1
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Rafieiolhosseini N, Killa M, Neumann T, Tötsch N, Grad JN, Höing A, Dirksmeyer T, Niemeyer J, Ottmann C, Knauer SK, Giese M, Voskuhl J, Hoffmann D. Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups. Beilstein J Org Chem 2022; 18:1322-1331. [PMID: 36225729 PMCID: PMC9520824 DOI: 10.3762/bjoc.18.137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/08/2022] [Indexed: 12/24/2022] Open
Abstract
The 14-3-3 protein family, one of the first discovered phosphoserine/phosphothreonine binding proteins, has attracted interest not only because of its important role in the cell regulatory processes but also due to its enormous number of interactions with other proteins. Here, we use a computational approach to predict the binding sites of the designed hybrid compound featuring aggregation-induced emission luminophores as a potential supramolecular ligand for 14-3-3ζ in the presence and absence of C-Raf peptides. Our results suggest that the area above and below the central pore of the dimeric 14-3-3ζ protein is the most probable binding site for the ligand. Moreover, we predict that the position of the ligand is sensitive to the presence of phosphorylated C-Raf peptides. With a series of experiments, we confirmed the computational prediction of two C2 related, dominating binding sites on 14-3-3ζ that may bind to two of the supramolecular ligand molecules.
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Affiliation(s)
- Neda Rafieiolhosseini
- Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Matthias Killa
- Faculty of Chemistry (Organic Chemistry) and CENIDE, University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
| | - Thorben Neumann
- Faculty of Chemistry (Organic Chemistry) and CENIDE, University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
| | - Niklas Tötsch
- Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Jean-Noël Grad
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Alexander Höing
- Department of Molecular Biology II, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Thies Dirksmeyer
- Faculty of Chemistry (Organic Chemistry) and CENIDE, University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
| | - Jochen Niemeyer
- Faculty of Chemistry (Organic Chemistry) and CENIDE, University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, Netherlands
| | - Shirley K Knauer
- Department of Molecular Biology II, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Michael Giese
- Faculty of Chemistry (Organic Chemistry) and CENIDE, University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
| | - Jens Voskuhl
- Faculty of Chemistry (Organic Chemistry) and CENIDE, University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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2
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Meiners A, Bäcker S, Hadrović I, Heid C, Beuck C, Ruiz-Blanco YB, Mieres-Perez J, Pörschke M, Grad JN, Vallet C, Hoffmann D, Bayer P, Sánchez-García E, Schrader T, Knauer SK. Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. Nat Commun 2021; 12:1505. [PMID: 33686072 PMCID: PMC7940618 DOI: 10.1038/s41467-021-21753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.
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Affiliation(s)
- Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sandra Bäcker
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Inesa Hadrović
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christian Heid
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Marius Pörschke
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Cecilia Vallet
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sánchez-García
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Shirley K Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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3
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Abstract
We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2 × 2 origami structure with increasing level of detail ranging from the mean-field level to an all-atom representation of the DNA structure. We observe a consistent pore conductivity as a function of salt concentration for all four models. However, a comparison of our data to recent experimental investigations on similar systems displays significant deviations. We discuss possible reasons for the discrepancies and propose extensions to our models for future investigations.
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Affiliation(s)
- Kai Szuttor
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Florian Weik
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Jean-Noël Grad
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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4
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Anzt H, Bach F, Druskat S, Löffler F, Loewe A, Renard BY, Seemann G, Struck A, Achhammer E, Aggarwal P, Appel F, Bader M, Brusch L, Busse C, Chourdakis G, Dabrowski PW, Ebert P, Flemisch B, Friedl S, Fritzsch B, Funk MD, Gast V, Goth F, Grad JN, Hegewald J, Hermann S, Hohmann F, Janosch S, Kutra D, Linxweiler J, Muth T, Peters-Kottig W, Rack F, Raters FH, Rave S, Reina G, Reißig M, Ropinski T, Schaarschmidt J, Seibold H, Thiele JP, Uekermann B, Unger S, Weeber R. An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action. F1000Res 2020; 9:295. [PMID: 33552475 PMCID: PMC7845155 DOI: 10.12688/f1000research.23224.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 08/22/2023] Open
