1
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The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Nat Commun 2020; 11:4187. [PMID: 32826901 PMCID: PMC7442826 DOI: 10.1038/s41467-020-17792-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/19/2020] [Indexed: 12/18/2022] Open
Abstract
EHBP1 is an adaptor protein that regulates vesicular trafficking by recruiting Rab8 family members and Eps15-homology domain-containing proteins 1/2 (EHD1/2). It also links endosomes to the actin cytoskeleton. However, the underlying molecular mechanism of activation of EHBP1 actin-binding activity is unclear. Here, we show that both termini of EHBP1 have membrane targeting potential. EHBP1 associates with PI(3)P, PI(5)P, and phosphatidylserine via its N-terminal C2 domain. We show that in the absence of Rab8 family members, the C-terminal bivalent Mical/EHBP Rab binding (bMERB) domain forms an intramolecular complex with its central calponin homology (CH) domain and auto-inhibits actin binding. Rab8 binding to the bMERB domain relieves this inhibition. We have analyzed the CH:bMERB auto-inhibited complex and the active bMERB:Rab8 complex biochemically and structurally. Together with structure-based mutational studies, this explains how binding of Rab8 frees the CH domain and allows it to interact with the actin cytoskeleton, leading to membrane tubulation. EHBP1 is an adaptor protein that regulates vesicular trafficking and links endosomes to the actin cytoskeleton. Here, authors show that both termini of EHBP1 have membrane targeting potential and that in the absence of its binding partner Rab8, the bMERB and CH domain of EHBP1 form an intramolecular complex which auto-inhibits actin binding.
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2
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Esposito A, Ventura V, Petoukhov MV, Rai A, Svergun DI, Vanoni MA. Human MICAL1: Activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8. Protein Sci 2018; 28:150-166. [PMID: 30242933 DOI: 10.1002/pro.3512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 12/18/2022]
Abstract
Human MICAL1 is a member of a recently discovered family of multidomain proteins that couple a FAD-containing monooxygenase-like domain to typical protein interaction domains. Growing evidence implicates the NADPH oxidase reaction catalyzed by the flavoprotein domain in generation of hydrogen peroxide as a second messenger in an increasing number of cell types and as a specific modulator of actin filaments stability. Several proteins of the Rab families of small GTPases are emerging as regulators of MICAL activity by binding to its C-terminal helical domain presumably shifting the equilibrium from the free - auto-inhibited - conformation to the active one. We here extend the characterization of the MICAL1-Rab8 interaction and show that indeed Rab8, in the active GTP-bound state, stabilizes the active MICAL1 conformation causing a specific four-fold increase of kcat of the NADPH oxidase reaction. Kinetic data and small-angle X-ray scattering (SAXS) measurements support the formation of a 1:1 complex between full-length MICAL1 and Rab8 with an apparent dissociation constant of approximately 8 μM. This finding supports the hypothesis that Rab8 is a physiological regulator of MICAL1 activity and shows how the protein region preceding the C-terminal Rab-binding domain may mask one of the Rab-binding sites detected with the isolated C-terminal fragment. SAXS-based modeling allowed us to propose the first model of the free full-length MICAL1, which is consistent with an auto-inhibited conformation in which the C-terminal region prevents catalysis by interfering with the conformational changes that are predicted to occur during the catalytic cycle.
