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Gebregiworgis T, Chan JYL, Kuntz DA, Privé GG, Marshall CB, Ikura M. Crystal structure of NRAS Q61K with a ligand-induced pocket near switch II. Eur J Cell Biol 2024; 103:151414. [PMID: 38640594 DOI: 10.1016/j.ejcb.2024.151414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024] Open
Abstract
The RAS isoforms (KRAS, HRAS and NRAS) have distinct cancer type-specific profiles. NRAS mutations are the second most prevalent RAS mutations in skin and hematological malignancies. Although RAS proteins were considered undruggable for decades, isoform and mutation-specific investigations have produced successful RAS inhibitors that are either specific to certain mutants, isoforms (pan-KRAS) or target all RAS proteins (pan-RAS). While extensive structural and biochemical investigations have focused mainly on K- and H-RAS mutations, NRAS mutations have received less attention, and the most prevalent NRAS mutations in human cancers, Q61K and Q61R, are rare in K- and H-RAS. This manuscript presents a crystal structure of the NRAS Q61K mutant in the GTP-bound form. Our structure reveals a previously unseen pocket near switch II induced by the binding of a ligand to the active form of the protein. This observation reveals a binding site that can potentially be exploited for development of inhibitors against mutant NRAS. Furthermore, the well-resolved catalytic site of this GTPase bound to native GTP provides insight into the stalled GTP hydrolysis observed for NRAS-Q61K.
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Affiliation(s)
- Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5W9, Canada.
| | - Jonathan Yui-Lai Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Douglas A Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada; Department of Biochemistry, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada.
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Stathopulos PB, Ikura M. Aromatically stacking the odds in favour of increased ORAI1 activation. Cell Calcium 2024; 117:102841. [PMID: 38154331 DOI: 10.1016/j.ceca.2023.102841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Affiliation(s)
- Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, London, ON, N6A 5C1, Canada.
| | - Mitsuhiko Ikura
- Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada
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Saitoh T, Kim HN, Narita R, Ohtsuka I, Mo W, Lee KY, Enomoto M, Gasmi-Seabrook GMC, Marshall CB, Ikura M. Biochemical and biophysical characterization of the RAS family small GTPase protein DiRAS3. Protein Expr Purif 2023; 212:106361. [PMID: 37652393 DOI: 10.1016/j.pep.2023.106361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
DiRAS3, also called ARHI, is a RAS (sub)family small GTPase protein that shares 50-60% sequence identity with H-, K-, and N-RAS, with substitutions in key conserved G-box motifs and a unique 34 amino acid extension at its N-terminus. Unlike the RAS proto-oncogenes, DiRAS3 exhibits tumor suppressor properties. DiRAS3 function has been studied through genetics and cell biology, but there has been a lack of understanding of the biochemical and biophysical properties of the protein, likely due to its instability and poor solubility. To overcome this solubility issue, we engineered a DiRAS3 variant (C75S/C80S), which significantly improved soluble protein expression in E. coli. Recombinant DiRAS3 was purified by Ni-NTA and size exclusion chromatography (SEC). Concentration dependence of the SEC chromatogram indicated that DiRAS3 exists in monomer-dimer equilibrium. We then produced truncations of the N-terminal (ΔN) and both (ΔNC) extensions to the GTPase domain. Unlike full-length DiRAS3, the SEC profiles showed that ΔNC is monomeric while ΔN was monomeric with aggregation, suggesting that the N and/or C-terminal tail(s) contribute to dimerization and aggregation. The 1H-15N HSQC NMR spectrum of ΔNC construct displayed well-dispersed peaks similar to spectra of other GTPase domains, which enabled us to demonstrate that DiRAS3 has a GTPase domain that can bind GDP and GTP. Taken together, we conclude that, despite the substitutions in the G-box motifs, DiRAS3 can switch between nucleotide-bound states and that the N- and C-terminal extensions interact transiently with the GTPase domain in intra- and inter-molecular fashions, mediating weak multimerization of this unique small GTPase.
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Affiliation(s)
- Takashi Saitoh
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.
| | - Ha-Neul Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Riku Narita
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan
| | - Ibuki Ohtsuka
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan
| | - Weiyu Mo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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Lee KY, Ikura M, Marshall CB. The Self-Association of the KRAS4b Protein is Altered by Lipid-Bilayer Composition and Electrostatics. Angew Chem Int Ed Engl 2023; 62:e202218698. [PMID: 36883374 DOI: 10.1002/anie.202218698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/07/2023] [Accepted: 03/07/2023] [Indexed: 03/09/2023]
Abstract
KRAS is a peripheral membrane protein that regulates multiple signaling pathways, and is mutated in ≈30 % of cancers. Transient self-association of KRAS is essential for activation of the downstream effector RAF and oncogenicity. The presence of anionic phosphatidylserine (PS) lipids in the membrane was shown to promote KRAS self-assembly, however, the structural mechanisms remain elusive. Here, we employed nanodisc bilayers of defined lipid compositions, and probed the impact of PS concentration on KRAS self-association. Paramagnetic NMR experiments demonstrated the existence of two transient dimer conformations involving alternate electrostatic contacts between R135 and either D153 or E168 on the "α4/5-α4/5" interface, and revealed that lipid composition and salt modulate their dynamic equilibrium. These dimer interfaces were validated by charge-reversal mutants. This plasticity demonstrates how the dynamic KRAS dimerization interface responds to the environment, and likely extends to the assembly of other signaling complexes on the membrane.
