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Maeda M, Arakawa M, Komatsu Y, Saito K. Small GTPase ActIvitY ANalyzing (SAIYAN) system: A method to detect GTPase activation in living cells. J Cell Biol 2024; 223:e202403179. [PMID: 39101946 PMCID: PMC11303508 DOI: 10.1083/jcb.202403179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/10/2024] [Accepted: 07/11/2024] [Indexed: 08/06/2024] Open
Abstract
Small GTPases are essential in various cellular signaling pathways, and detecting their activation within living cells is crucial for understanding cellular processes. The current methods for detecting GTPase activation using fluorescent proteins rely on the interaction between the GTPase and its effector. Consequently, these methods are not applicable to factors, such as Sar1, where the effector also functions as a GTPase-activating protein. Here, we present a novel method, the Small GTPase ActIvitY ANalyzing (SAIYAN) system, for detecting the activation of endogenous small GTPases via fluorescent signals utilizing a split mNeonGreen system. We demonstrated Sar1 activation at the endoplasmic reticulum (ER) exit site and successfully detected its activation state in various cellular conditions. Utilizing the SAIYAN system in collagen-secreting cells, we discovered activated Sar1 localized both at the ER exit sites and ER-Golgi intermediate compartment (ERGIC) regions. Additionally, impaired collagen secretion confined the activated Sar1 at the ER exit sites, implying the importance of Sar1 activation through the ERGIC in collagen secretion.
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Affiliation(s)
- Miharu Maeda
- Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, Japan
| | - Masashi Arakawa
- Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, Japan
| | - Yukie Komatsu
- Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, Japan
| | - Kota Saito
- Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, Japan
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2
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Van der Verren SE, Zanetti G. The small GTPase Sar1, control centre of COPII trafficking. FEBS Lett 2023; 597:865-882. [PMID: 36737236 DOI: 10.1002/1873-3468.14595] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Sar1 is a small GTPase of the ARF family. Upon exchange of GDP for GTP, Sar1 associates with the endoplasmic reticulum (ER) membrane and recruits COPII components, orchestrating cargo concentration and membrane deformation. Many aspects of the role of Sar1 and regulation of its GTP cycle remain unclear, especially as complexity increases in higher organisms that secrete a wider range of cargoes. This review focusses on the regulation of GTP hydrolysis and its role in coat assembly, as well as the mechanism of Sar1-induced membrane deformation and scission. Finally, we highlight the additional specialisation in higher eukaryotes and the outstanding questions on how Sar1 functions are orchestrated.
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Affiliation(s)
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College London, UK
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3
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Kustigian L, Gong X, Gai W, Thongchol J, Zhang J, Puchalla J, Carr CM, Rye HS. GTP-stimulated membrane fission by the N-BAR protein AMPH-1. Traffic 2023; 24:34-47. [PMID: 36435193 PMCID: PMC9825645 DOI: 10.1111/tra.12875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 10/24/2022] [Accepted: 11/19/2022] [Indexed: 11/28/2022]
Abstract
Membrane-enclosed transport carriers sort biological molecules between stations in the cell in a dynamic process that is fundamental to the physiology of eukaryotic organisms. While much is known about the formation and release of carriers from specific intracellular membranes, the mechanism of carrier formation from the recycling endosome, a compartment central to cellular signaling, remains to be resolved. In Caenorhabditis elegans, formation of transport carriers from the recycling endosome requires the dynamin-like, Eps15-homology domain (EHD) protein, RME-1, functioning with the Bin/Amphiphysin/Rvs (N-BAR) domain protein, AMPH-1. Here we show, using a free-solution single-particle technique known as burst analysis spectroscopy (BAS), that AMPH-1 alone creates small, tubular-vesicular products from large, unilamellar vesicles by membrane fission. Membrane fission requires the amphipathic H0 helix of AMPH-1 and is slowed in the presence of RME-1. Unexpectedly, AMPH-1-induced membrane fission is stimulated in the presence of GTP. Furthermore, the GTP-stimulated membrane fission activity seen for AMPH-1 is recapitulated by the heterodimeric N-BAR amphiphysin protein from yeast, Rvs161/167p, strongly suggesting that GTP-stimulated membrane fission is a general property of this important class of N-BAR proteins.
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Affiliation(s)
- Lauren Kustigian
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
- Current address: GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, Pennsylvania 19426, USA
| | - Xue Gong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Wei Gai
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Jirapat Thongchol
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Jason Puchalla
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Chavela M. Carr
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
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4
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Hannan JP, Swisher GH, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. HPLC method to resolve, identify and quantify guanine nucleotides bound to recombinant ras GTPase. Anal Biochem 2021; 631:114338. [PMID: 34433016 PMCID: PMC8511091 DOI: 10.1016/j.ab.2021.114338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/31/2022]
Abstract
The Ras superfamily of small G proteins play central roles in diverse signaling pathways. Superfamily members act as molecular on-off switches defined by their occupancy with GTP or GDP, respectively. In vitro functional studies require loading with a hydrolysis-resistant GTP analogue to increase the on-state lifetime, as well as knowledge of fractional loading with activating and inactivating nucleotides. The present study describes a method combining elements of previous approaches with new, optimized features to analyze the bound nucleotide composition of a G protein loaded with activating (GMPPNP) or inactivating (GDP) nucleotide. After nucleotide loading, the complex is washed to remove unbound nucleotides then bound nucleotides are heat-extracted and subjected to ion-paired, reverse-phase HPLC-UV to resolve, identify and quantify the individual nucleotide components. These data enable back-calculation to the nucleotide composition and fractional activation of the original, washed G protein population prior to heat extraction. The method is highly reproducible. Application to multiple HRas preparations and mutants confirms its ability to fully extract and analyze bound nucleotides, and to resolve the fractional on- and off-state populations. Furthermore, the findings yield a novel hypothesis for the molecular disease mechanism of Ras mutations at the E63 and Y64 positions.
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Affiliation(s)
- Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Justin G Martyr
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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5
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Gasper R, Wittinghofer F. The Ras switch in structural and historical perspective. Biol Chem 2020; 401:143-163. [PMID: 31600136 DOI: 10.1515/hsz-2019-0330] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022]
Abstract
Since its discovery as an oncogene more than 40 years ago, Ras has been and still is in the focus of many academic and pharmaceutical labs around the world. A huge amount of work has accumulated on its biology. However, many questions about the role of the different Ras isoforms in health and disease still exist and a full understanding will require more intensive work in the future. Here we try to survey some of the structural findings in a historical perspective and how it has influenced our understanding of structure-function and mechanistic relationships of Ras and its interactions. The structures show that Ras is a stable molecular machine that uses the dynamics of its switch regions for the interaction with all regulators and effectors. This conformational flexibility has been used to create small molecule drug candidates against this important oncoprotein.
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Affiliation(s)
- Raphael Gasper
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
| | - Fred Wittinghofer
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
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6
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Johnson CW, Reid D, Parker JA, Salter S, Knihtila R, Kuzmic P, Mattos C. The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects. J Biol Chem 2017; 292:12981-12993. [PMID: 28630043 PMCID: PMC5546037 DOI: 10.1074/jbc.m117.778886] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/09/2017] [Indexed: 11/06/2022] Open
Abstract
H-Ras, K-Ras, and N-Ras are small GTPases that are important in the control of cell proliferation, differentiation, and survival, and their mutants occur frequently in human cancers. The G-domain, which catalyzes GTP hydrolysis and mediates downstream signaling, is 95% conserved between the Ras isoforms. Because of their very high sequence identity, biochemical studies done on H-Ras have been considered representative of all three Ras proteins. We show here that this is not a valid assumption. Using enzyme kinetic assays under identical conditions, we observed clear differences between the three isoforms in intrinsic catalysis of GTP by Ras in the absence and presence of the Ras-binding domain (RBD) of the c-Raf kinase protein (Raf-RBD). Given their identical active sites, isoform G-domain differences must be allosteric in origin, due to remote isoform-specific residues that affect conformational states. We present the crystal structure of N-Ras bound to a GTP analogue and interpret the kinetic data in terms of structural features specific for H-, K-, and N-Ras.
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Affiliation(s)
- Christian W Johnson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Derion Reid
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Jillian A Parker
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Shores Salter
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Ryan Knihtila
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | | | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115.
