1
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Schumann W, Loschwitz J, Reiners J, Degrandi D, Legewie L, Stühler K, Pfeffer K, Poschmann G, Smits SHJ, Strodel B. Integrative modeling of guanylate binding protein dimers. Protein Sci 2023; 32:e4818. [PMID: 37916607 PMCID: PMC10683561 DOI: 10.1002/pro.4818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 11/03/2023]
Abstract
Guanylate-binding proteins (GBPs) are essential interferon-γ-activated large GTPases that play a crucial role in host defense against intracellular bacteria and parasites. While their protective functions rely on protein polymerization, our understanding of the structural intricacies of these multimerized states remains limited. To bridge this knowledge gap, we present dimer models for human GBP1 (hGBP1) and murine GBP2 and 7 (mGBP2 and mGBP7) using an integrative approach, incorporating the crystal structure of hGBP1's GTPase domain dimer, crosslinking mass spectrometry, small-angle X-ray scattering, protein-protein docking, and molecular dynamics simulations. Our investigation begins by comparing the protein dynamics of hGBP1, mGBP2, and mGBP7. We observe that the M/E domain in all three proteins exhibits significant mobility and hinge motion, with mGBP7 displaying a slightly less pronounced motion but greater flexibility in its GTPase domain. These dynamic distinctions can be attributed to variations in the sequences of mGBP7 and hGBP1/mGBP2, resulting in different dimerization modes. Unlike hGBP1 and its close ortholog mGBP2, which exclusively dimerize through their GTPase domains, we find that mGBP7 exhibits three equally probable alternative dimer structures. The GTPase domain of mGBP7 is only partially involved in its dimerization, primarily due to an accumulation of negative charge, allowing mGBP7 to dimerize independently of GTP. Instead, mGBP7 exhibits a strong tendency to dimerize in an antiparallel arrangement across its stalks. The results of this work go beyond the sequence-structure-function relationship, as the sequence differences in mGBP7 and mGBP2/hGBP1 do not lead to different structures, but to different protein dynamics and dimerization. The distinct GBP dimer structures are expected to encode specific functions crucial for disrupting pathogen membranes.
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Affiliation(s)
- Wibke Schumann
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
| | - Jennifer Loschwitz
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
| | - Jens Reiners
- Center for Structural StudiesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Larissa Legewie
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome ResearchMedical Faculty and University Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ)Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine UniversityDüsseldorfGermany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome ResearchMedical Faculty and University Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sander H. J. Smits
- Center for Structural StudiesHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute for BiochemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Birgit Strodel
- Institute of Theoretical and Computational ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Biological Information Processing: Structural BiochemistryForschungszentrum JülichJülichGermany
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2
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Hornbergs J, Montag K, Loschwitz J, Mohr I, Poschmann G, Schnake A, Gratz R, Brumbarova T, Eutebach M, Angrand K, Fink-Straube C, Stühler K, Zeier J, Hartmann L, Strodel B, Ivanov R, Bauer P. SEC14-GOLD protein PATELLIN2 binds IRON-REGULATED TRANSPORTER1 linking root iron uptake to vitamin E. Plant Physiol 2023; 192:504-526. [PMID: 36493393 PMCID: PMC10152663 DOI: 10.1093/plphys/kiac563] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Organisms require micronutrients, and Arabidopsis (Arabidopsis thaliana) IRON-REGULATED TRANSPORTER1 (IRT1) is essential for iron (Fe2+) acquisition into root cells. Uptake of reactive Fe2+ exposes cells to the risk of membrane lipid peroxidation. Surprisingly little is known about how this is avoided. IRT1 activity is controlled by an intracellular variable region (IRT1vr) that acts as a regulatory protein interaction platform. Here, we describe that IRT1vr interacted with peripheral plasma membrane SEC14-Golgi dynamics (SEC14-GOLD) protein PATELLIN2 (PATL2). SEC14 proteins bind lipophilic substrates and transport or present them at the membrane. To date, no direct roles have been attributed to SEC14 proteins in Fe import. PATL2 affected root Fe acquisition responses, interacted with ROS response proteins in roots, and alleviated root lipid peroxidation. PATL2 had high affinity in vitro for the major lipophilic antioxidant vitamin E compound α-tocopherol. Molecular dynamics simulations provided insight into energetic constraints and the orientation and stability of the PATL2-ligand interaction in atomic detail. Hence, this work highlights a compelling mechanism connecting vitamin E with root metal ion transport at the plasma membrane with the participation of an IRT1-interacting and α-tocopherol-binding SEC14 protein.
