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Determining the structure and mechanisms of all individual functional modules of cells at high molecular detail has often been seen as equal to understanding how cells work. Recent technical advances have led to a flush of high-resolution structures of various macromolecular machines, but despite this wealth of detailed information, our understanding of cellular function remains incomplete. Here, we discuss present-day limitations of structural biology and highlight novel technologies that may enable us to analyze molecular functions directly inside cells. We predict that the progression toward structural cell biology will involve a shift toward conceptualizing a 4D virtual reality of cells using digital twins. These will capture cellular segments in a highly enriched molecular detail, include dynamic changes, and facilitate simulations of molecular processes, leading to novel and experimentally testable predictions. Transferring biological questions into algorithms that learn from the existing wealth of data and explore novel solutions may ultimately unveil how cells work.
The ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different length, linkage-type and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying length, as well as, homotypic and heterotypic branched chains of the two most abundant linkage types – K48- and K63-linked Ub. We identified some of the first K48/K63 branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4 and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50 and p97-adaptor FAF1. Crucially, we compared datasets collected using two common DUB inhibitors – Chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.
Microbial rhodopsins are omnipresent on Earth, however the vast majority of them remain uncharacterized. Here we describe a new rhodopsin group from cold-adapted organisms and cold environments, such as glaciers, denoted as CryoRhodopsins (CryoRs). Our data suggest that CryoRs have dual functionality switching between inward transmembrane proton translocation and photosensory activity, both of which can be modulated with UV light. CryoR1 exhibits two subpopulations in the ground state, which upon light activation lead to transient photocurrents of opposing polarities. A distinguishing feature of the group is the presence of a buried arginine residue close to the cytoplasmic face of its members. Combining single-particle cryo-electron microscopy and X-ray crystallography with the rhodopsin activation by lit, we demonstrate that the arginine stabilizes a UV-absorbing intermediate of an extremely slow CryoRhodopsin photocycle. Together with extensive spectroscopic characterization, our investigations on CryoR1 and CryoR2 proteins reveal mechanisms of photoswitching in the newly identified group and demonstrate principles of the adaptation of these rhodopsins to low temperatures.Microbial rhodopsins are omnipresent on Earth, however the vast majority of them remain uncharacterized. Here we describe a new rhodopsin group from cold-adapted organisms and cold environments, such as glaciers, denoted as CryoRhodopsins (CryoRs). Our data suggest that CryoRs have dual functionality switching between inward transmembrane proton translocation and photosensory activity, both of which can be modulated with UV light. CryoR1 exhibits two subpopulations in the ground state, which upon light activation lead to transient photocurrents of opposing polarities. A distinguishing feature of the group is the presence of a buried arginine residue close to the cytoplasmic face of its members. Combining single-particle cryo-electron microscopy and X-ray crystallography with the rhodopsin activation by light, we demonstrate that the arginine stabilizes a UV-absorbing intermediate of an extremely slow CryoRhodopsin photocycle. Together with extensive spectroscopic characterization, our investigations on CryoR1 and CryoR2 proteins reveal mechanisms of photoswitching in the newly identified group and demonstrate principles of the adaptation of these rhodopsins to low temperatures.
Microbial rhodopsins are omnipresent on Earth, however the vast majority of them remain uncharacterized. Here we describe a new rhodopsin clade from cold-adapted organisms and cold environments, such as glaciers, denoted as CryoRhodopsins (CryoRs). Our data suggest that CryoRs have photosensory activity. A distinguishing feature of the clade is the presence of a buried arginine residue close to the cytoplasmic face of its members. Combining single-particle cryo-electron microscopy and X-ray crystallography with the rhodopsin activation by light, we demonstrate that the arginine stabilizes a strongly blue-shifted intermediate of an extremely slow CryoRhodopsin photocycle. Together with extensive spectroscopic characterization, our investigations on CryoR1 and CryoR2 proteins reveal mechanisms of photoswitching in the newly identified clade and demonstrate principles of the adaptation of these rhodopsins to low temperatures.
