1
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Barelli H, Camonis J, de Gunzburg J, Goud B, Moreau-Gachelin F, Wittinghofer A, Zahraoui A. Pierre Chardin, un pionnier de la découverte des gènes et protéines de la superfamille Ras. Med Sci (Paris) 2020; 36:394-398. [DOI: 10.1051/medsci/2020058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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2
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Abstract
The BBSome is a heterooctameric protein complex that plays a central role in primary cilia homeostasis. Its malfunction causes the severe ciliopathy Bardet-Biedl syndrome (BBS). The complex acts as a cargo adapter that recognizes signaling proteins such as GPCRs and links them to the intraflagellar transport machinery. The underlying mechanism is poorly understood. Here we present a high-resolution cryo-EM structure of a human heterohexameric core subcomplex of the BBSome. The structure reveals the architecture of the complex in atomic detail. It explains how the subunits interact with each other and how disease-causing mutations hamper this interaction. The complex adopts a conformation that is open for binding to membrane-associated GTPase Arl6 and a large positively charged patch likely strengthens the interaction with the membrane. A prominent negatively charged cleft at the center of the complex is likely involved in binding of positively charged signaling sequences of cargo proteins.
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Affiliation(s)
- Björn Udo Klink
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oliver Hofnagel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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3
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Wauters L, Terheyden S, Gilsbach BK, Leemans M, Athanasopoulos PS, Guaitoli G, Wittinghofer A, Gloeckner CJ, Versées W, Kortholt A. Biochemical and kinetic properties of the complex Roco G-protein cycle. Biol Chem 2019; 399:1447-1456. [PMID: 30067506 DOI: 10.1515/hsz-2018-0227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022]
Abstract
Roco proteins have come into focus after mutations in the gene coding for the human Roco protein Leucine-rich repeat kinase 2 (LRRK2) were discovered to be one of the most common genetic causes of late onset Parkinson's disease. Roco proteins are characterized by a Roc domain responsible for GTP binding and hydrolysis, followed by a COR dimerization device. The regulation and function of this RocCOR domain tandem is still not completely understood. To fully biochemically characterize Roco proteins, we performed a systematic survey of the kinetic properties of several Roco protein family members, including LRRK2. Together, our results show that Roco proteins have a unique G-protein cycle. Our results confirm that Roco proteins have a low nucleotide affinity in the micromolar range and thus do not strictly depend on G-nucleotide exchange factors. Measurement of multiple and single turnover reactions shows that neither Pi nor GDP release are rate-limiting, while this is the case for the GAP-mediated GTPase reaction of some small G-proteins like Ras and for most other high affinity Ras-like proteins, respectively. The KM values of the reactions are in the range of the physiological GTP concentration, suggesting that LRRK2 functioning might be regulated by the cellular GTP level.
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Affiliation(s)
- Lina Wauters
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.,Department of Cell Biochemistry, University of Groningen, Groningen NL-9747 AG, The Netherlands.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Susanne Terheyden
- Department of Cell Biochemistry, University of Groningen, Groningen NL-9747 AG, The Netherlands.,Structural Biology Group, Max-Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Bernd K Gilsbach
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, D-72076 Tübingen, Germany
| | - Margaux Leemans
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | | | - Giambattista Guaitoli
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, D-72076 Tübingen, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max-Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, D-72076 Tübingen, Germany.,University of Tübingen, Institute for Ophthalmic Research, Center for Ophthalmology, D-72076 Tübingen, Germany
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen NL-9747 AG, The Netherlands
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4
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Kösling SK, Fansa EK, Maffini S, Wittinghofer A. Mechanism and dynamics of INPP5E transport into and inside the ciliary compartment. Biol Chem 2018; 399:277-292. [PMID: 29140789 DOI: 10.1515/hsz-2017-0226] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 08/24/2017] [Accepted: 11/03/2017] [Indexed: 11/15/2022]
Abstract
The inositol polyphosphate 5'-phosphatase E (INPP5E) localizes to cilia. We showed that the carrier protein phosphodiesterase 6 delta subunit (PDE6δ) mediates the sorting of farnesylated INPP5E into cilia due to high affinity binding and release by the ADP-ribosylation factor (Arf)-like protein Arl3·GTP. However, the dynamics of INPP5E transport into and inside the ciliary compartment are not fully understood. Here, we investigate the movement of INPP5E using live cell fluorescence microscopy and fluorescence recovery after photobleaching (FRAP) analysis. We show that PDE6δ and the dynein transport system are essential for ciliary sorting and entry of INPP5E. However, its innerciliary transport is regulated solely by the intraflagellar transport (IFT) system, independent from PDE6δ activity and INPP5E farnesylation. By contrast, movement of Arl3 into and within cilia occurs freely by diffusion and IFT-independently. The farnesylation defective INPP5E CaaX box mutant loses the exclusive ciliary localization. The accumulation of this mutant at centrioles after photobleaching suggests an affinity trap mechanism for ciliary entry, that in case of the wild type is overcome by the interaction with PDE6δ. Collectively, we postulate a three-step mechanism regulating ciliary localization of INPP5E, consisting of farnesylation- and PDE6δ-mediated targeting, INPP5E-PDE6δ complex diffusion into the cilium with transfer to the IFT system, and retention inside cilia.
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Affiliation(s)
- Stefanie Kristine Kösling
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, D-44227 Dortmund, Germany
| | - Eyad Kalawy Fansa
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, D-44227 Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, D-44227 Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, D-44227 Dortmund, Germany
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5
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Lyraki R, Lokaj M, Soares DC, Little A, Vermeren M, Marsh JA, Wittinghofer A, Hurd T. Characterization of a novel RP2-OSTF1 interaction and its implication for actin remodelling. J Cell Sci 2018; 131:jcs.211748. [PMID: 29361551 DOI: 10.1242/jcs.211748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/21/2017] [Indexed: 11/20/2022] Open
Abstract
Retinitis pigmentosa 2 (RP2) is the causative gene for a form of X-linked retinal degeneration. RP2 was previously shown to have GTPase-activating protein (GAP) activity towards the small GTPase ARL3 via its N-terminus, but the function of the C-terminus remains elusive. Here, we report a novel interaction between RP2 and osteoclast-stimulating factor 1 (OSTF1), an intracellular protein that indirectly enhances osteoclast formation and activity and is a negative regulator of cell motility. Moreover, this interaction is abolished by a human pathogenic mutation in RP2. We utilized a structure-based approach to pinpoint the binding interface to a strictly conserved cluster of residues on the surface of RP2 that spans both the C- and N-terminal domains of the protein, and which is structurally distinct from the ARL3-binding site. In addition, we show that RP2 is a positive regulator of cell motility in vitro, recruiting OSTF1 to the cell membrane and preventing its interaction with the migration regulator Myo1E.
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Affiliation(s)
- Rodanthi Lyraki
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Mandy Lokaj
- Structural Biology Group, Max-Planck Institut für Molekulare Physiologie, Abteilung Strukturelle Biologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Dinesh C Soares
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Abigail Little
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Matthieu Vermeren
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.,MRC Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alfred Wittinghofer
- Structural Biology Group, Max-Planck Institut für Molekulare Physiologie, Abteilung Strukturelle Biologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Toby Hurd
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
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6
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Abstract
Rasal is a modular multi-domain protein of the GTPase-activating protein 1 (GAP1) family; its four known members, GAP1m, Rasal, GAP1IP4BP and Capri, have a Ras GTPase-activating domain (RasGAP). This domain supports the intrinsically slow GTPase activity of Ras by actively participating in the catalytic reaction. In the case of Rasal, GAP1IP4BP and Capri, their remaining domains are responsible for converting the RasGAP domains into dual Ras- and Rap-GAPs, via an incompletely understood mechanism. Although Rap proteins are small GTPase homologues of Ras, their catalytic residues are distinct, which reinforces the importance of determining the structure of full-length GAP1 family proteins. To date, these proteins have not been crystallized, and their size is not adequate for nuclear magnetic resonance (NMR) or for high-resolution cryo-electron microscopy (cryoEM). Here we present the low resolution structure of full-length Rasal, obtained by negative staining electron microscopy, which allows us to propose a model of its domain topology. These results help to understand the role of the different domains in controlling the dual GAP activity of GAP1 family proteins.
