The Faculty of Mathematics and Natural Sciences

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The Faculty of Mathematics and Natural Sciences (MNF) employs more than 800 Scientists in seven departments: Biology, Chemistry, Computer Sciences, Mathematics, Pharmacy, Physics and Psychology. Among the wide-ranging research areas covered by the faculty, several cooperative programmes put specific emphasis on Life Sciences and Physics.

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    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 Matthias
    Measured 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.
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    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 Matthias
    Absorption spectra (in wavenumber) of anisole in ethyl acetate between 258K and 348K in steps of 5K.
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    Table S4: Linearized laser induced fluroescence Stark spectrum of anisole at an electric field strength of 819:09Vcm􀀀1. 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-Luise
    Linearized 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.
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    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 Matthias
    Emission spectra (in wavenumber) of anisole in ethyl acetate between 258K and 348K in steps of 5K.
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    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, WF
    Supplement to a paper in GBE (title: Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled asgard archaea)
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    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-W641
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    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, Holger
    The 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"
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    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, Holger
    The 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"
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    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.1009200
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    TopDomain dataset
    (N/A, 2021) Mulnaes, Daniel; Golchin, Pegah; Koenig, Filip; Gohlke, Holger
    This 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.
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    Electronic Supporting Information for MOLSTRUC-D-21-03929
    (Journal of Molecular Structure, 2021) Hebestreit, Marie-Luise
    This 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/cm
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    Supporting Information for "Molecular modeling and simulations of DNA and RNA: DNAzyme as a model system"
    (N/A, 2021-03-17) Gertzen, Christoph; Gohlke, Holger
    Nowadays, 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.
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    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, Carsten
    Domain 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.
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    TopDomain dataset v2.0
    (N/A, 2021-05-01) Mulnaes, Daniel; Golchin, Pegah; Koenig, Filip; Gohlke, Holger
    This 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.
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    TopProperty dataset
    (N/A, 2021-07-07) Mulnaes, Daniel; Schott-Verdugo, Stephan; Koenig, Filip; Gohlke, Holger
    Transmembrane 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/.
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    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, Holger
    PlaF 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.
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    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, Holger
    Of 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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    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, Jana
    Hyperpolarization-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.
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    Structural and mechanistic insights into bacterial phospholipase A involved in membrane phospholipid degradation and virulence
    (N/A, 2022) Stephan, Schott-Verdugo; Holger, Gohlke; Renu, Batra-Safferling; Karl-Erich, Jaeger; Filip, Kovacic
    Cells steadily adapt their membrane glycerophospholipid (GPL) composition to changing environmental and developmental conditions. While the regulation of membrane homeostasis via GPL synthesis in bacteria has been studied in detail, the mechanisms underlying the controlled degradation of endogenous GPLs remain unknown. Thus far, the function of intracellular phospholipases A (PLAs) in GPL remodeling (Lands cycle) in bacteria is not clearly established. Here, we identified the first cytoplasmic membrane-bound phospholipase A1 (PlaF) from Pseudomonas aeruginosa, which might be involved in the Lands cycle. PlaF is an important virulence factor, as the P. aeruginosa ΔplaF mutant showed strongly attenuated virulence in Galleria mellonella and macrophages. We present a 2.0-Å-resolution crystal structure of PlaF, the first structure that reveals homodimerization of a single-pass transmembrane (TM) full-length protein. PlaF dimerization, mediated solely through the intermolecular interactions of TM and juxtamembrane regions, inhibits its activity. The dimerization site and the catalytic sites are linked by an intricate ligand-mediated interaction network, which might explain the product (fatty acid) feedback inhibition observed with the purified PlaF protein. We used molecular dynamics simulations and configurational free energy computations to suggest a model of PlaF activation through a coupled monomerization and tilting of the monomer in the membrane, which constrains the active site cavity into contact with the GPL substrates. Thus, these data indicate the importance of the PlaF mediated GPL remodeling pathway for virulence and could pave the way for the development of novel therapeutics targeting PlaF.
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    Manual for FCFit
    (No, 2022) Schmitt, Michael; Krügler, Daniel
    Manual for FCFit