1
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Roske Y, Cappel C, Cremer N, Hoffmann P, Koudelka T, Tholey A, Heinemann U, Daumke O, Damme M. Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation. Nucleic Acids Res 2024; 52:370-384. [PMID: 37994783 PMCID: PMC10783504 DOI: 10.1093/nar/gkad1114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023] Open
Abstract
The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in lysosomes, yielding a soluble active form. The deficiency of PLD3 leads to the slowed degradation of nucleic acids in lysosomes and chronic activation of nucleic acid-specific intracellular toll-like receptors. While the mechanism of PLD phospholipase activity has been extensively characterized, not much is known about how PLDs bind and hydrolyze nucleic acids. Here, we determined the high-resolution crystal structure of the luminal N-glycosylated domain of human PLD3 in its apo- and single-stranded DNA-bound forms. PLD3 has a typical phospholipase fold and forms homodimers with two independent catalytic centers via a newly identified dimerization interface. The structure of PLD3 in complex with an ssDNA-derived thymidine product in the catalytic center provides insights into the substrate binding mode of nucleic acids in the PLD family. Our structural data suggest a mechanism for substrate binding and nuclease activity in the PLD family and provide the structural basis to design immunomodulatory drugs targeting PLD3.
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Affiliation(s)
- Yvette Roske
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Cedric Cappel
- Biochemical Institute, Kiel University, Kiel, Germany
| | - Nils Cremer
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straβe 10, 13125 Berlin, Germany
| | | | - Tomas Koudelka
- Institute of Experimental Medicine, Kiel University, 24188 Kiel, Germany
| | - Andreas Tholey
- Institute of Experimental Medicine, Kiel University, 24188 Kiel, Germany
| | - Udo Heinemann
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Oliver Daumke
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Markus Damme
- Biochemical Institute, Kiel University, Kiel, Germany
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2
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Proft S, Leiz J, Heinemann U, Seelow D, Schmidt-Ott KM, Rutkiewicz M. Discovery of a non-canonical GRHL1 binding site using deep convolutional and recurrent neural networks. BMC Genomics 2023; 24:736. [PMID: 38049725 PMCID: PMC10696883 DOI: 10.1186/s12864-023-09830-3] [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: 08/17/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Transcription factors regulate gene expression by binding to transcription factor binding sites (TFBSs). Most models for predicting TFBSs are based on position weight matrices (PWMs), which require a specific motif to be present in the DNA sequence and do not consider interdependencies of nucleotides. Novel approaches such as Transcription Factor Flexible Models or recurrent neural networks consequently provide higher accuracies. However, it is unclear whether such approaches can uncover novel non-canonical, hitherto unexpected TFBSs relevant to human transcriptional regulation. RESULTS In this study, we trained a convolutional recurrent neural network with HT-SELEX data for GRHL1 binding and applied it to a set of GRHL1 binding sites obtained from ChIP-Seq experiments from human cells. We identified 46 non-canonical GRHL1 binding sites, which were not found by a conventional PWM approach. Unexpectedly, some of the newly predicted binding sequences lacked the CNNG core motif, so far considered obligatory for GRHL1 binding. Using isothermal titration calorimetry, we experimentally confirmed binding between the GRHL1-DNA binding domain and predicted GRHL1 binding sites, including a non-canonical GRHL1 binding site. Mutagenesis of individual nucleotides revealed a correlation between predicted binding strength and experimentally validated binding affinity across representative sequences. This correlation was neither observed with a PWM-based nor another deep learning approach. CONCLUSIONS Our results show that convolutional recurrent neural networks may uncover unanticipated binding sites and facilitate quantitative transcription factor binding predictions.
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Affiliation(s)
- Sebastian Proft
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353, Berlin, Germany
| | - Janna Leiz
- Department of Nephrology and Hypertension, Hannover Medical School, 30625, Hannover, Germany
- Department of Nephrology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203, Berlin, Germany
- Molecular and Translational Kidney Research, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Udo Heinemann
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
| | - Dominik Seelow
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany.
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353, Berlin, Germany.
| | - Kai M Schmidt-Ott
- Department of Nephrology and Hypertension, Hannover Medical School, 30625, Hannover, Germany.
- Department of Nephrology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203, Berlin, Germany.
- Molecular and Translational Kidney Research, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
| | - Maria Rutkiewicz
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, 61-704, Poland
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3
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Specker E, Wesolowski R, Schütz A, Matthes S, Mallow K, Wasinska-Kalwa M, Winkler L, Oder A, Alenina N, Pleimes D, von Kries JP, Heinemann U, Bader M, Nazaré M. Structure-Based Design of Xanthine-Imidazopyridines and -Imidazothiazoles as Highly Potent and In Vivo Efficacious Tryptophan Hydroxylase Inhibitors. J Med Chem 2023; 66:14866-14896. [PMID: 37905925 DOI: 10.1021/acs.jmedchem.3c01454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Tryptophan hydroxylases catalyze the first and rate-limiting step in the biosynthesis of serotonin, a well-known neurotransmitter that plays an important role in multiple physiological functions. A reduction of serotonin levels, especially in the brain, can cause dysregulation leading to depression or insomnia. In contrast, overproduction of peripheral serotonin is associated with symptoms like carcinoid syndrome and pulmonary arterial hypertension. Recently, we developed a class of TPH inhibitors based on xanthine-benzimidazoles, characterized by a tripartite-binding mode spanning the binding sites of the cosubstrate pterin and the substrate tryptophan and by chelation of the catalytic iron ion. Herein, we describe the structure-based development of a second generation of xanthine-imidiazopyridines and -imidazothiazoles designed to inhibit TPH1 in the periphery while preventing the interaction with TPH2 in the brain. Lead compound 32 (TPT-004) shows superior pharmacokinetic and pharmacodynamic properties as well as efficacy in preclinical models of peripheral serotonin attenuation and colorectal tumor growth.