Nuclear pore complexes (NPCs) constitute giant channels within the nuclear envelope that mediate nucleocytoplasmic exchange. NPC diameter is thought to be regulated by nuclear envelope tension, but how such diameter changes are physiologically linked to cell differentiation, where mechanical properties of nuclei are remodeled and nuclear mechanosensing occurs, remains unstudied. Here we used cryo-electron tomography to show that NPCs dilate during differentiation of mouse embryonic stem cells into neural progenitors. In Nup133-deficient cells, which are known to display impaired neural differentiation, NPCs however fail to dilate. By analyzing the architectures of individual NPCs with template matching, we revealed that the Nup133-deficient NPCs are structurally heterogeneous and frequently disintegrate, resulting in the formation of large nuclear envelope openings. We propose that the elasticity of the NPC scaffold mechanically safeguards the nuclear envelope. Our studies provide a molecular explanation for how genetic perturbation of scaffolding components of macromolecular complexes causes tissue-specific phenotypes.
Upon infection, human immunodeficiency virus (HIV-1) releases its cone-shaped capsid into the cytoplasm of infected T-cells and macrophages. As its largest known cargo, the capsid enters the nuclear pore complex (NPC), driven by interactions with numerous FG-repeat nucleoporins (FG-Nups). Whether NPCs structurally adapt to capsid passage and whether capsids are modified during passage remains unknown, however. Here, we combined super-resolution and correlative microscopy with cryo electron tomography and molecular simulations to study nuclear entry of HIV-1 capsids in primary human macrophages. We found that cytosolically bound cyclophilin A is stripped off capsids entering the NPC, and the capsid hexagonal lattice remains largely intact inside and beyond the central channel. Strikingly, the NPC scaffold rings frequently crack during capsid passage, consistent with computer simulations indicating the need for NPC widening. The unique cone shape of the HIV-1 capsid facilitates its entry into NPCs and helps to crack their rings.
The lipid content of skin plays a determinant role in its barrier function with a particularly important role attributed to linoleic acid and its derivatives. Here we explored the consequences of interfering with the soluble epoxide hydrolase (sEH) on skin homeostasis. sEH; which converts fatty acid epoxides generated by cytochrome P450 enzymes to their corresponding diols, was largely restricted to the epidermis which was enriched in sEH-generated diols. Global deletion of the sEH increased levels of epoxides, including the linoleic acid-derived epoxide; 12,13-epoxyoctadecenoic acid (12,13-EpOME), and increased basal keratinocyte proliferation. sEH deletion (sEH-/- mice) resulted in thicker differentiated spinous and corneocyte layers compared to wild-type mice, a hyperkeratosis phenotype that was reproduced in wild-type mice treated with a sEH inhibitor. sEH deletion made the skin sensitive to inflammation and sEH-/- mice developed thicker imiquimod-induced psoriasis plaques than the control group and were more prone to inflammation triggered by mechanical stress with pronounced infiltration and activation of neutrophils as well as vascular leak and increased 12,13-EpOME and leukotriene (LT) B4 levels. Topical treatment of LTB4 antagonist after stripping successfully inhibited inflammation and neutrophil infiltration both in wild type and sEH-/- skin. While 12,13-EpoME had no effect on the trans-endothelial migration of neutrophils, like LTB4, it effectively induced neutrophil adhesion and activation. These observations indicate that while the increased accumulation of neutrophils in sEH-deficient skin could be attributed to the increase in LTB4 levels, both 12,13-EpOME and LTB4 contribute to neutrophil activation. Our observations identify a protective role of the sEH in the skin and should be taken into account when designing future clinical trials with sEH inhibitors.