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Affiliation(s)
- Ki-Young Lee
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-Do, South Korea
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
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Lee KY, Ikura M, Marshall CB. The Self‐Association of the KRAS4b Protein is Altered by Lipid‐Bilayer Composition and Electrostatics. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202218698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Affiliation(s)
- Ki-Young Lee
- CHA University Pharmacy 120, Haeryong-ro 11160 Pocheon-si KOREA, REPUBLIC OF
| | - Mitsuhiko Ikura
- Princess Margaret Hospital: Princess Margaret Hospital Cancer Centre Medical biophysics CANADA
| | - Christopher B. Marshall
- Princess Margaret Hospital: Princess Margaret Hospital Cancer Centre Medical biophysics CANADA
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Gebregiworgis T, Kano Y, Ohh M, Marshall CB, Ikura M. Abstract 670: Distinct biochemical properties of KRAS Q61H mutant render cancer cells resistant to SHP2 inhibitors. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent reports suggest that specific KRAS mutations are associated with either resistance or sensitivity of cancer cells to SHP2 inhibitors (SHP2i). However, a lack of understanding of the underlying mechanism(s) is hindering the clinical advancement of SHP2i therapy for cancer. Here we report that cancer cells that harbor KRAS Q61H mutation (found in about 5% of pancreatic ductal adenocarcinoma tumors) or HEK293 cells that over-express KRAS Q61H are resistant to SHP2i. Our biochemical studies supported by all atom molecular dynamic simulations show that the Q61H mutation impairs intrinsic GTP hydrolysis and impedes stimulation of the GTPase cycle by both SOS1 and RASA1, but has negligible impact on binding to BRAF-RBD. Similar to wild-type KRAS, the Q61H mutant can be phosphorylated by Src at Tyr-32 and Tyr-64, and both site scan be dephosphorylated by SHP2, although SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. In vitro, phosphorylation of KRAS Q61H increased intrinsic nucleotide exchange without affecting its insensitivity to SOS1 and RASA1. Phosphorylation of wild-type and SHP2i-sensitive mutants (e.g., G12V) confers resistance to SOS1/RASA1 activities and impairs binding to BRAF-RBD, thus the constitutive resistance to upstream regulation and uncompromised ability of phosphorylated KRAS Q61H to activate MAPK signaling are distinct properties of this mutant. Decoupling of KRAS Q61H from upstream signaling and impaired intrinsic nucleotide hydrolysis lead to a highly GTP-loaded pool that is insensitive to the suppressive effects of Src phosphorylation. While SHP2 plays multiple roles in stimulating RAS signaling, including promoting the GEF function of SOS1, reducing p120 GAP-mediated inactivation of KRAS, and reversing Src phosphorylation of KRAS, we revealed that none of these are required by KRAS Q61H. These insights provide a mechanistic understanding of oncogenic KRAS mutants that can guide clinical trials of SHP2 inhibitors for patients with pancreatic and other cancers bearing KRAS Q61H.
Citation Format: Teklab Gebregiworgis, Yoshihito Kano, Michael Ohh, Christopher B. Marshall, Mitsuhiko Ikura. Distinct biochemical properties of KRAS Q61H mutant render cancer cells resistant to SHP2 inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 670.
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Affiliation(s)
| | | | - Michael Ohh
- 2University of Toronto, Toronto, Ontario, Canada
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Marshall CB, Ikura M. Hitting the hotspots. Nat Chem Biol 2022; 18:578-579. [DOI: 10.1038/s41589-022-01000-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Johnson CW, Seo HS, Terrell EM, Yang MH, KleinJan F, Gebregiworgis T, Gasmi-Seabrook GMC, Geffken EA, Lakhani J, Song K, Bashyal P, Popow O, Paulo JA, Liu A, Mattos C, Marshall CB, Ikura M, Morrison DK, Dhe-Paganon S, Haigis KM. Regulation of GTPase function by autophosphorylation. Mol Cell 2022; 82:950-968.e14. [PMID: 35202574 PMCID: PMC8986090 DOI: 10.1016/j.molcel.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/29/2021] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
Abstract
A unifying feature of the RAS superfamily is a conserved GTPase cycle by which these proteins transition between active and inactive states. We demonstrate that autophosphorylation of some GTPases is an intrinsic regulatory mechanism that reduces nucleotide hydrolysis and enhances nucleotide exchange, altering the on/off switch that forms the basis for their signaling functions. Using X-ray crystallography, nuclear magnetic resonance spectroscopy, binding assays, and molecular dynamics on autophosphorylated mutants of H-RAS and K-RAS, we show that phosphoryl transfer from GTP requires dynamic movement of the switch II region and that autophosphorylation promotes nucleotide exchange by opening the active site and extracting the stabilizing Mg2+. Finally, we demonstrate that autophosphorylated K-RAS exhibits altered effector interactions, including a reduced affinity for RAF proteins in mammalian cells. Thus, autophosphorylation leads to altered active site dynamics and effector interaction properties, creating a pool of GTPases that are functionally distinct from their non-phosphorylated counterparts.