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Affiliation(s)
- Jorge Cuellar
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - José María Valpuesta
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.,Unidad Asociada de Nanobiotecnología (CNB-CSIC e IMDEA Nanociencia), Madrid, Spain
| | - Alfred Wittinghofer
- Department of Structural Biology, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Begoña Sot
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.,Unidad Asociada de Nanobiotecnología (CNB-CSIC e IMDEA Nanociencia), Madrid, Spain.,IMDEA-Nanociencia, Faraday 9, Campus Universitario de Cantoblanco, 28048 Madrid, Spain
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7
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Klink BU, Zent E, Juneja P, Kuhlee A, Raunser S, Wittinghofer A. A recombinant BBSome core complex and how it interacts with ciliary cargo. eLife 2017; 6. [PMID: 29168691 PMCID: PMC5700813 DOI: 10.7554/elife.27434] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [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: 04/19/2017] [Accepted: 11/03/2017] [Indexed: 01/07/2023] Open
Abstract
Cilia are small, antenna-like structures on the surface of eukaryotic cells that harbor a unique set of sensory proteins, including GPCRs and other membrane proteins. The transport of these proteins involves the BBSome, an eight-membered protein complex that is recruited to ciliary membranes by the G-protein Arl6. BBSome malfunction leads to Bardet-Biedl syndrome, a ciliopathy with severe consequences. Short ciliary targeting sequences (CTS) have been identified that trigger the transport of ciliary proteins. However, mechanistic studies that relate ciliary targeting to BBSome binding are missing. Here we used heterologously expressed BBSome subcomplexes to analyze the complex architecture and to investigate the binding of GPCRs and other receptors to the BBSome. A stable heterohexameric complex was identified that binds to GPCRs with interactions that only partially overlap with previously described CTS, indicating a more complex recognition than anticipated. Arl6•GTP does not affect these interactions, suggesting no direct involvement in cargo loading/unloading.
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Affiliation(s)
- Björn Udo Klink
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Eldar Zent
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Puneet Juneja
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Anne Kuhlee
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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8
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Martín-Gago P, Fansa EK, Wittinghofer A, Waldmann H. Structure-based development of PDEδ inhibitors. Biol Chem 2017; 398:535-545. [PMID: 27935847 DOI: 10.1515/hsz-2016-0272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 08/25/2016] [Accepted: 11/06/2016] [Indexed: 11/15/2022]
Abstract
The prenyl binding protein PDEδ enhances the diffusion of farnesylated Ras proteins in the cytosol, ultimately affecting their correct localization and signaling. This has turned PDEδ into a promising target to prevent oncogenic KRas signaling. In this review we summarize and describe the structure-guided-development of the three different PDEδ inhibitor chemotypes that have been documented so far. We also compare both their potency for binding to the PDEδ pocket and their in vivo efficiency in suppressing oncogenic KRas signaling, as a result of the inhibition of the PDEδ/KRas interaction.
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Affiliation(s)
- Pablo Martín-Gago
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund
| | - Eyad Kalawy Fansa
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund
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9
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Mejuch T, Garivet G, Hofer W, Kaiser N, Fansa EK, Ehrt C, Koch O, Baumann M, Ziegler S, Wittinghofer A, Waldmann H. Small-Molecule Inhibition of the UNC119-Cargo Interaction. Angew Chem Int Ed Engl 2017; 56:6181-6186. [DOI: 10.1002/anie.201701905] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/30/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Tom Mejuch
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Guillaume Garivet
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Walter Hofer
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Nadine Kaiser
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Eyad K. Fansa
- Department of Structural Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Matthias Baumann
- Lead Discovery Center GmbH; Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Slava Ziegler
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Alfred Wittinghofer
- Department of Structural Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
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10
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Mejuch T, Garivet G, Hofer W, Kaiser N, Fansa EK, Ehrt C, Koch O, Baumann M, Ziegler S, Wittinghofer A, Waldmann H. Small-Molecule Inhibition of the UNC119-Cargo Interaction. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tom Mejuch
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Guillaume Garivet
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Walter Hofer
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Nadine Kaiser
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Eyad K. Fansa
- Department of Structural Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Matthias Baumann
- Lead Discovery Center GmbH; Otto-Hahn-Strasse 15 44227 Dortmund Germany
| | - Slava Ziegler
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Alfred Wittinghofer
- Department of Structural Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology; Max-Planck-Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
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11
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Murarka S, Martín-Gago P, Schultz-Fademrecht C, Al Saabi A, Baumann M, Fansa EK, Ismail S, Nussbaumer P, Wittinghofer A, Waldmann H. Development of Pyridazinone Chemotypes Targeting the PDEδ Prenyl Binding Site. Chemistry 2017; 23:6083-6093. [PMID: 27809361 DOI: 10.1002/chem.201603222] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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] [Received: 07/06/2016] [Indexed: 12/18/2022]
Abstract
The K-Ras GTPase is a major target in anticancer drug discovery. However, direct interference with signaling by K-Ras has not led to clinically useful drugs yet. Correct localization and signaling by farnesylated K-Ras is regulated by the prenyl binding protein PDEδ. Interfering with binding of PDEδ to K-Ras by means of small molecules provides a novel opportunity to suppress oncogenic signaling. Here we describe the identification and structure-guided development of novel K-Ras-PDEδ inhibitor chemotypes based on pyrrolopyridazinones and pyrazolopyridazinones that bind to the farnesyl binding pocket of PDEδ with low nanomolar affinity. We delineate the structure-property relationship and in vivo pharmacokinetic (PK) and toxicokinetic (Tox) studies for pyrazolopyridazinone-based K-Ras-PDEδ inhibitors. These findings may inspire novel drug discovery efforts aimed at the development of drugs targeting oncogenic Ras.
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Affiliation(s)
- Sandip Murarka
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Pablo Martín-Gago
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | | | - Alaa Al Saabi
- Lead Discovery Center GmbH, 44227, Dortmund, Germany
| | | | - Eyad K Fansa
- Max-Planck-Institut für Molekulare Physiologie, Structural Biology Group, 44227, Dortmund, Germany
| | - Shehab Ismail
- Beatson Institute for Cancer Research, Bearsden, Glasgow, G61 1BD, UK
| | | | - Alfred Wittinghofer
- Max-Planck-Institut für Molekulare Physiologie, Structural Biology Group, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Technische Universität Dortmund, Fakultät Chemie, Chemische Biologie, Otto-Hahn-Straße 6, 44221, Dortmund, Germany
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12
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Martín-Gago P, Fansa EK, Winzker M, Murarka S, Janning P, Schultz-Fademrecht C, Baumann M, Wittinghofer A, Waldmann H. Covalent Protein Labeling at Glutamic Acids. Cell Chem Biol 2017; 24:589-597.e5. [DOI: 10.1016/j.chembiol.2017.03.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/07/2017] [Accepted: 03/24/2017] [Indexed: 12/26/2022]
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13
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Blackburn GM, Cherfils J, Moss GP, Richards NGJ, Waltho JP, Williams NH, Wittinghofer A. How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016). PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-0202] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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
AbstractProcedures are proposed for the naming of individual atoms, P, O, F, N, and S in phosphate esters, amidates, thiophosphates, polyphosphates, their mimics, and analogues of transition states for enzyme-catalyzed phosphoryl transfer reactions. Their purpose is to enable scientists in very different fields, e.g. biochemistry, biophysics, chemistry, computational chemistry, crystallography, and molecular biology, to share standard protocols for the labelling of individual atoms in complex molecules. This will facilitate clear and unambiguous descriptions of structural results, as well as scientific intercommunication concerning them. At the present time, perusal of the Protein Data Bank (PDB) and other sources shows that there is a limited degree of commonality in nomenclature, but a large measure of irregularity in more complex structures. The recommendations described here adhere to established practice as closely as possible, in particular to IUPAC and IUBMB recommendations and to “best practice” in the PDB, especially to its atom labelling of amino acids, and particularly to Cahn-Ingold-Prelog rules for stereochemical nomenclature. They are designed to work in complex enzyme sites for binding phosphates but also to have utility for non-enzymatic systems. Above all, the recommendations are designed to be easy to comprehend and user-friendly.
