The Faculties
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The Heinrich Heine University (HHU) is divided up into five faculties which are all located on one campus. The oldest one and core of the university is the Faculty of Medicine, followed by the Faculty of Mathematics and Natural Sciences and the Faculty of Arts and Humanities. In the late 1980s and early 1990s the Faculty of Business and Economics and the Faculty of Law were then launched.
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Item Acoustics of word-final S(Heinrich-Heine-Universität Düsseldorf, 2019-03-19) Plag, Ingo; Homann, Julia; Kunter, GeroRecent research has shown that homophonous lexemes show systematic phonetic differences (e.g. Gahl 2008, Drager 2011), with important consequences for models of speech production such as Levelt et al. (1999). These findings also pose the question of whether similar differences hold for allegedly homophonous affixes (instead of free lexemes). Earlier experimental research found some evidence that morphemic and nonmorphemic sounds may differ acoustically (Walsh & Parker 1983, Losiewicz 1992). This paper investigates this question by analyzing the phonetic realization of non-morphemic /s/ and /z/, and of six different English /s/ and /z/ morphemes (plural, genitive, genitive-plural and 3rd person singular, as well as cliticized forms of has and is). The analysis is based on more than 600 tokens extracted from conversational speech (Buckeye Corpus, Pitt et al. 2007). Two important results emerge. First, there are significant differences in acoustic duration between some morphemic /s/’s and /z/’s and non-morphemic /s/ and /z/, respectively. Second, there are significant differences in duration between some of the morphemes. These findings challenge standard assumptions in morphological theory, lexical phonology and models of speech production.Item Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled asgard archaea(Genome Biology and Evolution, 2020) Garg, SG; Kapust, N; Lin, W; Knopp, M; Tria, FDK; Nelson-Sathi, S; Gould, SB; Fan, L; Zhu, R; Zhang, C; Martin, WFSupplement to a paper in GBE (title: Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled asgard archaea)Item Electronic Supporting Information for MOLSTRUC-D-21-03929(Journal of Molecular Structure, 2021) Hebestreit, Marie-LuiseThis collection gives a) the experimental and simulated zero-field spectrum of the electronic origin of 6-methylindole b) the experimental and simulated Stark spectrum of the electronic origin of 6-methylindole at 425.49 V/cmItem Item FC-Fit(No, 2022) Krügler, Daniel; Schmitt, MichaelFCfit is program for the simulation and fit of vibronic absorption and emission spectra based on the evaluation of relative Franck-Condon (FC) factors and/or Franck-Condon-Herzberg-Teller (FCHT) theory. The program computes the FC integrals of multidimensional, harmonic oscillators mainly based on the recursion formula given in the papers of Doktorov, Malkin, and Man’ko.Item Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation(Institute of Molecular Evolution, 2023) Brabender, Max; Henriques Pereira, Delfina P.; Mrnjavac, Natalia; Schlikker, Manon Laura; Kimura, Zen-Ichiro; Sucharitakul, Jeerus; Kleinermanns, Karl; Tüysüz, Harun; Buckel, Wolfgang; Preiner, Martina; Martin, William F.Raw data of UV-VIS spectraItem Functional and structural characterization of interactions between opposite subunits in HCN pacemaker channels(N/A, 2021-08-05) Kondapuram, Mahesh; Frieg, Benedikt; Yüksel, Sezin; Schwabe, Tina; Sattler, Christian; Lelle, Marco; Schweinitz, Andrea; Schmauder, Ralf; Benndorf, Klaus; Gohlke, Holger; Kusch, JanaHyperpolarization-activated and cyclic nucleotide (HCN) modulated channels are tetrameric cation channels. In each of the four subunits, the intracellular cyclic nucleotide-binding domain (CNBD) is coupled to the transmembrane domain via a helical structure, the C-linker. High-resolution channel structures suggest that the C-linker enables functionally relevant interactions with the opposite subunit, which might be critical for coupling the conformational changes in the CNBD to the channel pore. We combined mutagenesis, patch-clamp technique, confocal patch-clamp fluorometry, and molecular dynamics simulations to show that residue K464 of the C-linker is essential for stabilizing the closed state of the mHCN2 channel by forming interactions with the opposite subunit. MD simulations revealed that both cAMP and K464E induce a rotation of the intracellular domain relative to the channel pore, weakening the autoinhibitory effect of the unoccupied CL-CNBD region. The adopted poses are in excellent agreement with structural results.Item Item MD simulation data for: "Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa"(N/A, 2023-11) Gentile, Rocco; Schott-Verdugo, Stephan; Gohlke, HolgerPlaF is a membrane-bound phospholipase A1 from P. aeruginosa that is involved in remodeling membrane glycerophospholipids (GPLs) and modulation of virulence-associated signaling and metabolic pathways. Previously, we identified the role of medium-chain free fatty acids (FFA) in inhibiting PlaF activity and promoting homodimerization, yet the underlying molecular mechanism remained elusive. Here, we used unbiased and biased molecular