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Affiliation(s)
- Christian W Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Moon-Hee Yang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Ezekiel A Geffken
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jimit Lakhani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Puspalata Bashyal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Olesja Popow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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Eves BJ, Gebregiworgis T, Gasmi-Seabrook GM, Kuntz DA, Privé GG, Marshall CB, Ikura M. Structures of RGL1 RAS-Association domain in complex with KRAS and the oncogenic G12V mutant. J Mol Biol 2022; 434:167527. [DOI: 10.1016/j.jmb.2022.167527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
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Duong CN, Brückner R, Schmitt M, Nottebaum AF, Braun LJ, Meyer Zu Brickwedde M, Ipe U, Vom Bruch H, Schöler HR, Trapani G, Trappmann B, Ebrahimkutty MP, Huveneers S, de Rooij J, Ishiyama N, Ikura M, Vestweber D. Force-induced changes of α-catenin conformation stabilize vascular junctions independently of vinculin. J Cell Sci 2021; 134:273834. [PMID: 34851405 PMCID: PMC8729784 DOI: 10.1242/jcs.259012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/18/2021] [Indexed: 11/20/2022] Open
Abstract
Cadherin-mediated cell adhesion requires anchoring via the β-catenin–α-catenin complex to the actin cytoskeleton, yet, α-catenin only binds F-actin weakly. A covalent fusion of VE-cadherin to α-catenin enhances actin anchorage in endothelial cells and strongly stabilizes endothelial junctions in vivo, blocking inflammatory responses. Here, we have analyzed the underlying mechanism. We found that VE-cadherin–α-catenin constitutively recruits the actin adaptor vinculin. However, removal of the vinculin-binding region of α-catenin did not impair the ability of VE-cadherin–α-catenin to enhance junction integrity. Searching for an alternative explanation for the junction-stabilizing mechanism, we found that an antibody-defined epitope, normally buried in a short α1-helix of the actin-binding domain (ABD) of α-catenin, is openly displayed in junctional VE-cadherin–α-catenin chimera. We found that this epitope became exposed in normal α-catenin upon triggering thrombin-induced tension across the VE-cadherin complex. These results suggest that the VE-cadherin–α-catenin chimera stabilizes endothelial junctions due to conformational changes in the ABD of α-catenin that support constitutive strong binding to actin. Summary: There are novel antibody epitopes at the actin-binding domain of α-catenin that correlate with high affinity binding and are exposed in junction-stabilizing VE-cadherin–α-catenin fusion proteins.
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Affiliation(s)
- Cao Nguyen Duong
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Randy Brückner
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Martina Schmitt
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Astrid F Nottebaum
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Laura J Braun
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Marika Meyer Zu Brickwedde
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Ute Ipe
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Hermann Vom Bruch
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Giuseppe Trapani
- Bioactive Materials Laboratory, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Britta Trappmann
- Bioactive Materials Laboratory, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
| | - Mirsana P Ebrahimkutty
- Institute of Medical Physics and Biophysics, University of Muenster, Muenster 48149, Germany
| | - Stephan Huveneers
- Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Johan de Rooij
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Dietmar Vestweber
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, D-48149 Münster, Germany
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Huo KG, Notsuda H, Fang Z, Liu NF, Gebregiworgis T, Li Q, Pham NA, Li M, Liu N, Shepherd FA, Marshall CB, Ikura M, Moghal N, Tsao MS. Lung cancer driven by BRAF G469V mutation is targetable by EGFR kinase inhibitors. J Thorac Oncol 2021; 17:277-288. [PMID: 34648945 DOI: 10.1016/j.jtho.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Mutations in BRAF occur in 2-4% of lung adenocarcinoma (LUAD) patients. Combination dabrafenib/trametinib or single-agent vemurafenib is approved only for patients with cancers driven by the V600E BRAF mutation. Targeted therapy is not currently available for patients harboring non-V600 BRAF mutations. METHODS An LUAD patient-derived xenograft (PDX) model (PHLC12) with wild-type and non-amplified epidermal growth factor receptor (EGFR) was tested for response to EGFR tyrosine kinase inhibitors (TKI). A cell line derived from this model (X12CL) was also used to evaluate drug sensitivity and to identify potential drivers by siRNA knockdown. Kinase assays were used to test direct targeting of the candidate driver by the EGFR TKIs. Structural modeling including, molecular dynamics (MD) simulations, and binding assays were conducted to explore the mechanism of off-target inhibition by EGFR TKIs on the model 12 driver. RESULTS Both PDX PHLC12 and the X12CL cell line were sensitive to multiple EGFR TKIs. The BRAFG469V mutation was found to be the only known oncogenic mutation in this model. siRNA knockdown of BRAF, but not the EGFR, killed X12CL, confirming BRAFG469V as the oncogenic driver. Kinase activity of the BRAF protein isolated from X12CL was inhibited by treatment with the EGFR TKIs gefitinib and osimertinib, and expression of BRAFG469V in non-EGFR-expressing NR6 cells promoted growth in low serum, which was also sensitive to EGFR TKIs. . Structural modeling, MD simulations, and in vitro binding assays support BRAFG469V being a direct target of the TKIs. CONCLUSION Clinically approved EGFR TKIs can be repurposed to treat NSCLC patients harboring the BRAFG469V mutation.