Abstract
Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
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Affiliation(s)
- Hartwig Anzt
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- University of Tennessee, Knoxville, TN, USA
| | - Felix Bach
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Stephan Druskat
- Friedrich Schiller University, Jena, Germany
- German Aerospace Center (DLR), Berlin, Germany
- Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frank Löffler
- Friedrich Schiller University, Jena, Germany
- Louisiana State University, Baton Rouge, LA, USA
| | - Axel Loewe
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Bernhard Y. Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | - Gunnar Seemann
- University Heart Centre Freiburg Bad Krozingen, Freiburg, Germany
| | | | | | | | - Franziska Appel
- Leibniz Institute of Agricultural Development in Transition Economies (IAMO), Halle (Saale), Germany
| | | | - Lutz Brusch
- Technische Universität Dresden, Dresden, Germany
| | | | | | | | - Peter Ebert
- Saarland Informatics Campus, Saarbrücken, Germany
| | | | | | | | | | - Volker Gast
- Friedrich Schiller University, Jena, Germany
| | | | | | | | | | | | - Stephan Janosch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Dominik Kutra
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Linxweiler
- Technische Universität Braunschweig, Braunschweig, Germany
| | - Thilo Muth
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | | | - Fabian Rack
- FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Karlsruhe, Germany
| | | | | | | | - Malte Reißig
- Institute for Advanced Sustainability Studies, Potsdam, Germany
| | - Timo Ropinski
- Ulm University, Ulm, Germany
- Linköping University, Linköping, Sweden
| | | | - Heidi Seibold
- Ludwig Maximilian University of Munich, München, Germany
| | | | | | - Stefan Unger
- Julius Kühn-Institut (JKI), Quedlinburg, Germany
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5
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Anzt H, Bach F, Druskat S, Löffler F, Loewe A, Renard BY, Seemann G, Struck A, Achhammer E, Aggarwal P, Appel F, Bader M, Brusch L, Busse C, Chourdakis G, Dabrowski PW, Ebert P, Flemisch B, Friedl S, Fritzsch B, Funk MD, Gast V, Goth F, Grad JN, Hegewald J, Hermann S, Hohmann F, Janosch S, Kutra D, Linxweiler J, Muth T, Peters-Kottig W, Rack F, Raters FH, Rave S, Reina G, Reißig M, Ropinski T, Schaarschmidt J, Seibold H, Thiele JP, Uekermann B, Unger S, Weeber R. An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action. F1000Res 2020; 9:295. [PMID: 33552475 PMCID: PMC7845155 DOI: 10.12688/f1000research.23224.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/11/2021] [Indexed: 11/20/2022] Open
Abstract
Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
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Affiliation(s)
- Hartwig Anzt
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- University of Tennessee, Knoxville, TN, USA
| | - Felix Bach
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Stephan Druskat
- Friedrich Schiller University, Jena, Germany
- German Aerospace Center (DLR), Berlin, Germany
- Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frank Löffler
- Friedrich Schiller University, Jena, Germany
- Louisiana State University, Baton Rouge, LA, USA
| | - Axel Loewe
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Bernhard Y. Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | - Gunnar Seemann
- University Heart Centre Freiburg Bad Krozingen, Freiburg, Germany
| | | | | | | | - Franziska Appel
- Leibniz Institute of Agricultural Development in Transition Economies (IAMO), Halle (Saale), Germany
| | | | - Lutz Brusch
- Technische Universität Dresden, Dresden, Germany
| | | | | | | | - Peter Ebert
- Saarland Informatics Campus, Saarbrücken, Germany
| | | | | | | | | | - Volker Gast
- Friedrich Schiller University, Jena, Germany
| | | | | | | | | | | | - Stephan Janosch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Dominik Kutra
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Linxweiler
- Technische Universität Braunschweig, Braunschweig, Germany
| | - Thilo Muth
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | | | - Fabian Rack
- FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Karlsruhe, Germany
| | | | | | | | - Malte Reißig
- Institute for Advanced Sustainability Studies, Potsdam, Germany
| | - Timo Ropinski
- Ulm University, Ulm, Germany
- Linköping University, Linköping, Sweden
| | | | - Heidi Seibold
- Ludwig Maximilian University of Munich, München, Germany
| | | | | | - Stefan Unger
- Julius Kühn-Institut (JKI), Quedlinburg, Germany
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6
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Smolin D, Tötsch N, Grad JN, Linders J, Kaschani F, Kaiser M, Kirsch M, Hoffmann D, Schrader T. Accelerated trypsin autolysis by affinity polymer templates. RSC Adv 2020; 10:28711-28719. [PMID: 35520047 PMCID: PMC9055874 DOI: 10.1039/d0ra05827k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 11/21/2022] Open
Abstract
Affinity copolymers specifically recognize the trypsin surface and act as templates for multiple protease molecules, leading to drastically accelerated autolysis – an unusual way for highly efficient enzyme inhibition at physiological conditions.