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Affiliation(s)
- G. Michael Blackburn
- 1Department of Molecular Biology, Krebs Institute, University of Sheffield, S10 2TN, UK
| | - Jacqueline Cherfils
- 2Laboratoire de Biologie et Pharmacologie Appliquée, CNRS – École Normale Supérieure Paris-Saclay, Cachan, France. http://orcid.org/0000-0002-8966-3067
| | - Gerard P. Moss
- 3Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4NS, UK
| | - Nigel G. J. Richards
- 4Department of Chemistry, Indiana University Purdue University Indianapolis, IL 46202, USA; and School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | | | | | - Alfred Wittinghofer
- 7Group for Structural Biology, Max-Planck-Institut für Molekulare Physiologie, 44227 Dortmund, Deutschland
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14
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Martín-Gago P, Fansa EK, Klein CH, Murarka S, Janning P, Schürmann M, Metz M, Ismail S, Schultz-Fademrecht C, Baumann M, Bastiaens PIH, Wittinghofer A, Waldmann H. A PDE6δ-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2. Angew Chem Int Ed Engl 2017; 56:2423-2428. [PMID: 28106325 DOI: 10.1002/anie.201610957] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [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] [Received: 11/14/2016] [Indexed: 12/11/2022]
Abstract
Small-molecule inhibition of the interaction between the KRas oncoprotein and the chaperone PDE6δ impairs KRas spatial organization and signaling in cells. However, despite potent binding in vitro (KD <10 nm), interference with Ras signaling and growth inhibition require 5-20 μm compound concentrations. We demonstrate that these findings can be explained by fast release of high-affinity inhibitors from PDE6δ by the release factor Arl2. This limitation is overcome by novel highly selective inhibitors that bind to PDE6δ with up to 7 hydrogen bonds, resulting in picomolar affinity. Their release by Arl2 is greatly decreased, and representative compounds selectively inhibit growth of KRas mutated and -dependent cells with the highest activity recorded yet. Our findings indicate that very potent inhibitors of the KRas-PDE6δ interaction may impair the growth of tumors driven by oncogenic KRas.
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Affiliation(s)
- Pablo Martín-Gago
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Eyad K Fansa
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227, Dortmund, Germany
| | - Christian H Klein
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Sandip Murarka
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Marc Schürmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Malte Metz
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Shehab Ismail
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227, Dortmund, Germany
| | | | | | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- TU Dortmund, Faculty of Chemistry and Chemical Biology, 44227, Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- TU Dortmund, Faculty of Chemistry and Chemical Biology, 44227, Dortmund, Germany
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15
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Affiliation(s)
- Alfred Wittinghofer
- Department of Structural Biology, Max-Planck-Institute for Molecular Physiology Department of Structural Biology, Dortmund, Germany
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16
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Martín-Gago P, Fansa EK, Klein CH, Murarka S, Janning P, Schürmann M, Metz M, Ismail S, Schultz-Fademrecht C, Baumann M, Bastiaens PIH, Wittinghofer A, Waldmann H. A PDE6δ-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Pablo Martín-Gago
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Eyad K. Fansa
- Structural Biology Group; Max Planck Institute for Molecular Physiology; 44227 Dortmund Germany
| | - Christian H. Klein
- Department of Systemic Cell Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Sandip Murarka
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Marc Schürmann
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Malte Metz
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Shehab Ismail
- Structural Biology Group; Max Planck Institute for Molecular Physiology; 44227 Dortmund Germany
| | | | | | - Philippe I. H. Bastiaens
- Department of Systemic Cell Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
- TU Dortmund; Faculty of Chemistry and Chemical Biology; 44227 Dortmund Germany
| | - Alfred Wittinghofer
- Structural Biology Group; Max Planck Institute for Molecular Physiology; 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
- TU Dortmund; Faculty of Chemistry and Chemical Biology; 44227 Dortmund Germany
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17
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Abstract
Arl2 and Arl3 are Arf-like small GTP-binding proteins of the Arf subfamily of the Ras superfamily. Despite their structural similarity and sharing of many interacting partners, Arl2 and Arl3 have different biochemical properties and biological functions. Growing evidence suggest that Arl2 and Arl3 play a fundamental role as regulators of trafficking of lipid modified proteins between different compartments. Here we highlight the similarities and differences between these 2 homologous proteins and discuss the sorting mechanism of lipidated cargo into the ciliary compartment through the carriers PDE6δ and Unc119 and the release factors Arl2 and Arl3.
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Affiliation(s)
- Eyad K Fansa
- a Max Planck Institute of Molecular Physiology , Dortmund , Germany
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18
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Jaiswal M, Fansa EK, Kösling SK, Mejuch T, Waldmann H, Wittinghofer A. Novel Biochemical and Structural Insights into the Interaction of Myristoylated Cargo with Unc119 Protein and Their Release by Arl2/3. J Biol Chem 2016; 291:20766-78. [PMID: 27481943 DOI: 10.1074/jbc.m116.741827] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [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: 06/06/2016] [Indexed: 11/06/2022] Open
Abstract
Primary cilia are highly specialized small antenna-like cellular protrusions that extend from the cell surface of many eukaryotic cell types. The protein content inside cilia and cytoplasm is very different, but details of the sorting process are not understood for most ciliary proteins. Recently, we have shown that prenylated proteins are sorted according to their affinity to the carrier protein PDE6δ and the ability of Arl3 but not Arl2 to release high affinity cargo inside the cilia (Fansa, E. K., Kösling, S. K., Zent, E., Wittinghofer, A., and Ismail, S. (2016) Nat. Commun. 7, 11366). Here we address the question whether a similar principle governs the transport of myristoylated cargo by the carrier proteins Unc119a and Unc119b. We thus analyzed the binding strength of N-terminal myristoylated cargo peptides (GNAT1, NPHP3, Cystin1, RP2, and Src) to Unc119a and Unc119b proteins. The affinity between myristoylated cargo and carrier protein, Unc119, varies between subnanomolar and micromolar. Peptides derived from ciliary localizing proteins (GNAT1, NPHP3, and Cystin1) bind with high affinity to Unc119 proteins, whereas a peptide derived from a non-ciliary localizing protein (Src) has low affinity. The peptide with intermediate affinity (RP2) is localized at the ciliary transition zone as a gate keeper. We show that the low affinity peptides are released by both Arl2·GppNHp and Arl3·GppNHp, whereas the high affinity peptides are exclusively released by only Arl3·GppNHp. Determination of the x-ray structure of myristoylated NPHP3 peptide in complex with Unc119a reveals the molecular details of high affinity binding and suggests the importance of the residues at the +2 and +3 positions relative to the myristoylated glycine for high and low affinities. The mutational analysis of swapping the residues at the +2 and +3 positions between high and low affinity peptides results in reversing their affinities for Unc119a and leads to a partial mislocalization of a low affinity mutant of NPHP3.