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Affiliation(s)
- Ku-Geng Huo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Hirotsugu Notsuda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Thoracic Surgery Institute of Development, Aging and Cancer, Tohoku University. Sendai, Japan
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ningdi Feng Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ni Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Nadeem Moghal
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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12
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Lee KY, Enomoto M, Gebregiworgis T, Gasmi-Seabrook GMC, Ikura M, Marshall CB. Oncogenic KRAS G12D mutation promotes dimerization through a second, phosphatidylserine-dependent interface: a model for KRAS oligomerization. Chem Sci 2021; 12:12827-12837. [PMID: 34703570 PMCID: PMC8494122 DOI: 10.1039/d1sc03484g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/04/2021] [Indexed: 12/02/2022] Open
Abstract
KRAS forms transient dimers and higher-order multimers (nanoclusters) on the plasma membrane, which drive MAPK signaling and cell proliferation. KRAS is a frequently mutated oncogene, and while it is well known that the most prevalent mutation, G12D, impairs GTP hydrolysis, thereby increasing KRAS activation, G12D has also been shown to enhance nanoclustering. Elucidating structures of dynamic KRAS assemblies on a membrane has been challenging, thus we have refined our NMR approach that uses nanodiscs to study KRAS associated with membranes. We incorporated paramagnetic relaxation enhancement (PRE) titrations and interface mutagenesis, which revealed that, in addition to the symmetric ‘α–α’ dimerization interface shared with wild-type KRAS, the G12D mutant also self-associates through an asymmetric ‘α–β’ interface. The ‘α–β’ association is dependent on the presence of phosphatidylserine lipids, consistent with previous reports that this lipid promotes KRAS self-assembly on the plasma membrane in cells. Experiments using engineered mutants to spoil each interface, together with PRE probes attached to the membrane or free in solvent, suggest that dimerization through the primary ‘α–α’ interface releases β interfaces from the membrane promoting formation of the secondary ‘α–β’ interaction, potentially initiating nanoclustering. In addition, the small molecule BI-2852 binds at a β–β interface, stabilizing a new dimer configuration that outcompetes native dimerization and blocks the effector-binding site. Our data indicate that KRAS self-association involves a delicately balanced conformational equilibrium between transient states, which is sensitive to disease-associated mutation and small molecule inhibitors. The methods developed here are applicable to biologically important transient interactions involving other membrane-associated proteins. Studies of membrane-dependent dimerization of KRAS on nanodiscs using paramagnetic NMR titrations and mutagenesis revealed a novel asymmetric ‘α–β’ interface that provides a potential mechanism for the enhanced assembly of KRAS–G12D nanoclusters.![]()
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Affiliation(s)
- Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada .,Department of Medical Biophysics, University of Toronto Toronto Ontario M5G 1L7 Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada
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Kano Y, Gebregiworgis T, Marshall C, Ikura M, Miyake S, Ohh M. MO14-2 KRAS Q61H mutation evades the regulation of tyrosyl phosphorylation and renders cancer cells resistant to SHP2 inhibitor. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Chandrakumar AA, Coyaud É, Marshall CB, Ikura M, Raught B, Rottapel R. Tankyrase regulates epithelial lumen formation via suppression of Rab11 GEFs. J Cell Biol 2021; 220:212384. [PMID: 34128958 PMCID: PMC8221736 DOI: 10.1083/jcb.202008037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 01/08/2023] Open
Abstract
Rab11 GTPase proteins are required for cytokinesis, ciliogenesis, and lumenogenesis. Rab11a is critical for apical delivery of podocalyxin (PODXL) during lumen formation in epithelial cells. SH3BP5 and SH3BP5L are guanine nucleotide exchange factors (GEFs) for Rab11. We show that SH3BP5 and SH3BP5L are required for activation of Rab11a and cyst lumen formation. Using proximity-dependent biotin identification (BioID) interaction proteomics, we have identified SH3BP5 and its paralogue SH3BP5L as new substrates of the poly-ADP-ribose polymerase Tankyrase and the E3 ligase RNF146. We provide data demonstrating that epithelial polarity via cyst lumen formation is governed by Tankyrase, which inhibits Rab11a activation through the suppression of SH3BP5 and SH3BP5L. RNF146 reduces Tankyrase protein abundance and restores Rab11a activation and lumen formation. Thus, Rab11a activation is controlled by a signaling pathway composed of the sequential inhibition of SH3BP5 paralogues by Tankyrase, which is itself suppressed by RNF146.
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Affiliation(s)
- Arun A Chandrakumar
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | | | - Mitsuhiko Ikura
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Robert Rottapel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Division of Rheumatology, St. Michael's Hospital, Toronto, Ontario, Canada
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15
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Zhao Q, Fujimiya R, Kubo S, Marshall CB, Ikura M, Shimada I, Nishida N. Real-Time In-Cell NMR Reveals the Intracellular Modulation of GTP-Bound Levels of RAS. Cell Rep 2021; 32:108074. [PMID: 32846131 DOI: 10.1016/j.celrep.2020.108074] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/03/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
The small guanosine triphosphatase (GTPase) RAS serves as a molecular switch in signal transduction, and its mutation and aberrant activation are implicated in tumorigenesis. Here, we perform real-time, in-cell nuclear magnetic resonance (NMR) analyses of non-farnesylated RAS to measure time courses of the fraction of the active GTP-bound form (fGTP) within cytosol of live mammalian cells. The observed intracellular fGTP is significantly lower than that measured in vitro for wild-type RAS as well as oncogenic mutants, due to both decrease of the guanosine diphosphate (GDP)-GTP exchange rate (kex) and increase of GTP hydrolysis rate (khy). In vitro reconstitution experiments show that highly viscous environments promote a reduction of kex, whereas the increase of khy is stimulated by unidentified cytosolic proteins. This study demonstrates the power of in-cell NMR to directly detect the GTP-bound levels of RAS in mammalian cells, thereby revealing that the khy and kex of RAS are modulated by various intracellular factors.
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Affiliation(s)
- Qingci Zhao
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryu Fujimiya
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Kubo
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.