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7
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Gerwert K, Mann D, Kötting C. Common mechanisms of catalysis in small and heterotrimeric GTPases and their respective GAPs. Biol Chem 2017; 398:523-533. [PMID: 28245182 DOI: 10.1515/hsz-2016-0314] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/15/2017] [Indexed: 01/15/2023]
Abstract
GTPases are central switches in cells. Their dysfunctions are involved in severe diseases. The small GTPase Ras regulates cell growth, differentiation and apoptosis by transmitting external signals to the nucleus. In one group of oncogenic mutations, the 'switch-off' reaction is inhibited, leading to persistent activation of the signaling pathway. The switch reaction is regulated by GTPase-activating proteins (GAPs), which catalyze GTP hydrolysis in Ras, and by guanine nucleotide exchange factors, which catalyze the exchange of GDP for GTP. Heterotrimeric G-proteins are activated by G-protein coupled receptors and are inactivated by GTP hydrolysis in the Gα subunit. Their GAPs are called regulators of G-protein signaling. In the same way that Ras serves as a prototype for small GTPases, Gαi1 is the most well-studied Gα subunit. By utilizing X-ray structural models, time-resolved infrared-difference spectroscopy, and biomolecular simulations, we elucidated the detailed molecular reaction mechanism of the GTP hydrolysis in Ras and Gαi1. In both proteins, the charge distribution of GTP is driven towards the transition state, and an arginine is precisely positioned to facilitate nucleophilic attack of water. In addition to these mechanistic details of GTP hydrolysis, Ras dimerization as an emerging factor in signal transduction is discussed in this review.
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Affiliation(s)
- Klaus Gerwert
- Department of Biophysics, Ruhr-University Bochum, Universitätsstrasse 150, D-44801 Bochum
| | - Daniel Mann
- Department of Biophysics, Ruhr-University Bochum, Universitätsstrasse 150, D-44801 Bochum
| | - Carsten Kötting
- Department of Biophysics, Ruhr-University Bochum, Universitätsstrasse 150, D-44801 Bochum
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8
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Goody PR. Intrinsic protein fluorescence assays for GEF, GAP and post-translational modifications of small GTPases. Anal Biochem 2016; 515:22-25. [DOI: 10.1016/j.ab.2016.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
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9
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Abstract
SUMMARYEvidence is emerging that the role of protein structure in disease needs to be rethought. Sequence mutations in proteins are often found to affect the rate at which a protein switches between structures. Modeling structural transitions in wildtype and variant proteins is central to understanding the molecular basis of disease. This paper investigates an efficient algorithmic realization of the stochastic roadmap simulation framework to model structural transitions in wildtype and variants of proteins implicated in human disorders. Our results indicate that the algorithm is able to extract useful information on the impact of mutations on protein structure and function.
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10
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Noé F, Krachtus D, Smith JC, Fischer S. Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. J Chem Theory Comput 2015; 2:840-57. [PMID: 26626691 DOI: 10.1021/ct050162r] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functionally relevant transitions between native conformations of a protein can be complex, involving, for example, the reorganization of parts of the backbone fold, and may occur via a multitude of pathways. Such transitions can be characterized by a transition network (TN), in which the experimentally determined end state structures are connected by a dense network of subtransitions via low-energy intermediates. We show here how the computation of a TN can be achieved for a complex protein transition. First, an efficient hierarchical procedure is used to uniformly sample the conformational subspace relevant to the transition. Then, the best path which connects the end states is determined as well as the rate-limiting ridge on the energy surface which separates them. Graph-theoretical algorithms permit this to be achived by computing the barriers of only a small number out of the many subtransitions in the TN. These barriers are computed using the Conjugate Peak Refinement method. The approach is illustrated on the conformational switch of Ras p21. The best and the 12 next-best transition pathways, having rate-limiting barriers within a range of 10 kcal/mol, were identified. Two main energy ridges, which respectively involve rearrangements of the switch I and switch II loops, show that switch I must rearrange by threading Tyr32 underneath the protein backbone before the rate-limiting switch II rearrangement can occur, while the details of the switch II rearrangement differ significantly among the low-energy pathways.
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Affiliation(s)
- Frank Noé
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, and Computational Biochemistry, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Dieter Krachtus
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, and Computational Biochemistry, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Jeremy C Smith
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, and Computational Biochemistry, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Stefan Fischer
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, and Computational Biochemistry, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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11
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Huecas S, Marcelo F, Perona A, Ruiz-Ávila LB, Morreale A, Cañada FJ, Jiménez-Barbero J, Andreu JM. Beyond a Fluorescent Probe: Inhibition of Cell Division Protein FtsZ by mant-GTP Elucidated by NMR and Biochemical Approaches. ACS Chem Biol 2015; 10:2382-92. [PMID: 26247422 DOI: 10.1021/acschembio.5b00444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FtsZ is the organizer of cell division in most bacteria and a target in the quest for new antibiotics. FtsZ is a tubulin-like GTPase, in which the active site is completed at the interface with the next subunit in an assembled FtsZ filament. Fluorescent mant-GTP has been extensively used for competitive binding studies of nucleotide analogs and synthetic GTP-replacing inhibitors possessing antibacterial activity. However, its mode of binding and whether the mant tag interferes with FtsZ assembly function were unknown. Mant-GTP exists in equilibrium as a mixture of C2'- and C3'-substituted isomers. We have unraveled the molecular recognition process of mant-GTP by FtsZ monomers. Both isomers bind in the anti glycosidic bond conformation: 2'-mant-GTP in two ribose puckering conformations and 3'-mant-GTP in the preferred C2' endo conformation. In each case, the mant tag strongly interacts with FtsZ at an extension of the GTP binding site, which is also supported by molecular dynamics simulations. Importantly, mant-GTP binding induces archaeal FtsZ polymerization into inactive curved filaments that cannot hydrolyze the nucleotide, rather than straight GTP-hydrolyzing assemblies, and also inhibits normal assembly of FtsZ from the Gram-negative bacterium Escherichia coli but is hydrolyzed by FtsZ from Gram-positive Bacillus subtilis. Thus, the specific interactions provided by the fluorescent mant tag indicate a new way to search for synthetic FtsZ inhibitors that selectively suppress the cell division of bacterial pathogens.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Filipa Marcelo
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- UCIBIO, REQUIMTE, Dept. de Química, Faculdade de Ciências
e Tecnologia, UNL, 2829-516 Caparica, Portugal
| | - Almudena Perona
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa, CBMSO−CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Laura B. Ruiz-Ávila
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Antonio Morreale
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa, CBMSO−CSIC, Cantoblanco, 28049 Madrid, Spain
| | - F. Javier Cañada
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José M. Andreu
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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12
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Marshall CB, Meiri D, Smith MJ, Mazhab-Jafari MT, Gasmi-Seabrook GMC, Rottapel R, Stambolic V, Ikura M. Probing the GTPase cycle with real-time NMR: GAP and GEF activities in cell extracts. Methods 2012; 57:473-85. [PMID: 22750304 DOI: 10.1016/j.ymeth.2012.06.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 06/19/2012] [Accepted: 06/21/2012] [Indexed: 01/18/2023] Open
Abstract
The Ras superfamily of small GTPases is a large family of switch-like proteins that control diverse cellular functions, and their deregulation is associated with multiple disease processes. When bound to GTP they adopt a conformation that interacts with effector proteins, whereas the GDP-bound state is generally biologically inactive. GTPase activating proteins (GAPs) promote hydrolysis of GTP, thus impeding the biological activity of GTPases, whereas guanine nucleotide exchange factors (GEFs) promote exchange of GDP for GTP and activate GTPase proteins. A number of methods have been developed to assay GTPase nucleotide hydrolysis and exchange, as well as the activity of GAPs and GEFs. The kinetics of these reactions are often studied with purified proteins and fluorescent nucleotide analogs, which have been shown to non-specifically impact hydrolysis and exchange. Most GAPs and GEFs are large multidomain proteins subject to complex regulation that is challenging to reconstitute in vitro. In cells, the activities of full-length GAPs or GEFs are typically assayed indirectly on the basis of nucleotide loading of the cognate GTPase, or by exploiting their interaction with effector proteins. Here, we describe a recently developed real-time NMR method to assay kinetics of nucleotide exchange and hydrolysis reactions by direct monitoring of nucleotide-dependent structural changes in an isotopically labeled GTPase. The unambiguous readout of this method makes it possible to precisely measure GAP and GEF activities from extracts of mammalian cells, enabling studies of their catalytic and regulatory mechanisms. We present examples of NMR-based assays of full-length GAPs and GEFs overexpressed in mammalian cells.