dynamics simulations and free energy computations to assess how PlaF interacts with FFAs localized in the water milieu surrounding the bilayer or within the bilayer, and how these interactions regulate PlaF activity. Medium-chain FFAs localized in the upper bilayer leaflet can stabilize inactive dimeric PlaF, likely through interactions with charged surface residues as experimentally validated. Potential of mean force (PMF) computations indicate that membrane-bound FFAs may facilitate the activation of monomeric PlaF by lowering the activation barrier of changing into a tilted, active configuration. We estimated that the coupled equilibria of PlaF monomerization-dimerization and tilting at the physiological concentration of PlaF lead to the majority of PlaF forming inactive dimers when in a cell membrane loaded with decanoic acid (C10). This is in agreement with a suggested in vivo product feedback loop and GC-MS profiling results indicating that PlaF catalyzes the release of C10 from P. aeruginosa membranes. Additionally, we found that C10 in the water milieu can access the catalytic site of active monomeric PlaF, contributing to the competitive component of C10-mediated PlaF inhibition. Our study provides mechanistic insights into how medium-chain FFA may regulate the activity of PlaF, a potential bacterial drug target.Item MD simulation data for: "The cyclophilin A binding loop of the capsid regulates the human TRIM5α sensitivity of nonpandemic HIV-1"(N/A, 2023-11) Becker, Daniel; Münk, Carsten; Gohlke, HolgerAll MD input structures, MD infiles, umbrella sampling files, and scripts that were used to analyze the umbrella sampling results are provided in this supporting repository.Item Millisecond-long sampling for a comprehensive energetic evaluation of aqueous ionic liquid effects on amino acid interactions(N/A, 2022-09-01) El Harrar, Till; Gohlke, HolgerThe interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data is available describing the energetic effect of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of > 1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol 1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provides explanations at the atomistic and energetic level for complex IL effects on protein stability and should help improve the prediction accuracy of computational tools that estimate protein stability based on (free) energy functions.Item Molecular dynamics simulations data and analysis scripts used for Grx5 in the publication "Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins"(N/A, 2020-02) Wäschenbach, Lucas; Gohlke, HolgerThe files in this directory contain the molecular dynamics simulations data and analysis scripts for Grx5 used in the publication "Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins"Item Molecular dynamics simulations data and analysis scripts used for Grx7 in the publication "Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins"(N/A, 2020-02) Wäschenbach, Lucas; Gohlke, HolgerThe files in this directory contain the molecular dynamics simulations data and analysis scripts for Grx7 used in the publication "Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins"Item Movie for: The architecture of the 10-23 DNAzyme and its implications for DNA-mediated catalysis(N/A, 2022-09-19) Christoph, Gertzen; Jan, Borggräfe; Aldino, Viegas; Manuel, Etzkorn; Holger, GohlkeUnderstanding the molecular features of catalytically active DNA sequences, so-called DNAzymes, is not only essential for our understanding of the fundamental properties of catalytic nucleic acids in general but may well be the key to unraveling their full potential via tailored modifications. Our recent findings contributed to the endeavor to assemble a mechanistic picture of DNA-mediated catalysis by providing high-resolution structural insights into the 10-23 DNAzyme (Dz) and exposing a complex interplay between the Dz´s unique molecular architecture, conformational plasticity, and dynamic modulation by metal ions as central elements of the DNA catalyst. To illustrate the sampled conformational space, the movie depicts one MD trajectory of the Dz:RNA complex.Item Petersilie et al. 2023 - Figure 1(iScience, 2023) Petersilie, Laura; Heiduschka, Sonja; Nelson, Joel S. E.; Neu, Louis A.; Le, Stephanie; Anand, Ruchika; Kafitz, Karl W.; Prigione, Alessandro; Rose, Christine R.Brain organoids derived from human pluripotent stem cells (hPSCs) are a promising tool for studying human neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We demonstrate that cBOS host mature neurons and astrocytes organized in complex architecture. By leveraging the fact that cBOS allow direct access to the developing neural cells, we carried out an array of functional analyses. Whole-cell patch-clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large-scale calcium oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Lastly, FRET-based imaging with the genetically-encoded nanosensor ATeam1.03YEMK revealed the high sensitivity of neurons to acute metabolic inhibition. Altogether, cBOS represent a powerful platform for assessing the morphological and functional aspects of organized human neural cells in intact minimal networks.Item Petersilie et al. 2023 - Figure 2(iScience, 