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16
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Burgos M, Philippe R, Antigny F, Buscaglia P, Masson E, Mukherjee S, Dubar P, Le Maréchal C, Campeotto F, Lebonvallet N, Frieden M, Llopis J, Domingo B, Stathopulos PB, Ikura M, Brooks W, Guida W, Chen JM, Ferec C, Capiod T, Mignen O. The p.E152K-STIM1 mutation deregulates Ca 2+ signaling contributing to chronic pancreatitis. J Cell Sci 2021; 134:jcs.244012. [PMID: 33468626 DOI: 10.1242/jcs.244012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 12/24/2020] [Indexed: 11/20/2022] Open
Abstract
Since deregulation of intracellular Ca2+ can lead to intracellular trypsin activation, and stromal interaction molecule-1 (STIM1) protein is the main regulator of Ca2+ homeostasis in pancreatic acinar cells, we explored the Ca2+ signaling in 37 STIM1 variants found in three pancreatitis patient cohorts. Extensive functional analysis of one particular variant, p.E152K, identified in three patients, provided a plausible link between dysregulated Ca2+ signaling within pancreatic acinar cells and chronic pancreatitis susceptibility. Specifically, p.E152K, located within the STIM1 EF-hand and sterile α-motif domain, increased the release of Ca2+ from the endoplasmic reticulum in patient-derived fibroblasts and transfected HEK293T cells. This event was mediated by altered STIM1-sarco/endoplasmic reticulum calcium transport ATPase (SERCA) conformational change and enhanced SERCA pump activity leading to increased store-operated Ca2+ entry (SOCE). In pancreatic AR42J cells expressing the p.E152K variant, Ca2+ signaling perturbations correlated with defects in trypsin activation and secretion, and increased cytotoxicity after cholecystokinin stimulation.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Miguel Burgos
- Université de Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France .,Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, 02002 Albacete, Spain.,Complejo Hospitalario Universitario de Albacete (UI-CHUA), 02002 Albacete, Spain
| | - Reginald Philippe
- Université de Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Fabrice Antigny
- Univ. Paris-Sud, Faculté de Médecine, Université Paris-Saclay, 94270 Le Kremlin Bicêtre, France.,Inserm UMR_S 999, Hôpital Marie Lannelongue, 92350 Le Plessis Robinson, France.,Department of Cell Physiology and Metabolism, Geneva Medical Center, CH-1211 Geneva, Switzerland
| | - Paul Buscaglia
- Université de Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France.,UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, INSERM, CHU de Brest, BP824, F29609 Brest, France
| | - Emmanuelle Masson
- Université de Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Sreya Mukherjee
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - Pauline Dubar
- Université de Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | | | - Florence Campeotto
- Hôpital Necker, AP-HP, Service de Gastroentérologie et Explorations Fonctionnelles Digestives Pédiatriques, Paris Descartes-Sorbonne Paris Cité Université, Institut Imagine, 75015 Paris, France
| | - Nicolas Lebonvallet
- Laboratory of Interactions Keratinocytes Neurons (EA4685), University of Western Brittany, F-29200 Brest, France
| | - Maud Frieden
- Department of Cell Physiology and Metabolism, Geneva Medical Center, CH-1211 Geneva, Switzerland
| | - Juan Llopis
- Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, 02002 Albacete, Spain
| | - Beatriz Domingo
- Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, 02002 Albacete, Spain
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, London, ON N6A 5C1, Canada
| | - Mitsuhiko Ikura
- Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Wesley Brooks
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - Wayne Guida
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - Jian-Min Chen
- Université de Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Claude Ferec
- Université de Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Thierry Capiod
- INSERM Unit 1151, Institut Necker Enfants Malades (INEM), Université Paris Descartes, Paris 75014, France
| | - Olivier Mignen
- Université de Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France .,UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, INSERM, CHU de Brest, BP824, F29609 Brest, France
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17
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Marshall CB, KleinJan F, Gebregiworgis T, Lee KY, Fang Z, Eves BJ, Liu NF, Gasmi-Seabrook GMC, Enomoto M, Ikura M. NMR in integrated biophysical drug discovery for RAS: past, present, and future. J Biomol NMR 2020; 74:531-554. [PMID: 32804298 DOI: 10.1007/s10858-020-00338-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Mutations in RAS oncogenes occur in ~ 30% of human cancers, with KRAS being the most frequently altered isoform. RAS proteins comprise a conserved GTPase domain and a C-terminal lipid-modified tail that is unique to each isoform. The GTPase domain is a 'switch' that regulates multiple signaling cascades that drive cell growth and proliferation when activated by binding GTP, and the signal is terminated by GTP hydrolysis. Oncogenic RAS mutations disrupt the GTPase cycle, leading to accumulation of the activated GTP-bound state and promoting proliferation. RAS is a key target in oncology, however it lacks classic druggable pockets and has been extremely challenging to target. RAS signaling has thus been targeted indirectly, by harnessing key downstream effectors as well as upstream regulators, or disrupting the proper membrane localization required for signaling, by inhibiting either lipid modification or 'carrier' proteins. As a small (20 kDa) protein with multiple conformers in dynamic equilibrium, RAS is an excellent candidate for NMR-driven characterization and screening for direct inhibitors. Several molecules have been discovered that bind RAS and stabilize shallow pockets through conformational selection, and recent compounds have achieved substantial improvements in affinity. NMR-derived insight into targeting the RAS-membrane interface has revealed a new strategy to enhance the potency of small molecules, while another approach has been development of peptidyl inhibitors that bind through large interfaces rather than deep pockets. Remarkable progress has been made with mutation-specific covalent inhibitors that target the thiol of a G12C mutant, and these are now in clinical trials. Here we review the history of RAS inhibitor development and highlight the utility of NMR and integrated biophysical approaches in RAS drug discovery.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Ben J Eves
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ningdi F Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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18
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Lee KY, Fang Z, Enomoto M, Gasmi-Seabrook G, Zheng L, Koide S, Ikura M, Marshall CB. Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2020; 59:11037-11045. [PMID: 32227412 PMCID: PMC7395670 DOI: 10.1002/anie.202001758] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Indexed: 11/07/2022]
Abstract
KRAS homo-dimerization has been implicated in the activation of RAF kinases, however, the mechanism and structural basis remain elusive. We developed a system to study KRAS dimerization on nanodiscs using paramagnetic relaxation enhancement (PRE) NMR spectroscopy, and determined distinct structures of membrane-anchored KRAS dimers in the active GTP- and inactive GDP-loaded states. Both dimerize through an α4-α5 interface, but the relative orientation of the protomers and their contacts differ substantially. Dimerization of KRAS-GTP, stabilized by electrostatic interactions between R135 and E168, favors an orientation on the membrane that promotes accessibility of the effector-binding site. Remarkably, "cross"-dimerization between GTP- and GDP-bound KRAS molecules is unfavorable. These models provide a platform to elucidate the structural basis of RAF activation by RAS and to develop inhibitors that can disrupt the KRAS dimerization. The methodology is applicable to many other farnesylated small GTPases.