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Affiliation(s)
- Christopher B Marshall
- Ontario Cancer Institute and The Campbell Family Cancer Research Institute, University Health Network, 101 College Street, Rm 4-804 Toronto Medical Discovery Tower, MaRS Building, Toronto, ON, Canada M5G 1L7
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13
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Flaherty KT, Sosman JA, Atkins MB. New options and new questions: how to select and sequence therapies for patients with metastatic melanoma. Am Soc Clin Oncol Educ Book 2012:524-530. [PMID: 24451790 DOI: 10.14694/edbook_am.2012.32.211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Recent advances in the understanding of the melanoma biology and tumor immunology have yielded new treatment strategies for patients with advanced melanoma. Within the past year, the selective BRAF inhibitor vemurafenib and immune checkpoint inhibitor ipilimumab have been added to the treatment armamentarium. In addition, other molecularly targeted agents and immunotherapies are showing considerable promise. The availability of multiple, effective treatment options for patients with melanoma, although long sought, has complicated treatment decisions. This article will review the advances in our understanding of melanoma biology and tumor immunology, the current status of immunotherapy, the advances in molecularly targeted therapy for patients with BRAF mutant melanomas, the possible approaches to patients with BRAF wild-type (WT) tumors, and the current considerations for treatment selection of individual patients.
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Affiliation(s)
- Keith T Flaherty
- From the Massachusetts General Hospital Cancer Center, Boston, MA; Vanderbilt University Medical Center, Nashville, TN; Beth Israel Deaconess Medical Center, Boston, MA
| | - Jeff A Sosman
- From the Massachusetts General Hospital Cancer Center, Boston, MA; Vanderbilt University Medical Center, Nashville, TN; Beth Israel Deaconess Medical Center, Boston, MA
| | - Michael B Atkins
- From the Massachusetts General Hospital Cancer Center, Boston, MA; Vanderbilt University Medical Center, Nashville, TN; Beth Israel Deaconess Medical Center, Boston, MA
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14
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Abstract
The development of novel fluorescence methods for the detection of key biomolecules is of great interest, both in basic research and in drug discovery. Particularly relevant and widespread molecules in cells are ADP and GDP, which are the products of a large number of cellular reactions, including reactions catalysed by nucleoside triphosphatases and kinases. Previously, biosensors for ADP were developed in this laboratory, based on fluorophore adducts with the bacterial actin homologue ParM. It is shown in the present study that one of these biosensors, tetramethylrhodamine–ParM, can also monitor GDP. The biosensor can be used to measure micromolar concentrations of GDP on the background of millimolar concentrations of GTP. The fluorescence response of the biosensor is fast, the response time being <0.2 s. Thus the biosensor allows real-time measurements of GTPase and GTP-dependent kinase reactions. Applications of the GDP biosensor are exemplified with two different GTPases, measuring the rates of GTP hydrolysis and nucleotide exchange.
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15
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Jones JC, Temple BRS, Jones AM, Dohlman HG. Functional reconstitution of an atypical G protein heterotrimer and regulator of G protein signaling protein (RGS1) from Arabidopsis thaliana. J Biol Chem 2011; 286:13143-50. [PMID: 21325279 PMCID: PMC3075661 DOI: 10.1074/jbc.m110.190355] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 02/01/2011] [Indexed: 11/06/2022] Open
Abstract
It has long been known that animal heterotrimeric Gαβγ proteins are activated by cell-surface receptors that promote GTP binding to the Gα subunit and dissociation of the heterotrimer. In contrast, the Gα protein from Arabidopsis thaliana (AtGPA1) can activate itself without a receptor or other exchange factor. It is unknown how AtGPA1 is regulated by Gβγ and the RGS (regulator of G protein signaling) protein AtRGS1, which is comprised of an RGS domain fused to a receptor-like domain. To better understand the cycle of G protein activation and inactivation in plants, we purified and reconstituted AtGPA1, full-length AtRGS1, and two putative Gβγ dimers. We show that the Arabidopsis Gα protein binds to its cognate Gβγ dimer directly and in a nucleotide-dependent manner. Although animal Gβγ dimers inhibit GTP binding to the Gα subunit, AtGPA1 retains fast activation in the presence of its cognate Gβγ dimer. We show further that the full-length AtRGS1 protein accelerates GTP hydrolysis and thereby counteracts the fast nucleotide exchange rate of AtGPA1. Finally, we show that AtGPA1 is less stable in complex with GDP than in complex with GTP or the Gβγ dimer. Molecular dynamics simulations and biophysical studies reveal that altered stability is likely due to increased dynamic motion in the N-terminal α-helix and Switch II of AtGPA1. Thus, despite profound differences in the mechanisms of activation, the Arabidopsis G protein is readily inactivated by its cognate RGS protein and forms a stable, GDP-bound, heterotrimeric complex similar to that found in animals.
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Affiliation(s)
| | - Brenda R. S. Temple
- From the Department of Biochemistry and Biophysics
- R. L. Juliano Structural Bioinformatics Core Facility, and
| | - Alan M. Jones
- Departments of Pharmacology and
- Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Henrik G. Dohlman
- From the Department of Biochemistry and Biophysics
- Departments of Pharmacology and
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16
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Mazhab-Jafari MT, Marshall CB, Smith M, Gasmi-Seabrook GMC, Stambolic V, Rottapel R, Neel BG, Ikura M. Real-time NMR study of three small GTPases reveals that fluorescent 2'(3')-O-(N-methylanthraniloyl)-tagged nucleotides alter hydrolysis and exchange kinetics. J Biol Chem 2009; 285:5132-6. [PMID: 20018863 DOI: 10.1074/jbc.c109.064766] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Ras family of small GTPases control diverse signaling pathways through a conserved "switch" mechanism, which is turned on by binding of GTP and turned off by GTP hydrolysis to GDP. Full understanding of GTPase switch functions requires reliable, quantitative assays for nucleotide binding and hydrolysis. Fluorescently labeled guanine nucleotides, such as 2'(3')-O-(N-methylanthraniloyl) (mant)-substituted GTP and GDP analogs, have been widely used to investigate the molecular properties of small GTPases, including Ras and Rho. Using a recently developed NMR method, we show that the kinetics of nucleotide hydrolysis and exchange by three small GTPases, alone and in the presence of their cognate GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors, are affected by the presence of the fluorescent mant moiety. Intrinsic hydrolysis of mantGTP by Ras homolog enriched in brain (Rheb) is approximately 10 times faster than that of GTP, whereas it is 3.4 times slower with RhoA. On the other hand, the mant tag inhibits TSC2GAP-catalyzed GTP hydrolysis by Rheb but promotes p120 RasGAP-catalyzed GTP hydrolysis by H-Ras. Guanine nucleotide exchange factor-catalyzed nucleotide exchange for both H-Ras and RhoA was inhibited by mant-substituted nucleotides, and the degree of inhibition depends highly on the GTPase and whether the assay measures association of mantGTP with, or dissociation of mantGDP from the GTPase. These results indicate that the mant moiety has significant and unpredictable effects on GTPase reaction kinetics and underscore the importance of validating its use in each assay.
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Affiliation(s)
- Mohammad T Mazhab-Jafari
- Division of Signaling Biology, Ontario Cancer Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada
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17
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Padovani D, Banerjee R. A rotary mechanism for coenzyme B(12) synthesis by adenosyltransferase. Biochemistry 2009; 48:5350-7. [PMID: 19413290 DOI: 10.1021/bi900454s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosyltransferases (ATRs) catalyze the synthesis of the reactive cobalt-carbon bond found in coenzyme B(12) or 5'-deoxyadenosylcobalamin (AdoCbl), which serves as a cofactor for a number of isomerases. The reaction involves a reductive adenosylation of cob(II)alamin in which an electron delivered by a reductase reduces cob(II)alamin to cob(I)alamin, which attacks the 5'-carbon of ATP to form AdoCbl and inorganic triphosphate. Of the three classes of ATRs found in nature, the PduO type, which is also the only one found in mammals, is the most extensively studied. The crystal structures of a number of PduO-type ATRs are available and reveal a trimeric organization with the active sites located at the subunit interfaces. We have previously demonstrated that the ATR from Methylobacterium extorquens, which supports methylmalonyl-CoA mutase activity, serves dual functions; i.e., it tailors the active AdoCbl form of the cofactor and then transfers it directly to the dependent mutase (Padovani et al. (2008) Nat. Chem. Biol. 4, 194). Only two of the three active sites in ATR are simultaneously occupied by AdoCbl. In this study, we demonstrate that binding of the substrate ATP to ATR that is fully loaded with AdoCbl leads to the ejection of 1 equivalent of the cofactor into solution. In the presence of methylmalonyl-CoA mutase and ATP, AdoCbl is transferred from ATR to the acceptor protein in a process that exhibits an approximately 3.5-fold lower K(act) for ATP compared to the one in which cofactor is released into solution. Furthermore, ATP favorably influences cofactor transfer in the forward direction by reducing the ratio of apo-methylmalonyl-CoA mutase/holo-ATR required for delivery of 1 equivalent of AdoCbl, from 4 to 1. These results lead us to propose a rotary mechanism for ATR function in which, at any given time, only two of its active sites are used for AdoCbl synthesis and where binding of ATP to the vacant site leads to the transfer of the high value AdoCbl product to the acceptor mutase.
