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A hallmark of Huntington's disease (HD) is a prolonged polyglutamine sequence in the huntingtin protein and, correspondingly, an expanded cytosine, adenine, and guanine (CAG) triplet repeat region in the mRNA. A majority of studies investigating disease pathology were concerned with toxic huntingtin protein, but the mRNA moved into focus due to its recruitment to RNA foci and emerging novel therapeutic approaches targeting the mRNA. A hallmark of CAG-RNA is that it forms a stable hairpin in vitro which seems to be crucial for specific protein interactions. Using in-cell folding experiments, we show that the CAG-RNA is largely destabilized in cells compared to dilute buffer solutions but remains folded in the cytoplasm and nucleus. Surprisingly, we found the same folding stability in the nucleoplasm and in nuclear speckles under physiological conditions suggesting that CAG-RNA does not undergo a conformational transition upon recruitment to the nuclear speckles. We found that the metabolite adenosine triphosphate (ATP) plays a crucial role in promoting unfolding, enabling its recruitment to nuclear speckles and preserving its mobility. Using in vitro experiments and molecular dynamics simulations, we found that the ATP effects can be attributed to a direct interaction of ATP with the nucleobases of the CAG-RNA rather than ATP acting as "a fuel" for helicase activity. ATP-driven changes in CAG-RNA homeostasis could be disease-relevant since mitochondrial function is affected in HD disease progression leading to a decline in cellular ATP levels., Journal of the American Chemical Society, 145 (17), ISSN:0002-7863, ISSN:1520-5126

The thermoforming of unidirectional fibre reinforced thermoplastics facilitates the manufacturing of parts within short cycle times. Within the scope of this thesis the influences of different process parameters on the resulting part quality are studied. Besides the experimental studies, the forming behaviour is analysed using finite element simulations. The results are then compared to the outcome of the experimental studies and the possibilities and limits of the used simulation method are presented. Das Thermoformen von unidirektional faserverstärkten Thermoplasten bietet die Möglichkeit, Bauteile mit kurzen Zykluszeiten herzustellen. Die vorliegende Arbeit untersucht den Einfluss verschiedener Parameter auf die erreichbare Bauteilqualität. Daneben findet eine Betrachtung des Umformverhaltens auch mit Hilfe einer FE-Simulation statt. Abschließend werden die Resultate der Simulationen mit den Ergebnissen der experimentellen Studien verglichen und die Möglichkeiten der verwendeten Simulationsmethodik aufgezeigt.

During embryogenesis, morphogens form a concentration gradient in responsive tissue, which is then translated into a spatial cellular pattern. The mechanisms by which morphogens spread through a tissue to establish such a morphogenetic field remain elusive. Here, we investigate by mutually complementary simulations and in vivo experiments how Wnt morphogen transport by cytonemes differs from typically assumed diffusion-based transport for patterning of highly dynamic tissue such as the neural plate in zebrafish. Stochasticity strongly influences fate acquisition at the single cell level and results in fluctuating boundaries between pattern regions. Stable patterning can be achieved by sorting through concentration dependent cell migration and apoptosis, independent of the morphogen transport mechanism. We show that Wnt transport by cytonemes achieves distinct Wnt thresholds for the brain primordia earlier compared with diffusion-based transport. We conclude that a cytoneme-mediated morphogen transport together with directed cell sorting is a potentially favored mechanism to establish morphogen gradients in rapidly expanding developmental systems., Author summary How entire organisms develop out of single cells is a long-term challenge in the life sciences. Morphogens are crucial signaling molecules organizing cell fates and patterning by their local concentrations. While many morphogens diffuse freely, specialized cell extrusions can facilitate directed cell-to-cell transport for morphogens of the Wnt/β-Catenin family. We performed simulations of quickly growing tissue take this into account, back to back with in-vivo experiments. Our simulations suggest that stochasticity effects lead to non-physiological fluctuating boundaries of tissue regions if not properly controlled. Such control can be achieved via directed cell sorting and apoptosis. We provide experimental evidence for both mechanisms. We observe a distinct temporal difference between the transport mechanisms, with cytonemes facilitating an earlier establishment of a stable pre-pattern. Overall, simulations suggest that cytoneme-mediated Wnt transport is advantageous over diffusion-based transport and a potential general mechanism to establish morphogen gradients in rapidly expanding developmental systems.

Small-angle X-ray scattering (SAXS) is an experimental method for structural characterization of biomolecules in solution. As SAXS measures averaged low-resolution scattering intensities, the sparse information obtained is not sufficient to reconstruct unique atomistic models. We integrate this information into molecular dynamics (MD) simulations using computationally efficient structure-based models (SBMs). Based on a dynamic fit of scattering intensities, such simulations produce reasonable structural models in agreement with the target data. Simulations are faster than explicit-solvent approaches by more than two orders of magnitude and achieve comparable accuracy.

Proteins are complex biomolecules which perform critical tasks in living organisms. Knowledge of a protein's structure is essential for understanding its physiological function in detail. Despite the incredible progress in experimental techniques, protein structure determination is still expensive, time-consuming, and arduous. That is why computer simulations are often used to complement or interpret experimental data. Here, we explore how in silico protein structure determination based on replica-exchange molecular dynamics (REMD) can benefit from including contact information derived from theoretical and experimental sources, such as direct coupling analysis or NMR spectroscopy. To reflect the influence from erroneous and noisy data we probe how false-positive contacts influence the simulated ensemble. Specifically, we integrate varying numbers of randomly selected native and non-native contacts and explore how such a bias can guide simulations towards the native state. We investigate the number of contacts needed for a significant enrichment of native-like conformations and show the capabilities and limitations of this method. Adhering to a threshold of approximately 75% true-positive contacts within a simulation, we obtain an ensemble with native-like conformations of high quality. We find that contact-guided REMD is capable of delivering physically reasonable models of a protein's structure. CA extern

The temporal and spatial resolution in the microscopy of tissues has increased significantly within the last years, yielding new insights into the dynamics of tissue development and the role of single cells within it. Still, the theoretical description of the connection of single cell processes to macroscopic tissue reorganisations is lacking. Especially in tumour development, single cells play a crucial role in the advance of tumour properties. We developed a simulation framework that can model tissue development up to the centimetre scale with micrometre resolution of single cells. Through parallelisation, it enables the efficient use of high-performance computing systems, therefore enabling detailed simulations on 10.000s of cores. Our generalised tumour model respects adhesion driven cell migration, cell-to-cell signalling, and mutation-driven tumour heterogeneity. We scan the response of the tumour development depending on division inhibiting substances such as cytostatic agents. Furthermore, we are investigating the interaction with radiotherapy to find a suitable therapy plan. Currently, the emergence of ever-more-powerful experimental techniques such as light sheet microscopy already offers unprecedented subcellular insight into tissue dynamics. Combined with powerful machine learning techniques, such large data sets (TB’s +) can be effectively evaluated promising realistic parameters for our simulations for topics ranging from cancer development to embryogenesis or morphogenesis with considerable impact both for basic science and applied biomedical fields.