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Affiliation(s)
- Alessandro Esposito
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Valeria Ventura
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Maxim V Petoukhov
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Leninsky prospect 59, 119333, Moscow, Russia.,A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Leninsky Prospect 31, 119071, Moscow, Russia.,N.N. Semenov Institute of Chemical Physics of Russian Academy of Sciences, Kosygina str. 4, 119991, Moscow, Russia.,European Molecular Biology Laboratory, EMBL Hamburg Unit, c/o DESY, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Amrita Rai
- Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, EMBL Hamburg Unit, c/o DESY, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Maria A Vanoni
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
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3
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Cossé MM, Barta ML, Fisher DJ, Oesterlin LK, Niragire B, Perrinet S, Millot GA, Hefty PS, Subtil A. The Loss of Expression of a Single Type 3 Effector (CT622) Strongly Reduces Chlamydia trachomatis Infectivity and Growth. Front Cell Infect Microbiol 2018; 8:145. [PMID: 29868501 PMCID: PMC5962693 DOI: 10.3389/fcimb.2018.00145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/20/2018] [Indexed: 12/20/2022] Open
Abstract
Invasion of epithelial cells by the obligate intracellular bacterium Chlamydia trachomatis results in its enclosure inside a membrane-bound compartment termed an inclusion. The bacterium quickly begins manipulating interactions between host intracellular trafficking and the inclusion interface, diverging from the endocytic pathway and escaping lysosomal fusion. We have identified a previously uncharacterized protein, CT622, unique to the Chlamydiaceae, in the absence of which most bacteria failed to establish a successful infection. CT622 is abundant in the infectious form of the bacteria, in which it associates with CT635, a putative novel chaperone protein. We show that CT622 is translocated into the host cytoplasm via type three secretion throughout the developmental cycle of the bacteria. Two separate domains of roughly equal size have been identified within CT622 and a 1.9 Å crystal structure of the C-terminal domain has been determined. Genetic disruption of ct622 expression resulted in a strong bacterial growth defect, which was due to deficiencies in proliferation and in the generation of infectious bacteria. Our results converge to identify CT622 as a secreted protein that plays multiple and crucial roles in the initiation and support of the C. trachomatis growth cycle. They reveal that genetic disruption of a single effector can deeply affect bacterial fitness.
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Affiliation(s)
- Mathilde M Cossé
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Michael L Barta
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Derek J Fisher
- Department of Microbiology, Southern Illinois University, Carbondale, IL, United States
| | - Lena K Oesterlin
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique UMR 144, Molecular Mechanisms of Intracellular Transport, Paris, France
| | - Béatrice Niragire
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France
| | - Stéphanie Perrinet
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France
| | - Gaël A Millot
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR3756 IP Centre National de la Recherche Scientifique, Paris, France
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Agathe Subtil
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France
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4
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Rai A, Oprisko A, Campos J, Fu Y, Friese T, Itzen A, Goody RS, Gazdag EM, Müller MP. bMERB domains are bivalent Rab8 family effectors evolved by gene duplication. eLife 2016; 5. [PMID: 27552051 PMCID: PMC5026484 DOI: 10.7554/elife.18675] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022] Open
Abstract
In their active GTP-bound form, Rab proteins interact with proteins termed effector molecules. In this study, we have thoroughly characterized a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. Within our study, we show that these effectors display a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and that some of the effector domains can bind two Rab proteins via separate binding sites. Structural analysis allowed us to explain the specificity towards Rab8 family members and the presence of two similar Rab binding sites that must have evolved via gene duplication. This study is the first to thoroughly characterize a Rab effector protein that contains two separate Rab binding sites within a single domain, allowing Micals and EHBPs to bind two Rabs simultaneously, thus suggesting previously unknown functions of these effector molecules in endosomal trafficking. DOI:http://dx.doi.org/10.7554/eLife.18675.001
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Affiliation(s)
- Amrita Rai
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Anastasia Oprisko
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jeremy Campos
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Yangxue Fu
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Timon Friese
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Garching, Germany
| | - Roger S Goody
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Emerich Mihai Gazdag
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias P Müller
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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5
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Cromm PM, Spiegel J, Küchler P, Dietrich L, Kriegesmann J, Wendt M, Goody RS, Waldmann H, Grossmann TN. Protease-Resistant and Cell-Permeable Double-Stapled Peptides Targeting the Rab8a GTPase. ACS Chem Biol 2016; 11:2375-82. [PMID: 27336832 DOI: 10.1021/acschembio.6b00386] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Small GTPases comprise a family of highly relevant targets in chemical biology and medicinal chemistry research and have been considered "undruggable" due to the persisting lack of effective synthetic modulators and suitable binding pockets. As molecular switches, small GTPases control a multitude of pivotal cellular functions, and their dysregulation is associated with many human diseases such as various forms of cancer. Rab-GTPases represent the largest subfamily of small GTPases and are master regulators of vesicular transport interacting with various proteins via flat and extensive protein-protein interactions (PPIs). The only reported synthetic inhibitor of a PPI involving an activated Rab GTPase is the hydrocarbon stapled peptide StRIP3. However, this macrocyclic peptide shows low proteolytic stability and cell permeability. Here, we report the design of a bioavailable StRIP3 analogue that harbors two hydrophobic cross-links and exhibits increased binding affinity, combined with robust cellular uptake and extremely high proteolytic stability. Localization experiments reveal that this double-stapled peptide and its target protein Rab8a accumulate in the same cellular compartments. The reported approach offers a strategy for the implementation of biostability into conformationally constrained peptides while supporting cellular uptake and target affinity, thereby conveying drug-like properties.