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Affiliation(s)
- Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Le Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, and Perlmutter Cancer Center, New York University Langone Health, New York, NY, 10016, USA
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
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19
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Lee K, Fang Z, Enomoto M, Gasmi‐Seabrook G, Zheng L, Koide S, Ikura M, Marshall CB. Two Distinct Structures of Membrane‐Associated Homodimers of GTP‐ and GDP‐Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ki‐Young Lee
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
| | - Zhenhao Fang
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
| | | | - Le Zheng
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
| | - Shohei Koide
- Department of Biochemistry and Molecular PharmacologyNew York University School of Medicine, and Perlmutter Cancer CenterNew York University Langone Health New York NY 10016 USA
| | - Mitsuhiko Ikura
- Princess Margaret Cancer CentreUniversity Health Network Toronto Ontario M5G 1L7 Canada
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20
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Gebregiworgis T, Marshall CB, Kano Y, Ohh M, Ikura M. Abstract A04: Biophysical and biochemical characterization of Src-phosphorylated KRas. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-a04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tyrosine phosphorylation of several small GTPase proteins including Ras has been reported; however, investigations to understand the biologic role of tyrosine phosphorylated small GTPases have been limited. We will present the detailed characterization of the impact of tyrosyl phosphorylation of KRas on each stage of the GTPase cycle, and on the binding to the RBD of BRaf. Using NMR and MS analysis we demonstrate that a catalytic amount of Src (1 mole of Src into 250 moles of KRas) specifically phosphorylates KRas at two of the eight tyrosine residues (Y32 and Y64) in vitro. In HEK293 cells, ectopic expression of Src with KRas results in tyrosyl phosphorylation of the same sites in KRas. Tyrosyl phosphorylation of KRas perturbs the chemical shifts of residues in the two switch regions. Using our real-time NMR-based small GTPase assay, we illustrate that tyrosyl phosphorylation alters regulation of the KRas GTPase cycle by guanine exchange factor (SOScat) and GTPase activating protein (p120GAP), rendering KRas resistant to both activities. Furthermore, using an Octet BLI binding assay, we demonstrated that tyrosyl phosphorylation of KRas strongly impairs BRaf-RBD binding. In vitro, Src-phosphorylated KRas can be completely dephosphorylated by the phosphatase SHP2. In cells, we were able to detect endogenous tyrosyl phosphorylated Ras upon SHP2 CRISPR knockout. Together, our findings demonstrate that the GTPase cycle and effector binding affinity of KRas can be regulated by the balance of Src and SHP2 activities.
Citation Format: Teklab Gebregiworgis, Christopher B. Marshall, Yoshihito Kano, Michael Ohh, Mitsuhiko Ikura. Biophysical and biochemical characterization of Src-phosphorylated KRas [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A04.
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Affiliation(s)
- Teklab Gebregiworgis
- 1Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada,
| | - Christopher B. Marshall
- 1Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada,
| | - Yoshihito Kano
- 2Departments of Laboratory Medicine and Pathobiology, and Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Michael Ohh
- 2Departments of Laboratory Medicine and Pathobiology, and Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Mitsuhiko Ikura
- 1Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada,
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21
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Grant BMM, Enomoto M, Back SI, Lee KY, Gebregiworgis T, Ishiyama N, Ikura M, Marshall CB. Calmodulin disrupts plasma membrane localization of farnesylated KRAS4b by sequestering its lipid moiety. Sci Signal 2020; 13:13/625/eaaz0344. [PMID: 32234958 DOI: 10.1126/scisignal.aaz0344] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
KRAS4b is a small guanosine triphosphatase (GTPase) protein that regulates several signal transduction pathways that underlie cell proliferation, differentiation, and survival. KRAS4b function requires prenylation of its C terminus and recruitment to the plasma membrane, where KRAS4b activates effector proteins including the RAF family of kinases. The Ca2+-sensing protein calmodulin (CaM) has been suggested to regulate the localization of KRAS4b through direct, Ca2+-dependent interaction, but how CaM and KRAS4b functionally interact is controversial. Here, we determined a crystal structure, which was supported by solution nuclear magnetic resonance (NMR), that revealed the sequestration of the prenyl moiety of KRAS4b in the hydrophobic pocket of the C-terminal lobe of Ca2+-bound CaM. Our engineered fluorescence resonance energy transfer (FRET)-based biosensor probes (CaMeRAS) showed that, upon stimulation of Ca2+ influx by extracellular ligands, KRAS4b reversibly translocated in a Ca2+-CaM-dependent manner from the plasma membrane to the cytoplasm in live HeLa and HEK293 cells. These results reveal a mechanism underlying the inhibition of KRAS4b activity by Ca2+ signaling pathways.
