Open Access Atom probe reconstruction with a locally varying tip shape(2019) Beinke, Daniel; Schmitz, Guido (Prof. Dr. Dr. h.c.)In this thesis, a new approach for the reconstruction of data taken from an atom probe tomography experiment is presented. The goal of the study is to develop an algorithm, which is able to overcome well-known drawbacks of the conventional reconstruction technique, mainly caused by local magnification effects. At the same time, the algorithm should be easy to use and also fast enough, so that it might be routinely used as an improved alternative to the established reconstruction technique. The idea is based on the already existing possibility to simulate an entire atom probe experiment on a realistic length. Since the successive calculation of ion trajectories starting at the emitter surface and hitting the detector after a flight of a few centimeters can be realized, the concept is designed to invert the field evaporation process by making use of this trajectory calculation. To this end, the detected emitter volume needs to be rebuilt from the bottom to the top, which is an important difference compared to the conventional technique. In a first test, this inversion of the simulated experiment is demonstrated for a few prominent example cases. The decisive criterion for the positioning of an atom at a specific lattice site on the current emitter surface is the accordance of the impact position of the corresponding calculated trajectory with the measured coordinates on the detector. For every possible surface position, first an ion trajectory is calculated and its detector impact position is compared to the measured impact position. Finally, the best-matching trajectory defines the reconstruction coordinates. The approach is performed for some prominent example emitter structures with strongly varying evaporation fields of the involved material, which is known for causing tremendous artifacts in the reconstruction derived by the standard technique. In this first attempt, the algorithm is restricted to a rigid lattice, which means that detected atoms can only be positioned at sites belonging to the former lattice of the emitter. In a second step, the restriction to a rigid lattice is dropped. In this way, the reconstruction algorithm describes a more realistic scenario, since the exact lattice structure and its orientation might be unknown in the majority of experiments. The possibilities and limitations of the approach are discussed. It is found that an additional criterion for the determination of the reconstruction coordinates is needed in this case, since the algorithm is very sensitive to the misplacement of atoms. The stability can be significantly improved by the consideration of an inter-atomic potential, which acts as a filter that exclusively allows surface sites with a sufficiently high amount of neighbor atoms. For a perfect detector efficiency the algorithm yields promising results, but a decrease of the efficiency towards realistic values gives rise to artifacts. As a consequence of these numerical experiments, a new concept has been developed, which neglects the consideration of exact ion trajectories in order to make the algorithm more stable and fast. This third approach assumes rotational symmetry for the investigated emitter volume. An absolutely new characteristic of the technique is the capability to extract the shape of a field emitter directly from the observed pattern of ion impacts on the detector. This feature is a very important difference to the conventional technique, which assumes a constant spherical emitter shape. To the best of the authors knowledge, such a technique with this capability did not exist before. The promising features are demonstrated for several simulated but nevertheless realistic emitter structures. The improved quality of the reconstruction that can be achieved by the application of the here developed technique is shown by direct comparison to the result of the established reconstruction approach. The impressive benefits are illustrated for relevant emitter structures containing either precipitates or layers of different materials with strongly varying evaporation fields (44% or 56% relative variation). In addition, a simple modification of the technique is described, which yields homogenized atomic densities in the reconstructed volumes. Without this modification, the emitter surface is treated like a rigid curved plane, which is shifted upwards with every reconstructed atom during reconstruction. Once the surface is no longer considered to be rigid, individual parts can be lifted separately, yielding a significantly homogenized atomic density. Finally, the new concept of shape extraction is extended for the application to arbitrary emitter structures. The main idea of extracting the information about the emitter shape from the local density of measured events on the detector is maintained. In order to extend the approach to the application to structures without rotational symmetry, a relation between the local density of events on the detector and the Gaussian curvature on the emitter surface is derived. With the help of an iterative finite difference method, the Gaussian curvature at several positions on the tip surface is set. Consequently, a reasonable description of the emitter surface can be obtained and the reconstruction of an arbitrary data set can be performed. The concept is tested and discussed for a simulated example emitter structure.Item Open Access Tuning aggregation by molecular design in n-type donor-acceptor copolymers : from synthesis towards application in organic electronics(2019) Gross, Yannic Martin; Ludwigs, Sabine (Prof. Dr.)
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