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Affiliation(s)
- Philipp M. Cromm
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Jochen Spiegel
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Philipp Küchler
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Laura Dietrich
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Julia Kriegesmann
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Mathias Wendt
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Roger S. Goody
- Structural
Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse
11, D-44227 Dortmund, Germany
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Tom N. Grossmann
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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6
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Cromm PM, Schaubach S, Spiegel J, Fürstner A, Grossmann TN, Waldmann H. Orthogonal ring-closing alkyne and olefin metathesis for the synthesis of small GTPase-targeting bicyclic peptides. Nat Commun 2016; 7:11300. [PMID: 27075966 PMCID: PMC4834642 DOI: 10.1038/ncomms11300] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/11/2016] [Indexed: 02/06/2023] Open
Abstract
Bicyclic peptides are promising scaffolds for the development of inhibitors of biological targets that proved intractable by typical small molecules. So far, access to bioactive bicyclic peptide architectures is limited due to a lack of appropriate orthogonal ring-closing reactions. Here, we report chemically orthogonal ring-closing olefin (RCM) and alkyne metathesis (RCAM), which enable an efficient chemo- and regioselective synthesis of complex bicyclic peptide scaffolds with variable macrocycle geometries. We also demonstrate that the formed alkyne macrocycle can be functionalized subsequently. The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand. This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far. The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets. Bicyclic peptides can inhibit biological targets hard to address with small molecules. Here, the authors combine two orthogonal ring-closing reactions to produce bicyclic peptides with improved bioactivity thereby providing a strategy that can greatly improve the structural diversity of such peptides.
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Affiliation(s)
- Philipp M Cromm
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Sebastian Schaubach
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany
| | - Jochen Spiegel
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Alois Fürstner
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany
| | - Tom N Grossmann
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany.,Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
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7
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Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MAS, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M. Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases. eLife 2016; 5:e12813. [PMID: 26824392 PMCID: PMC4769169 DOI: 10.7554/elife.12813] [Citation(s) in RCA: 663] [Impact Index Per Article: 82.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/21/2016] [Indexed: 12/18/2022] Open
Abstract
Mutations in Park8, encoding for the multidomain Leucine-rich repeat kinase 2 (LRRK2) protein, comprise the predominant genetic cause of Parkinson's disease (PD). G2019S, the most common amino acid substitution activates the kinase two- to threefold. This has motivated the development of LRRK2 kinase inhibitors; however, poor consensus on physiological LRRK2 substrates has hampered clinical development of such therapeutics. We employ a combination of phosphoproteomics, genetics, and pharmacology to unambiguously identify a subset of Rab GTPases as key LRRK2 substrates. LRRK2 directly phosphorylates these both in vivo and in vitro on an evolutionary conserved residue in the switch II domain. Pathogenic LRRK2 variants mapping to different functional domains increase phosphorylation of Rabs and this strongly decreases their affinity to regulatory proteins including Rab GDP dissociation inhibitors (GDIs). Our findings uncover a key class of bona-fide LRRK2 substrates and a novel regulatory mechanism of Rabs that connects them to PD.
