Goethe University Data Repository (GUDe)
The archiving and publication platform for scientific research data at Goethe University Frankfurt.
The Goethe University Data Repository (GUDe) provides a platform for its members to electronically archive, share, and publish their research data. GUDe is jointly operated by the University Library and the University Data Center of the Goethe University. The metadata of all public content is freely available and indexed by search engines as well as scientific web services. GUDe follows the FAIR principles for long-term accessibility (minimum 10 years), allows for reliable citation via DOIs as well as cooperative access to non-public data and operates on DSpace-CRIS v7.
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Research Data
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Recent Additions
- Research DataReconstitution of glycan-driven MHC I recycling reveals calreticulin as mediator between TAPBPR and tapasin2026-05-22Protein folding in the endoplasmic reticulum (ER) relies on N-linked glycosylation and glycan remodeling to guide quality control. Major histocompatibility complex class I (MHC I) molecules, essential for adaptive immunity, undergo a specialized maturation pathway involving the peptide-loading complex (PLC), the editor TAPBPR, the UDP-glucose:glycoprotein glucosyltransferase, and the lectin chaperone calreticulin. However, how glycan-dependent mechanisms coordinate MHC I transfer between these factors has remained unclear. Using a fully reconstituted system, we show that retrograde transfer of peptide-receptive MHC I from TAPBPR to tapasin requires calreticulin recognition of monoglucosylated MHC I glycans. While calreticulin’s C-terminal acidic helix is dispensable for releasing reglucosylated MHC I from TAPBPR, it is essential for productive docking of MHC I onto tapasin. These findings reveal a glycan-surveillance mechanism that enables retrieval of suboptimally loaded MHC I molecules missed by the initial quality control at the PLC. Our work defines a glycan-dependent chaperone network, finely tuned by a combination of low-micromolar interactions between the constituents, that ensures efficient MHC I maturation and illustrates fundamental principles of ER protein quality control.
1 5 - Research DataATP-driven conformational dynamics reveal hidden intermediates in a heterodimeric ABC transporter2026-05-11ATP-binding cassette (ABC) transporters are essential molecular machines whose conformational dynamics have largely been inferred from ensemble-averaged measurements. Resolving dynamic heterogeneity and transient intermediates, however, requires single-molecule approaches. Here, we use single-molecule Förster resonance energy transfer (smFRET) to resolve ATP-driven conformational dynamics of the heterodimeric type IV ABC transporter TmrAB, a functional homolog of the human antigen transporter TAP, at the level of individual molecules. Fluorophores positioned at the nucleotide-binding domains and periplasmic gate were validated by accessible-volume simulations, fluorescence lifetimes, and ensemble FRET, demonstrating that these reporters reliably track conformational transitions. Single-molecule analysis distinguishes ATP-free and ATP-bound states and quantifies ATP-dependent population shifts from nucleotide-free to physiological ATP concentrations. Kinetic analysis further reveals an unexpectedly long ATP-bound dwell time of ~300 ms. Using complementary stabilization strategies, we directly resolve a previously hidden outward-facing open state that is kinetically masked under turnover conditions. These results provide the first single-molecule characterization of TmrAB and establish a quantitative single-molecule framework for dissecting ATP-coupled conformational dynamics in heterodimeric ABC transporters.
17 1 - Research DataIntegrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops2026-05-08While the GNRA tetraloops are an extensively studied and common folding motif, their dynamic NMR structures in solution integrating state-of-the-art NMR parameters such as residual dipolar couplings (RDC) and cross correlated relaxation rates (CCR) have previously not been determined. Given their dominant occurrence among tetraloops in the PDB and the advance of experimentally reweighted MD simulations, the present work aims at investigating the entire conformational space of two literature known GNRA tetraloops sequences by an extensive NMR investigation of NOEs, J-couplings constants, RDCs and CCRs as rich experimental base for MD Bayesian/maximum entropy reweighting, as classical structure calculation proofed insufficient for the more dynamic tetraloop. The resulting ensembles were clustered and compared to classically restrained structure calculations, structures from the PDB and models predicted by the prediction algorithms FarFar and Alphafold 3. Our results show that GNRA tetraloops can vary in dynamic sampling of conformational space. They highlight the importance of individual experimental validation of computationally obtained dynamic ensembles and model predictions.
42 1 - Research DataTEI/XML encoded transcription Na_50-714 from the Arthur Schopenhauer Legacy2026-04-30This document is a TEI/XML encoded transcription of the document Na_50-714 from the Arthur Schopenhauer Legacy - 'Schopenhauer-Archive': "Schreiben über die Hintergründe der angebotenen Leibrente des Bankhauses Muhl" from Adele Schopenhauer to Arthur Schopenhauer. Transcribed by Rüdiger Weyer, TEI encoded by Hannah Völker (https://sammlungen.ub.uni-frankfurt.de/schopenhauer/content/titleinfo/4236201)
8 2 - Research DataBiophysical characterization of the conformational landscape underlying SARS-CoV-2 RNA genome circularization2026-04-20RNA viruses possess strictly conserved RNA segments that adopt local structures and act as regulatory cis-acting elements. In addition, long-range RNA-RNA interactions between distant parts of their genome add additional layers of regulatory control. In SARS-CoV-2, crosslinking experiments identified multiple transiently formed long-range interactions within its genome. The longest distance interaction occurs between nucleotides in the 5’- and the 3’-terminal, untranslated regions (UTR’s). Their interaction requires opening of the 5’SL3 element that contains the transcription regulatory core sequence (TRS-L) in the 5’-UTR and of the 3’SL3base element in the 3’-UTR. In this study, we investigate the minimal sequence context necessary for formation of this long-range interaction. We determine alternative secondary structures formed by these elements, their thermodynamic stability and the stability of individual base-pairs. Further, we quantify populations and kinetic parameters in a three-strand equilibrium between the circularized form and the alternative structures formed within the UTR’s. We demonstrate that the stability of circularization is significantly reduced in subgenomic RNAs, pointing at a role of circularization in differentiating between genomic and subgenomic RNA during the viral life cycle.