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Affiliation(s)
- Edgar Specker
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
- Trypto Therapeutics GmbH, Robert-Rössle Straße 10, 13125 Berlin, Germany
| | - Radoslaw Wesolowski
- Trypto Therapeutics GmbH, Robert-Rössle Straße 10, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Anja Schütz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Keven Mallow
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Malgorzata Wasinska-Kalwa
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Lars Winkler
- Experimental Pharmacology and Oncology GmbH, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Andreas Oder
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Natalia Alenina
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Potsdamer Straße 58, 10785 Berlin, Germany
| | - Dirk Pleimes
- Trypto Therapeutics GmbH, Robert-Rössle Straße 10, 13125 Berlin, Germany
| | - Jens Peter von Kries
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Udo Heinemann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Trypto Therapeutics GmbH, Robert-Rössle Straße 10, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Potsdamer Straße 58, 10785 Berlin, Germany
- Charité─Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Marc Nazaré
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
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4
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Roske Y, Lindemann F, Diehl A, Cremer N, Higman VA, Schlegel B, Leidert M, Driller K, Turgay K, Schmieder P, Heinemann U, Oschkinat H. TapA acts as specific chaperone in TasA filament formation by strand complementation. Proc Natl Acad Sci U S A 2023; 120:e2217070120. [PMID: 37068239 PMCID: PMC10151520 DOI: 10.1073/pnas.2217070120] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Studying mechanisms of bacterial biofilm generation is of vital importance to understanding bacterial cell-cell communication, multicellular cohabitation principles, and the higher resilience of microorganisms in a biofilm against antibiotics. Biofilms of the nonpathogenic, gram-positive soil bacterium Bacillus subtilis serve as a model system with biotechnological potential toward plant protection. Its major extracellular matrix protein components are TasA and TapA. The nature of TasA filaments has been of debate, and several forms, amyloidic and non-Thioflavin T-stainable have been observed. Here, we present the three-dimensional structure of TapA and uncover the mechanism of TapA-supported growth of nonamyloidic TasA filaments. By analytical ultracentrifugation and NMR, we demonstrate TapA-dependent acceleration of filament formation from solutions of folded TasA. Solid-state NMR revealed intercalation of the N-terminal TasA peptide segment into subsequent protomers to form a filament composed of β-sandwich subunits. The secondary structure around the intercalated N-terminal strand β0 is conserved between filamentous TasA and the Fim and Pap proteins, which form bacterial type I pili, demonstrating such construction principles in a gram-positive organism. Analogous to the chaperones of the chaperone-usher pathway, the role of TapA is in donating its N terminus to serve for TasA folding into an Ig domain-similar filament structure by donor-strand complementation. According to NMR and since the V-set Ig fold of TapA is already complete, its participation within a filament beyond initiation is unlikely. Intriguingly, the most conserved residues in TasA-like proteins (camelysines) of Bacillaceae are located within the protomer interface.
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Affiliation(s)
- Yvette Roske
- Structural Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Florian Lindemann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Anne Diehl
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Nils Cremer
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Victoria A Higman
- Department for Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7HB, United Kingdom
| | - Brigitte Schlegel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Martina Leidert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Kristina Driller
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Kürşad Turgay
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Udo Heinemann
- Structural Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
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5
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Heinemann U, Ming Q, Roske Y, Rutkiewicz M, Wang J. Target sequence recognition and gene regulation by Grainyhead/CP2 transcription factors. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322093688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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6
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Specker E, Matthes S, Wesolowski R, Schütz A, Grohmann M, Alenina N, Pleimes D, Mallow K, Neuenschwander M, Gogolin A, Weise M, Pfeifer J, Ziebart N, Heinemann U, von Kries JP, Nazaré M, Bader M. Structure-Based Design of Xanthine-Benzimidazole Derivatives as Novel and Potent Tryptophan Hydroxylase Inhibitors. J Med Chem 2022; 65:11126-11149. [PMID: 35921615 DOI: 10.1021/acs.jmedchem.2c00598] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tryptophan hydroxylases catalyze the first and rate-limiting step in the synthesis of serotonin. Serotonin is a key neurotransmitter in the central nervous system and, in the periphery, functions as a local hormone with multiple physiological functions. Studies in genetically altered mouse models have shown that dysregulation of peripheral serotonin levels leads to metabolic, inflammatory, and fibrotic diseases. Overproduction of serotonin by tumor cells causes severe symptoms typical for the carcinoid syndrome, and tryptophan hydroxylase inhibitors are already in clinical use for patients suffering from this disease. Here, we describe a novel class of potent tryptophan hydroxylase inhibitors, characterized by spanning all active binding sites important for catalysis, specifically those of the cosubstrate pterin, the substrate tryptophan as well as directly chelating the catalytic iron ion. The inhibitors were designed to efficiently reduce serotonin in the periphery while not passing the blood-brain barrier, thus preserving serotonin levels in the brain.
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Affiliation(s)
- Edgar Specker
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str.10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany
| | - Radoslaw Wesolowski
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany
| | - Anja Schütz
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany
| | - Maik Grohmann
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany
| | - Natalia Alenina
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Potsdamer Str. 58, 10785 Berlin, Germany
| | - Dirk Pleimes
- SCINSPIRE Holding & Consulting GmbH, Dunckerstr. 25, 10437 Berlin, Germany
| | - Keven Mallow
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str.10, 13125 Berlin-Buch, Germany
| | - Martin Neuenschwander
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str.10, 13125 Berlin-Buch, Germany
| | - Angelina Gogolin
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str.10, 13125 Berlin-Buch, Germany.,Berliner Hochschule für Technik (BHT), Luxemburger Str. 10, 13353 Berlin, Germany
| | - Marie Weise
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str.10, 13125 Berlin-Buch, Germany.,Berliner Hochschule für Technik (BHT), Luxemburger Str. 10, 13353 Berlin, Germany
| | - Jochen Pfeifer
- Berliner Hochschule für Technik (BHT), Luxemburger Str. 10, 13353 Berlin, Germany
| | - Nandor Ziebart
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str.10, 13125 Berlin-Buch, Germany.,Freie Universität Berlin, Chemistry and Biochemistry Institute, Takustr. 3, 14195 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany.,Freie Universität Berlin, Chemistry and Biochemistry Institute, Takustr. 3, 14195 Berlin, Germany
| | - Jens Peter von Kries
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str.10, 13125 Berlin-Buch, Germany
| | - Marc Nazaré
- Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str.10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Potsdamer Str. 58, 10785 Berlin, Germany.,University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany.,Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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7
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Ellson CD, Goretti Riça I, Kim JS, Huang YMM, Lim D, Mitra T, Hsu A, Wei EX, Barrett CD, Wahl M, Delbrück H, Heinemann U, Oschkinat H, Chang CEA, Yaffe MB. An integrated pharmacological, structural, and genetic analysis of extracellular versus intracellular ROS production in neutrophils. J Mol Biol 2022; 434:167533. [DOI: 10.1016/j.jmb.2022.167533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/03/2022] [Indexed: 11/28/2022]
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8
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Carter DM, Specker E, Małecki PH, Przygodda J, Dudaniec K, Weiss MS, Heinemann U, Nazaré M, Gohlke U. Enhanced Properties of a Benzimidazole Benzylpyrazole Lysine Demethylase Inhibitor: Mechanism-of-Action, Binding Site Analysis, and Activity in Cellular Models of Prostate Cancer. J Med Chem 2021; 64:14266-14282. [PMID: 34555281 DOI: 10.1021/acs.jmedchem.1c00693] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Jumonji domain-containing lysine demethylase (KDM) enzymes are encoded by genes of the KDM superfamily. Activities of the KDM4 subfamily promote aggressive phenotypes associated with prostate cancer (PCa). Previously, we discovered a benzimidazole pyrazole molecule that inhibited KDM4 isoforms with properties tractable for development. Here, we demonstrate that a benzyl-substituted variant of this inhibitor exhibits improved potency in biochemical assays, is cell-permeable, and kills PCa cells at low micromolar concentrations. By X-ray crystallography and kinetics-based assays, we demonstrate that the mechanism of inhibition is complex, proceeding via competition with the enzyme for binding of active-site Fe2+ and by populating a distal site on the enzyme surface. Furthermore, we provide evidence that the inhibitor's cytostatic properties arise from direct intracellular inhibition of KDM4 enzymes. PCa cells treated with the inhibitor exhibit reduced expression of genes regulated by the androgen receptor, an outcome accompanied by epigenetic maintenance of a heterochromatic state.