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Affiliation(s)
- Martin Steger
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Francesca Tonelli
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Genta Ito
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Davies
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Matthias Trost
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Melanie Vetter
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefanie Wachter
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Graham Duddy
- Molecular Discovery Research, GlaxoSmithKline Pharmaceuticals R&D, Harlow, United Kingdom
| | - Stephen Wilson
- RD Platform Technology and Science, GlaxoSmithKline Pharmaceuticals R&D, Stevenage, United Kingdom
| | - Marco AS Baptista
- The Michael J. Fox Foundation for Parkinson's Research, New York, United States
| | - Brian K Fiske
- The Michael J. Fox Foundation for Parkinson's Research, New York, United States
| | - Matthew J Fell
- Early Discovery Neuroscience, Merck Research Laboratories, Boston, United States
| | - John A Morrow
- Neuroscience, Merck Research Laboratories, Westpoint, United States
| | - Alastair D Reith
- Neurodegeneration Discovery Performance Unit, GlaxoSmithKline Pharmaceuticals R&D, Stevenage, United Kingdom
| | - Dario R Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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8
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Gao Y, Tan L, Dong CH, Hou X. Expression, purification and guanine nucleotide binding characterization of Arabidopsis RabE1d13-185 GTPase. Protein Expr Purif 2015; 119:57-62. [PMID: 26611608 DOI: 10.1016/j.pep.2015.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/03/2015] [Accepted: 11/15/2015] [Indexed: 01/27/2023]
Abstract
Arabidopsis RabE1d subclass plays important plant-specific functions in plant growth and development, response to ethylene and defence to plant pathogen, besides their basic cellular role in membrane trafficking. In this study, we present the expression, purification, and characterization of the recombinant core domain of AtRabE1d13-185. AtRabE1d13-185 was successfully expressed in Escherichia coli and purified via two-step nickel affinity chromatography followed by gel filtration, and identified single band in SDS-PAGE. The resultant protein was functionally active, as determined by interaction with guanine nucleotide by a fluorescence-based assay. The intrinsic tryptophan of AtRabE1d13-185 showed fluorescence resonance energy transfer (FRET) effect upon forming complex with fluorescent methylanthraniloyl (mant)-GDP, but quenched when binding with non-labelled guanine nucleotide. The association rate of mantGDP with AtRabE1d13-185 was determined to be 3.48 × 10(7) s(-1) M(-1). The dissociation rates of GDP and mantGDP from the complex with AtRabE1d13-185 were similar. The koff values were determined to be 4.02 × 10(-4) s(-1) based on the FRET effect for the AtRabE1d13-185:GDP and 5.41 × 10(-4) s(-1) for mantGDP excited directly.