Correlative dynamic imaging of cellular landmarks, such as nuclei and nucleoli, cell membranes, nuclear envelope and lipid droplets is critical for systems cell biology and drug discovery, but challenging to achieve with molecular labels. Virtual staining of label-free images with deep neural networks is an emerging solution for correlative dynamic imaging. Multiplexed imaging of cellular landmarks from scattered light and subsequent demultiplexing with virtual staining leaves the light spectrum for imaging additional molecular reporters, photomanipulation, or other tasks. Current approaches for virtual staining of landmark organelles are fragile in the presence of nuisance variations in imaging, culture conditions, and cell types. We report training protocols for virtual staining of nuclei and membranes robust to variations in imaging parameters, cell states, and cell types. We describe a flexible and scalable convolutional architecture, UNeXt2, for supervised training and self-supervised pre-training. The strategies we report here enable robust virtual staining of nuclei and cell membranes in multiple cell types, including human cell lines, neuromasts of zebrafish and stem cell (iPSC)-derived neurons, across a range of imaging conditions. We assess the models by comparing the intensity, segmentations, and application-specific measurements obtained from virtually stained and experimentally stained nuclei and cell membranes. The models rescue missing labels, non-uniform expression of labels, and photobleaching. We share three pre-trained models (VSCyto3D, VSNeuromast, and VSCyto2D) and a PyTorch-based pipeline (VisCy) for training, inference, and deployment that leverages current community standards for image data and metadata.
Hidradenitis suppurativa ist eine multifaktoriell-bedingte chronisch entzündliche Hauterkrankung, die durch eine Okklusion der Talgdrüseneinheit des Haarfollikels entsteht. Aus der anschließend mit Entzündung einhergehenden Ruptur des Haarfollikels entwickeln sich entzündliche Knoten, Abszesse und Fistelgänge. (39–41) In der weiteren Progression der Erkrankung kommt es zur Störung der Hautarchitektur und fibrotischen Narbenbildungen. (52) Durch Untersuchungen des entzündlichen Infiltrates konnte bereits die Beteiligung einer Reihe von Immunzellen und Entzündungsmediatoren identifiziert werden. Hierzu zählen Makrophagen, neutrophile Granulozyten, Dendritische Zellen, Lymphozyten, IL-1β sowie TNF-α. (41,45,46,51,53) Da die genaue Pathophysiologie der Hidradenitis suppurativa bislang unzureichend aufgeklärt ist, gibt es aktuell keine kausale Therapiemöglichkeit für die Betroffenen. (52) Die Wahl der Therapie wird anhand der Bewertung des Schweregrades nach Hurley getroffen. (25) Obwohl meisten Patientinnen und Patienten von der milden bis mittelschweren Form der Hidradenitis suppurativa (Hurley I und Hurley II) betroffen sind (98), werden die meisten Arzneimittel für die Behandlung von Hurley II und Hurley III von den Leitlinien empfohlen. Zu den empfohlenen Medikamenten gehören u. a. Rifampicin, meist in Kombination mit Clindamycin, sowie der TNF-α-Inhibitor Adalimumab (18,85), welche effektiv und systemisch wirken. Durch die entstehenden Nebenwirkungen wäre die Behandlung der milden bis mittelschweren Hidradenitis suppurativa mit diesen Medikamenten allerdings unverhältnismäßig. Um jedoch den im Verlauf der Krankheit entstehenden Hautdestruktionen vorbeugen zu können, müssten die Medikamente möglichst früh eingesetzt werden. (228) Vor diesem Hintergrund sollte in Kooperation mit dem Institut für Pharmazeutische Technologie der Goethe Universität Frankfurt eine Rifampicin-Nanoformulierung zur Behandlung milder bis mittelschwerer Hidradenitis suppurativa entwickelt und im Labor der dermatologischen Klinik präklinisch validiert werden.
Daher wurde im ersten Teil der vorliegenden Arbeit ein Epidermismodell aus der Haut betroffener Patientinnen und Patienten generiert, um die Rifampicin-Nanoformulierung validieren zu können. Dieses wies eine mehrschichtige Epidermis mit allen wichtigen Differenzierungsmarkern ähnlich der läsionalen Hidradenitis suppurativa auf und schüttete die proinflammatorischen Zytokine IL-1β und TNF-α aus. Als weiteres Modell wurden ex vivo Explantate aus läsionaler Hidradenitis suppurativa Haut etabliert. Für die Bewertung der Validität der Explantatkulturen wurde die Morphologie und Integrität der Epidermis mittels Hämatoxylin-Eosin sowie der Proliferationsmarker Ki-67 näher beleuchtet. Im zweiten Teil dieser Arbeit wurden Untersuchungen für die Festlegung eines Konzentrationsbereichs, unter Verwendung von Rifampicin in DMSO gelöst als in vitro Behandlung, durchgeführt.