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Affiliation(s)
- David M Carter
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany
| | - Edgar Specker
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Piotr H Małecki
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany.,Helmholtz-Zentrum Berlin (HZB) Macromolecular Crystallography, Berlin 14109, Germany
| | - Jessica Przygodda
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Krystyna Dudaniec
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin (HZB) Macromolecular Crystallography, Berlin 14109, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Ulrich Gohlke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Gemeinschaft (MDC), Berlin 13125 Germany
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9
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Leiz J, Rutkiewicz M, Birchmeier C, Heinemann U, Schmidt-Ott KM. Technologies for profiling the impact of genomic variants on transcription factor binding. MED GENET-BERLIN 2021. [DOI: 10.1515/medgen-2021-2073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Transcription factors (TFs) bind DNA in a sequence-specific manner and thereby regulate target gene expression. TF binding and its regulatory activity is highly context dependent, and is not only determined by specific cell types or differentiation stages but also relies on other regulatory mechanisms, such as DNA and chromatin modifications. Interactions between TFs and their DNA binding sites are critical mediators of phenotypic variation and play important roles in the onset of disease. A continuously growing number of studies therefore attempts to elucidate TF:DNA interactions to gain knowledge about regulatory mechanisms and disease-causing variants. Here we summarize how TF-binding characteristics and the impact of variants can be investigated, how bioinformatic tools can be used to analyze and predict TF:DNA binding, and what additional information can be obtained from the TF protein structure.
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Affiliation(s)
- Janna Leiz
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin , Department of Nephrology and Intensive Care Medicine , Hindenburgdamm 30 , Berlin , Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) , Molecular and Translational Kidney Research , Robert-Rössle-Str. 10 , Berlin , Germany
| | - Maria Rutkiewicz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) , Macromolecular Structure and Interaction , Berlin , Germany
| | - Carmen Birchmeier
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) , Developmental Biology and Signal Transduction , Berlin , Germany
| | - Udo Heinemann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) , Macromolecular Structure and Interaction , Berlin , Germany
| | - Kai M. Schmidt-Ott
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin , Department of Nephrology and Intensive Care Medicine , Hindenburgdamm 30 , Berlin , Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) , Molecular and Translational Kidney Research , Robert-Rössle-Str. 10 , Berlin , Germany
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10
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Heinemann U. Regulation of gene expression by transcription factors and RNA-binding proteins. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321096446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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11
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Garg A, Roske Y, Yamada S, Uehata T, Takeuchi O, Heinemann U. PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases. Nucleic Acids Res 2021; 49:5369-5381. [PMID: 33950203 PMCID: PMC8136824 DOI: 10.1093/nar/gkab316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
The CCCH-type zinc finger (ZnF) containing ZC3H12 ribonucleases are crucial in post-transcriptional immune homoeostasis with ZC3H12A being the only structurally studied member of the family. In this study, we present a structural-biochemical characterization of ZC3H12C, which is linked with chronic immune disorders like psoriasis. We established that the RNA substrate is cooperatively recognized by the PIN and ZnF domains of ZC3H12C and analyzed the crystal structure of ZC3H12C bound to a single-stranded RNA substrate. The RNA engages in hydrogen-bonded contacts and stacking interactions with the PIN and ZnF domains simultaneously. The ZC3H12 ZnF shows unprecedented structural features not previously observed in any member of the CCCH-ZnF family and utilizes stacking interactions via a unique combination of spatially conserved aromatic residues to align the target transcript in a bent conformation onto the ZnF scaffold. Further comparative structural analysis of ZC3H12 CCCH-ZnF suggests that a trinucleotide sequence is recognized by ZC3H12 ZnF in target RNA. Our work not only describes the initial structure-biochemical study on ZC3H12C, but also provides the first molecular insight into RNA recognition by a ZC3H12 family member. Finally, our work points to an evolutionary code for RNA recognition adopted by CCCH-type ZnF proteins.
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Affiliation(s)
- Ankur Garg
- Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Yvette Roske
- Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Shinnosuke Yamada
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Udo Heinemann
- Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
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12
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Kamdem N, Roske Y, Kovalskyy D, Platonov M, Balinskyi O, Kreuchwig A, Saupe J, Fang L, Diehl A, Schmieder P, Krause G, Rademann J, Heinemann U, Birchmeier W, Oschkinat H. Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling. Magn Reson (Gott) 2021; 2:355-374. [PMID: 37904770 PMCID: PMC10539800 DOI: 10.5194/mr-2-355-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/28/2021] [Indexed: 11/01/2023]
Abstract
Dishevelled (Dvl) proteins are important regulators of the Wnt signalling pathway, interacting through their PDZ domains with the Wnt receptor Frizzled. Blocking the Dvl PDZ-Frizzled interaction represents a potential approach for cancer treatment, which stimulated the identification of small-molecule inhibitors, among them the anti-inflammatory drug Sulindac and Ky-02327. Aiming to develop tighter binding compounds without side effects, we investigated structure-activity relationships of sulfonamides. X-ray crystallography showed high complementarity of anthranilic acid derivatives in the GLGF loop cavity and space for ligand growth towards the PDZ surface. Our best binding compound inhibits Wnt signalling in a dose-dependent manner as demonstrated by TOP-GFP assays (IC50 ∼ 50 µ M ) and Western blotting of β -catenin levels. Real-time PCR showed reduction in the expression of Wnt-specific genes. Our compound interacted with Dvl-1 PDZ (KD = 2.4 µ M ) stronger than Ky-02327 and may be developed into a lead compound interfering with the Wnt pathway.