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Affiliation(s)
- Yi Gao
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Lingling Tan
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Chun-Hai Dong
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaomin Hou
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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9
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Lai YC, Kondapalli C, Lehneck R, Procter JB, Dill BD, Woodroof HI, Gourlay R, Peggie M, Macartney TJ, Corti O, Corvol JC, Campbell DG, Itzen A, Trost M, Muqit MM. Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1. EMBO J 2015; 34:2840-61. [PMID: 26471730 PMCID: PMC4654935 DOI: 10.15252/embj.201591593] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 09/18/2015] [Indexed: 12/21/2022] Open
Abstract
Mutations in the PTEN‐induced kinase 1 (PINK1) are causative of autosomal recessive Parkinson's disease (PD). We have previously reported that PINK1 is activated by mitochondrial depolarisation and phosphorylates serine 65 (Ser65) of the ubiquitin ligase Parkin and ubiquitin to stimulate Parkin E3 ligase activity. Here, we have employed quantitative phosphoproteomics to search for novel PINK1‐dependent phosphorylation targets in HEK (human embryonic kidney) 293 cells stimulated by mitochondrial depolarisation. This led to the identification of 14,213 phosphosites from 4,499 gene products. Whilst most phosphosites were unaffected, we strikingly observed three members of a sub‐family of Rab GTPases namely Rab8A, 8B and 13 that are all phosphorylated at the highly conserved residue of serine 111 (Ser111) in response to PINK1 activation. Using phospho‐specific antibodies raised against Ser111 of each of the Rabs, we demonstrate that Rab Ser111 phosphorylation occurs specifically in response to PINK1 activation and is abolished in HeLa PINK1 knockout cells and mutant PINK1 PD patient‐derived fibroblasts stimulated by mitochondrial depolarisation. We provide evidence that Rab8A GTPase Ser111 phosphorylation is not directly regulated by PINK1 in vitro and demonstrate in cells the time course of Ser111 phosphorylation of Rab8A, 8B and 13 is markedly delayed compared to phosphorylation of Parkin at Ser65. We further show mechanistically that phosphorylation at Ser111 significantly impairs Rab8A activation by its cognate guanine nucleotide exchange factor (GEF), Rabin8 (by using the Ser111Glu phosphorylation mimic). These findings provide the first evidence that PINK1 is able to regulate the phosphorylation of Rab GTPases and indicate that monitoring phosphorylation of Rab8A/8B/13 at Ser111 may represent novel biomarkers of PINK1 activity in vivo. Our findings also suggest that disruption of Rab GTPase‐mediated signalling may represent a major mechanism in the neurodegenerative cascade of Parkinson's disease.
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Affiliation(s)
- Yu-Chiang Lai
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Chandana Kondapalli
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Ronny Lehneck
- Centre for Integrated Protein Science Munich, Department Chemistry Technische Universität München, Garching, Germany
| | - James B Procter
- Division of Computational Biology, College of Life Sciences University of Dundee, Dundee, UK
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Helen I Woodroof
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Robert Gourlay
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Mark Peggie
- Division of Signal Transduction Therapy, College of Life Sciences University of Dundee, Dundee, UK
| | - Thomas J Macartney
- Division of Signal Transduction Therapy, College of Life Sciences University of Dundee, Dundee, UK
| | - Olga Corti
- Inserm U 1127, Paris, France CNRS UMR 7225, Paris, France Sorbonne Universités UPMC Paris 06 UMR S 1127, Paris, France Institut du Cerveau et de la Moelle épinière ICM, Paris, France
| | - Jean-Christophe Corvol
- Inserm U 1127, Paris, France CNRS UMR 7225, Paris, France Sorbonne Universités UPMC Paris 06 UMR S 1127, Paris, France Institut du Cerveau et de la Moelle épinière ICM, Paris, France Inserm Centre d'Investigation Clinique (CIC), Paris, France AP-HP, Département des maladies du système nerveux, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - David G Campbell
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Aymelt Itzen
- Centre for Integrated Protein Science Munich, Department Chemistry Technische Universität München, Garching, Germany
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Miratul Mk Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK College of Medicine, Dentistry & Nursing, University of Dundee, Dundee, UK
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10
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Yin G, Lopes da Fonseca T, Eisbach SE, Anduaga AM, Breda C, Orcellet ML, Szegő ÉM, Guerreiro P, Lázaro DF, Braus GH, Fernandez CO, Griesinger C, Becker S, Goody RS, Itzen A, Giorgini F, Outeiro TF, Zweckstetter M. α-Synuclein interacts with the switch region of Rab8a in a Ser129 phosphorylation-dependent manner. Neurobiol Dis 2014; 70:149-61. [PMID: 24983211 DOI: 10.1016/j.nbd.2014.06.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 06/16/2014] [Accepted: 06/22/2014] [Indexed: 12/13/2022] Open
Abstract
Alpha-synuclein (αS) misfolding is associated with Parkinson's disease (PD) but little is known about the mechanisms underlying αS toxicity. Increasing evidence suggests that defects in membrane transport play an important role in neuronal dysfunction. Here we demonstrate that the GTPase Rab8a interacts with αS in rodent brain. NMR spectroscopy reveals that the C-terminus of αS binds to the functionally important switch region as well as the C-terminal tail of Rab8a. In line with a direct Rab8a/αS interaction, Rab8a enhanced αS aggregation and reduced αS-induced cellular toxicity. In addition, Rab8 - the Drosophila ortholog of Rab8a - ameliorated αS-oligomer specific locomotor impairment and neuron loss in fruit flies. In support of the pathogenic relevance of the αS-Rab8a interaction, phosphorylation of αS at S129 enhanced binding to Rab8a, increased formation of insoluble αS aggregates and reduced cellular toxicity. Our study provides novel mechanistic insights into the interplay of the GTPase Rab8a and αS cytotoxicity, and underscores the therapeutic potential of targeting this interaction.