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Affiliation(s)
| | | | | | - Tom Mejuch
- the Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Herbert Waldmann
- the Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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19
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Wittinghofer A, Martin JB, Blacklow S. Proteins special issue of biopolymers. Biopolymers 2016; 99:807-8. [PMID: 23893350 DOI: 10.1002/bip.22353] [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)
- Alfred Wittinghofer
- Department of Structural Biology, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
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20
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Papke B, Murarka S, Vogel HA, Martín-Gago P, Kovacevic M, Truxius DC, Fansa EK, Ismail S, Zimmermann G, Heinelt K, Schultz-Fademrecht C, Al Saabi A, Baumann M, Nussbaumer P, Wittinghofer A, Waldmann H, Bastiaens PI. Identification of pyrazolopyridazinones as PDEδ inhibitors. Nat Commun 2016; 7:11360. [PMID: 27094677 PMCID: PMC4843002 DOI: 10.1038/ncomms11360] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 03/17/2016] [Indexed: 12/21/2022] Open
Abstract
The prenyl-binding protein PDEδ is crucial for the plasma membrane localization of prenylated Ras. Recently, we have reported that the small-molecule Deltarasin binds to the prenyl-binding pocket of PDEδ, and impairs Ras enrichment at the plasma membrane, thereby affecting the proliferation of KRas-dependent human pancreatic ductal adenocarcinoma cell lines. Here, using structure-based compound design, we have now identified pyrazolopyridazinones as a novel, unrelated chemotype that binds to the prenyl-binding pocket of PDEδ with high affinity, thereby displacing prenylated Ras proteins in cells. Our results show that the new PDEδ inhibitor, named Deltazinone 1, is highly selective, exhibits less unspecific cytotoxicity than the previously reported Deltarasin and demonstrates a high correlation with the phenotypic effect of PDEδ knockdown in a set of human pancreatic cancer cell lines.
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Affiliation(s)
- Björn Papke
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Sandip Murarka
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Holger A Vogel
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Pablo Martín-Gago
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Marija Kovacevic
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Dina C Truxius
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Eyad K Fansa
- Structural Biology Group, Max Planck Institute for Molecular Physiology, D-44227 Dortmund, Germany
| | - Shehab Ismail
- Structural Biology Group, Max Planck Institute for Molecular Physiology, D-44227 Dortmund, Germany
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, UK
| | - Gunther Zimmermann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Kaatje Heinelt
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | | | - Alaa Al Saabi
- Lead Discovery Center GmbH, D-44227 Dortmund, Germany
| | | | | | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute for Molecular Physiology, D-44227 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
- TU Dortmund, Faculty of Chemistry and Chemical Biology, D-44227 Dortmund, Germany
| | - Philippe I.H. Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
- TU Dortmund, Faculty of Chemistry and Chemical Biology, D-44227 Dortmund, Germany
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21
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Blaževitš O, Mideksa YG, Šolman M, Ligabue A, Ariotti N, Nakhaeizadeh H, Fansa EK, Papageorgiou AC, Wittinghofer A, Ahmadian MR, Abankwa D. Galectin-1 dimers can scaffold Raf-effectors to increase H-ras nanoclustering. Sci Rep 2016; 6:24165. [PMID: 27087647 PMCID: PMC4834570 DOI: 10.1038/srep24165] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 03/22/2016] [Indexed: 12/12/2022] Open
Abstract
Galectin-1 (Gal-1) dimers crosslink carbohydrates on cell surface receptors. Carbohydrate-derived inhibitors have been developed for cancer treatment. Intracellularly, Gal-1 was suggested to interact with the farnesylated C-terminus of Ras thus specifically stabilizing GTP-H-ras nanoscale signalling hubs in the membrane, termed nanoclusters. The latter activity may present an alternative mechanism for how overexpressed Gal-1 stimulates tumourigenesis. Here we revise the current model for the interaction of Gal-1 with H-ras. We show that it indirectly forms a complex with GTP-H-ras via a high-affinity interaction with the Ras binding domain (RBD) of Ras effectors. A computationally generated model of the Gal-1/C-Raf-RBD complex is validated by mutational analysis. Both cellular FRET as well as proximity ligation assay experiments confirm interaction of Gal-1 with Raf proteins in mammalian cells. Consistently, interference with H-rasG12V-effector interactions basically abolishes H-ras nanoclustering. In addition, an intact dimer interface of Gal-1 is required for it to positively regulate H-rasG12V nanoclustering, but negatively K-rasG12V nanoclustering. Our findings suggest stacked dimers of H-ras, Raf and Gal-1 as building blocks of GTP-H-ras-nanocluster at high Gal-1 levels. Based on our results the Gal-1/effector interface represents a potential drug target site in diseases with aberrant Ras signalling.
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Affiliation(s)
- Olga Blaževitš
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Yonatan G Mideksa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Maja Šolman
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Alessio Ligabue
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Nicholas Ariotti
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Hossein Nakhaeizadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Eyad K Fansa
- Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | | | | | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
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22
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Fansa EK, Kösling SK, Zent E, Wittinghofer A, Ismail S. PDE6δ-mediated sorting of INPP5E into the cilium is determined by cargo-carrier affinity. Nat Commun 2016; 7:11366. [PMID: 27063844 PMCID: PMC5512577 DOI: 10.1038/ncomms11366] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 03/18/2016] [Indexed: 01/06/2023] Open
Abstract
The phosphodiesterase 6 delta subunit (PDE6δ) shuttles several farnesylated cargos between membranes. The cargo sorting mechanism between cilia and other compartments is not understood. Here we show using the inositol polyphosphate 5'-phosphatase E (INPP5E) and the GTP-binding protein (Rheb) that cargo sorting depends on the affinity towards PDE6δ and the specificity of cargo release. High-affinity cargo is exclusively released by the ciliary transport regulator Arl3, while low-affinity cargo is released by Arl3 and its non-ciliary homologue Arl2. Structures of PDE6δ/cargo complexes reveal the molecular basis of the sorting signal which depends on the residues at the -1 and -3 positions relative to farnesylated cysteine. Structure-guided mutation allows the generation of a low-affinity INPP5E mutant which loses exclusive ciliary localization. We postulate that the affinity to PDE6δ and the release by Arl2/3 in addition to a retention signal are the determinants for cargo sorting and enrichment at its destination.
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Affiliation(s)
- Eyad Kalawy Fansa
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | | | - Eldar Zent
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Alfred Wittinghofer
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Shehab Ismail
- CR-UK Beatson Institute, Garscube Estate Switchback Road, Glasgow G61 1BD, UK
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23
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Abstract
Two recent studies evaluated a small molecule that specifically binds to and inactivates the KRAS G12C mutant. The new findings argue that the perception that mutant KRAS is persistently frozen in its active GTP-bound form may not be accurate.
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Affiliation(s)
- G Aaron Hobbs
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alfred Wittinghofer
- Department of Structural Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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24
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Ismail-Ali A, Fansa EK, Pryk N, Yahiaoui S, Kushnir S, Pflieger M, Wittinghofer A, Schulz F. Biosynthesis-driven structure–activity relationship study of premonensin-derivatives. Org Biomol Chem 2016; 14:7671-5. [DOI: 10.1039/c6ob01201a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The controlled derivatization of natural products is of great importance for their use in drug discovery.