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Most viewed
- Research DataThe global water resources and use model WaterGAP v2.2e - model output driven by gswp3-w5e5 and historical setup of direct human impacts2023-10-20Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download model output for the time period 1901-2019 that was computed by driving WaterGAP v2.2e by four alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. For two climate datasets, model runs up to 2021 or 2022 are available. For comparison, output of a version of WaterGAP v2.2d that is calibrated to the same dataset of observed streamflow as WaterGAP v2.2e is provided. Each of the climate forcing-model version combinations is run in two socio-economic settings, histsoc and nosoc. In nosoc, human water use is set to zero and man-made reservoirs are assumed to be non-existant. In the paper connected to this dataset (to be submitted to Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. The most important and requested model outputs (total water storage variations, streamflow and water use) are evaluated against observation data. Standard model output is described as well as the specifics of the WaterGAP contribution within the ISIMIP framework. Müller Schmied, H., Cáceres, D., Eisner, S., Flörke, M., Herbert, C., Niemann, C., Peiris, T. A., Popat, E., Portmann, F. T., Reinecke, R., Schumacher, M., Shadkam, S., Telteu, C.-E., Trautmann, T., Döll, P. (2021): The global water resources and use model WaterGAP v2.2d: Model description and evaluation. Geosci. Model Dev., 14, 1037–1079. https://doi.org/10.5194/gmd-14-1037-2021
1537 1034 - Research DataThe global water resources and use model WaterGAP v2.2e - model output driven by gswp3-era5 and historical setup of direct human impacts2023-10-20Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download model output for the time period 1901-2019 that was computed by driving WaterGAP v2.2e by four alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. For two climate datasets, model runs up to 2021 or 2023 are available. For comparison, output of a version of WaterGAP v2.2d that is calibrated to the same dataset of observed streamflow as WaterGAP v2.2e is provided. Each of the climate forcing-model version combinations is run in two socio-economic settings, histsoc and nosoc. In nosoc, human water use is set to zero and man-made reservoirs are assumed to be non-existant. In the paper connected to this dataset (in review with Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. The most important and requested model outputs (total water storage variations, streamflow and water use) are evaluated against observation data. Standard model output is described as well as the specifics of the WaterGAP contribution within the ISIMIP framework. Müller Schmied, H., Cáceres, D., Eisner, S., Flörke, M., Herbert, C., Niemann, C., Peiris, T. A., Popat, E., Portmann, F. T., Reinecke, R., Schumacher, M., Shadkam, S., Telteu, C.-E., Trautmann, T., Döll, P. (2021): The global water resources and use model WaterGAP v2.2d: Model description and evaluation. Geosci. Model Dev., 14, 1037–1079. https://doi.org/10.5194/gmd-14-1037-2021
950 991 - Research DataThe global water resources and use model WaterGAP v2.2e - daily water storage model output driven by gswp3-era5 and historical setup of direct human impacts2024-04-04Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download daily model output for water storage variables for the time period 1901-2019 (2023) that was computed by driving WaterGAP v2.2e by two alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. In the paper connected to this dataset (in review with Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. Here, the single water storage compartments and terrestrial (total) water storage are provided.
429 326 - Research DataThe global water resources and use model WaterGAP v2.2e - daily water storage model output driven by gswp3-w5e5 and historical setup of direct human impacts2024-04-04Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download daily model output for water storage variables for the time period 1901-2019 (2023) that was computed by driving WaterGAP v2.2e by two alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. In the paper connected to this dataset (in review with Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. Here, the single water storage compartments and terrestrial (total) water storage are provided.
399 198 - Research DataA j_eff 12 Kitaev material on the triangular lattice: The case of NaRuO22023-06-07Motivated by recent reports of a quantum disordered ground state in the triangular lattice compound NaRuO$_2$, we derive a $j_{\rm eff}=1/2$ magnetic model for this system by means of first-principles calculations. The pseudospin Hamiltonian is dominated by bond-dependent off-diagonal $\Gamma$ interactions, complemented by a ferromagnetic Heisenberg exchange and a notably \emph{antiferromagnetic} Kitaev term. In addition to bilinear interactions, we find a sizable four-spin ring exchange contribution with a \emph{strongly anisotropic} character, which has been so far overlooked when modeling Kitaev materials. The analysis of the magnetic model, based on the minimization of the classical energy and exact diagonalization of the quantum Hamiltonian, points toward the existence of a rather robust easy-plane ferromagnetic order, which cannot be easily destabilized by physically relevant perturbations.
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