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Affiliation(s)
- Guowei Yin
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tomas Lopes da Fonseca
- Department of Neurodegeneration and Restorative Research, University Medicine Göttingen, Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Sibylle E Eisbach
- Department of Neurodegeneration and Restorative Research, University Medicine Göttingen, Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | | | - Carlo Breda
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Maria L Orcellet
- Max Planck for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR), Universidad Nacional de Rosario, IBR-CONICET, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Éva M Szegő
- Department of Neurodegeneration and Restorative Research, University Medicine Göttingen, Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Patricia Guerreiro
- Department of Neurodegeneration and Restorative Research, University Medicine Göttingen, Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Diana F Lázaro
- Department of Neurodegeneration and Restorative Research, University Medicine Göttingen, Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Gerhard H Braus
- Dept. Molecular Microbiology and Genetics, Institute of Microbiology & Genetics, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Claudio O Fernandez
- Max Planck for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR), Universidad Nacional de Rosario, IBR-CONICET, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Roger S Goody
- Max-Planck-Institute of Molecular Physiology, Department of Physical Biochemistry, Dortmund 44227, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany; Max-Planck-Institute of Molecular Physiology, Department of Physical Biochemistry, Dortmund 44227, Germany
| | - Flaviano Giorgini
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Tiago F Outeiro
- Department of Neurodegeneration and Restorative Research, University Medicine Göttingen, Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.
| | - Markus Zweckstetter
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; German Center for Neurodegenerative Diseases (DZNE), D-37077 Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.
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11
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Guo Z, Hou X, Goody RS, Itzen A. Intermediates in the guanine nucleotide exchange reaction of Rab8 protein catalyzed by guanine nucleotide exchange factors Rabin8 and GRAB. J Biol Chem 2013; 288:32466-32474. [PMID: 24072714 DOI: 10.1074/jbc.m113.498329] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small G-proteins of the Ras superfamily control the temporal and spatial coordination of intracellular signaling networks by acting as molecular on/off switches. Guanine nucleotide exchange factors (GEFs) regulate the activation of these G-proteins through catalytic replacement of GDP by GTP. During nucleotide exchange, three distinct substrate·enzyme complexes occur: a ternary complex with GDP at the start of the reaction (G-protein·GEF·GDP), an intermediary nucleotide-free binary complex (G-protein·GEF), and a ternary GTP complex after productive G-protein activation (G-protein·GEF·GTP). Here, we show structural snapshots of the full nucleotide exchange reaction sequence together with the G-protein substrates and products using Rabin8/GRAB (GEF) and Rab8 (G-protein) as a model system. Together with a thorough enzymatic characterization, our data provide a detailed view into the mechanism of Rabin8/GRAB-mediated nucleotide exchange.
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Affiliation(s)
- Zhong Guo
- From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Xiaomin Hou
- From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany,; the College of Life Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Roger S Goody
- From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany,.
| | - Aymelt Itzen
- From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany,; the Center for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, 85747 Garching, Germany.