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Affiliation(s)
- A. Ismail-Ali
- Fakultät für Chemie und Biochemie
- Organische Chemie 1
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - E. K. Fansa
- Max-Planck-Institut für Molekulare Physiologie
- 44227 Dortmund
- Germany
| | - N. Pryk
- Fakultät für Chemie und Biochemie
- Organische Chemie 1
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - S. Yahiaoui
- Centre d'Etudes et de Recherche sur le Médicament de Normandie UPRES EA 4258
- Université de Caen Basse-Normandie
- 14032 Caen Cedex
- France
| | - S. Kushnir
- Fakultät für Chemie und Biochemie
- Organische Chemie 1
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - M. Pflieger
- Fakultät für Chemie und Biochemie
- Organische Chemie 1
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - A. Wittinghofer
- Max-Planck-Institut für Molekulare Physiologie
- 44227 Dortmund
- Germany
| | - F. Schulz
- Fakultät für Chemie und Biochemie
- Organische Chemie 1
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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25
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Abstract
This study shows that the prenylated C‐terminus of RPGR can bind to PDE6δ with high affinity, suggesting two distinct binding sites of the RPGR/PDE6δ complex. The serine residue at the −3 position relative to the prenylated cysteine seems to play a key role in defining the selectivity of PDE6δ towards ciliary prenylated cargo.
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26
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Remans K, Bürger M, Vetter I, Wittinghofer A. C2 domains as protein-protein interaction modules in the ciliary transition zone. Cilia 2015. [PMCID: PMC4519163 DOI: 10.1186/2046-2530-4-s1-p65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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27
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Gotthardt K, Lokaj M, Koerner C, Falk N, Gießl A, Wittinghofer A. A G-protein activation cascade from Arl13B to Arl3 and implications for ciliary targeting of lipidated proteins. eLife 2015; 4. [PMID: 26551564 PMCID: PMC4868535 DOI: 10.7554/elife.11859] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [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: 09/24/2015] [Accepted: 11/06/2015] [Indexed: 12/11/2022] Open
Abstract
Small G-proteins of the ADP-ribosylation-factor-like (Arl) subfamily have been shown to be crucial to ciliogenesis and cilia maintenance. Active Arl3 is involved in targeting and releasing lipidated cargo proteins from their carriers PDE6δ and UNC119a/b to the cilium. However, the guanine nucleotide exchange factor (GEF) which activates Arl3 is unknown. Here we show that the ciliary G-protein Arl13B mutated in Joubert syndrome is the GEF for Arl3, and its function is conserved in evolution. The GEF activity of Arl13B is mediated by the G-domain plus an additional C-terminal helix. The switch regions of Arl13B are involved in the interaction with Arl3. Overexpression of Arl13B in mammalian cell lines leads to an increased Arl3·GTP level, whereas Arl13B Joubert-Syndrome patient mutations impair GEF activity and thus Arl3 activation. We anticipate that through Arl13B's exclusive ciliary localization, Arl3 activation is spatially restricted and thereby an Arl3·GTP compartment generated where ciliary cargo is specifically released.
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Affiliation(s)
- Katja Gotthardt
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Mandy Lokaj
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Carolin Koerner
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Nathalie Falk
- Department of Biology, Animal Physiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Andreas Gießl
- Department of Biology, Animal Physiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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28
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Kapoor S, Fansa EK, Möbitz S, Ismail SA, Winter R, Wittinghofer A, Weise K. Effect of the N-Terminal Helix and Nucleotide Loading on the Membrane and Effector Binding of Arl2/3. Biophys J 2015; 109:1619-29. [PMID: 26488653 PMCID: PMC4624342 DOI: 10.1016/j.bpj.2015.08.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 03/24/2015] [Revised: 08/05/2015] [Accepted: 08/10/2015] [Indexed: 01/02/2023] Open
Abstract
The small GTP-binding proteins Arl2 and Arl3, which are close homologs, share a number of interacting partners and act as displacement factors for prenylated and myristoylated cargo. Nevertheless, both proteins have distinct biological functions. Whereas Arl3 is considered a ciliary protein, Arl2 has been reported to be involved in tubulin folding, mitochondrial function, and Ras signaling. How these different roles are attained by the two homolog proteins is not fully understood. Recently, we showed that the N-terminal amphipathic helix of Arl3, but not that of Arl2, regulates the release of myristoylated ciliary proteins from the GDI-like solubilizing factor UNC119a/b. In the biophysical study presented here, both proteins are shown to exhibit a preferential localization and clustering in liquid-disordered domains of phase-separated membranes. However, the membrane interaction behavior differs significantly between both proteins with regard to their nucleotide loading. Whereas Arl3 and other Arf proteins with an N-terminal amphipathic helix require GTP loading for the interaction with membranes, Arl2 binds to membranes in a nucleotide-independent manner. In contrast to Arl2, the N-terminal helix of Arl3 increases the binding affinity to UNC119a. Furthermore, UNC119a impedes membrane binding of Arl3, but not of Arl2. Taken together, these results suggest an interplay among the nucleotide status of Arl3, the location of the N-terminal helix, membrane fluidity and binding, and the release of lipid modified cargos from carriers such as UNC119a. Since a specific Arl3-GEF is postulated to reside inside cilia, the N-terminal helix of Arl3•GTP would be available for allosteric regulation of UNC119a cargo release only inside cilia.
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Affiliation(s)
- Shobhna Kapoor
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Eyad K Fansa
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Simone Möbitz
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Shehab A Ismail
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany; Structural Biology of Cilia, CR-UK Beatson Institute, Glasgow, United Kingdom
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Katrin Weise
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany.
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29
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Lokaj M, Kösling SK, Koerner C, Lange SM, van Beersum SEC, van Reeuwijk J, Roepman R, Horn N, Ueffing M, Boldt K, Wittinghofer A. The Interaction of CCDC104/BARTL1 with Arl3 and Implications for Ciliary Function. Structure 2015; 23:2122-32. [PMID: 26455799 PMCID: PMC4635315 DOI: 10.1016/j.str.2015.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/26/2015] [Accepted: 08/29/2015] [Indexed: 01/23/2023]
Abstract
Cilia are small antenna-like cellular protrusions critical for many developmental signaling pathways. The ciliary protein Arl3 has been shown to act as a specific release factor for myristoylated and farnesylated ciliary cargo molecules by binding to the effectors Unc119 and PDE6δ. Here we describe a newly identified Arl3 binding partner, CCDC104/CFAP36. Biochemical and structural analyses reveal that the protein contains a BART-like domain and is called BARTL1. It recognizes an LLxILxxL motif at the N-terminal amphipathic helix of Arl3, which is crucial for the interaction with the BART-like domain but also for the ciliary localization of Arl3 itself. These results seem to suggest a ciliary role of BARTL1, and possibly link it to the Arl3 transport network. We thus speculate on a regulatory mechanism whereby BARTL1 aids the presentation of active Arl3 to its GTPase-activating protein RP2 or hinders Arl3 membrane binding in the area of the transition zone.
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Affiliation(s)
- Mandy Lokaj
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Stefanie K Kösling
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Carolin Koerner
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Sven M Lange
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Sylvia E C van Beersum
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Jeroen van Reeuwijk
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Nicola Horn
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Marius Ueffing
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Karsten Boldt
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Alfred Wittinghofer
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany.