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Affiliation(s)
- Dominique Padovani
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-5606, USA
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18
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Leskovar A, Reinstein J. Photophysical properties of popular fluorescent adenosine nucleotide analogs used in enzyme mechanism probing. Arch Biochem Biophys 2008; 473:16-24. [PMID: 18342617 DOI: 10.1016/j.abb.2008.02.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 02/26/2008] [Accepted: 02/26/2008] [Indexed: 11/24/2022]
Abstract
Fluorescent nucleotide analogs are widely used in mechanistic studies of nucleotide binding and utilizing proteins. We describe here an overview of the photophysical parameters of the most popular nucleotide analogs that have a fluorescent N-methylanthraniloyl-group attached at various positions of the nucleotide. Steady state absorption and fluorescence spectra of free chromophores depend on the type of modification (ribose, base or phosphate moiety) and the addition of proteins suggests that the labeled nucleotides also vary in sensitivity depending upon their local protein environment. Fluorescence lifetime measurements imply two to three lifetimes for each nucleotide with complex changes in dependence on solvent but more importantly also on the protein. The measured quantum yields quantify the increase in fluorescence for (C8)-MABA-ADP, MANT-ATP and (Pgamma)-MABA-ATP as 153%, 93% and 14% when bound to DnaK, ClpB and Trap1, respectively, compared to free in buffer solution.
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Affiliation(s)
- Adriane Leskovar
- Max-Planck-Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29, D-69120 Heidelberg, Germany
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19
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Wittinghofer A, Franken SM, Scheidig AJ, Rensland H, Lautwein A, Pai EF, Goody RS. Three-dimensional structure and properties of wild-type and mutant H-ras-encoded p21. CIBA FOUNDATION SYMPOSIUM 2007; 176:6-21; discussion 21-7. [PMID: 8299426 DOI: 10.1002/9780470514450.ch2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ras (or p21) is the product of the ras proto-oncogene and is believed to be involved in growth-promoting signal transduction. The structure of the guanine nucleotide-binding domain of H-Ras (or p21H-ras) in the triphosphate conformation was determined at very high resolution (1.4 A). All the binding interactions between protein and Gpp[NH]p and Mg2+ can be resolved in great detail. The region around amino acids 61-65 is flexible and exists in two conformations, one of which seems to be important for catalysis. The properties and structures of several oncogenic and non-oncogenic mutant forms of Ras have also been determined. Since the structure of the GDP-bound form is also known, the nature of the conformational change from the GTP-bound to the GDP-bound form can be inferred from the 3-D structure. A mechanism for the intrinsic GTP hydrolysis has been proposed. Its implications for the GAP-stimulated GTPase reaction is discussed in the light of recent kinetic and mutational experiments.
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Affiliation(s)
- A Wittinghofer
- Max Planck Institute for Medical Research, Heidelberg, Germany
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20
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Abstract
Biochemical systems and processes in living cells generally operate far from equilibrium. This review presents an overview of a statistical thermodynamic treatment for such systems, with examples from several key components in cellular signal transduction. Open-system nonequilibrium steady-state (NESS) models are introduced. The models account quantitatively for the energetics and thermodynamics in phosphorylation-dephosphorylation switches, GTPase timers, and specificity amplification through kinetic proofreading. The chemical energy derived from ATP and GTP hydrolysis establishes the NESS of a cell and makes the cell--a mesoscopic-biochemical reaction system that consists of a collection of thermally driven fluctuating macromolecules--a genetically programmed chemical machine.
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Affiliation(s)
- Hong Qian
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA.
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21
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Sprang SR, Chen Z, Du X. Structural basis of effector regulation and signal termination in heterotrimeric Galpha proteins. ADVANCES IN PROTEIN CHEMISTRY 2007; 74:1-65. [PMID: 17854654 DOI: 10.1016/s0065-3233(07)74001-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This chapter addresses, from a molecular structural perspective gained from examination of x-ray crystallographic and biochemical data, the mechanisms by which GTP-bound Galpha subunits of heterotrimeric G proteins recognize and regulate effectors. The mechanism of GTP hydrolysis by Galpha and rate acceleration by GAPs are also considered. The effector recognition site in all Galpha homologues is formed almost entirely of the residues extending from the C-terminal half of alpha2 (Switch II) together with the alpha3 helix and its junction with the beta5 strand. Effector binding does not induce substantial changes in the structure of Galpha*GTP. Effectors are structurally diverse. Different effectors may recognize distinct subsets of effector-binding residues of the same Galpha protein. Specificity may also be conferred by differences in the main chain conformation of effector-binding regions of Galpha subunits. Several Galpha regulatory mechanisms are operative. In the regulation of GMP phospodiesterase, Galphat sequesters an inhibitory subunit. Galphas is an allosteric activator and inhibitor of adenylyl cyclase, and Galphai is an allosteric inhibitor. Galphaq does not appear to regulate GRK, but is rather sequestered by it. GTP hydrolysis terminates the signaling state of Galpha. The binding energy of GTP that is used to stabilize the Galpha:effector complex is dissipated in this reaction. Chemical steps of GTP hydrolysis, specifically, formation of a dissociative transition state, is rate limiting in Ras, a model G protein GTPase, even in the presence of a GAP; however, the energy of enzyme reorganization to produce a catalytically active conformation appears to be substantial. It is possible that the collapse of the switch regions, associated with Galpha deactivation, also encounters a kinetic barrier, and is coupled to product (Pi) release or an event preceding formation of the GDP*Pi complex. Evidence for a catalytic intermediate, possibly metaphosphate, is discussed. Galpha GAPs, whether exogenous proteins or effector-linked domains, bind to a discrete locus of Galpha that is composed of Switch I and the N-terminus of Switch II. This site is immediately adjacent to, but does not substantially overlap, the Galpha effector binding site. Interactions of effectors and exogenous GAPs with Galpha proteins can be synergistic or antagonistic, mediated by allosteric interactions among the three molecules. Unlike GAPs for small GTPases, Galpha GAPs supply no catalytic residues, but rather appear to reduce the activation energy for catalytic activation of the Galpha catalytic site.
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Affiliation(s)
- Stephen R Sprang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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22
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Alfonzo MJ, de Aguilar EP, de Murillo AG, de Villarroel SS, de Alfonzo RG, Borges A, de Becemberg IL. Characterization of a G protein-coupled guanylyl cyclase-B receptor from bovine tracheal smooth muscle. J Recept Signal Transduct Res 2006; 26:269-97. [PMID: 16818377 DOI: 10.1080/10799890600766446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A G protein-coupled natriuretic peptide-guanylyl cyclase receptor-B (NPR-B) located in plasma membranes from bovine tracheal smooth muscle shows complex kinetics and regulation. NPR-B was activated by natriuretic peptides (CNP-53 > ANP-28) at the ligand extracellular domain, stimulated by Gq-protein activators, such as mastoparan, and inhibited by Gi-sensitive chloride, interacting at the juxtamembrane domain. The kinase homology domain was evaluated by the ATP inhibition of Mn2+-activated NPR-B, which was partially reversed by mastoparan. The catalytic domain was studied by kinetics of Mn2+/Mg2+ and GTP, and the catalytic effect with GTP analogues with modifications of the /gamma phosphates and ribose moieties. Most NPR-B biochemical properties remained after detergent solubilization but the mastoparan activation and chloride inhibition of NPR-B disappeared. Our results indicate that NPR-B is a highly regulated nano-machinery with domains acting at cross-talk points with other signal transducing cascades initiated by G protein-coupled receptors and affected by intracellular ligands such as chloride, Mn2+, Mg2+, ATP, and GTP.
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Affiliation(s)
- Marcelo J Alfonzo
- Sección de Biomembranas, Instituto de Medicina Experimental, Facultad de Medicina. Universidad Central de Venezuela, Caracas, Venezuela.
