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 The phonetics of newly derived words: Testing the effect of morphological segmentability on affix duration(HHU, 2018) Plag, Ingo; Ben Hedia, SoniaNewly derived morphologically complex words have played a prominent role in research on morphological productivity and lexical innovation (e.g. Baayen 1989, 1996; Plag 1999; Mühleisen 2010). Most of the attention concerning the properties of such words has been devoted to their phonological, morphological, semantic and syntactic properties (see, for example, Bauer et al. 2013 for such analyses). This paper takes a look at the phonetic properties of affixed words, testing Hay’s (2003) ‘segmentability hypothesis’, according to which newly derived words are expected to show less phonetic integration, hence less phonetic reduction, of the affix involved than established forms. This hypothesis is based on the idea that morphological segmentability negatively correlates with phonological integration. To date there is only one study that clearly confirmed the segmentability hypothesis (i.e. Hay 2007), while other studies have failed to replicate the effect (see Hanique and Ernestus 2012 for an overview). The present study investigates the issue with data from the Switchboard corpus for five affixes of English: un-, locative in-, negative in-, dis- and adverbial -ly. Using different measures of morphological segmentability, we demonstrate that the durations of the two prefixes un- and dis- (unlike the durations of in- and -ly) largely support the segmentability hypothesis. With un- and dis- prefixed words, prefixes that are more easily segmentable have longer durations.Item Table S1: Measured density of the solution of anisole in ethyl acetate versus the weight fraction between 0 and 0.013 of the solute between 258K and 348K. The densities are given as kg/m^-3.(Data in Brief, 2018-10-03) Lindic, Mirko MatthiasMeasured density of the solution of anisole in ethyl acetate versus the weight fraction between 0 and 0.013 of the solute between 258 K and 348 K.Item Table S2: Absorption spectra (in wavenumber) of anisole in ethyl acetate between 258K and 348K in steps of 5K. These data are available as Table S2.doc and Table S2.csv. The raw data (in nm) are available as Table 2.dat(Data in Brief, 2018-10-03) Lindic, Mirko MatthiasAbsorption spectra (in wavenumber) of anisole in ethyl acetate between 258K and 348K in steps of 5K.Item Table S4: Linearized laser induced fluroescence Stark spectrum of anisole at an electric field strength of 819:09Vcm1. The first column gives the relative frequeny in 1MHz increment, the second column the relative intensities.(Data in Brief, 2018-10-03) Schneider, Michael; Hebestreit, Marie-LuiseLinearized laser induced fluroescence Stark spectrum of anisole at an electric field strength of 819:09V/cm. The first column gives the relative frequeny in 1MHz increment, the second column the relative intensities.Item Table S3: Emission spectra (in wavenumber) of anisole in ethyl acetate between 258K and 348K in steps of 5K. These data are available as Table S3.doc and Table S3.csv. The raw data (in nm) are available as Table 3.dat(Data in Brief, 2018-10-03) Lindic, Mirko MatthiasEmission spectra (in wavenumber) of anisole in ethyl acetate between 258K and 348K in steps of 5K.Item Anis an , or is it? Plural and genitive-plural are not homophonous(hhu, 2019) Ingo Plag, Arne Lohmann, Sonia Ben Hedia, & Julia ZimmermannItem 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 Sequence alignments of alpha and beta spectrin(N/A, 2020) Wäschenbach, Lucas; Gohlke, Holger*** Multiple sequence alignment of erythrocytic α-spectrin sequences from 58 different species Sequences of erythrocytic α-spectrin were collected from the UniProtKB database at uniprot.org. 58 sequences with “erythrocytic α-spectrin” annotation were selected with an additional criterium being a comparable sequence length to human erythrocytic α-spectrin (2,419 residues). Multiple sequence alignment was performed with Clustal Omega (webserver version accessed at https://www.ebi.ac.uk/Tools/msa/clustalo/ on 04.30.2020) with default parameters. The result is given in the file with the ending .clustal_num. In addition, the sequence alignment is displayed as a .tif file, with colored residues indicating high identiy according to the ‘identity’ coloring option of Mview; colors vary according to physicochemical properties as specified in the MView documentation (Madeira, Park et al. 2019). *** Multiple sequence alignment of erythrocytic β-spectrin sequences from 11 different species Sequences of erythrocytic β-spectrin were collected from the UniProtKB database at uniprot.org. 11 sequences with “erythrocytic β -spectrin” annotation were selected with an additional criterium being a comparable sequence length to human erythrocytic β-spectrin (2,137 residues). Multiple sequence alignment was performed with Clustal Omega (webserver version accessed at https://www.ebi.ac.uk/Tools/msa/clustalo/ on 04.30.2020) with default parameters. The result is given in the file with the ending .clustal_num. In addition, the sequence alignment is displayed as a .tif file, with colored residues indicating high identiy according to the ‘identity’ coloring option of Mview; colors vary according to physicochemical properties as specified in the MView documentation (Madeira, Park et al. 2019). *** Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., and Lopez, R. (2019) The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 47, W636-W641Item 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 A spectrum of verticality across genes(PLoS Genetics, 2020-11-02) Nagies, Falk S. P.; Brueckner, Julia; Tria, Fernando T. K.; Martin, Willam F.Supplementary Table S9 - A spectrum of verticality across genes - https://doi.org/10.1371/journal.pgen.1009200Item TopDomain dataset(N/A, 2021) Mulnaes, Daniel; Golchin, Pegah; Koenig, Filip; Gohlke, HolgerThis is the TopDomain dataset as described in: "TopDomain: Exhaustive Protein Domain Boundary Meta-Prediction Combining Multi-Source Information and Deep Learning" by Daniel Mulnaes, Pegah Golchin, Filip Koenig, and Holger Gohlke. This dataset contains two folder: training_set : Contains the fasta files of the TopDomain training set; test_set: Contains the fasta files of the TopDomain test set. Each fasta file has a header with three fields, in the following format: ">system_name|domain_type|boundary_list". Where: system_name contains the PDB ID and chain ID of the target protein; domain_type contains target type, either single-domain or multi-domain; boundary_list contains a list of residues annotated as domain boundaries separated by spaces, this field is empty for single-domain proteins as they have no domain boundaries. The sequence is the fasta-sequence of the protein, each line contains at most 100 residues of the protein sequence. No protein in the test set shares more than 20% sequence identity to any protein in the training set.