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Wiegandt D, Vieweg S, Hofmann F, Koch D, Li F, Wu YW, Itzen A, Müller MP, Goody RS. Locking GTPases covalently in their functional states. Nat Commun 2015; 6:7773. [PMID: 26178622 PMCID: PMC4518245 DOI: 10.1038/ncomms8773] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/09/2015] [Indexed: 11/29/2022] Open
Abstract
GTPases act as key regulators of many cellular processes by switching between active (GTP-bound) and inactive (GDP-bound) states. In many cases, understanding their mode of action has been aided by artificially stabilizing one of these states either by designing mutant proteins or by complexation with non-hydrolysable GTP analogues. Because of inherent disadvantages in these approaches, we have developed acryl-bearing GTP and GDP derivatives that can be covalently linked with strategically placed cysteines within the GTPase of interest. Binding studies with GTPase-interacting proteins and X-ray crystallography analysis demonstrate that the molecular properties of the covalent GTPase–acryl–nucleotide adducts are a faithful reflection of those of the corresponding native states and are advantageously permanently locked in a defined nucleotide (that is active or inactive) state. In a first application, in vivo experiments using covalently locked Rab5 variants provide new insights into the mechanism of correct intracellular localization of Rab proteins. The cellular function of small GTPases is regulated by switching between active (GTP-bound) and inactive (GDP-bound) states. Here the authors develop nucleotide analogues that can be covalently linked to GTPases via a strategically placed cysteine residue to lock the target GTPase in defined activation states.
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Affiliation(s)
- David Wiegandt
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sophie Vieweg
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Frank Hofmann
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Daniel Koch
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Fu Li
- 1] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany [2] Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
| | - Yao-Wen Wu
- 1] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany [2] Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Matthias P Müller
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Roger S Goody
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Luo Y, Fischer JJ, Baessler OYGN, Schrey AK, Ungewiss J, Glinski M, Sefkow M, Dreger M, Koester H. GDP-capture compound--a novel tool for the profiling of GTPases in pro- and eukaryotes by capture compound mass spectrometry (CCMS). J Proteomics 2009; 73:815-9. [PMID: 20026263 DOI: 10.1016/j.jprot.2009.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 12/01/2009] [Accepted: 12/02/2009] [Indexed: 12/28/2022]
Abstract
The functional isolation of proteome subsets based on small molecule-protein interactions is an increasingly popular and promising field in functional proteomics. Entire protein families may be profiled on the basis of their common interaction with a metabolite or small molecule inhibitor. This is enabled by novel multifunctional small molecule probes. One platform approach in this field are Capture Compounds that contain a small molecule of interest to bind target proteins, a photo-activatable reactivity function to covalently trap bound proteins, and a sorting function to isolate Capture Compound-protein conjugates from complex biological samples for direct trypsinisation and protein identification by liquid chromatography/mass spectrometry (CCMS). We here present the synthesis and application of a novel GDP-Capture Compound for the functional enrichment of GTPases, a pivotal protein family that exerts key functions in signal transduction. We present data from CCMS experiments on two biological lysates from Escherichia coli and from human-derived Hek293 cells. The GDP-Capture Compound robustly captures a wide range of different GTPases from both systems and will be a valuable tool for the proteomic profiling of this important protein family.
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Affiliation(s)
- Yan Luo
- Caprotec Bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
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Vincent SP, Grenier S, Mioskowski C, Salesse C, Lebeau L. Probing the transducin nucleotide binding site with GDP analogues. Bioorg Med Chem Lett 2001; 11:1185-8. [PMID: 11354373 DOI: 10.1016/s0960-894x(01)00172-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An affinity study between the G protein of the visual photoreceptor, transducin, and eight different non-hydrolyzable GDP analogues is described. Imidodiphosphate derivatives have been shown to exhibit good affinities to transducin. This very important heterotrimeric G protein is shown to be highly restrictive with regard to structural modifications of the nucleotide at the pyrophosphate moiety, at the 3' position on ribose, as well as at the N1 position of the purine.
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Affiliation(s)
- S P Vincent
- Laboratoire de Synthèse Bioorganique associé au CNRS, Université Louis Pasteur, Illkirch, France
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