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Affiliation(s)
- Nestor Kamdem
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Dmytro Kovalskyy
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
| | - Maxim O. Platonov
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
| | - Oleksii Balinskyi
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
| | - Annika Kreuchwig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Jörn Saupe
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Liang Fang
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Anne Diehl
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Gerd Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Jörg Rademann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Pharmazie, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Udo Heinemann
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Walter Birchmeier
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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13
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Irmscher T, Roske Y, Gayk I, Dunsing V, Chiantia S, Heinemann U, Barbirz S. Pantoea stewartii WceF is a glycan biofilm-modifying enzyme with a bacteriophage tailspike-like fold. J Biol Chem 2021; 296:100286. [PMID: 33450228 PMCID: PMC7949094 DOI: 10.1016/j.jbc.2021.100286] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 11/19/2022] Open
Abstract
Pathogenic microorganisms often reside in glycan-based biofilms. Concentration and chain length distribution of these mostly anionic exopolysaccharides (EPS) determine the overall biophysical properties of a biofilm and result in a highly viscous environment. Bacterial communities regulate this biofilm state via intracellular small-molecule signaling to initiate EPS synthesis. Reorganization or degradation of this glycan matrix, however, requires the action of extracellular glycosidases. So far, these were mainly described for bacteriophages that must degrade biofilms for gaining access to host bacteria. The plant pathogen Pantoea stewartii (P. stewartii) encodes the protein WceF within its EPS synthesis cluster. WceF has homologs in various biofilm forming plant pathogens of the Erwinia family. In this work, we show that WceF is a glycosidase active on stewartan, the main P. stewartii EPS biofilm component. WceF has remarkable structural similarity with bacteriophage tailspike proteins (TSPs). Crystal structure analysis showed a native trimer of right-handed parallel β-helices. Despite its similar fold, WceF lacks the high stability found in bacteriophage TSPs. WceF is a stewartan hydrolase and produces oligosaccharides, corresponding to single stewartan repeat units. However, compared with a stewartan-specific glycan hydrolase of bacteriophage origin, WceF showed lectin-like autoagglutination with stewartan, resulting in notably slower EPS cleavage velocities. This emphasizes that the bacterial enzyme WceF has a role in P. stewartii biofilm glycan matrix reorganization clearly different from that of a bacteriophage exopolysaccharide depolymerase.
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Affiliation(s)
- Tobias Irmscher
- Physikalische Biochemie, Universität Potsdam, Potsdam, Germany; Department Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Yvette Roske
- Crystallography, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Igor Gayk
- Physikalische Biochemie, Universität Potsdam, Potsdam, Germany
| | - Valentin Dunsing
- Physikalische Zellbiochemie, Universität Potsdam, Potsdam, Germany
| | | | - Udo Heinemann
- Crystallography, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität, Berlin, Germany.
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14
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Heinemann U, Roske Y. Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. Cancers (Basel) 2021; 13:cancers13020190. [PMID: 33430354 PMCID: PMC7825780 DOI: 10.3390/cancers13020190] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains. Abstract The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.
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15
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Mostinski Y, Heynen GJJE, López-Alberca MP, Paul J, Miksche S, Radetzki S, Schaller D, Shanina E, Seyffarth C, Kolomeets Y, Ziebart N, de Schryver J, Oestreich S, Neuenschwander M, Roske Y, Heinemann U, Rademacher C, Volkamer A, von Kries JP, Birchmeier W, Nazaré M. From Pyrazolones to Azaindoles: Evolution of Active-Site SHP2 Inhibitors Based on Scaffold Hopping and Bioisosteric Replacement. J Med Chem 2020; 63:14780-14804. [PMID: 33210922 DOI: 10.1021/acs.jmedchem.0c01265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The tyrosine phosphatase SHP2 controls the activity of pivotal signaling pathways, including MAPK, JAK-STAT, and PI3K-Akt. Aberrant SHP2 activity leads to uncontrolled cell proliferation, tumorigenesis, and metastasis. SHP2 signaling was recently linked to drug resistance against cancer medications such as MEK and BRAF inhibitors. In this work, we present the development of a novel class of azaindole SHP2 inhibitors. We applied scaffold hopping and bioisosteric replacement concepts to eliminate unwanted structural motifs and to improve the inhibitor characteristics of the previously reported pyrazolone SHP2 inhibitors. The most potent azaindole 45 inhibits SHP2 with an IC50 = 0.031 μM in an enzymatic assay and with an IC50 = 2.6 μM in human pancreas cells (HPAF-II). Evaluation in a series of cellular assays for metastasis and drug resistance demonstrated efficient SHP2 blockade. Finally, 45 inhibited proliferation of two cancer cell lines that are resistant to cancer drugs and diminished ERK signaling.
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Affiliation(s)
- Yelena Mostinski
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Guus J J E Heynen
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Maria Pascual López-Alberca
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jerome Paul
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sandra Miksche
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Silke Radetzki
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - David Schaller
- Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Elena Shanina
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg, 1, 14476 Potsdam, Germany
| | - Carola Seyffarth
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Yuliya Kolomeets
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Nandor Ziebart
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Judith de Schryver
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sylvia Oestreich
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christoph Rademacher
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg, 1, 14476 Potsdam, Germany
| | - Andrea Volkamer
- Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Walter Birchmeier
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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D'Andréa ÉD, Roske Y, Oliveira GAD, Cremer N, Diehl A, Schmieder P, Heinemann U, Oschkinat H, Pires JR. Crystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from Trypanosoma cruzi. J Struct Biol 2020; 211:107536. [DOI: 10.1016/j.jsb.2020.107536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 10/24/2022]
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Chouhan OP, Roske Y, Heinemann U, Biswas S. Structure of the active GGEEF domain of a diguanylate cyclase from Vibrio cholerae. Biochem Biophys Res Commun 2019; 523:287-292. [PMID: 31862141 DOI: 10.1016/j.bbrc.2019.11.179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 11/26/2019] [Indexed: 01/05/2023]
Abstract
Cyclic-di-GMP (c-di-GMP) synthesized by diguanylate cyclases has been an important and ubiquitous secondary messenger in almost all bacterial systems. In Vibrio cholerae, c-di-GMP plays an intricate role in the production of the exopolysaccharide matrix, and thereby, in biofilm formation. The formation of the surface biofilm enables the bacteria to survive in aquatic bodies, when not infecting a human host. Diguanylate cyclases are the class of enzymes which synthesize c-di-GMP from two molecules of GTP and are endowed with a GGDEF or, a GGEEF signature domain. The VC0395_0300 protein from V. cholerae, has been established as a diguanylate cyclase with a necessary role in biofilm formation. Here we present the structure of an N-terminally truncated form of VC0395_0300, which retains the active GGEEF domain for diguanylate cyclase activity but lacks 160 residues from the poorly organized N-terminal domain. X-ray diffraction data was collected from a crystal of VC0395_0300(161-321) to a resolution of 1.9 Å. The structure displays remarkable topological similarity with diguanylate cyclases from other bacterial systems, but lacks the binding site for c-di-GMP present in its homologues. Finally, we demonstrate the ability of the truncated diguanylate cyclase VC0395_0300(161-321) to produce c-di-GMP, and its role in biofilm formation for the bacteria.
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Affiliation(s)
| | - Yvette Roske
- Macromolecular Structure and Interaction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Udo Heinemann
- Macromolecular Structure and Interaction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Chemistry and Biochemistry Institute, Freie Universität, Berlin, Germany
| | - Sumit Biswas
- ViStA Lab, BITS, Pilani - K K Birla Goa Campus, Zuarinagar, Goa, India.
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18
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Abstract
Tight junctions are complex supramolecular entities composed of integral membrane proteins, membrane-associated and soluble cytoplasmic proteins engaging in an intricate and dynamic system of protein-protein interactions. Three-dimensional structures of several tight-junction proteins or their isolated domains have been determined by X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy. These structures provide direct insight into molecular interactions that contribute to the formation, integrity, or function of tight junctions. In addition, the known experimental structures have allowed the modeling of ligand-binding events involving tight-junction proteins. Here, we review the published structures of tight-junction proteins. We show that these proteins are composed of a limited set of structural motifs and highlight common types of interactions between tight-junction proteins and their ligands involving these motifs.