2023) Petersilie, Laura; Heiduschka, Sonja; Nelson, Joel S. E.; Neu, Louis A.; Le, Stephanie; Anand, Ruchika; Kafitz, Karl W.; Prigione, Alessandro; Rose, Christine R.Brain organoids derived from human pluripotent stem cells (hPSCs) are a promising tool for studying human neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We demonstrate that cBOS host mature neurons and astrocytes organized in complex architecture. By leveraging the fact that cBOS allow direct access to the developing neural cells, we carried out an array of functional analyses. Whole-cell patch-clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large-scale calcium oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Lastly, FRET-based imaging with the genetically-encoded nanosensor ATeam1.03YEMK revealed the high sensitivity of neurons to acute metabolic inhibition. Altogether, cBOS represent a powerful platform for assessing the morphological and functional aspects of organized human neural cells in intact minimal networks.Item Petersilie et al. 2023 - Figure 3(iScience, 2023) Petersilie, Laura; Heiduschka, Sonja; Nelson, Joel S. E.; Neu, Louis A.; Le, Stephanie; Anand, Ruchika; Kafitz, Karl W.; Prigione, Alessandro; Rose, Christine R.Brain organoids derived from human pluripotent stem cells (hPSCs) are a promising tool for studying human neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We demonstrate that cBOS host mature neurons and astrocytes organized in complex architecture. By leveraging the fact that cBOS allow direct access to the developing neural cells, we carried out an array of functional analyses. Whole-cell patch-clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large-scale calcium oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Lastly, FRET-based imaging with the genetically-encoded nanosensor ATeam1.03YEMK revealed the high sensitivity of neurons to acute metabolic inhibition. Altogether, cBOS represent a powerful platform for assessing the morphological and functional aspects of organized human neural cells in intact minimal networks.Item Petersilie et al. 2023 - Figure 4(iScience, 2023) Petersilie, Laura; Heiduschka, Sonja; Nelson, Joel S. E.; Neu, Louis A.; Le, Stephanie; Anand, Ruchika; Kafitz, Karl W.; Prigione, Alessandro; Rose, Christine R.Brain organoids derived from human pluripotent stem cells (hPSCs) are a promising tool for studying human neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We demonstrate that cBOS host mature neurons and astrocytes organized in complex architecture. By leveraging the fact that cBOS allow direct access to the developing neural cells, we carried out an array of functional analyses. Whole-cell patch-clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large-scale calcium oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Lastly, FRET-based imaging with the genetically-encoded nanosensor ATeam1.03YEMK revealed the high sensitivity of neurons to acute metabolic inhibition. Altogether, cBOS represent a powerful platform for assessing the morphological and functional aspects of organized human neural cells in intact minimal networks.Item Petersilie et al. 2023 - Figure 5(iScience, 2023) Petersilie, Laura; Heiduschka, Sonja; Nelson, Joel S. E.; Neu, Louis A.; Le, Stephanie; Anand, Ruchika; Kafitz, Karl W.; Prigione, Alessandro; Rose, Christine R.Brain organoids derived from human pluripotent stem cells (hPSCs) are a promising tool for studying human neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We demonstrate that cBOS host mature neurons and astrocytes organized in complex architecture. By leveraging the fact that cBOS allow direct access to the developing neural cells, we carried out an array of functional analyses. Whole-cell patch-clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large-scale calcium oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Lastly, FRET-based imaging with the genetically-encoded nanosensor ATeam1.03YEMK revealed the high sensitivity of neurons to acute metabolic inhibition. Altogether, cBOS represent a powerful platform for assessing the morphological and functional aspects of organized human neural cells in intact minimal networks.Item Petersilie et al. 2023 - Figure 6(iScience, 2023) Petersilie, Laura; Heiduschka, Sonja; Nelson, Joel S. E.; Neu, Louis A.; Le, Stephanie; Anand, Ruchika; Kafitz, Karl W.; Prigione, Alessandro; Rose, Christine R.Brain organoids derived from human pluripotent stem cells (hPSCs) are a promising tool for studying human neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We demonstrate that cBOS host mature neurons and astrocytes organized in complex architecture. By leveraging the fact that cBOS allow direct access to the developing neural cells, we carried out an array of functional analyses. Whole-cell patch-clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large scale calcium oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Lastly, FRET-based imaging with the genetically-encoded nanosensor ATeam1.03YEMK revealed the high sensitivity of neurons to acute metabolic inhibition. Altogether, cBOS represent a powerful platform for assessing the morphological and functional aspects of organized human neural cells in intact minimal networks.
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