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Affiliation(s)
- Daniel Smolin
- Faculty of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Niklas Tötsch
- Faculty of Biology
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Jean-Noël Grad
- Faculty of Biology
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Jürgen Linders
- Faculty of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | | | - Markus Kaiser
- Faculty of Biology
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | | | - Daniel Hoffmann
- Faculty of Biology
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - Thomas Schrader
- Faculty of Chemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
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7
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Ehlers M, Grad JN, Mittal S, Bier D, Mertel M, Ohl L, Bartel M, Briels J, Heimann M, Ottmann C, Sanchez-Garcia E, Hoffmann D, Schmuck C. Rational Design, Binding Studies, and Crystal-Structure Evaluation of the First Ligand Targeting the Dimerization Interface of the 14-3-3ζ Adapter Protein. Chembiochem 2018; 19:591-595. [DOI: 10.1002/cbic.201700588] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Martin Ehlers
- Institute of Organic Chemistry; University of Duisburg-Essen (Germany); Universitätsstrasse 7 45141 Essen Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics; ZMB/Faculty of Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Sumit Mittal
- Computational Biochemistry; University of Duisburg-Essen; Universitätsstrasse 3 45141 Essen Germany
| | - David Bier
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
| | - Marcel Mertel
- Institute of Organic Chemistry; University of Duisburg-Essen (Germany); Universitätsstrasse 7 45141 Essen Germany
| | - Ludwig Ohl
- Department of Bioinformatics and Computational Biophysics; ZMB/Faculty of Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Maria Bartel
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
- Department of Biomedical Engineering and; Institute for Complex Molecular Systems; Technische Universiteit Eindhoven; P. O. Box 513 5600 MB Eindhoven Netherlands
| | - Jeroen Briels
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
- Department of Biomedical Engineering and; Institute for Complex Molecular Systems; Technische Universiteit Eindhoven; P. O. Box 513 5600 MB Eindhoven Netherlands
| | - Marius Heimann
- Institute of Organic Chemistry; University of Duisburg-Essen (Germany); Universitätsstrasse 7 45141 Essen Germany
| | - Christian Ottmann
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
- Department of Biomedical Engineering and; Institute for Complex Molecular Systems; Technische Universiteit Eindhoven; P. O. Box 513 5600 MB Eindhoven Netherlands
| | - Elsa Sanchez-Garcia
- Computational Biochemistry; University of Duisburg-Essen; Universitätsstrasse 3 45141 Essen Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics; ZMB/Faculty of Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Carsten Schmuck
- Institute of Organic Chemistry; University of Duisburg-Essen (Germany); Universitätsstrasse 7 45141 Essen Germany
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8
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Grad JN, Gigante A, Wilms C, Dybowski JN, Ohl L, Ottmann C, Schmuck C, Hoffmann D. Locating Large, Flexible Ligands on Proteins. J Chem Inf Model 2018; 58:315-327. [PMID: 29266929 DOI: 10.1021/acs.jcim.7b00413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many biologically important ligands of proteins are large, flexible, and in many cases charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods such as docking or molecular dynamics (MD) simulation. The alternative approach proposed here is scanning of a spatial and angular grid around the protein with smaller fragments of the large ligand. Energy values for complete grids can be computed efficiently with a well-known fast Fourier transform-accelerated algorithm and a physically meaningful interaction model. We show that the approach can readily incorporate flexibility of the protein and ligand. The energy grids (EGs) resulting from the ligand fragment scans can be transformed into probability distributions and then directly compared to probability distributions estimated from MD simulations and experimental structural data. We test the approach on a diverse set of complexes between proteins and large, flexible ligands, including a complex of sonic hedgehog protein and heparin, three heparin sulfate substrates or nonsubstrates of an epimerase, a multibranched supramolecular ligand that stabilizes a protein-peptide complex, a flexible zwitterionic ligand that binds to a surface basin of a Kringle domain, and binding of ATP to a flexible site of an ion channel. In all cases, the EG approach gives results that are in good agreement with experimental data or MD simulations.
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Affiliation(s)
- Jean-Noël Grad
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen , Universitätstraße 7, 45141 Essen, Germany
| | - Alba Gigante
- Institute of Organic Chemistry, University of Duisburg-Essen , Universitätstraße 7, 45141 Essen, Germany
| | - Christoph Wilms
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen , Universitätstraße 7, 45141 Essen, Germany
| | - Jan Nikolaj Dybowski
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen , Universitätstraße 7, 45141 Essen, Germany
| | - Ludwig Ohl
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen , Universitätstraße 7, 45141 Essen, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology , Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen , Universitätstraße 7, 45141 Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen , Universitätstraße 7, 45141 Essen, Germany
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9
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Pellegrini S, Grad JN, Bousquet T, Pélinski L. A novel multicomponent reaction: easy access to ferrocenyl (alkylimino)-1,4-dihydroquinolines. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.01.144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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