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Affiliation(s)
- Udo Heinemann
- Macromolecular Structure and Interaction Laboratory, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Anja Schuetz
- Protein Production & Characterization Platform, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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19
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Małecki PH, Rüger N, Roatsch M, Krylova O, Link A, Jung M, Heinemann U, Weiss MS. Front Cover: Structure‐Based Screening of Tetrazolylhydrazide Inhibitors versus KDM4 Histone Demethylases (ChemMedChem 21/2019). ChemMedChem 2019. [DOI: 10.1002/cmdc.201900598] [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: 11/08/2022]
Affiliation(s)
- Piotr H. Małecki
- Macromolecular Crystallography Helmholtz-Zentrum Berlin für Materialien und Energie Albert-Einstein-Str. 15 12489 Berlin Germany
- Macromolecular Structure and Interaction Max Delbrück Center for Molecular Medicine Robert-Rössle-Str. 10 13125 Berlin Germany
- Current address: International Institute of Molecular and Cell Biology Ks. Trojdena Street 4 02-109 Warsaw Poland
| | - Nicole Rüger
- Institute of Pharmacy Universität Greifswald Friedrich-Ludwig-Jahn-Str. 17 17489 Greifswald Germany
| | - Martin Roatsch
- Institute of Pharmaceutical Sciences University of Freiburg Albertstr. 25 79104 Freiburg Germany
- Current address: Københavns Universitet Center for Biopharmaceuticals Universitetsparken 2 2100 Copenhagen Denmark
| | - Oxana Krylova
- Department of Molecular Biophysics Forschungsinstitut für Molekulare Pharmakologie Robert-Rössle-Str. 10 13125 Berlin Germany
| | - Andreas Link
- Institute of Pharmacy Universität Greifswald Friedrich-Ludwig-Jahn-Str. 17 17489 Greifswald Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Udo Heinemann
- Macromolecular Structure and Interaction Max Delbrück Center for Molecular Medicine Robert-Rössle-Str. 10 13125 Berlin Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography Helmholtz-Zentrum Berlin für Materialien und Energie Albert-Einstein-Str. 15 12489 Berlin Germany
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20
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Banchenko S, Arumughan A, Petrović S, Schwefel D, Wanker EE, Roske Y, Heinemann U. Common Mode of Remodeling AAA ATPases p97/CDC48 by Their Disassembling Cofactors ASPL/PUX1. Structure 2019; 27:1830-1841.e3. [PMID: 31648844 DOI: 10.1016/j.str.2019.10.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/16/2019] [Accepted: 09/30/2019] [Indexed: 10/25/2022]
Abstract
The hexameric ring structure of the type II AAA+ ATPases is considered as stable and permanent. Recently, the UBX domain-containing cofactors Arabidopsis thaliana PUX1 and human alveolar soft part sarcoma locus (ASPL) were reported to bind and disassemble the cognate AAA+ ATPases AtCDC48 and human p97. Here, we present two crystal structures related to these complexes: a truncated AtCDC48 (AtCDC48-ND1) and a hybrid complex containing human p97-ND1 and the UBX domain of plant PUX1 (p97-ND1:PUX1-UBX). These structures reveal close similarity between the human and plant AAA+ ATPases, but also highlight differences between disassembling and non-disassembling AAA+ ATPase cofactors. Based on an AtCDC48 disassembly assay with PUX1 and known crystal structures of the p97-bound human cofactor ASPL, we propose a general ATPase disassembly model. Thus, our structural and biophysical investigations provide detailed insight into the mechanism of AAA+ ATPase disassembly by UBX domain cofactors and suggest a general mode of regulating the cellular activity of these molecular machines.
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Affiliation(s)
- Sofia Banchenko
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Anup Arumughan
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Saša Petrović
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - David Schwefel
- Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Erich E Wanker
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany.
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany.
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21
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Małecki PH, Rüger N, Roatsch M, Krylova O, Link A, Jung M, Heinemann U, Weiss MS. Structure-Based Screening of Tetrazolylhydrazide Inhibitors versus KDM4 Histone Demethylases. ChemMedChem 2019; 14:1828-1839. [PMID: 31475772 PMCID: PMC6899576 DOI: 10.1002/cmdc.201900441] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/02/2019] [Indexed: 12/12/2022]
Abstract
Human histone demethylases are known to play an important role in the development of several tumor types. Consequently, they have emerged as important medical targets for the treatment of human cancer. Herein, structural studies on tetrazolylhydrazide inhibitors as a new scaffold for a certain class of histone demethylases, the JmjC proteins, are reported. A series of compounds are structurally described and their respective binding modes to the KDM4D protein, which serves as a high-resolution model to represent the KDM4 subfamily in crystallographic studies, are examined. Similar to previously reported inhibitors, the compounds described herein are competitors for the natural KDM4 cofactor, 2-oxoglutarate. The tetrazolylhydrazide scaffold fills an important gap in KDM4 inhibition and newly described, detailed interactions of inhibitor moieties pave the way to the development of compounds with high target-binding affinity and increased membrane permeability, at the same time.
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Affiliation(s)
- Piotr H Małecki
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489, Berlin, Germany.,Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Current address: International Institute of Molecular and Cell Biology, Ks. Trojdena Street 4, 02-109, Warsaw, Poland
| | - Nicole Rüger
- Institute of Pharmacy, Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Martin Roatsch
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany.,Current address: Københavns Universitet, Center for Biopharmaceuticals, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Oxana Krylova
- Department of Molecular Biophysics, Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Andreas Link
- Institute of Pharmacy, Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Udo Heinemann
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489, Berlin, Germany
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22
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Heinemann U, Arumughan A, Banchenko S, Petrovic S, Roske Y, Wanker EE. Regulation of p97 ATPase activity by cofactor-mediated remodelling and post-translational modification. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319094129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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Broeker NK, Roske Y, Valleriani A, Stephan MS, Andres D, Koetz J, Heinemann U, Barbirz S. Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail. J Biol Chem 2019; 294:11751-11761. [PMID: 31189652 PMCID: PMC6682738 DOI: 10.1074/jbc.ra119.008133] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 02/28/2019] [Revised: 06/11/2019] [Indexed: 12/20/2022] Open
Abstract
Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 Å resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an ϵ15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.