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Affiliation(s)
- Benjamin M M Grant
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Sung-In Back
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Noboru Ishiyama
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.
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22
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Kano Y, Gebregiworgis T, Marshall CB, Radulovich N, Poon BPK, St-Germain J, Cook JD, Valencia-Sama I, Grant BMM, Herrera SG, Miao J, Raught B, Irwin MS, Lee JE, Yeh JJ, Zhang ZY, Tsao MS, Ikura M, Ohh M. Tyrosyl phosphorylation of KRAS stalls GTPase cycle via alteration of switch I and II conformation. Nat Commun 2019; 10:224. [PMID: 30644389 PMCID: PMC6333830 DOI: 10.1038/s41467-018-08115-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
Deregulation of the RAS GTPase cycle due to mutations in the three RAS genes is commonly associated with cancer development. Protein tyrosine phosphatase SHP2 promotes RAF-to-MAPK signaling pathway and is an essential factor in RAS-driven oncogenesis. Despite the emergence of SHP2 inhibitors for the treatment of cancers harbouring mutant KRAS, the mechanism underlying SHP2 activation of KRAS signaling remains unclear. Here we report tyrosyl-phosphorylation of endogenous RAS and demonstrate that KRAS phosphorylation via Src on Tyr32 and Tyr64 alters the conformation of switch I and II regions, which stalls multiple steps of the GTPase cycle and impairs binding to effectors. In contrast, SHP2 dephosphorylates KRAS, a process that is required to maintain dynamic canonical KRAS GTPase cycle. Notably, Src- and SHP2-mediated regulation of KRAS activity extends to oncogenic KRAS and the inhibition of SHP2 disrupts the phosphorylation cycle, shifting the equilibrium of the GTPase cycle towards the stalled ‘dark state’. Deregulation of the RAS GTPase cycle due to mutations in RAS genes is commonly associated with cancer development. Here authors use NMR and mass spectrometry to shows that KRAS phosphorylation via Src alters the conformation of switch I and II regions and thereby impacts the GTPase cycle.
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Affiliation(s)
- Yoshihito Kano
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network and Department of Pathology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Betty P K Poon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Ivette Valencia-Sama
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, 5G OA4, Canada
| | - Benjamin M M Grant
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Silvia Gabriela Herrera
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jinmin Miao
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Meredith S Irwin
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, 5G OA4, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network and Department of Pathology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada. .,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.
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23
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Abstract
Calmodulin (CaM) is a ubiquitous calcium-sensing protein that has one of the most highly conserved sequences among eukaryotes. CaM has been a useful tool for biologists studying calcium signaling for decades. In recent years, CaM has also been implicated in numerous cancer-associated pathways, and rare CaM mutations have been identified as a cause of human cardiac arrhythmias. Here, we present a collection of our most recent and effective protocols for the expression and purification of recombinant CaM from Escherichia coli, including various isotopic labeling schemes, primarily for nuclear magnetic resonance (NMR) spectroscopy and other biophysical applications.
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Affiliation(s)
- Benjamin M M Grant
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Mitsuhiko Ikura
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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24
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Stathopulos PB, Ikura M. Does stromal interaction molecule-1 have five senses? Cell Calcium 2018; 77:79-80. [PMID: 30528613 DOI: 10.1016/j.ceca.2018.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/01/2018] [Accepted: 12/01/2018] [Indexed: 01/04/2023]
Abstract
A single calcium (Ca2+) binding site within the canonical EF-hand loop was thought to govern the stromal interaction molecule-1 (STIM1) structural changes that lead to activation of Orai1 Ca2+ channels. Recent work by Gudlur et al., published in Nat Commun [9(1):4536], suggests that the STIM1 endoplasmic reticulum (ER) luminal domain has ∼5 additional Ca2+ binding sites, which underlie a surprising new proposal for Ca2+ sensing.
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Affiliation(s)
- Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, London, ON, N6A 5C1, Canada.
| | - Mitsuhiko Ikura
- Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.
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25
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Inoue M, Nakashima R, Enomoto M, Koike Y, Zhao X, Yip K, Huang SH, Waldron JN, Ikura M, Liu FF, Bratman SV. Plasma redox imbalance caused by albumin oxidation promotes lung-predominant NETosis and pulmonary cancer metastasis. Nat Commun 2018; 9:5116. [PMID: 30504805 PMCID: PMC6269536 DOI: 10.1038/s41467-018-07550-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/08/2018] [Indexed: 12/29/2022] Open
Abstract
Neutrophil extracellular traps (NETs) promote cancer metastasis in preclinical models following massive exogenous inflammatory stimuli. It remains unknown whether cancer hosts under physiologic conditions experience NETosis and consequent metastasis. Here we show that plasma redox imbalance caused by albumin oxidation promotes inflammation-independent NETosis. Albumin is the major source of free thiol that maintains redox balance. Oxidation of albumin-derived free thiol is sufficient to trigger NETosis via accumulation of reactive oxygen species within neutrophils. The resultant NETs are found predominantly within lungs where they contribute to the colonization of circulating tumor cells leading to pulmonary metastases. These effects are abrogated by pharmacologic inhibition of NET formation. Moreover, albumin oxidation is associated with pulmonary metastasis in a cohort of head and neck cancer patients. These results implicate plasma redox balance as an endogenous and physiologic regulator of NETosis and pulmonary cancer metastasis, providing new therapeutic and diagnostic opportunities for combatting cancer progression. Neutrophil extracellular traps (NETs) are known to promote metastasis in mouse models. Here the authors show plasma redox imbalance caused by albumin oxidation to induce inflammation-independent NETosis and lung metastasis, and albumin oxidation and reduced plasma free thiol to be associated with lung metastasis in a cohort of head and neck cancer patients.