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23
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Noé F, Ille F, Smith JC, Fischer S. Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21. Proteins 2006; 59:534-44. [PMID: 15778967 DOI: 10.1002/prot.20422] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The computation of minimum energy paths (MEPs) is an approach for gaining insight into protein conformational transitions that are too slow to be observed with unconstrained molecular dynamics simulations. MEPs have the advantage of providing the energy barrier of the rate-limiting step(s), allowing discrimination among different paths. Finding low-energy MEPs for complex transitions, such as those involving rearrangements of the backbone fold or repacking of buried side chains, has hitherto been unfeasible in a reliable, automated manner, the MEP often displaying unphysical behavior, such as the crossing of bonds. Here, this problem is addressed by combining a counterintuitive procedure for generating an initial guess of the path, in which all side chains are shrunk, with the conjugate peak refinement (CPR) method. The effectiveness of the approach is tested on the conformational switch in Ras p21. This conformational transition involves some partial unfolding and re-folding, a process for which a multitude of pathways are likely to exist and for which a single MEP does not provide a complete description. However, this transition requires some sterically demanding rearrangements, thus testing the ability of a method to find low-energy pathways free of structurally unphysical events. This is achieved by the present approach, which finds a path whose rate-limiting barrier is compatible with experiment. This demonstrates that the method can be used to compute plausible pathways for complex rearrangements in proteins in an automated manner that is unbiased by external driving constraints.
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Affiliation(s)
- Frank Noé
- Computational Molecular Biophysics, IWR, University of Heidelberg, Heidelberg, Germany
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24
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Eberth A, Dvorsky R, Becker CFW, Beste A, Goody RS, Ahmadian MR. Monitoring the real-time kinetics of the hydrolysis reaction of guanine nucleotide-binding proteins. Biol Chem 2006; 386:1105-14. [PMID: 16307476 DOI: 10.1515/bc.2005.127] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The conversion of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by guanine nucleotide-binding proteins (GNBPs) is a fundamental enzyme reaction in living cells that acts as an important timer in a variety of biological processes. This reaction is intrinsically slow but can be stimulated by GTPase-activating proteins (GAPs) by several orders of magnitude. In the present study, we synthesized and characterized a new fluorescent nucleotide, 2'(3')-O-(N-ethylcarbamoyl-(5''-carboxytetramethylrhodamine) amide)-GTP, or tamraGTP, which is sensitive towards conformational changes of certain GNBPs induced by GTP hydrolysis. Unlike other fluorescent nucleotides, tamra-GTP allows real-time monitoring of the kinetics of the intrinsic and GAP-catalyzed GTP hydrolysis reactions of small GNBPs from the Rho family.
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Affiliation(s)
- Alexander Eberth
- Department of Structural Biology, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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25
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Pasqualato S, Cherfils J. Crystallographic evidence for substrate-assisted GTP hydrolysis by a small GTP binding protein. Structure 2005; 13:533-40. [PMID: 15837192 DOI: 10.1016/j.str.2005.01.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2004] [Revised: 12/17/2004] [Accepted: 01/08/2005] [Indexed: 01/27/2023]
Abstract
GTP hydrolysis by small GTP binding proteins of the Ras superfamily is a universal reaction that controls multiple cellular regulations. Its enzymic mechanism has been the subject of long-standing debates as to the existence/identity of the general base and the electronic nature of its transition state. Here we report the high-resolution crystal structure of a small GTP binding protein, Rab11, solved in complex with GDP and Pi. Unexpectedly, a Pi oxygen and the GDP-cleaved oxygen are located less than 2.5 A apart, suggesting that they share a proton, likely in the form of a low-barrier hydrogen bond. This implies that the gamma-phosphate of GTP was protonated; hence, that GTP acts as a general base. Furthermore, this interaction should establish at, and stabilize, the transition state. Altogether, we propose a revised model for the GTPase reaction that should reconcile earlier models into a unique substrate-assisted mechanism.
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Affiliation(s)
- Sebastiano Pasqualato
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
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26
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Sun M, Andreassi JL, Liu S, Pinto R, Triccas JA, Leyh TS. The trifunctional sulfate-activating complex (SAC) of Mycobacterium tuberculosis. J Biol Chem 2004; 280:7861-6. [PMID: 15615729 DOI: 10.1074/jbc.m409613200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sulfate activation pathway is essential for the assimilation of sulfate and, in many bacteria, is comprised of three reactions: the synthesis of adenosine 5'-phosphosulfate (APS), the hydrolysis of GTP, and the 3'-phosphorylation of APS to produce 3'-phosphoadenosine 5'-phosphosulfate (PAPS), whose sulfuryl group is reduced or transferred to other metabolites. The entire sulfate activation pathway is organized into a single complex in Mycobacterium tuberculosis. Although present in many bacteria, these tripartite complexes have not been studied in detail. Initial rate characterization of the mycobacterial system reveals that it is poised for extremely efficient throughput: at saturating ATP, PAPS synthesis is 5800 times more efficient than APS synthesis. The APS kinase domain of the complex does not appear to form the covalent E.P intermediate observed in the closely related APS kinase from Escherichia coli. The stoichiometry of GTP hydrolysis and APS synthesis is 1:1, and the APS synthesis reaction is driven 1.1 x 10(6)-fold further during GTP hydrolysis; the system harnesses the full chemical potential of the hydrolysis reaction to the synthesis of APS. A key energy-coupling step in the mechanism is a ligand-induced isomerization that enhances the affinity of GTP and commits APS synthesis and GTP hydrolysis to the completion of the catalytic cycle. Ligand-induced increases in guanine nucleotide affinity observed in the mycobacterial system suggest that it too undergoes the energy-coupling isomerization.
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Affiliation(s)
- Meihao Sun
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461-1926, USA
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27
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Jameson EE, Roof RA, Whorton MR, Mosberg HI, Sunahara RK, Neubig RR, Kennedy RT. Real-time detection of basal and stimulated G protein GTPase activity using fluorescent GTP analogues. J Biol Chem 2004; 280:7712-9. [PMID: 15613467 DOI: 10.1074/jbc.m413810200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrolysis of fluorescent GTP analogues BODIPY FL guanosine 5 '-O-(thiotriphosphate) (BGTPgammaS) and BODIPY FL GTP (BGTP) by Galpha(i1) and Galpha was characterized using on-line capillary electrophoresis (o) laser-induced fluorescence assays in order that changes in sub-strate, substrate-enzyme complex, and product could be monitored separately. Apparent k values (V /[E]) (max cat) steady-state and K(m) values were determined from assays for each substrate-protein pair. When BGTP was the substrate, maximum turnover numbers for Galpha and Galpha(i1) were 8.3 +/- 1 x 10(-3) and 3.0 +/- 0.2 x 10(-2) s(-1), respectively, and K(m) values were 120 +/- 60 and 940 +/- 160 nm. Assays with BGTPgammaS yielded maximum turnover numbers of 1.6 +/- 0.1 x 10(-4) and 5.5 +/- 0.3 x 10(-4) s(-1) for Galpha and Galpha(i1); K(m) values were 14 (o)(+/-)8 and 87 +/- 22 nm. Acceleration of Galpha GTPase activity by regulators of G protein signaling (RGS) was demonstrated in both steady-state and pseudo-single-turnover assay formats with BGTP. Nanomolar RGS increased the rate of enzyme product formation (BODIPY(R) FL GDP (BGDP)) by 117-213% under steady-state conditions and accelerated the rate of G protein-BGTP complex decay by 199 -778% in pseudo-single-turnover assays. Stimulation of GTPase activity by RGS proteins was inhibited 38-81% by 40 mum YJ34, a previously reported peptide RGS inhibitor. Taken together, these results illustrate that Galpha subunits utilize BGTP as a substrate similarly to GTP, making BGTP a useful fluorescent indicator of G protein activity. The unexpected levels of BGTPgammaS hydrolysis detected suggest that caution should be used when interpreting data from fluorescence assays with this probe.
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Affiliation(s)
- Emily E Jameson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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28
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Becker EW. Relevance of the kinetic equilibrium of forces to the control of the cell cycle by Ras proteins. Biol Chem 2004; 385:41-7. [PMID: 14977045 DOI: 10.1515/bc.2004.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In higher organisms, the replacement of GDP bound to Ras proteins with GTP, under the participation of an exchange factor, is an important step in the initiation of cell division. Ras-GTP activates kinases and other effectors, which pass signals to the cell nucleus and to the cytoskeleton. The active state of Ras is terminated by hydrolysis of the bound GTP with the assistance of an activating protein (GAP). Knowledge of these regulatory events is based on extensive experimental data, but many aspects of their interpretation are still controversial. It is assumed here that a significant part of the free energy released when two partners associate is stored in a 'kinetic equilibrium of forces' (KEF), and used to facilitate the separation from a third partner. The activation of the Raf kinase is explained primarily in terms of an allosteric effect of Ras-GTP on the phosphate transfer in the catalytic region of the kinase. A mechanism is proposed for the modification of GAP by Ras-GTP, which is believed to be a prerequisite for the well-known crosstalk between the Ras- and Rho-dependent signalling pathways. The cell, by meeting the requirements for KEF, manages to reduce activation barriers, thus significantly accelerating the regulatory events and other complex biological reaction sequences.