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 Supporting Information for "Molecular modeling and simulations of DNA and RNA: DNAzyme as a model system"(N/A, 2021-03-17) Gertzen, Christoph; Gohlke, HolgerNowadays, the structural dynamics of DNA and RNA is accessible on an atomistic level on a micro- to millisecond time scale via molecular dynamics simulations. However, as DNA or RNA are highly charged molecules, performing such simulations is challenging as to the representation of intramolecular electrostatic interactions and those to solvent molecules and ions. This is particularly true for DNAzymes, where DNA and RNA backbones can come as close as 2.4 Å with their charged phosphate groups during the catalytic cycle. Here, we present tools to simulate the structural dynamics of a DNAzyme, with a focus on detailed instructions for the Amber suite of programs. Furthermore, we will show how to analyze metal ion binding within the DNAzyme.Item Structural models of SFV Bet protein as SI for "Foamy Viruses, Bet, and APOBEC3 Restriction"(N/A, 2021-03-18) Vasudevan, Ananda; Becker, Daniel; Luedde, Tom; Gohlke, Holger; Muenk, CarstenDomain boundaries within the sequence of the SFV-chimpanzee Bet protein sequence were predicted with TopDomain. The two domains were modeled using the ROBETTA webserver. For each domain, ROBETTA generated five models. The best model was chosen based on the lowest Cα atom RMSD between the generated models and the corresponding ab initio modeled domain of PFV Bet. This consensus approach was also validated by TopScore in that domains with the lowest RMSD also have the lowest TopScore compared to the other four models. For the N-terminal domain, the overall TopScore is 0.47 and for the C-terminal one 0.45, indicating a moderate quality of the models. In the N-terminal domain, the helical part of the structure has low local TopScores, indicating good quality, but the N-terminal loops high local TopScores, indicating low quality. In the C-terminal domain, the β-strands have low local TopScores, indicating good quality, but helices and loops from residues 358–403 have high local TopScores, indicating low quality.Item TopDomain dataset v2.0(N/A, 2021-05-01) Mulnaes, Daniel; Golchin, Pegah; Koenig, Filip; Gohlke, HolgerThis is the TopDomain dataset v2.0 as described in: "TopDomain: Exhaustive Protein Domain Boundary Meta-Prediction Combining Multi-Source Information and Deep Learning" by Daniel Mulnaes, Pegah Golchin, Filip Koenig, and Holger Gohlke. This dataset contains three folder: dataset : Contains the full dataset and the TopDomain and TopDomainSeq predictions for the dataset training_set : Contains the fasta files of the TopDomain training set test_set : Contains the fasta files of the TopDomain test set Each fasta file has a header with three fields, in the following format: >system_name|domain_type|boundary_list Where: system_name contains the PDB ID and chain ID of the target protein domain_type contains target type, either single-domain or multi-domain boundary_list contains a list of residues annotated as domain boundaries separated by spaces, this field is empty for single-domain proteins as they have no domain boundaries The sequence is the fasta-sequence of the protein each line contains at most 100 residues of the protein sequence No protein in the test set shares more than 20% sequence identity to any protein in the training set.Item TopProperty dataset(N/A, 2021-07-07) Mulnaes, Daniel; Schott-Verdugo, Stephan; Koenig, Filip; Gohlke, HolgerTransmembrane proteins (TMPs) are critical components of cellular life. However, due to experimental challenges, the number of experimentally resolved TMP structures is severely underrepresented in databases compared to their cellular abundance. Prediction of (per-residue) features such as transmembrane topology, membrane exposure, secondary structure, and solvent accessibility can be a useful starting point for experimental design or protein structure prediction, but often requires different computational tools for different features or types of proteins. We present TopProperty, a meta-predictor that predicts all of these features for TMPs or globular proteins. TopProperty predictions are robust, especially for proteins with few sequence homologs, and significantly better than the evaluated state-of-the-art primary predictors on all quality metrics. TopProperty eliminates the need for protein type- or feature-tailored tools, specifically for TMPs. TopProperty is freely available as web server and standalone at https://cpclab.uni-duesseldorf.de/topsuite/.Item Simulation data for "Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity"(N/A, 2021-07-12) Ahmad, Sabahuddin; Strunk, Christoph; Schott-Verdugo, Stephan; Jaeger, Karl-Erich; Kovacic, Filip; Gohlke, HolgerPlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates has remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by fatty acid-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.Item Supporting Information for "F/G-Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism"(N/A, 2021-07-13) Becker, Daniel; Bharatam, Prasad; Gohlke, HolgerOf 57 human Cytochrome P450 (CYP) enzymes, twelve metabolize 90% of xenobiotics. To our knowledge, no study has addressed the relation between enzyme dynamics and substrate promiscuity for more than three CYPs. Here, we show by constraint dilution simulations with the Constraint Network Analysis for the twelve isoforms that structural rigidity of the F/G-region is significantly inversely correlated to the enzymes’ substrate promiscuity. This highlights the functional importance of structural dynamics of the substrate tunnel.
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