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Affiliation(s)
- Jannik Hornbergs
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Karolin Montag
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Jennifer Loschwitz
- Institute of Theoretical Chemistry and Computer Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Inga Mohr
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anika Schnake
- Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Regina Gratz
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | | | - Monique Eutebach
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Kalina Angrand
- Department of Biosciences-Plant Biology, Saarland University, Campus A2.4, D-66123 Saarbrücken, Germany
| | | | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Molecular Proteomics Laboratory, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Jürgen Zeier
- Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
| | - Laura Hartmann
- Institute of Macromolecular Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Birgit Strodel
- Institute of Theoretical Chemistry and Computer Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
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3
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Forsberg Chaaban H, Loschwitz J, de Weert MV, Strodel B, Stahlhul M, Foderà V. Biophysics of IL-22 receptor interaction with selected interleukins. Biophys J 2023; 122:457a. [PMID: 36784344 DOI: 10.1016/j.bpj.2022.11.2459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Hussein Forsberg Chaaban
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; Leo Pharma A/S, Copenhagen, Denmark
| | - Jennifer Loschwitz
- Structural Biochemistry, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
| | | | - Birgit Strodel
- Structural Biochemistry, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
| | | | - Vito Foderà
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
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4
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Loschwitz J, Steffens N, Wang X, Schäffler M, Pfeffer K, Degrandi D, Strodel B. Domain motions, dimerization, and membrane interactions of the murine guanylate binding protein 2. Sci Rep 2023; 13:679. [PMID: 36639389 PMCID: PMC9839784 DOI: 10.1038/s41598-023-27520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Guanylate-binding proteins (GBPs) are a group of GTPases that are induced by interferon-[Formula: see text] and are crucial components of cell-autonomous immunity against intracellular pathogens. Here, we examine murine GBP2 (mGBP2), which we have previously shown to be an essential effector protein for the control of Toxoplasma gondii replication, with its recruitment through the membrane of the parasitophorous vacuole and its involvement in the destruction of this membrane likely playing a role. The overall aim of our work is to provide a molecular-level understanding of the mutual influences of mGBP2 and the parasitophorous vacuole membrane. To this end, we performed lipid-binding assays which revealed that mGBP2 has a particular affinity for cardiolipin. This observation was confirmed by fluorescence microscopy using giant unilamellar vesicles of different lipid compositions. To obtain an understanding of the protein dynamics and how this is affected by GTP binding, mGBP2 dimerization, and membrane binding, assuming that each of these steps are relevant for the function of the protein, we carried out standard as well as replica exchange molecular dynamics simulations with an accumulated simulation time of more than 30 μs. The main findings from these simulations are that mGBP2 features a large-scale hinge motion in its M/E domain, which is present in each of the studied protein states. When bound to a cardiolipin-containing membrane, this hinge motion is particularly pronounced, leading to an up and down motion of the M/E domain on the membrane, which did not occur on a membrane without cardiolipin. Our prognosis is that this up and down motion has the potential to destroy the membrane following the formation of supramolecular mGBP2 complexes on the membrane surface.
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Affiliation(s)
- Jennifer Loschwitz
- grid.411327.20000 0001 2176 9917Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Nora Steffens
- grid.411327.20000 0001 2176 9917Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Xue Wang
- grid.411327.20000 0001 2176 9917Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Moritz Schäffler
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Klaus Pfeffer
- grid.411327.20000 0001 2176 9917Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany. .,Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425, Jülich, Germany.