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Affiliation(s)
- Erwin W Becker
- Institut für Mikrostrukturtechnik, Forschungszentrum Karlsruhe, Universität Karlsruhe, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany.
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29
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Wout P, Pu K, Sullivan SM, Reese V, Zhou S, Lin B, Maddock JR. The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase. J Bacteriol 2004; 186:5249-57. [PMID: 15292126 PMCID: PMC490892 DOI: 10.1128/jb.186.16.5249-5257.2004] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CgtA(E)/Obg(E)/YhbZ is an Escherichia coli guanine nucleotide binding protein of the Obg/GTP1 subfamily whose members have been implicated in a number of cellular functions including GTP-GDP sensing, sporulation initiation, and translation. Here we describe a kinetic analysis of CgtA(E) with guanine nucleotides and show that its properties are similar to those of the Caulobacter crescentus homolog CgtA(C). CgtA(E) binds both GTP and GDP with moderate affinity, shows high guanine nucleotide exchange rate constants for both nucleotides, and has a relatively low GTP hydrolysis rate. We show that CgtA(E) is associated predominantly with the 50S ribosomal subunit. Interestingly, CgtA(E) copurifies with SpoT, a ribosome-associated ppGpp hydrolase/synthetase involved in the stress response. The interaction between CgtA(E) and SpoT was confirmed by reciprocal coprecipitation experiments and by two-hybrid assays. These studies raise the possibility that the ribosome-associated CgtA(E) is involved in the SpoT-mediated stress response.
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Affiliation(s)
- P Wout
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, 48109, USA
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30
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Topol IA, Cachau RE, Nemukhin AV, Grigorenko BL, Burt SK. Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1700:125-36. [PMID: 15210132 DOI: 10.1016/j.bbapap.2004.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Revised: 03/29/2004] [Accepted: 04/22/2004] [Indexed: 11/22/2022]
Abstract
We present results of the modeling for the hydrolysis reaction of guanosine triphosphate (GTP) in the RAS-GAP protein complex using essentially ab initio quantum chemistry methods. One of the approaches considers a supermolecular cluster composed of 150 atoms at a consistent quantum level. Another is a hybrid QM/MM method based on the effective fragment potential technique, which describes interactions between quantum and molecular mechanical subsystems at the ab initio level of the theory. Our results show that the GTP hydrolysis in the RAS-GAP protein complex can be modeled by a substrate-assisted catalytic mechanism. We can locate a configuration on the top of the barrier corresponding to the transition state of the hydrolysis reaction such that the straightforward descents from this point lead either to reactants GTP+H(2)O or to products guanosine diphosphate (GDP)+H(2)PO(4)(-). However, in all calculations such a single-step process is characterized by an activation barrier that is too high. Another possibility is a two-step reaction consistent with formation of an intermediate. Here the Pgamma-O(Pbeta) bond is already broken, but the lytic water molecule is still in the pre-reactive state. We present arguments favoring the assumption that the first step of the GTP hydrolysis reaction in the RAS-GAP protein complex may be assigned to the breaking of the Pgamma-O(Pbeta) bond prior to the creation of the inorganic phosphate.
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Affiliation(s)
- Igor A Topol
- Advanced Biomedical Computing Center, SAIC Frederick, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702-1201, USA.
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31
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Du X, Black GE, Lecchi P, Abramson FP, Sprang SR. Kinetic isotope effects in Ras-catalyzed GTP hydrolysis: evidence for a loose transition state. Proc Natl Acad Sci U S A 2004; 101:8858-63. [PMID: 15178760 PMCID: PMC428437 DOI: 10.1073/pnas.0401675101] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Indexed: 11/18/2022] Open
Abstract
A remote labeling method has been developed to determine (18)O kinetic isotope effects (KIEs) in Ras-catalyzed GTP hydrolysis. Substrate mixtures consist of (13)C-depleted GTP and [(18)O,(13)C]GTP that contains (18)O at phosphoryl positions of mechanistic interest and (13)C at all carbon positions of the guanosine moiety. Isotope ratios of the nonvolatile substrates and products are measured by using a chemical reaction interface/isotope ratio mass spectrometer. The isotope effects are 1.0012 (0.0026) in the gamma nonbridge oxygens, 1.0194 (0.0025) in the leaving group oxygens (the beta-gamma oxygen and the two beta nonbridge oxygens), and 1.0105 (0.0016) in the two beta nonbridge oxygens. The KIE in the beta-gamma bridge oxygen was computed to be 1.0116 or 1.0088 by two different methods. The significant KIE in the leaving group reveals that chemistry is largely rate-limiting whereas the KIEs in the gamma nonbridge oxygens and the leaving group indicate a loose transition state that approaches a metaphosphate. The KIE in the two beta nonbridge oxygens is roughly equal to that in the beta-gamma bridge oxygen. This indicates that, in the transition state, Ras shifts one-half of the negative charge that arises from P(gamma)-O(beta-gamma) fission from the beta-gamma bridge oxygen to the two beta nonbridge oxygens. The KIE effects, interpreted in light of structural and spectroscopic data, suggest that Ras promotes a loose transition state by stabilizing negative charge in the beta-gamma bridge and beta nonbridge oxygens of GTP.
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Affiliation(s)
- Xinlin Du
- Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Korlach J, Baird DW, Heikal AA, Gee KR, Hoffman GR, Webb WW. Spontaneous nucleotide exchange in low molecular weight GTPases by fluorescently labeled gamma-phosphate-linked GTP analogs. Proc Natl Acad Sci U S A 2004; 101:2800-5. [PMID: 14973186 PMCID: PMC365700 DOI: 10.1073/pnas.0308579100] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulated guanosine nucleotide exchange and hydrolysis constitute the fundamental activities of low molecular weight GTPases. We show that three guanosine 5'-triphosphate analogs with BODIPY fluorophores coupled via the gamma phosphate bind to the GTPases Cdc42, Rac1, RhoA, and Ras and displace guanosine 5'-diphosphate with high intrinsic exchange rates in the presence of Mg(2+) ions, thereby acting as synthetic, low molecular weight guanine nucleotide exchange factors. The accompanying large fluorescence enhancements (as high as 12-fold), caused by a reduction in guanine quenching of the environmentally sensitive BODIPY dye fluorescence on protein binding, allow for real-time monitoring of this spontaneous nucleotide exchange in the visible spectrum with high signal-to-noise ratios. Binding affinities increased with longer aliphatic linkers connecting the nucleotide and BODIPY fluorophore and were in the 10-100 nM range. Steady-state and time-resolved fluorescence spectroscopy showed an inverse relationship between linker length and fluorescence enhancement factors and differences in protein-bound fluorophore mobilities, providing optimization criteria for future applications of such compounds as efficient elicitors and reporters of nucleotide exchange. EDTA markedly enhanced nucleotide exchange, enabling rapid loading of GTPases with these probes. Differences in active site geometries, in the absence of Mg(2+), caused qualitatively different reporting of the bound state by the different analogs. The BODIPY analogs also prevented the interaction of Cdc42 with p21 activated kinase. Together, these results validate the use of these analogs as valuable tools for studying GTPase functions and for developing potent synthetic nucleotide exchange factors for this important class of signaling molecules.
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Affiliation(s)
- Jonas Korlach
- Field of Biochemistry, Molecular and Cell Biology, School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
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Li G, Qian H. Kinetic timing: a novel mechanism that improves the accuracy of GTPase timers in endosome fusion and other biological processes. Traffic 2002; 3:249-55. [PMID: 11929606 DOI: 10.1034/j.1600-0854.2002.030402.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The GTPase superfamily contains a large number of proteins that function as molecular switches by binding and hydrolyzing GTP molecules. They are localized at various intracellular organelles and control diverse cellular processes. For many GTPases, the lifetime of the activated, GTP-bound state is believed to serve as a timer in determining the activation time of a biological event such as membrane fusion and signal transduction. However, such a timer is intrinsically stochastic due to thermal noise at the level of single GTPase molecules. Here, we describe a mathematical model that shows how a directional GTPase cycle, in a nonequilibrium steady-state driven by GTP hydrolysis, can significantly reduce the variance in the lifetime of an activated GTPase molecule and thereby increase the accuracy and efficiency of the timer. This mechanism, termed kinetic timing, articulates a clear function for the energy consumption in GTPase-controlled biological processes. It provides a rationale for why biological timers utilize a GTP hydrolysis cycle rather than a simple GTP binding-dissociation equilibrium, and why the GTP-bound state is a better timer than the GDP-bound state. It also explains the necessity for the existence of multiple GTP-bound intermediates identified by fluorescence spectroscopy and nuclear magnetic resonance studies.