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30
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Chen YX, Koch S, Uhlenbrock K, Weise K, Das D, Gremer L, Brunsveld L, Wittinghofer A, Winter R, Triola G, Waldmann H. Synthesis of the Rheb and K-Ras4B GTPases. Angew Chem Int Ed Engl 2015; 49:6090-5. [PMID: 20652921 DOI: 10.1002/anie.201001884] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [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)
- Yong-Xiang Chen
- Abteilung Chemische Biologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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31
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Abstract
Kinase inhibition is considered to be an important therapeutic target for LRRK2 mediated Parkinson's disease (PD). Many LRRK2 kinase inhibitors have been reported but have yet to be optimized in order to qualify as drug candidates for the treatment of the disease. In order to start a structure-function analysis of such inhibitors, we mutated the active site of Dictyostelium Roco4 kinase to resemble LRRK2. Here, we show saturation transfer difference (STD) NMR and the first cocrystal structures of two potent in vitro inhibitors, LRRK2-IN-1 and compound 19, with mutated Roco4. Our data demonstrate that this system can serve as an excellent tool for the structural characterization and optimization of LRRK2 inhibitors using X-ray crystallography and NMR spectroscopy.
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Affiliation(s)
- Bernd K Gilsbach
- †Department of Cell Biochemistry, University of Groningen, 9747AG Groningen, The Netherlands
| | - Ana C Messias
- ‡Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,§Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching bei München, Germany
| | - Genta Ito
- ∥University of Dundee, DD1 4HN Dundee, Scotland
| | - Michael Sattler
- ‡Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,§Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching bei München, Germany
| | | | | | - Arjan Kortholt
- †Department of Cell Biochemistry, University of Groningen, 9747AG Groningen, The Netherlands
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32
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Kapoor S, Möbitz S, Ismail SA, Fansa EK, Wittinghofer A, Winter R, Weise K. The Difference in Arl2 and Arl3 Membrane Binding and Localization. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2091] [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: 10/24/2022] Open
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33
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Wittinghofer A. Abstract IA01: Ras membrane localization, ciliary trafficking and anti-Ras drug candidates. Mol Cancer Res 2014. [DOI: 10.1158/1557-3125.rasonc14-ia01] [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: 11/16/2022]
Abstract
Abstract
GTP-binding (G) proteins are molecular switches that cycle between a GDP-bound OFF and a GTP-bound ON state and are regulated by Guanine nucleotide exchange factors (GEFs) and GTPase Activating Proteins (GAPs). The Ras superfamily of G proteins are 20-25 kDa proteins involved in almost every aspect of cell function. Members of the Ras subfamily such as the oncoprotein Ras itself or RheB, but also ciliary proteins such as the inositol phosphatase INPP5E or the α-subunit of phosphodiesterase PDE6, have a C-terminal CaaX motif, the cysteine residue of which is modified with the lipophilic farnesyl moiety. The farnesyl group and further modifications are required for membrane attachment and function. Spatiotemporal regulation of Ras proteins relies on a highly dynamic shuttling between different membrane compartments. Transport between membrane compartments in the cell is mediated by factors such as PDEδ, the delta subunit of phosphodiesterase and possibly similar proteins.
Arl3 is a member of the Arf subfamily of the Ras superfamily. In the GTP-bound form Arl3 interacts with a variety of proteins called downstream effectors. These are the delta subunit of phosphodiesterase PDEδ, HRG4 (human retina gene 4) also called Unc119 and various other proteins such as BART (Binder of Arl2). Arl3 regulates the binding of ciliary and other cargo to PDEδ and HRG4.
We will discuss how spatiotemporal regulation of Ras proteins is mediated by the Arl2 and 3 conformational switch cycle and how this has suggested a new avenue towards anti-Ras drugs.
Citation Format: Alfred Wittinghofer. Ras membrane localization, ciliary trafficking and anti-Ras drug candidates. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr IA01. doi: 10.1158/1557-3125.RASONC14-IA01
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Gasper R, Sot B, Wittinghofer A. GTPase activity of Di-Ras proteins is stimulated by Rap1GAP proteins. Small GTPases 2014; 1:133-141. [PMID: 21686267 DOI: 10.4161/sgtp.1.3.14742] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 01/06/2011] [Accepted: 01/06/2011] [Indexed: 11/19/2022] Open
Abstract
The Ras family is the largest and most diverse sub-group of Ras-like G proteins. This complexity is further increased by the high number of regulatory Guanine nucleotide Exchange Factors (GEFs) and GTPase Activating Proteins (GAPs) that target specific members of this subfamily. Di-Ras1 and Di-Ras2 are little characterized members of the Ras-like sub-group with still unidentified regulatory and effector proteins. Here we determined the nucleotide binding properties of Di-Ras1/Di-Ras2. The above nanomolar affinity and the inability to react with members of the Cdc25 RasGEF family might suggest that activation does not require a GEF. We identified Rap1GAP1 and Rap1GAP2 as specific GTPase activating proteins of the Di-Ras family. Dual-specificity GAPs of the GAP1(m) family could not activate Di-Ras proteins, despite the presence of the required catalytic residue. Although Di-Ras proteins share GAPs with Rap G proteins, no common effectors could be identified in vitro.
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Affiliation(s)
- Raphael Gasper
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Strukturelle Biologie; Dortmund, Germany
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35
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Abstract
Septins form oligomeric complexes consisting of septins from different subgroups, which form filaments that are involved in a number of biological processes. They are GTP-binding proteins that contain all the necessary elements to perform the general GDP-to-GTP conformational switch. It is however unclear whether or not such a switch is important for the dynamics of septin filaments. Here we investigate the complex GTPase reaction of members of each of the four human septin groups, which is dominated by the stability of dimer formation via the nucleotide binding or so-called G-interface. The results also show that the actual hydrolysis reaction is very similar for three septin groups in the monomeric state while the Sept6 has no GTPase activity. Sept7, the only member of the Sept7 subgroup, forms a very tight G-interface dimer in the GDP-bound state. Here we show that the stability of the interface is dramatically decreased by exchanging GDP with a nucleoside triphosphate, which is believed to influence filament formation and dynamics via Sept7.
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36
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Bravo-Rodriguez K, Ismail-Ali AF, Klopries S, Kushnir S, Ismail S, Fansa EK, Wittinghofer A, Schulz F, Sanchez-Garcia E. Predicted incorporation of non-native substrates by a polyketide synthase yields bioactive natural product derivatives. Chembiochem 2014; 15:1991-7. [PMID: 25044264 DOI: 10.1002/cbic.201402206] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [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: 04/30/2014] [Indexed: 11/08/2022]
Abstract
The polyether ionophore monensin is biosynthesized by a polyketide synthase that delivers a mixture of monensins A and B by the incorporation of ethyl- or methyl-malonyl-CoA at its fifth module. Here we present the first computational model of the fifth acyltransferase domain (AT5mon ) of this polyketide synthase, thus affording an investigation of the basis of the relaxed specificity in AT5mon , insights into the activation for the nucleophilic attack on the substrate, and prediction of the incorporation of synthetic malonic acid building blocks by this enzyme. Our predictions are supported by experimental studies, including the isolation of a predicted derivative of the monensin precursor premonensin. The incorporation of non-native building blocks was found to alter the ratio of premonensins A and B. The bioactivity of the natural product derivatives was investigated and revealed binding to prenyl-binding protein. We thus show the potential of engineered biosynthetic polyketides as a source of ligands for biological macromolecules.