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5
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Bhatia S, Spanier L, Bickel D, Dienstbier N, Woloschin V, Vogt M, Pols H, Lungerich B, Reiners J, Aghaallaei N, Diedrich D, Frieg B, Schliehe-Diecks J, Bopp B, Lang F, Gopalswamy M, Loschwitz J, Bajohgli B, Skokowa J, Borkhardt A, Hauer J, Hansen FK, Smits SHJ, Jose J, Gohlke H, Kurz T. Development of a First-in-Class Small-Molecule Inhibitor of the C-Terminal Hsp90 Dimerization. ACS Cent Sci 2022; 8:636-655. [PMID: 35647282 PMCID: PMC9136973 DOI: 10.1021/acscentsci.2c00013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Indexed: 05/04/2023]
Abstract
Heat shock proteins 90 (Hsp90) are promising therapeutic targets due to their involvement in stabilizing several aberrantly expressed oncoproteins. In cancerous cells, Hsp90 expression is elevated, thereby exerting antiapoptotic effects, which is essential for the malignant transformation and tumor progression. Most of the Hsp90 inhibitors (Hsp90i) under investigation target the ATP binding site in the N-terminal domain of Hsp90. However, adverse effects, including induction of the prosurvival resistance mechanism (heat shock response or HSR) and associated dose-limiting toxicity, have so far precluded their clinical approval. In contrast, modulators that interfere with the C-terminal domain (CTD) of Hsp90 do not inflict HSR. Since the CTD dimerization of Hsp90 is essential for its chaperone activity, interfering with the dimerization process by small-molecule protein-protein interaction inhibitors is a promising strategy for anticancer drug research. We have developed a first-in-class small-molecule inhibitor (5b) targeting the Hsp90 CTD dimerization interface, based on a tripyrimidonamide scaffold through structure-based molecular design, chemical synthesis, binding mode model prediction, assessment of the biochemical affinity, and efficacy against therapy-resistant leukemia cells. 5b reduces xenotransplantation of leukemia cells in zebrafish models and induces apoptosis in BCR-ABL1+ (T315I) tyrosine kinase inhibitor-resistant leukemia cells, without inducing HSR.
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Affiliation(s)
- Sanil Bhatia
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Phone: (+49) 211 81 04896.
| | - Lukas Spanier
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - David Bickel
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Niklas Dienstbier
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Vitalij Woloschin
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Melina Vogt
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Henrik Pols
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Beate Lungerich
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Jens Reiners
- Center
for Structural Studies, Heinrich Heine University
Düsseldorf, Düsseldorf 40225, Germany
| | - Narges Aghaallaei
- Department
of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen 72076, Germany
| | - Daniela Diedrich
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Benedikt Frieg
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Institute of Biological Information Processing (IBI-7:
Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4:
Bioinformatics), Forschungszentrum Jülich
GmbH, Jülich 52425, Germany
| | - Julian Schliehe-Diecks
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Bertan Bopp
- Institute
for Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Münster 48149, Germany
| | - Franziska Lang
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Mohanraj Gopalswamy
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Jennifer Loschwitz
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Baubak Bajohgli
- Department
of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen 72076, Germany
| | - Julia Skokowa
- Department
of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen 72076, Germany
| | - Arndt Borkhardt
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Julia Hauer
- Department
of Pediatrics, Pediatric Hematology and Oncology, University Hospital Carl Gustav Carus, Dresden 01307, Germany
- Partner
Site Dresden, National Center for Tumor
Diseases (NCT), Dresden 01307, Germany
| | - Finn K. Hansen
- Pharmaceutical
and Cell Biological Chemistry, Pharmaceutical
Institute University of Bonn, Bonn 53121, Germany
| | - Sander H. J. Smits
- Center
for Structural Studies, Heinrich Heine University
Düsseldorf, Düsseldorf 40225, Germany
- Institute
of Biochemistry, Heinrich Heine University
Düsseldorf, Düsseldorf 40225, Germany
| | - Joachim Jose
- Institute
for Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Münster 48149, Germany
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Institute of Biological Information Processing (IBI-7:
Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4:
Bioinformatics), Forschungszentrum Jülich
GmbH, Jülich 52425, Germany
- Phone: (+49)
211 81 13662.
| | - Thomas Kurz
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Phone: (+49)
211 81 14984.