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Affiliation(s)
- Nina K Broeker
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Mareike S Stephan
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Dorothee Andres
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Joachim Koetz
- Kolloidchemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität, Takustrasse 6, 14195 Berlin, Germany
| | - Stefanie Barbirz
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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24
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Ming Q, Roske Y, Schuetz A, Walentin K, Ibraimi I, Schmidt-Ott KM, Heinemann U. Structural basis of gene regulation by the Grainyhead/CP2 transcription factor family. Nucleic Acids Res 2019; 46:2082-2095. [PMID: 29309642 PMCID: PMC5829564 DOI: 10.1093/nar/gkx1299] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 09/26/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Grainyhead (Grh)/CP2 transcription factors are highly conserved in multicellular organisms as key regulators of epithelial differentiation, organ development and skin barrier formation. In addition, they have been implicated as being tumor suppressors in a variety of human cancers. Despite their physiological importance, little is known about their structure and DNA binding mode. Here, we report the first structural study of mammalian Grh/CP2 factors. Crystal structures of the DNA-binding domains of grainyhead-like (Grhl) 1 and Grhl2 reveal a closely similar conformation with immunoglobulin-like core. Both share a common fold with the tumor suppressor p53, but differ in important structural features. The Grhl1 DNA-binding domain binds duplex DNA containing the consensus recognition element in a dimeric arrangement, supporting parsimonious target-sequence selection through two conserved arginine residues. We elucidate the molecular basis of a cancer-related mutation in Grhl1 involving one of these arginines, which completely abrogates DNA binding in biochemical assays and transcriptional activation of a reporter gene in a human cell line. Thus, our studies establish the structural basis of DNA target-site recognition by Grh transcription factors and reveal how tumor-associated mutations inactivate Grhl proteins. They may serve as points of departure for the structure-based development of Grh/CP2 inhibitors for therapeutic applications.
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Affiliation(s)
- Qianqian Ming
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Chemistry and Biochemistry Institute, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Yvette Roske
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Anja Schuetz
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Helmholtz Protein Sample Production Facility, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Katharina Walentin
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Ibraim Ibraimi
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Kai M Schmidt-Ott
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Department of Nephrology, Charité Medical University, Charitéplatz 1, 10117 Berlin, Germany
| | - Udo Heinemann
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Chemistry and Biochemistry Institute, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.,Helmholtz Protein Sample Production Facility, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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25
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Bommer M, Heinemann U. Prototyping protein expression constructs with PCR, cell-free expression and fluorescence detection size exclusion chromatography. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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26
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Petrovic S, Roske Y, Heinemann U. Structural basis of ASPL-mediated regulation of p97 methylation by METTL21D. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Heinemann U, Garg A, Roske Y, Schütz A. Post-translational regulation of gene expression in the immune system by Roquin/RC3H1 and ribonucleases of the Regnase/ZC3H12/MCPIP family. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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28
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Roske Y, Diehl A, Ball L, Turgay K, Heinemann U, Akbey Ü, Oschkinat H. Structural insight into protein-aided bacterial biofilm formation. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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29
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Kunstmann S, Gohlke U, Broeker NK, Roske Y, Heinemann U, Santer M, Barbirz S. Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site. J Am Chem Soc 2018; 140:10447-10455. [DOI: 10.1021/jacs.8b03719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonja Kunstmann
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ulrich Gohlke
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Nina K. Broeker
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Mark Santer
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Stefanie Barbirz
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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30
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Abstract
Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double-helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A+ wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds. Combined with the two G·U pairs, the C·A+ base pairs facilitate formation of a half turn of W-helical RNA flanked by six regular Watson-Crick base pairs in standard A conformation on either side. RNA melting experiments monitored by differential scanning calorimetry, UV and circular dichroism spectroscopy demonstrate that the RNA octadecamer undergoes a pH-induced structural transition which is consistent with the presence of a duplex with C·A+ base pairs at acidic pH. Our crystal structure provides a first glimpse of an RNA double helix based entirely on wobble base pairs with possible applications in RNA or DNA nanotechnology and pH biosensors.
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Affiliation(s)
- Ankur Garg
- Crystallography, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie University Berlin, 14195 Berlin, Germany
| | - Udo Heinemann
- Crystallography, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie University Berlin, 14195 Berlin, Germany
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31
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Jurk CM, Roske Y, Heinemann U. Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130. CROAT CHEM ACTA 2018. [DOI: 10.5562/cca3341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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32
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Heinemann U, Ming Q, Roske Y, Schuetz A, Schmidt-Ott KM. Parsimonious DNA target-site recognition by Grh/CP2 transcription factors. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317092750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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Garg A, Takeuchi O, Heinemann U. Immune response regulation by paralogous endoribonucleases: ZC3H12C and N4BP1. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317091215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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34
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Roske Y, Diehl A, Heinemann U, Oschkinat H, Turgay K. Structural insight into protein-aided bacterial biofilm formation. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317091823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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Schuetz A, Radusheva V, Krug SM, Heinemann U. Crystal structure of the tricellulin C-terminal coiled-coil domain reveals a unique mode of dimerization. Ann N Y Acad Sci 2017; 1405:147-159. [DOI: 10.1111/nyas.13408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Anja Schuetz
- Helmholtz Protein Sample Production Facility; Max Delbrück Center for Molecular Medicine; Berlin Germany
| | - Veselina Radusheva
- Helmholtz Protein Sample Production Facility; Max Delbrück Center for Molecular Medicine; Berlin Germany
| | - Susanne M. Krug
- Institute of Clinical Physiology, Campus Benjamin Franklin; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Udo Heinemann
- Helmholtz Protein Sample Production Facility; Max Delbrück Center for Molecular Medicine; Berlin Germany
- Macromolecular Structure and Interaction; Max Delbrück Center for Molecular Medicine; Berlin Germany
- Chemistry and Biochemistry Institute; Freie Universität Berlin; Berlin Germany
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36
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Jennek S, Mittag S, Reiche J, Westphal JK, Seelk S, Dörfel MJ, Pfirrmann T, Friedrich K, Schütz A, Heinemann U, Huber O. Tricellulin is a target of the ubiquitin ligase Itch. Ann N Y Acad Sci 2017; 1397:157-168. [DOI: 10.1111/nyas.13349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Susanne Jennek
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Sonnhild Mittag
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Juliane Reiche
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Julie K. Westphal
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Stefanie Seelk
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Max J. Dörfel
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Thorsten Pfirrmann
- Institute of Physiological Chemistry, University Hospital Halle; Martin Luther University Halle-Wittenberg; Halle/Saale Germany
| | - Karlheinz Friedrich
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Anja Schütz
- Helmholtz Protein Sample Production Facility; Max-Delbrück-Center for Molecular Medicine; Berlin Germany
| | - Udo Heinemann
- Helmholtz Protein Sample Production Facility; Max-Delbrück-Center for Molecular Medicine; Berlin Germany
- Crystallography; Max Delbrück Center for Molecular Medicine; Berlin Germany
- Chemistry and Biochemistry Institute; Freie Universität Berlin; Berlin Germany
| | - Otmar Huber
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
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37
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Carter DM, Specker E, Przygodda J, Neuenschwander M, von Kries JP, Heinemann U, Nazaré M, Gohlke U. Identification of a Novel Benzimidazole Pyrazolone Scaffold That Inhibits KDM4 Lysine Demethylases and Reduces Proliferation of Prostate Cancer Cells. SLAS Discov 2017; 22:801-812. [PMID: 28346812 DOI: 10.1177/2472555217699157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human lysine demethylase (KDM) enzymes (KDM1-7) constitute an emerging class of therapeutic targets, with activities that support growth and development of metastatic disease. By interacting with and co-activating the androgen receptor, the KDM4 subfamily (KDM4A-E) promotes aggressive phenotypes of prostate cancer (PCa). Knockdown of KDM4 expression or inhibition of KDM4 enzyme activity reduces the proliferation of PCa cell lines and highlights inhibition of lysine demethylation as a possible therapeutic method for PCa treatment. To address this possibility, we screened the ChemBioNet small molecule library for inhibitors of the human KDM4E isoform and identified several compounds with IC50 values in the low micromolar range. Two hits, validated as active by an orthogonal enzyme-linked immunosorbent assay, displayed moderate selectivity toward the KDM4 subfamily and exhibited antiproliferative effects in cellular models of PCa. These compounds were further characterized by their ability to maintain the transcriptionally silent histone H3 tri-methyl K9 epigenetic mark at subcytotoxic concentrations. Taken together, these efforts identify and validate a hydroxyquinoline scaffold and a novel benzimidazole pyrazolone scaffold as tractable for entry into hit-to-lead chemical optimization campaigns.