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12
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Posttranslational modifications of Rab proteins cause effective displacement of GDP dissociation inhibitor. Proc Natl Acad Sci U S A 2012; 109:5621-6. [PMID: 22411835 DOI: 10.1073/pnas.1121161109] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intracellular vesicular trafficking is regulated by approximately 60 members of the Rab subfamily of small Ras-like GDP/GTP binding proteins. Rab proteins cycle between inactive and active states as well as between cytosolic and membrane bound forms. Membrane extraction/delivery and cytosolic distribution of Rabs is mediated by interaction with the protein GDP dissociation inhibitor (GDI) that binds to prenylated inactive (GDP-bound) Rab proteins. Because the Rab:GDP:GDI complex is of high affinity, the question arises of how GDI can be displaced efficiently from Rab protein in order to allow the necessary recruitment of the Rab to its specific target membrane. While there is strong evidence that DrrA, as a bacterially encoded GDP/GTP exchange factor, contributes to this event, we show here that posttranslational modifications of Rabs can also modulate the affinity for GDI and thus cause effective displacement of GDI from Rab:GDI complexes. These activities have been found associated with the phosphocholination and adenylylation activities of the enzymes AnkX and DrrA/SidM, respectively, from the pathogenic bacterium Legionella pneumophila. Both modifications occur after spontaneous dissociation of Rab:GDI complexes within their natural equilibrium. Therefore, the effective GDI displacement that is observed is caused by inhibition of reformation of Rab:GDI complexes. Interestingly, in contrast to adenylylation by DrrA, AnkX can covalently modify inactive Rabs with high catalytic efficiency even when GDP is bound to the GTPase and hence can inhibit binding of GDI to Rab:GDP complexes. We therefore speculate that human cells could employ similar mechanisms in the absence of infection to effectively displace Rabs from GDI.
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13
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Hokanson DE, Bretscher AP. EPI64 interacts with Slp1/JFC1 to coordinate Rab8a and Arf6 membrane trafficking. Mol Biol Cell 2012; 23:701-15. [PMID: 22219378 PMCID: PMC3279397 DOI: 10.1091/mbc.e11-06-0521] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
ETOC: EPI64 is a TBC domain containing a microvillar protein that binds to Arf6 and induces actin-coated vacuole accumulation when overexpressed. EPI64 does this by stabilizing Arf6-GTP levels to induce clathrin-independent endocytosis and by preventing endosomes from maturing to the tubular endosome by lowering Rab8a GTP levels via association with JFC1. Cell function requires the integration of cytoskeletal organization and membrane trafficking. Small GTP-binding proteins are key regulators of these processes. We find that EPI64, an apical microvillar protein with a Tre-2/Bub2/Cdc16 (TBC) domain that stabilizes active Arf6 and has RabGAP activity, regulates Arf6-dependent membrane trafficking. Expression of EPI64 in HeLa cells induces the accumulation of actin-coated vacuoles, a distinctive phenotype seen in cells expressing constitutively active Arf6. Expression of EPI64 with defective RabGAP activity does not induce vacuole formation. Coexpression of Rab8a suppresses the vacuole phenotype induced by EPI64, and EPI64 expression lowers the level of Rab8-GTP in cells, strongly suggesting that EPI64 has GAP activity toward Rab8a. JFC1, an effector for Rab8a, colocalizes with and binds directly to a C-terminal region of EPI64. Together this region and the N-terminal TBC domain of EPI64 are required for the accumulation of vacuoles. Through analysis of mutants that uncouple JFC1 from either EPI64 or from Rab8-GTP, our data suggest a model in which EPI64 binds JFC1 to recruit Rab8a-GTP for deactivation by the RabGAP activity of EPI64. We propose that EPI64 regulates membrane trafficking both by stabilizing Arf6-GTP and by inhibiting the recycling of membrane through the tubular endosome by decreasing Rab8a-GTP levels.