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6
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Olagunju MO, Loschwitz J, Olubiyi OO, Strodel B. Multiscale
MD
simulations of wild‐type and sickle hemoglobin aggregation. Proteins 2022; 90:1811-1824. [DOI: 10.1002/prot.26352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/02/2022] [Accepted: 04/20/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Maryam O. Olagunju
- Institute of Biological Information Processing Structural Biochemistry, Forschungszentrum Jülich Jülich Germany
| | - Jennifer Loschwitz
- Institute of Biological Information Processing Structural Biochemistry, Forschungszentrum Jülich Jülich Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf Düsseldorf Germany
| | - Olujide O. Olubiyi
- Institute of Biological Information Processing Structural Biochemistry, Forschungszentrum Jülich Jülich Germany
- Department of Pharmaceutical and Medicinal Chemistry, College of Pharmacy Afe Babalola University Ado‐Ekiti Nigeria
- Institute of Drug Research and Development, Bogoro Centre Afe Babalola University Ado‐Ekiti Nigeria
| | - Birgit Strodel
- Institute of Biological Information Processing Structural Biochemistry, Forschungszentrum Jülich Jülich Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf Düsseldorf Germany
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7
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Fatafta H, Kav B, Bundschuh BF, Loschwitz J, Strodel B. Disorder-to-order transition of the amyloid-β peptide upon lipid binding. Biophys Chem 2021; 280:106700. [PMID: 34784548 DOI: 10.1016/j.bpc.2021.106700] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022]
Abstract
There is mounting evidence that Alzheimer's disease progression and severity are linked to neuronal membrane damage caused by aggregates of the amyloid-β (Aβ) peptide. However, the detailed mechanism behind the membrane damage is not well understood yet. Recently, the lipid-chaperone hypothesis has been put forward, based on which the formation of complexes between Aβ and free lipids enables an easy insertion of Aβ into membranes. In order to test this hypothesis, we performed numerous all-atom molecular dynamics simulations. We studied the complex formation between individual lipids, considering both POPC and DPPC, and Aβ and examined whether the resulting complexes would be able to insert into lipid membranes. Complex formation at a one-to-one ratio was readily observed, yet with minimal effects on Aβ's characteristics. Most importantly, the peptide remains largely disordered in 1:1 complexes, and the complex does not insert into the membrane; instead, it is adsorbed to the membrane surface. The results change considerably once Aβ forms a complex with a POPC cluster composed of three lipid molecules. The hydrophobic interactions between Aβ and the lipid tails cause the peptide to fold into either a helical or a β-sheet structure. These observations provide atomic insight into the disorder-to-order transition that is needed for membrane insertion or amyloid aggregation to proceed.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Bastian F Bundschuh
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany
| | - Jennifer Loschwitz
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany.
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8
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Loschwitz J, Jäckering A, Keutmann M, Olagunju M, Olubiyi OO, Strodel B. Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS. Data Brief 2021; 35:106948. [PMID: 33855133 PMCID: PMC8027721 DOI: 10.1016/j.dib.2021.106948] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 11/20/2022] Open
Abstract
We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these parameters based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory. For each molecule we provide a coordinate file of the three-dimensional molecular structure, the topology and the parameter file. The applicability of these parameters was demonstrated by MD simulations of these molecules bound to the active site of the main protease of the coronavirus SARS-CoV-2, 3CLpro, which is a main player during viral replication causing COVID-19.