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Affiliation(s)
- Kenny Bravo-Rodriguez
- Department of Theoretical Chemistry, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)
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37
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Zimmermann G, Schultz-Fademrecht C, Küchler P, Murarka S, Ismail S, Triola G, Nussbaumer P, Wittinghofer A, Waldmann H. Structure guided design and kinetic analysis of highly potent benzimidazole inhibitors targeting the PDEδ prenyl binding site. J Med Chem 2014; 57:5435-48. [PMID: 24884780 DOI: 10.1021/jm500632s] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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] [Indexed: 12/29/2022]
Abstract
K-Ras is one of the most frequently mutated signal transducing human oncogenes. Ras signaling activity requires correct cellular localization of the GTPase. The spatial organization of K-Ras is controlled by the prenyl binding protein PDEδ, which enhances Ras diffusion in the cytosol. Inhibition of the Ras-PDEδ interaction by small molecules impairs Ras localization and signaling. Here we describe in detail the identification and structure guided development of Ras-PDEδ inhibitors targeting the farnesyl binding pocket of PDEδ with nanomolar affinity. We report kinetic data that characterize the binding of the most potent small molecule ligands to PDEδ and prove their binding to endogenous PDEδ in cell lysates. The PDEδ inhibitors provide promising starting points for the establishment of new drug discovery programs aimed at cancers harboring oncogenic K-Ras.
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Affiliation(s)
- Gunther Zimmermann
- Max Planck Institute of Molecular Physiology , Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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38
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Remans K, Bürger M, Vetter IR, Wittinghofer A. C2 domains as protein-protein interaction modules in the ciliary transition zone. Cell Rep 2014; 8:1-9. [PMID: 24981858 DOI: 10.1016/j.celrep.2014.05.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/22/2014] [Accepted: 05/27/2014] [Indexed: 11/16/2022] Open
Abstract
RPGR-interacting protein 1 (RPGRIP1) is mutated in the eye disease Leber congenital amaurosis (LCA) and its structural homolog, RPGRIP1-like (RPGRIP1L), is mutated in many different ciliopathies. Both are multidomain proteins that are predicted to interact with retinitis pigmentosa G-protein regulator (RPGR). RPGR is mutated in X-linked retinitis pigmentosa and is located in photoreceptors and primary cilia. We solved the crystal structure of the complex between the RPGR-interacting domain (RID) of RPGRIP1 and RPGR and demonstrate that RPGRIP1L binds to RPGR similarly. RPGRIP1 binding to RPGR affects the interaction with PDEδ, the cargo shuttling factor for prenylated ciliary proteins. RPGRIP1-RID is a C2 domain with a canonical β sandwich structure that does not bind Ca(2+) and/or phospholipids and thus constitutes a unique type of protein-protein interaction module. Judging from the large number of C2 domains in most of the ciliary transition zone proteins identified thus far, the structure presented here seems to constitute a cilia-specific module that is present in multiprotein transition zone complexes.
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Affiliation(s)
- Kim Remans
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Marco Bürger
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Ingrid R Vetter
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Alfred Wittinghofer
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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39
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Wittinghofer A. Arf Proteins and Their Regulators: At the Interface Between Membrane Lipids and the Protein Trafficking Machinery. Ras Superfamily Small G Proteins: Biology and Mechanisms 2 2014. [PMCID: PMC7123483 DOI: 10.1007/978-3-319-07761-1_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The Arf small GTP-binding (G) proteins regulate membrane traffic and organelle structure in eukaryotic cells through a regulated cycle of GTP binding and hydrolysis. The first function identified for Arf proteins was recruitment of cytosolic coat complexes to membranes to mediate vesicle formation. However, subsequent studies have uncovered additional functions, including roles in plasma membrane signalling pathways, cytoskeleton regulation, lipid droplet function, and non-vesicular lipid transport. In contrast to other families of G proteins, there are only a few Arf proteins in each organism, yet they function specifically at many different cellular locations. Part of this specificity is achieved by formation of complexes with their guanine nucleotide-exchange factors (GEFs) and GTPase activating proteins (GAPs) that catalyse GTP binding and hydrolysis, respectively. Because these regulators outnumber their Arf substrates by at least 3-to-1, an important aspect of understanding Arf function is elucidating the mechanisms by which a single Arf protein is incorporated into different GEF, GAP, and effector complexes. New insights into these mechanisms have come from recent studies showing GEF–effector interactions, Arf activation cascades, and positive feedback loops. A unifying theme in the function of Arf proteins, carried out in conjunction with their regulators and effectors, is sensing and modulating the properties of the lipids that make up cellular membranes.
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Affiliation(s)
- Alfred Wittinghofer
- Max-Planck-Institute of Molecular Physiology, Dortmund, Nordrhein-Westfalen Germany
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40
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Miertzschke M, Koerner C, Spoerner M, Wittinghofer A. Structural insights into the small G-protein Arl13B and implications for Joubert syndrome. Biochem J 2014; 457:301-11. [PMID: 24168557 DOI: 10.1042/bj20131097] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [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: 12/30/2022]
Abstract
Ciliopathies are human diseases arising from defects in primary or motile cilia. The small G-protein Arl13B (ADP-ribosylation factor-like 13B) localizes to microtubule doublets of the ciliary axoneme and is mutated in Joubert syndrome. Its GDP/GTP mechanistic cycle and the effect of its mutations in patients with Joubert syndrome remain elusive. In the present study we applied high resolution structural and biochemical approaches to study Arl13B. The crystal structure of Chlamydomonas rheinhardtii Arl13B, comprising the G-domain and part of its unique C-terminus, revealed an incomplete active site, and together with biochemical data the present study accounts for the absence of intrinsic GTP hydrolysis by this protein. The structure shows that the residues representing patient mutations R79Q and R200C are involved in stabilizing important intramolecular interactions. Our studies suggest that Arg79 is crucial for the GDP/GTP conformational change by stabilizing the large two-residue register shift typical for Arf (ADP-ribosylation factor) and Arl subfamily proteins. A corresponding mutation in Arl3 induces considerable defects in effector and GAP (GTPase-activating protein) binding, suggesting a loss of Arl13B function in patients with Joubert syndrome.
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Affiliation(s)
- Mandy Miertzschke
- *Emeritus group A. Wittinghofer, Max-Planck-Institute for Molecular Physiology, BMZ, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Carolin Koerner
- *Emeritus group A. Wittinghofer, Max-Planck-Institute for Molecular Physiology, BMZ, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Michael Spoerner
- †Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Alfred Wittinghofer
- *Emeritus group A. Wittinghofer, Max-Planck-Institute for Molecular Physiology, BMZ, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
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41
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Abstract
The ARF-like (ARL) proteins, within the ARF family, are a collection of functionally diverse GTPases that share extensive (>40 %) identity with the ARFs and each other and are assumed to share basic mechanisms of regulation and a very incompletely documented degree of overlapping regulators. At least four ARLs were already present in the last eukaryotic common ancestor, along with one ARF, and these have been expanded to >20 members in mammals. We know little about the majority of these proteins so our review will focus on those about which the most is known, including ARL1, ARL2, ARL3, ARL4s, ARL6, ARL13s, and ARFRP1. From this fragmentary information we extract some generalizations and conclusions regarding the sources and extent of specificity and functions of the ARLs.
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Affiliation(s)
- Alfred Wittinghofer
- Max-Planck-Institute of Molecular Physiology, Dortmund, Nordrhein-Westfalen Germany
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42
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Abstract
The crystal structure of a nucleotide exchange factor in white blood cells reveals an autoinhibitory mechanism that reinforces the switch-like behaviour of the signalling protein Ras.