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Affiliation(s)
- David M Carter
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Edgar Specker
- 2 Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Jessica Przygodda
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,2 Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | | | | | - Udo Heinemann
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marc Nazaré
- 2 Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Ulrich Gohlke
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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38
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Consentius P, Loll B, Gohlke U, Alings C, Müller C, Müller R, Teutloff C, Heinemann U, Kaupp M, Wahl MC, Risse T. Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins. J Phys Chem Lett 2017; 8:1113-1117. [PMID: 28221042 DOI: 10.1021/acs.jpclett.6b02971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature. We have used quantum chemical calculations to explore the potential energy that determines the ring dynamics as well as the impact of the geometry on the magnetic parameters probed by EPR spectroscopy.
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Affiliation(s)
- Philipp Consentius
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
| | - Bernhard Loll
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
| | - Ulrich Gohlke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Claudia Alings
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
| | - Carsten Müller
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
| | - Robert Müller
- Institute of Chemistry, Technische Universität Berlin , Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Teutloff
- Department of Physics, Freie Universität Berlin , Arnimallee 14, D-14195 Berlin, Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin , 14195 Berlin, Germany
| | - Udo Heinemann
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Martin Kaupp
- Institute of Chemistry, Technische Universität Berlin , Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Markus C Wahl
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography , Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Thomas Risse
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin , 14195 Berlin, Germany
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39
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Consentius P, Gohlke U, Loll B, Alings C, Heinemann U, Wahl MC, Risse T. Combining EPR spectroscopy and X-ray crystallography to elucidate the structure and dynamics of conformationally constrained spin labels in T4 lysozyme single crystals. Phys Chem Chem Phys 2017; 19:20723-20734. [DOI: 10.1039/c7cp03144k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unraveling structural and dynamic details of spin labeled proteins using a combination of single crystal EPR spectroscopy and X-ray crystallography.
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Affiliation(s)
- Philipp Consentius
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
| | - Ulrich Gohlke
- Medicine in the Helmholtz Association
- 13125 Berlin
- Germany
| | - Bernhard Loll
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Claudia Alings
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Udo Heinemann
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
- Medicine in the Helmholtz Association
| | - Markus C. Wahl
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Thomas Risse
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin
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40
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Arumughan A, Roske Y, Barth C, Forero LL, Bravo-Rodriguez K, Redel A, Kostova S, McShane E, Opitz R, Faelber K, Rau K, Mielke T, Daumke O, Selbach M, Sanchez-Garcia E, Rocks O, Panáková D, Heinemann U, Wanker EE. Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers. Nat Commun 2016; 7:13047. [PMID: 27762274 PMCID: PMC5080433 DOI: 10.1038/ncomms13047] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 02/16/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022] Open
Abstract
Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers. This spontaneous process is accompanied by a reorientation of the D2 ATPase domain in p97 and a loss of its activity. Finally, we demonstrate that overproduction of ASPL disrupts p97 hexamer function in ERAD and that engineered eUBX polypeptides can induce cell death, providing a rationale for developing anti-cancer polypeptide inhibitors that may target p97 activity. The AAA+ ATPase p97 is an essential hexameric protein with multiple protein interaction partners and cellular functions. Here, the authors use interaction mapping to examine partner proteins of this large complex, and assess the effects of these proteins on the disassembly of the p97 complex.
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Affiliation(s)
- Anup Arumughan
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Carolin Barth
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Laura Lleras Forero
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Kenny Bravo-Rodriguez
- Max-Planck-Institute for Coal Research, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Alexandra Redel
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Simona Kostova
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Erik McShane
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Robert Opitz
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Katja Faelber
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Kirstin Rau
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14194 Berlin, Germany
| | - Oliver Daumke
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Elsa Sanchez-Garcia
- Max-Planck-Institute for Coal Research, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Oliver Rocks
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Daniela Panáková
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
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41
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Consentius P, Gohlke U, Loll B, Alings C, Müller R, Heinemann U, Kaupp M, Wahl M, Risse T. Tracking Transient Conformational States of T4 Lysozyme at Room Temperature Combining X-ray Crystallography and Site-Directed Spin Labeling. J Am Chem Soc 2016; 138:12868-12875. [DOI: 10.1021/jacs.6b05507] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philipp Consentius
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Ulrich Gohlke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Bernhard Loll
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Claudia Alings
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Robert Müller
- Institute
of Chemistry, Sekr. C7, Technische Universität Berlin, Straße des
17. Juni 135, 10623 Berlin, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Martin Kaupp
- Institute
of Chemistry, Sekr. C7, Technische Universität Berlin, Straße des
17. Juni 135, 10623 Berlin, Germany
| | - Markus Wahl
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Thomas Risse
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
- Berlin
Joint EPR Laboratory, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
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42
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Abstract
An evacuable guarded hot plate for thermal conductivity measurements between 200 and 800 C was used to investigate the heat transfer in barley straw. The different thermal transfer mechanisms (solid, gaseous conduction and infrared-radiative heat transfer) as well as coupling effects were separated. The measured thermal conductivities (λ = 0.041 W m−1 K−1) are similar to those of conventional insulation materials such as foams, glass or mineral fibres which are widely used as building insulation materials. Straw from barley or wheat, which is a low-cost, renewable material readily available world-wide, is therefore an interesting alternative to conventional insulation materials.