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Affiliation(s)
- Jennifer Loschwitz
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Anna Jäckering
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Monika Keutmann
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Maryam Olagunju
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Olujide O. Olubiyi
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Birgit Strodel
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
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9
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Olubiyi OO, Olagunju M, Keutmann M, Loschwitz J, Strodel B. High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2. Molecules 2020; 25:E3193. [PMID: 32668701 PMCID: PMC7396980 DOI: 10.3390/molecules25143193] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [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: 06/11/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/24/2022] Open
Abstract
We use state-of-the-art computer-aided drug design (CADD) techniques to identify prospective inhibitors of the main protease enzyme, 3CLpro of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19. From our screening of over one million compounds including approved drugs, investigational drugs, natural products, and organic compounds, and a rescreening protocol incorporating enzyme dynamics via ensemble docking, we have been able to identify a range of prospective 3CLpro inhibitors. Importantly, some of the identified compounds had previously been reported to exhibit inhibitory activities against the 3CLpro enzyme of the closely related SARS-CoV virus. The top-ranking compounds are characterized by the presence of multiple bi- and monocyclic rings, many of them being heterocycles and aromatic, which are flexibly linked allowing the ligands to adapt to the geometry of the 3CLpro substrate site and involve a high amount of functional groups enabling hydrogen bond formation with surrounding amino acid residues, including the catalytic dyad residues H41 and C145. Among the top binding compounds we identified several tyrosine kinase inhibitors, which include a bioflavonoid, the group of natural products that binds best to 3CLpro. Another class of compounds that decently binds to the SARS-CoV-2 main protease are steroid hormones, which thus may be endogenous inhibitors and might provide an explanation for the age-dependent severity of COVID-19. Many of the compounds identified by our work show a considerably stronger binding than found for reference compounds with in vitro demonstrated 3CLpro inhibition and anticoronavirus activity. The compounds determined in this work thus represent a good starting point for the design of inhibitors of SARS-CoV-2 replication.
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Affiliation(s)
- Olujide O. Olubiyi
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany; (M.O.); (M.K.); (J.L.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife 220005, Nigeria
| | - Maryam Olagunju
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany; (M.O.); (M.K.); (J.L.)
| | - Monika Keutmann
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany; (M.O.); (M.K.); (J.L.)
| | - Jennifer Loschwitz
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany; (M.O.); (M.K.); (J.L.)
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany; (M.O.); (M.K.); (J.L.)
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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Abstract
The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.
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Affiliation(s)
- Jennifer Loschwitz
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Olujide O Olubiyi
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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Barz B, Loschwitz J, Strodel B. Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations. PLoS Comput Biol 2019; 15:e1007193. [PMID: 31589600 PMCID: PMC6797221 DOI: 10.1371/journal.pcbi.1007193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/17/2019] [Accepted: 08/15/2019] [Indexed: 12/23/2022] Open
Abstract
Guanylate binding proteins (GBPs) belong to the dynamin-related superfamily and exhibit various functions in the fight against infections. The functions of the human guanylate binding protein 1 (hGBP1) are tightly coupled to GTP hydrolysis and dimerization. Despite known crystal structures of the hGBP1 monomer and GTPase domain dimer, little is known about the dynamics of hGBP1. To gain a mechanistic understanding of hGBP1, we performed sub-millisecond multi-resolution molecular dynamics simulations of both the hGBP1 monomer and dimer. We found that hGBP1 is a highly flexible protein that undergoes a hinge motion similar to the movements observed for other dynamin-like proteins. Another large-scale motion was observed for the C-terminal helix α13, providing a molecular view for the α13-α13 distances previously reported for the hGBP1 dimer. Most of the loops of the GTPase domain were found to be flexible, revealing why GTP binding is needed for hGBP1 dimerization to occur.
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Affiliation(s)
- Bogdan Barz
- Institute of Physical Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Jennifer Loschwitz
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University, Düsseldorf, Germany
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Zhang T, Loschwitz J, Strodel B, Nagel-Steger L, Willbold D. Interference with Amyloid-β Nucleation by Transient Ligand Interaction. Molecules 2019; 24:E2129. [PMID: 31195746 PMCID: PMC6600523 DOI: 10.3390/molecules24112129] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 12/20/2022] Open
Abstract
Amyloid-β peptide (Aβ) is an intrinsically disordered protein (IDP) associated with Alzheimer's disease. The structural flexibility and aggregation propensity of Aβ pose major challenges for elucidating the interaction between Aβ monomers and ligands. All-D-peptides consisting solely of D-enantiomeric amino acid residues are interesting drug candidates that combine high binding specificity with high metabolic stability. Here we characterized the interaction between the 12-residue all-D-peptide D3 and Aβ42 monomers, and how the interaction influences Aβ42 aggregation. We demonstrate for the first time that D3 binds to Aβ42 monomers with submicromolar affinities. These two highly unstructured molecules are able to form complexes with 1:1 and other stoichiometries. Further, D3 at substoichiometric concentrations effectively slows down the β-sheet formation and Aβ42 fibrillation by modulating the nucleation process. The study provides new insights into the molecular mechanism of how D3 affects Aβ assemblies and contributes to our knowledge on the interaction between two IDPs.