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Affiliation(s)
- Christopher Hein
- is at the Institute of Biophysical Chemistry and the Buchmann Institute of Molecular Life Sciences , Goethe University , Frankfurt , Germany
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43
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Wätzlich D, Vetter I, Gotthardt K, Miertzschke M, Chen YX, Wittinghofer A, Ismail S. The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo. EMBO Rep 2013; 14:465-72. [PMID: 23559067 DOI: 10.1038/embor.2013.37] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 11/09/2022] Open
Abstract
Defects in primary cilia result in human diseases known as ciliopathies. The retinitis pigmentosa GTPase regulator (RPGR), mutated in the most severe form of the eye disease, is located at the transition zone of the ciliary organelle. The RPGR-interacting partner PDEδ is involved in trafficking of farnesylated ciliary cargo, but the significance of this interaction is unknown. The crystal structure of the propeller domain of RPGR shows the location of patient mutations and how they perturb the structure. The RPGR·PDEδ complex structure shows PDEδ on a highly conserved surface patch of RPGR. Biochemical experiments and structural considerations show that RPGR can bind with high affinity to cargo-loaded PDEδ and exposes the Arl2/Arl3-binding site on PDEδ. On the basis of these results, we propose a model where RPGR is acting as a scaffold protein recruiting cargo-loaded PDEδ and Arl3 to release lipidated cargo into cilia.
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Affiliation(s)
- Denise Wätzlich
- Structural Biology Group, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
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44
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Zent E, Vetter I, Wittinghofer A. Structural and biochemical properties of Sept7, a unique septin required for filament formation. Biol Chem 2012; 392:791-7. [PMID: 21824007 DOI: 10.1515/bc.2011.082] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Septins constitute a family of conserved guanine nucleotide binding proteins found in a wide range of organisms from fungi to mammals. Members of the family share a canonical G-domain with N- and C-terminal extensions. G-domains assemble into hetero-oligomeric complexes which form non-polarised filaments or rings. Linear filaments are formed between the G-domains using either the guanine nucleotide binding site (G interface) or N- and C-terminal extensions (NC interface). Sept7 is a unique among the 13 human septins in that it occupies the ends of hexameric building blocks which assemble into non-polarised filaments. To gain insight into its particular properties we performed structural and biochemical studies on Sept7. We solved the crystal structure of a Sept7 dimer in the GDP-bound state. The structure and biochemistry of Sept7 provide new insights into the dynamics of the G interface and outline the differences in the properties of Sept7 compared to the members of group 2 septins.
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Affiliation(s)
- Eldar Zent
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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45
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Chandra A, Grecco HE, Pisupati V, Perera D, Cassidy L, Skoulidis F, Ismail SA, Hedberg C, Hanzal-Bayer M, Venkitaraman AR, Wittinghofer A, Bastiaens PIH. The GDI-like solubilizing factor PDEδ sustains the spatial organization and signalling of Ras family proteins. Nat Cell Biol 2011; 14:148-58. [PMID: 22179043 DOI: 10.1038/ncb2394] [Citation(s) in RCA: 254] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 11/04/2011] [Indexed: 12/31/2022]
Abstract
We identify a role for the GDI-like solubilizing factor (GSF) PDEδ in modulating signalling through Ras family G proteins by sustaining their dynamic distribution in cellular membranes. We show that the GDI-like pocket of PDEδ binds and solubilizes farnesylated Ras proteins, thereby enhancing their diffusion in the cytoplasm. This mechanism allows more effective trapping of depalmitoylated Ras proteins at the Golgi and polycationic Ras proteins at the plasma membrane to counter the entropic tendency to distribute these proteins over all intracellular membranes. Thus, PDEδ activity augments K/Hras signalling by enriching Ras at the plasma membrane; conversely, PDEδ down-modulation randomizes Ras distributions to all membranes in the cell and suppresses regulated signalling through wild-type Ras and also constitutive oncogenic Ras signalling in cancer cells. Our findings link the activity of PDEδ in determining Ras protein topography to Ras-dependent signalling.
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Affiliation(s)
- Anchal Chandra
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
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46
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Mucha E, Fricke I, Schaefer A, Wittinghofer A, Berken A. Rho proteins of plants – Functional cycle and regulation of cytoskeletal dynamics. Eur J Cell Biol 2011; 90:934-43. [PMID: 21277045 DOI: 10.1016/j.ejcb.2010.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 11/25/2010] [Accepted: 11/25/2010] [Indexed: 10/24/2022] Open
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47
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Ismail SA, Chen YX, Rusinova A, Chandra A, Bierbaum M, Gremer L, Triola G, Waldmann H, Bastiaens PIH, Wittinghofer A. Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo. Nat Chem Biol 2011; 7:942-9. [PMID: 22002721 DOI: 10.1038/nchembio.686] [Citation(s) in RCA: 208] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 08/31/2011] [Indexed: 01/21/2023]
Abstract
Lipidated Rho and Rab GTP-binding proteins are transported between membranes in complex with solubilizing factors called 'guanine nucleotide dissociation inhibitors' (GDIs). Unloading from GDIs using GDI displacement factors (GDFs) has been proposed but remains mechanistically elusive. PDEδ is a putative solubilizing factor for several prenylated Ras-subfamily proteins. Here we report the structure of fully modified farnesylated Rheb-GDP in complex with PDEδ. The structure explains the nucleotide-independent binding of Rheb to PDEδ and the relaxed specificity of PDEδ. We demonstrate that the G proteins Arl2 and Arl3 act in a GTP-dependent manner as allosteric release factors for farnesylated cargo. We thus describe a new transport system for farnesylated G proteins involving a GDI-like molecule and an unequivocal GDF. Considering the importance of PDEδ for proper Ras and Rheb signaling, this study is instrumental in developing a new target for anticancer therapy.
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Affiliation(s)
- Shehab A Ismail
- Structural Biology Group, Max Planck Institute for Molecular Physiology, Dortmund, Germany
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Abstract
GTP-binding (G) proteins constitute a class of P-loop (phosphate-binding loop) proteins that work as molecular switches between the GDP-bound OFF and the GTP-bound ON state. The common principle is the 160-180-residue G domain with an α,β topology that is responsible for nucleotide-dependent conformational changes and drives many biological functions. Although the G domain uses a universally conserved switching mechanism, its structure, function, and GTPase reaction are modified for many different pathways and processes.
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Schaefer A, Höhner K, Berken A, Wittinghofer A. The unique plant RhoGAPs are dimeric and contain a CRIB motif required for affinity and specificity towards cognate small G proteins. Biopolymers 2011; 95:420-33. [PMID: 21294109 DOI: 10.1002/bip.21601] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plant Rho proteins (ROPs) are inactivated by specific GTPase activating proteins, called RopGAPs. Many of these comprise the exclusive combination of a classic, catalytic Arg-containing RhoGAP domain, and a Cdc42/ Rac interactive binding (CRIB) motif which in animal and fungi has been identified in effectors for Cdc42 and Rac1, but never in any GAP protein. Both elements are required for an efficient RopGAP activity. Here, we analyzed the effect of the CRIB motif on the complex formation and the binding reaction with plant and human Rho proteins by using kinetic and equilibrium methods. We show that RopGAP2 from Arabidopsis thaliana dimerizes via its GAP domain and forms a 2:2 complex with ROP. The CRIB effector motif mediates high affinity and specificity in binding. The catalytic Arg in the context of the CRIB motif is inhibitory for binding. The unusually slow association and dissociation reactions suggest a major conformational change whereby the CRIB motif functions as a lid for binding and/or release of ROP. We propose a two-site interaction model where ROP binds to the CRIB motif as described for the human CRIB effectors and to the catalytic GAP domain as described for animal RhoGAPs.
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Affiliation(s)
- Antje Schaefer
- Department of Structural Biology, Max Planck Institute of Molecular Physiology, Otto Hahn Str. 11, 44227 Dortmund, Germany
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Wittinghofer A. Highlight on septins. Biol Chem 2011; 392:679-80. [DOI: 10.1515/bc.2011.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
No abstract available
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