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Affiliation(s)
- A. Beck
- Bavarian Centre for Applied Energy Research Am Hubland, D-97074 Würzburg, Germany
| | - U. Heinemann
- Bavarian Centre for Applied Energy Research Am Hubland, D-97074 Würzburg, Germany,
| | - M. Reidinger
- Bavarian Centre for Applied Energy Research Am Hubland, D-97074 Würzburg, Germany
| | - J. Fricke
- Bavarian Centre for Applied Energy Research Am Hubland, D-97074 Würzburg, Germany
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43
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Biedermann A, Kudoke C, Merten A, Minogue E, Rotermund U, Ebert HP, Heinemann U, Fricke J, Seifert H. Analysis of Heat Transfer Mechanisms in Polyurethane Rigid Foam. J CELL PLAST 2016. [DOI: 10.1106/kemu-lh63-v9h2-kfa3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Polyurethane closed cell rigid foams have been widely used as insulants in the building and refrigeration industry and also for district heating pipes. It is the special combination of its excellent insulation performance and the mechanical stability due to the foaming process which makes this material very attractive for these applications. The replacement of CFCs, which have been banned as blowing agents since 1993, by hydrocarbons in Europe caused a decrease in the insulation capability of polyurethane (PU) rigid foams. The additional global requirement to reduce energy losses also adds an incentive to search for potentials which would improve the thermal performance of rigid foams. To overcome this problem, the heat transfer within PU rigid foams via
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Affiliation(s)
- A. Biedermann
- BASF Schwarzheide GmbH Schwarzheide, Germany; Elastogran GmbH, D-49448 Lemförde, Germany
| | | | | | | | | | | | | | - J. Fricke
- Bavarian Center for Applied Energy Research (ZAE Bayern) Würzburg, Germany
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44
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45
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Heinemann U, Ming Q, Roske Y, Schütz A. Klf4 and Grhl1: two distinct ways of achieving DNA target site recognition. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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46
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Garg A, Takeuchi O, Heinemann U. MCPIP3 (ZC 3H 12C) regulates the innate immune response by acting as a ribonuclease. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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47
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Rösner J, Liotta A, Angamo EA, Spies C, Heinemann U, Kovács R. Minimizing photodecomposition of flavin adenine dinucleotide fluorescence by the use of pulsed LEDs. J Microsc 2016; 264:215-223. [PMID: 27368071 DOI: 10.1111/jmi.12436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/27/2016] [Accepted: 05/30/2016] [Indexed: 01/08/2023]
Abstract
Dynamic alterations in flavin adenine dinucleotide (FAD) fluorescence permit insight into energy metabolism-dependent changes of intramitochondrial redox potential. Monitoring FAD fluorescence in living tissue is impeded by photobleaching, restricting the length of microfluorimetric recordings. In addition, photodecomposition of these essential electron carriers negatively interferes with energy metabolism and viability of the biological specimen. Taking advantage of pulsed LED illumination, here we determined the optimal excitation settings giving the largest fluorescence yield with the lowest photobleaching and interference with metabolism in hippocampal brain slices. The effects of FAD bleaching on energy metabolism and viability were studied by monitoring tissue pO2 , field potentials and changes in extracellular potassium concentration ([K+ ]o ). Photobleaching with continuous illumination consisted of an initial exponential decrease followed by a nearly linear decay. The exponential decay was significantly decelerated with pulsed illumination. Pulse length of 5 ms was sufficient to reach a fluorescence output comparable to continuous illumination, whereas further increasing duration increased photobleaching. Similarly, photobleaching increased with shortening of the interpulse interval. Photobleaching was partially reversible indicating the existence of a transient nonfluorescent flavin derivative. Pulsed illumination decreased FAD photodecomposition, improved slice viability and reproducibility of stimulus-induced FAD, field potential, [K+ ]o and pO2 changes as compared to continuous illumination.
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Affiliation(s)
- J Rösner
- Neuroscience Research Center, Charité Universitätsmedizin, Berlin
| | - A Liotta
- Department of Anesthesiology and Intensive Care Medicine, Charité Universitätsmedizin, Berlin
| | - E A Angamo
- Neuroscience Research Center, Charité Universitätsmedizin, Berlin
| | - C Spies
- Department of Anesthesiology and Intensive Care Medicine, Charité Universitätsmedizin, Berlin
| | - U Heinemann
- Neuroscience Research Center, Charité Universitätsmedizin, Berlin
| | - R Kovács
- Institute for Neurophysiology, Charité Universitätsmedizin, Berlin.
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48
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Kowenz-Leutz E, Schuetz A, Liu Q, Knoblich M, Heinemann U, Leutz A. Functional interaction of CCAAT/enhancer-binding-protein-α basic region mutants with E2F transcription factors and DNA. Biochim Biophys Acta 2016; 1859:841-7. [PMID: 27131901 DOI: 10.1016/j.bbagrm.2016.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 03/24/2016] [Accepted: 04/19/2016] [Indexed: 11/28/2022]
Abstract
The transcription factor CCAAT/enhancer-binding protein α (C/EBPα) regulates cell cycle arrest and terminal differentiation of neutrophils and adipocytes. Mutations in the basic leucine zipper domain (bZip) of C/EBPα are associated with acute myeloid leukemia. A widely used murine transforming C/EBPα basic region mutant (BRM2) entails two bZip point mutations (I294A/R297A). BRM2 has been discordantly described as defective for DNA binding or defective for interaction with E2F. We have separated the two BRM2 mutations to shed light on the intertwined reciprocity between C/EBPα-E2F-DNA interactions. Both, C/EBPα I294A and R297A retain transactivation capacity and interaction with E2F-DP. The C/EBPα R297A mutation destabilized DNA binding, whereas the C/EBPα I294A mutation enhanced binding to DNA. The C/EBPα R297A mutant, like BRM2, displayed enhanced interaction with E2F-DP but failed to repress E2F-dependent transactivation although both mutants were readily suppressed by E2F1 for transcription through C/EBP cis-regulatory sites. In contrast, the DNA binding enhanced C/EBPα I294A mutant displayed increased repression of E2F-DP mediated transactivation and resisted E2F-DP mediated repression. Thus, the efficient repression of E2F dependent S-phase genes and the activation of differentiation genes reside in the balanced DNA binding capacity of C/EBPα.
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Affiliation(s)
- Elisabeth Kowenz-Leutz
- Tumorigenesis and Cell Differentiation, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anja Schuetz
- Protein Sample Production Facility, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Qingbin Liu
- Tumorigenesis and Cell Differentiation, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Maria Knoblich
- Tumorigenesis and Cell Differentiation, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Udo Heinemann
- Protein Sample Production Facility, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Chemistry and Biochemistry Institute, Freie Universität Berlin, Berlin, Germany
| | - Achim Leutz
- Tumorigenesis and Cell Differentiation, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Institute of Biology, Humboldt University of Berlin, Berlin, Germany.
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49
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Kang Y, Gohlke U, Engström O, Hamark C, Scheidt T, Kunstmann S, Heinemann U, Widmalm G, Santer M, Barbirz S. Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions. J Am Chem Soc 2016; 138:9109-18. [DOI: 10.1021/jacs.6b00240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yu Kang
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ulrich Gohlke
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Olof Engström
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Christoffer Hamark
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Tom Scheidt
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Sonja Kunstmann
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut
für Chemie und Biochemie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Mark Santer
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Stefanie Barbirz
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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50
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Abstract
XDSAPPis an expert system and graphical user interface (GUI) for the automated processing of diffraction images using theXDSprogram suite and other programs. The latest major update and the extension of the program are presented here. The update includes new features, as well as improvements in the GUI and the underlying decision-making system.XDSAPPis freely available for academic users.
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