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Affiliation(s)
- Tao Zhang
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Jennifer Loschwitz
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Luitgard Nagel-Steger
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
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Legewie L, Loschwitz J, Smits S, Prescher M, Wang X, Steffens N, Degrandi D, Strodel B, Schmitt L, Pfeffer K. mGBP7 interacting proteins in Toxoplasma gondii infection and biochemical characteristics of mGBP7. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.127.8] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Toxoplasma gondii (T. gondii) is an obligate intracellular parasite and the causative agent of toxoplasmosis. During host cell invasion, T. gondii forms an unique membranous compartment called the parasitophorous vacuole (PV). Members of the murine guanylate binding protein (mGBP) family localize around the PV leading to its disruption, but the underlying molecular mechanisms are poorly understood. The aim of this project is to provide a better understanding of the biochemistry of mGBPs as well as to elucidate the molecular mechanisms by which this IFNγ-inducible protein family is able to attack the parasite directly.
The GTPase activity of mGBP7 and its oligomerization status were analyzed using a colorimetric assay and multi-angle light scattering (MALS). The structure model of mGBP7 was obtained using I-TASSER homology modeling. For the identification of potential mGBP7 interaction partners co-immunoprecipitation (IP) and mass spectrometry (MS) experiments were performed.
The obtained biochemical data for mGBP7 display a GTPase activity in the μM range and a positive cooperativity of GTP hydrolysis. Furthermore, the MALS results indicate a transient oligomer formation independent of the presence of nucleotides. Homology modeling reveals an extended C-terminal domain for mGBP7 probably responsible for its oligomerization pattern. The initial mGBP7 IP-MS results offer hints about potential mGBP7 interaction partners and indicate that mGBP7 is ubiquitinated and ISGylated even in the absence of T. gondii infection.
The biochemical characterization of mGBP7 as well as the identification of potential mGBP7 interacting proteins will provide new insights into the dynamic interactions at the interface of parasite and host.
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Affiliation(s)
- Larissa Legewie
- 1Institute of Medical Microbiology & Hospital Hygiene, Heinrich-Heine University Duesseldorf, Germany
| | - Jennifer Loschwitz
- 2Institute of Theoretical & Computational Chemistry, Heinrich-Heine University Duesseldorf, Germany
| | - Sander Smits
- 3Institute of Biochemistry, Heinrich-Heine University Duesseldorf, Germany
| | - Martin Prescher
- 3Institute of Biochemistry, Heinrich-Heine University Duesseldorf, Germany
| | - Xue Wang
- 2Institute of Theoretical & Computational Chemistry, Heinrich-Heine University Duesseldorf, Germany
| | - Nora Steffens
- 1Institute of Medical Microbiology & Hospital Hygiene, Heinrich-Heine University Duesseldorf, Germany
| | - Daniel Degrandi
- 1Institute of Medical Microbiology & Hospital Hygiene, Heinrich-Heine University Duesseldorf, Germany
| | - Birgit Strodel
- 2Institute of Theoretical & Computational Chemistry, Heinrich-Heine University Duesseldorf, Germany
| | - Lutz Schmitt
- 3Institute of Biochemistry, Heinrich-Heine University Duesseldorf, Germany
| | - Klaus Pfeffer
- 1Institute of Medical Microbiology & Hospital Hygiene, Heinrich-Heine University Duesseldorf, Germany
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