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Affiliation(s)
- Guangpu Li
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 940 SL. Young Blvd., BMSB 853, Oklahoma City, OK 73104, USA.
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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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35
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Abstract
Several coumarin-labeled nucleotides have been synthesized, based on 2'(3')-O-(2-aminoethyl)carbamoyl-ATP (edaATP). The fluorescent coumarins coupled with the free amino group are 7-diethylaminocoumarin-3-carboxylic acid (to give deac-edaATP), coumarin 343 (but-edaATP) and 7-ethylamino-8-bromocoumarin-3-carboxylic acid (mbc-edaATP). The carbamoyl linkage of these nucleotide analogs undergoes interconversion between 2'- and 3'-hydroxyl attachment very slowly, so that the 2'- and 3'-isomers were separated and stored with minimal equilibration. 3'-Deac-edaADP had fluorescence excitation and emission maxima at 430 nm and 477 nm, with a fluorescence quantum yield of 0.012. The equivalent data for 3'-but-edaADP are 445 nm, 494 nm, and 0.51, respectively, and for 3'-mbc-edaADP, 405 nm, 464 nm, and 0.62. The interaction with skeletal myosin subfragment 1 was measured in the absence and presence of actin. In each case the fluorescence was decreased when bound to subfragment 1, 3-fold for 3'-deac-edaADP, 7-fold for 3'-but-edaADP, and 11-fold for 3'-mbc-edaADP. Steady-state ATPase measurements and the kinetics of binding and release of nucleotides were similar to those reported for the natural nucleotide. Large fluorescence changes could be observed for the release of these analogs from actomyosin subfragment 1, enabling a direct measurement of the kinetics of this process. In the case of 3'-deac-edaADP a rate constant of 474 s(-1) was measured (at pH 7.0, 20 degrees C, and low ionic strength).
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Affiliation(s)
- M R Webb
- National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom.
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Klockow B, Ahmadian MR, Block C, Wittinghofer A. Oncogenic insertional mutations in the P-loop of Ras are overactive in MAP kinase signaling. Oncogene 2000; 19:5367-76. [PMID: 11103938 DOI: 10.1038/sj.onc.1203909] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mutations of Ras with three extra amino acids inserted into the phosphate-binding (P) loop have been investigated both in vitro and in vivo. Such mutants have originally been detected as oncogenes both in the ras and the TC21 genes. Biochemical experiments reveal the molecular basis of their oncogenic potential: the mutants show a strongly attenuated binding affinity for nucleotides, most notably for GDP, leading to a preference for GTP binding. Furthermore, both the intrinsic as well as the GAP-stimulated GTP hydrolysis are drastically diminished. The binding interaction with GAP is reduced, whereas binding to the Ras-binding domain of the downstream effector c-Raf1 is not altered appreciably. Microinjection into PC12 cells shows the mutants to be as potent to induce neurite outgrowth as conventional oncogenic Ras mutants. Unexpectedly, their ability to stimulate the MAP kinase pathway as measured by a reporter gene assay in RK13 cells is much higher than that of the normal oncogenic mutant G12V. This characteristic was attributed to an increased stimulation of c-Raf1 kinase activity by the insertional Ras mutants.
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Affiliation(s)
- B Klockow
- Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany
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39
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Murthy SN, Lorand L. Nucleotide binding by the erythrocyte transglutaminase/Gh protein, probed with fluorescent analogs of GTP and GDP. Proc Natl Acad Sci U S A 2000; 97:7744-7. [PMID: 10869438 PMCID: PMC16615 DOI: 10.1073/pnas.140210197] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
GTP is known to be a potent inhibitor of the protein crosslinking activity of transglutaminase (TG), probably the most abundant G protein in the human red cell. Nucleotide binding to TG was examined by fluorescence spectroscopy and anisotropy in mixtures of TG with methylanthraniloyl analogs of GTP and GDP. A characteristic feature was the appearance of a major energy transfer band (lambda(exc, max) = 290 nm, lambda(em) = 444 nm) from protein tryptophans to the bound nucleotides. Quenching of the bound fluorophore (lambda(exc) = 360 nm, lambda(em) = 444 nm) by acrylamide was barely different from that of free ligand. However, major changes were observed in anisotropy, which was used to demonstrate a facile exchange between bound and free nucleotides and to evaluate affinity constants for the binding of methylanthraniloyl GTP and GDP to TG.
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Affiliation(s)
- S N Murthy
- Department of Cell and Molecular Biology, and Feinberg Cardiovascular Research Institute, Northwestern University Medical School, Chicago, IL 60611-3008, USA
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40
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Abstract
The currently understood function for Ras in signal transduction is in mediating the transmission of signals from external growth factors to the cell nucleus. Mutated forms of this GTP-binding protein are found in 30% of human cancers with particularly high prevalence in colon and pancreatic carcinomas. These mutations destroy the GTPase activity of Ras and cause the protein to be locked in its active, GTP bound form. As a result, the signaling pathways are activated, leading to uncontrolled tumor growth. Ras function in signaling requires its association with the plasma membrane. This is achieved by posttranslational farnesylation of a cysteine residue present as part of the CA1A2X carboxyl terminal tetrapeptide of all Ras proteins. The enzyme that recognizes and farnesylates the CA1A2X sequence, Ras farnesyltransferase (FTase), has become an important target for the design of inhibitors that might be interesting as antitumor agents. Several approaches have been taken in the search for in vivo active inhibitors of farnesyltransferase. These include the identification of natural products such as the chaetomellic and zaragozic acids that mimic farnesylpyrophosphate, bisubstrate transition state analogs combining elements of the farnesyl and tetrapeptide substrates and peptidomimetics that reproduce features of the carboxyl terminal tetrapeptide CA1A2X sequence. This last group of compounds has been most successful in showing highly potent inhibition of FTase and selective blocking of Ras processing in a range of Ras transformed tumor cell lines at concentrations as low as 10 nM. Certain peptidomimetics will also block tumor growth in various mouse models, with apparently few toxic side effects. These results suggest that farnesyltransferase inhibitors hold considerable promise as anticancer drugs in the clinic.
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Affiliation(s)
- Y Qian
- Department of Chemistry and Pharmacology, University of Pittsburgh, PA 15215, USA
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41
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Sullivan SM, Mishra R, Neubig RR, Maddock JR. Analysis of guanine nucleotide binding and exchange kinetics of the Escherichia coli GTPase Era. J Bacteriol 2000; 182:3460-6. [PMID: 10852878 PMCID: PMC101928 DOI: 10.1128/jb.182.12.3460-3466.2000] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Era is an essential Escherichia coli guanine nucleotide binding protein that appears to play a number of cellular roles. Although the kinetics of Era guanine nucleotide binding and hydrolysis have been described, guanine nucleotide exchange rates have never been reported. Here we describe a kinetic analysis of guanine nucleotide binding, exchange, and hydrolysis by Era using the fluorescent mant (N-methyl-3'-O-anthraniloyl) guanine nucleotide analogs. The equilibrium binding constants (K(D)) for mGDP and mGTP (0.61 +/- 0. 12 microgM and 3.6 +/- 0.80 microM, respectively) are similar to those of the unmodified nucleotides. The single turnover rates for mGTP hydrolysis by Era were 3.1 +/- 0.2 mmol of mGTP hydrolyzed/min/mol in the presence of 5 mM MgCl(2) and 5.6 +/- 0.3 mmol of mGTP hydrolyzed/min/mol in the presence of 0.2 mM MgCl(2). Moreover, Era associates with and exchanges guanine nucleotide rapidly (on the order of seconds) in both the presence and absence of Mg(2+). We suggest that models of Era function should reflect the rapid exchange of nucleotides in addition to the GTPase activity inherent to Era.
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Affiliation(s)
- S M Sullivan
- Department of Biology, University of Michigan, Ann Arbor 48109, USA
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Díaz JF, Escalona MM, Kuppens S, Engelborghs Y. Role of the switch II region in the conformational transition of activation of Ha-ras-p21. Protein Sci 2000; 9:361-8. [PMID: 10716188 PMCID: PMC2144537 DOI: 10.1110/ps.9.2.361] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The role of the switch II region in the conformational transition of activation of Ha-ras-p21 has been investigated by mutating residues predicted to act as hinges for the conformational transition of this loop (Ala59, Gly60, and Gly75) (Díaz JF, Wroblowski B, Schlitter J, Engelborghs Y, 1997, Proteins 28:434-451), as well as mutating the catalytic residue Gln61. The proposed mutations of the hinge residues decrease the rate of the conformational transition of activation as measured by the binding of BeF3- to the GDP-p21 complex. Also, the thermodynamic parameters of the binding reaction are altered by a factor between three and five, depending on the temperature. (Due to changes in activation and reaction enthalpies, partially compensated by entropy changes.) The control mutation Q61H in which only the catalytic residue is changed has only a limited effect on the kinetic rate constants of the conformational transition and on the thermodynamic parameters of the reaction. The fact that mutations of the hinge residues of the switch II region affect both the binding of the phosphate analog and the conformational transition of activation indicates that the switch II is implicated both in the early and the late states of the transition.