Hierbei wurde gezeigt, dass die eingesetzten Konzentrationen keine negativen Effekte bezüglich Proliferationsfähigkeit der Keratinozyten oder Apoptoseinduktion ausüben. Die Behandlung von nicht entzündlichen Epidermismodellen sowie Explantatkulturen mit der Rifampicin-Nanoformulierung mit einem Wirkstoffgehalt von 0,3 % führte ebenfalls zu keinen Proliferationsverlusten, induzierte keine Apoptose oder Zytotoxizität und hatte keinen Einfluss auf die Differenzierung der Keratinozyten. Im letzten Teil der Arbeit sollte die Wirksamkeit der Rifampicin-Nanoformulierung näher beleuchtet werden. Als Antibiotikum inhibiert Rifampicin die DNA-abhängige RNA-Polymerase von Bakterien (107,108), weshalb es bei der Behandlung der Tuberkulose eingesetzt wird. (111–113) Die Hidradenitis suppurativa ist aber primär keine Infektionskrankheit, sondern eine von Bakterien getriggerte, entzündliche Erkrankung. (19,52,82) Aus diesem Grund ist der positive Effekt der systemischen Rifampicintherapie vermutlich vielmehr auf eine antiphlogistische Wirkung zurückzuführen. Diese Überlegung wird durch mehrere Artikel gestützt, die zeigten, dass Rifampicin die Ausschüttung von IL-1β und TNF-α in unterschiedlichen in vitro und in vivo Modellen hemmt. (89–91,96,97) Die anschließenden Untersuchungen zur Wirksamkeit einer in vitro Rifampicinbehandlung bestätigten die antientzündliche Wirkung in den Explantatkulturen indem es die Sekretion von IL-1β, IL-6, IL-8, IL-10 und TNF-α verminderte. Ebenso senkte die Rifampicin-Nanoformulierung die Ausschüttung von IL-1β in den ex vivo Explantaten, was somit die in der klinischen Praxis beobachteten antiinflammatorischen Wirkung von Rifampicin belegt. Des Weiteren stellte sich in Untersuchungen heraus, dass Rifampicin zu einer reduzierten Zahl CD4(+)-T-Zellen führte, aber auf die CD3(+)-T-Zellen keine Auswirkungen hatte, was auf eine Veränderung des T-Zell Phänotyps hinweist.
Aufgrund der vorliegenden Ergebnisse zur Validierung der Rifampicin-Nanoformulierung, spricht nichts gegen die Testung der Rifampicin-Nanoformulierung in einem individuellen Heilversuch am Menschen.
Highlights
• Cryo-EM structures of the yeast low-affinity phosphate importer ScPho90
• Complementary structures reveal insights into the substrate translocation mechanism
• Comparisons with homologous transporters highlight the conserved transport mechanism
• Regulation by the SPX domain is discussed
Summary
Phosphate homeostasis is essential for all living organisms. Low-affinity phosphate transporters are involved in phosphate import and regulation in a range of eukaryotic organisms. We have determined the structures of the Saccharomyces cerevisiae phosphate importer Pho90 by electron cryomicroscopy in two complementary states at 2.3 and 3.1 Å resolution. The symmetrical, outward-open structure in the presence of phosphate indicates bound substrate ions in the binding pocket. In the absence of phosphate, Pho90 assumes an asymmetric structure with one monomer facing inward and one monomer facing outward, providing insights into the transport mechanism. The Pho90 transport domain binds phosphate ions on one side of the membrane, then flips to the other side where the substrate is released. Together with functional experiments, these complementary structures illustrate the transport mechanism of eukaryotic low-affinity phosphate transporters.