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Affiliation(s)
- David E Hokanson
- Weill Institute of Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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14
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Wen WS, Hsieh MC, Wang SSS. High-level expression and purification of human γD-crystallin in Escherichia coli. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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A structural basis for Lowe syndrome caused by mutations in the Rab-binding domain of OCRL1. EMBO J 2011; 30:1659-70. [PMID: 21378754 DOI: 10.1038/emboj.2011.60] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 02/04/2011] [Indexed: 01/31/2023] Open
Abstract
The oculocerebrorenal syndrome of Lowe (OCRL), also called Lowe syndrome, is characterized by defects of the nervous system, the eye and the kidney. Lowe syndrome is a monogenetic X-linked disease caused by mutations of the inositol-5-phosphatase OCRL1. OCRL1 is a membrane-bound protein recruited to membranes via interaction with a variety of Rab proteins. The structural and kinetic basis of OCRL1 for the recognition of several Rab proteins is unknown. In this study, we report the crystal structure of the Rab-binding domain (RBD) of OCRL1 in complex with Rab8a and the kinetic binding analysis of OCRL1 with several Rab GTPases (Rab1b, Rab5a, Rab6a and Rab8a). In contrast to other effectors that bind their respective Rab predominantly via α-helical structure elements, the Rab-binding interface of OCRL1 consists mainly of the IgG-like β-strand structure of the ASPM-SPD-2-Hydin domain as well as one α-helix. Our results give a deeper structural understanding of disease-causing mutations of OCRL1 affecting Rab binding.
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16
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Wixler V, Wixler L, Altenfeld A, Ludwig S, Goody RS, Itzen A. Identification and characterisation of novel Mss4-binding Rab GTPases. Biol Chem 2011; 392:239-48. [DOI: 10.1515/bc.2011.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The Mss4 (mammalian suppressor of yeast Sec4) is an evolutionarily highly conserved protein and is expressed in all mammalian tissues. Although its precise biological function is still elusive, it has been shown to associate with a subset of secretory Rab proteins (Rab1b, Rab3a, Rab8a, Rab10) and to possess a rather low guanine nucleotide exchange factor (GEF) activity towards them in vitro (Rab1, Rab3a and Rab8a). By screening a human placenta cDNA library with Mss4 as bait, we identified several Rab GTPases (Rab12, Rab13 and Rab18) as novel Mss4-binding Rab proteins. Only exocytic but no endocytic Rab GTPases were found in our search. The binding of Mss4 to Rab proteins was confirmed by direct yeast two-hybrid interaction, by co-immunoprecipitation from lysates of mammalian cells, by immunofluorescence colocalisation as well as by direct in vitro binding studies. Analysis of Mss4 catalytic activity towards different Rab substrates confirmed that it is a somewhat inefficient GEF. These data, together with our mutational analysis of Mss4-Rab binding capacity, support the already proposed idea that Mss4 functions rather as a chaperone for exocytic Rab GTPases than as a GEF.
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17
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Expression, purification, and characterization of soluble K-Ras4B for structural analysis. Protein Expr Purif 2010; 73:125-31. [PMID: 20566322 DOI: 10.1016/j.pep.2010.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 05/26/2010] [Accepted: 05/28/2010] [Indexed: 11/23/2022]
Abstract
A p21 GTPase K-Ras4B plays an important role in human cancer and represents an excellent target for cancer therapeutics. Currently, there are no drugs directly targeting K-Ras4B. In part, this is due to the lack of structural information describing unique features of K-Ras4B. Here we describe a methodology allowing production of soluble, well-folded K-Ras4B for structural analysis. The key points in K-Ras4B preparation are low temperature expression and extraction of K-Ras4B from the insoluble fraction using a nucleotide loading procedure in the presence of Mg(2+) and citrate, a low affinity chelator. Additionally, a significant amount of K-Ras4B could be extracted from the soluble fraction. We show that recombinant K-Ras4B is monomeric in solution. Excellent NMR signal dispersion suggests that the protein is well-folded and is amenable to solution structure determination. In addition, using phospholipid bilayer nanodiscs we show that recombinant K-Ras4B interacts with lipids and that this interaction is mediated by the C-terminal hypervariable region.
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