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Affiliation(s)
- J F Díaz
- Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Heverlee, Belgium
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Scheidig AJ, Burmester C, Goody RS. The pre-hydrolysis state of p21(ras) in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins. Structure 1999; 7:1311-24. [PMID: 10574788 DOI: 10.1016/s0969-2126(00)80021-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND In numerous biological events the hydrolysis of guanine triphosphate (GTP) is a trigger to switch from the active to the inactive protein form. In spite of the availability of several high-resolution crystal structures, the details of the mechanism of nucleotide hydrolysis by GTPases are still unclear. This is partly because the structures of the proteins in their active states had to be determined in the presence of non-hydrolyzable GTP analogues (e.g. GppNHp). Knowledge of the structure of the true Michaelis complex might provide additional insights into the intrinsic protein hydrolysis mechanism of GTP and related nucleotides. RESULTS The structure of the complex formed between p21(ras) and GTP has been determined by X-ray diffraction at 1.6 A using a combination of photolysis of an inactive GTP precursor (caged GTP) and rapid freezing (100K). The structure of this complex differs from that of p21(ras)-GppNHp (determined at 277K) with respect to the degree of order and conformation of the catalytic loop (loop 4 of the switch II region) and the positioning of water molecules around the gamma-phosphate group. The changes in the arrangement of water molecules were induced by the cryo-temperature technique. CONCLUSIONS The results shed light on the function of Gln61 in the intrinsic GTP hydrolysis reaction. Furthermore, the possibility of a proton shuffling mechanism between two attacking water molecules and an oxygen of the gamma-phosphate group can be proposed for the basal GTPase mechanism, but arguments are presented that render this protonation mechanism unlikely for the GTPase activating protein (GAP)-activated GTPase.
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Affiliation(s)
- A J Scheidig
- Abteilung für Physikalische Biochemie, Max-Planck Institute for Molecular Physiology, Dortmund, 44227, Germany.
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45
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Lin B, Covalle KL, Maddock JR. The Caulobacter crescentus CgtA protein displays unusual guanine nucleotide binding and exchange properties. J Bacteriol 1999; 181:5825-32. [PMID: 10482526 PMCID: PMC94105 DOI: 10.1128/jb.181.18.5825-5832.1999] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Caulobacter crescentus CgtA protein is a member of the Obg-GTP1 subfamily of monomeric GTP-binding proteins. In vitro, CgtA specifically bound GTP and GDP but not GMP or ATP. CgtA bound GTP and GDP with moderate affinity at 30 degrees C and displayed equilibrium binding constants of 1.2 and 0.5 microM, respectively, in the presence of Mg(2+). In the absence of Mg(2+), the affinity of CgtA for GTP and GDP was reduced 59- and 6-fold, respectively. N-Methyl-3'-O-anthranoyl (mant)-guanine nucleotide analogs were used to quantify GDP and GTP exchange. Spontaneous dissociation of both GDP and GTP in the presence of 5 to 12 mM Mg(2+) was extremely rapid (k(d) = 1.4 and 1.5 s(-1), respectively), 10(3)- to 10(5)-fold faster than that of the well-characterized eukaryotic Ras-like GTP-binding proteins. The dissociation rate constant of GDP increased sevenfold in the absence of Mg(2+). Finally, there was a low inherent GTPase activity with a single-turnover rate constant of 5.0 x 10(-4) s(-1) corresponding to a half-life of hydrolysis of 23 min. These data clearly demonstrate that the guanine nucleotide binding and exchange properties of CgtA are different from those of the well-characterized Ras-like GTP-binding proteins. Furthermore, these data are consistent with a model whereby the nucleotide occupancy of CgtA is controlled by the intracellular levels of guanine nucleotides.
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Affiliation(s)
- B Lin
- Department of Biology, University of Michigan, Ann Arbor, Michigan 48109-1048, USA
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46
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Kuppens S, Díaz JF, Engelborghs Y. Characterization of the hinges of the effector loop in the reaction pathway of the activation of ras-proteins. Kinetics of binding of beryllium trifluoride to V29G and I36G mutants of Ha-ras-p21. Protein Sci 1999; 8:1860-6. [PMID: 10493587 PMCID: PMC2144410 DOI: 10.1110/ps.8.9.1860] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This work experimentally confirms the pathway of activation of Ha-ras-p21, which was calculated by the method of Targeted Molecular Dynamics (TMD) (Díaz JF, Wroblowski B, Schlitter J, Engelborghs Y, 1997a, Proteins Struct Funct Genet 28:434-451). The process can be studied experimentally by analyzing the binding of BeF3- to the GDP complex of the active fluorescent mutant Y32W (Díaz JF, Sillen A, Engelborghs Y, 1997b, J Biol Chem 227:23138-23143). Two mutants, V29G and 136G, have been constructed at both sides of the effector loop of the active fluorescent mutant. This was done to check the proposed reaction pathway and to provide further insight into the mechanism of the activation of ras proteins. Both mutations accelerate the conformational isomerization with two orders of magnitude, demonstrating convincingly the role of these residues as hinges of the effector loop in one or more of the transitions of the conformational change. These results provide experimental support to the pathway calculated by TMD analysis.
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Affiliation(s)
- S Kuppens
- Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Heverlee, Belgium
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47
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Ostermann N, Ahmadian MR, Wittinghofer A, Goody RS. New N-2-Labelled Fluorescent Derivatives of Guanosine Nucleotides and Their Interaction with GTP-Binding Proteins. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/15257779908043072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Affiliation(s)
- I M Krab
- Equipe 2 du Groupe de Biophysique, Ecole Polytechnique, F-91128 Palaiseau, France
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49
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Scheffzek K, Ahmadian MR, Wittinghofer A. GTPase-activating proteins: helping hands to complement an active site. Trends Biochem Sci 1998; 23:257-62. [PMID: 9697416 DOI: 10.1016/s0968-0004(98)01224-9] [Citation(s) in RCA: 306] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stimulation of the intrinsic GTPase activity of GTP-binding proteins by GTPase-activating proteins (GAPs) is a basic principle of GTP-binding-protein downregulation. Recently, the molecular mechanism behind this reaction has been elucidated by studies on Ras and Rho, and their respective GAPs. The basic features involve stabilizing the existing catalytic machinery and supplementing it by an external arginine residue. This represents a novel mechanism for enzyme active-site formation.
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Affiliation(s)
- K Scheffzek
- Max-Planck-Institut für Molekulare Physiologie, Dortmund, Germany
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50
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Leonard DA, Lin R, Cerione RA, Manor D. Biochemical studies of the mechanism of action of the Cdc42-GTPase-activating protein. J Biol Chem 1998; 273:16210-5. [PMID: 9632678 DOI: 10.1074/jbc.273.26.16210] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The small GTP-binding proteins Rac, Rho, and Cdc42 were shown to mediate a variety of signaling pathways including cytoskeletal rearrangements, cell-cycle progression, and transformation. Key to the proper function of these GTP-binding proteins is an efficient shut-off mechanism that ensures the decay of the signal. Regulatory proteins termed GAPs (GTPase-activating proteins) enhance the intrinsic GTP hydrolysis of the GTP-binding proteins, thereby ensuring signal termination. We have used site-specific mutagenesis to elucidate the limit domain for GAP activity in Cdc42-GAP, and show that in addition to the known GAP-homology domain (three conserved boxes), a C-terminal region outside that domain is also essential for GAP activity. In addition, we have replaced the conserved arginine (Arg305), which was suggested by structural studies to be a key catalytic residue, with an alanine and found that the R305A Cdc42-GAP mutant has a greatly diminished catalytic capacity but is still able to bind Cdc42 with high affinity. Thus, a key catalytic role for this residue is confirmed. However, we also present evidence for the involvement of an additional residue(s), since the R305A Cdc42-GAP mutant still exhibits measurable activity. Some of this residual activity might result from a neighboring arginine, since a double mutant R305A/R306A shows a further decrease in catalytic activity.
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Affiliation(s)
- D A Leonard
- Department of Pharmacology, Veterinary Medical Center, Cornell University, Ithaca, New York 14853, USA
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