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Affiliation(s)
- Minoru Inoue
- Princess Margaret Cancer Centre Research Institute, University Health Network, Toronto, M5G2M9, ON, Canada
| | - Ryota Nakashima
- Princess Margaret Cancer Centre Research Institute, University Health Network, Toronto, M5G2M9, ON, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre Research Institute, University Health Network, Toronto, M5G2M9, ON, Canada
| | - Yuhki Koike
- Department of Gastrointestinal and Pediatric Surgery, Mie University Graduate School of Medicine, Tsu City, 514-8507, Mie Prefecture, Japan
| | - Xiao Zhao
- Princess Margaret Cancer Centre Research Institute, University Health Network, Toronto, M5G2M9, ON, Canada
| | - Kenneth Yip
- Princess Margaret Cancer Centre Research Institute, University Health Network, Toronto, M5G2M9, ON, Canada
| | - Shao Hui Huang
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Healthy Network, Toronto, M5G2M9, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, M5G2M9, ON, Canada
| | - John N Waldron
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Healthy Network, Toronto, M5G2M9, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, M5G2M9, ON, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre Research Institute, University Health Network, Toronto, M5G2M9, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G2M9, ON, Canada
| | - Fei-Fei Liu
- Princess Margaret Cancer Centre Research Institute, University Health Network, Toronto, M5G2M9, ON, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Healthy Network, Toronto, M5G2M9, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, M5G2M9, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G2M9, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre Research Institute, University Health Network, Toronto, M5G2M9, ON, Canada. .,Radiation Medicine Program, Princess Margaret Cancer Centre, University Healthy Network, Toronto, M5G2M9, ON, Canada. .,Department of Radiation Oncology, University of Toronto, Toronto, M5G2M9, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, M5G2M9, ON, Canada.
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26
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Ishiyama N, Sarpal R, Wood MN, Barrick SK, Nishikawa T, Hayashi H, Kobb AB, Flozak AS, Yemelyanov A, Fernandez-Gonzalez R, Yonemura S, Leckband DE, Gottardi CJ, Tepass U, Ikura M. Force-dependent allostery of the α-catenin actin-binding domain controls adherens junction dynamics and functions. Nat Commun 2018; 9:5121. [PMID: 30504777 PMCID: PMC6269467 DOI: 10.1038/s41467-018-07481-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/26/2018] [Indexed: 01/26/2023] Open
Abstract
α-catenin is a key mechanosensor that forms force-dependent interactions with F-actin, thereby coupling the cadherin-catenin complex to the actin cytoskeleton at adherens junctions (AJs). However, the molecular mechanisms by which α-catenin engages F-actin under tension remained elusive. Here we show that the α1-helix of the α-catenin actin-binding domain (αcat-ABD) is a mechanosensing motif that regulates tension-dependent F-actin binding and bundling. αcat-ABD containing an α1-helix-unfolding mutation (H1) shows enhanced binding to F-actin in vitro. Although full-length α-catenin-H1 can generate epithelial monolayers that resist mechanical disruption, it fails to support normal AJ regulation in vivo. Structural and simulation analyses suggest that α1-helix allosterically controls the actin-binding residue V796 dynamics. Crystal structures of αcat-ABD-H1 homodimer suggest that α-catenin can facilitate actin bundling while it remains bound to E-cadherin. We propose that force-dependent allosteric regulation of αcat-ABD promotes dynamic interactions with F-actin involved in actin bundling, cadherin clustering, and AJ remodeling during tissue morphogenesis.
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Affiliation(s)
- Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
| | - Ritu Sarpal
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Megan N Wood
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | | | - Tadateru Nishikawa
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Hanako Hayashi
- RIKEN Center for Life Science Technologies, Kobe, Hyogo, 650-0047, Japan
| | - Anna B Kobb
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Annette S Flozak
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Alex Yemelyanov
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Rodrigo Fernandez-Gonzalez
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Shigenobu Yonemura
- RIKEN Center for Life Science Technologies, Kobe, Hyogo, 650-0047, Japan
- Department of Cell Biology, Tokushima University Graduate School of Medical Science, Tokushima, 770-8503, Japan
| | - Deborah E Leckband
- Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, 61801, USA
| | - Cara J Gottardi
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Cellular and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ulrich Tepass
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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27
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Fang Z, Marshall CB, Nishikawa T, Gossert AD, Jansen JM, Jahnke W, Ikura M. Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site. Cell Chem Biol 2018; 25:1327-1336.e4. [DOI: 10.1016/j.chembiol.2018.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/21/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022]
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28
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Notsuda H, Pham N, Li M, Liu N, Raghavan V, Fang Z, Marshall C, Moghal N, Ikura M, Tsao M. MA27.07 Lung Adenocarcinoma Harboring BRAF G469V Mutation is Uniquely Sensitive to EGFR Tyrosine Kinase Inhibitors. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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29
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Gebregiworgis T, Marshall CB, Kano Y, Radulovich N, Tsao MS, Ohh M, Ikura M. Abstract 4360: Altering the regulation of KRAS GTPase cycle via Src and SHP2 creates a potential therapeutic vulnerability for pancreatic cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
More than 30% of all human cancers have Ras mutations and more than 95% of pancreatic cancers harbor KRAS mutations. However, therapeutically targeting cancers driven by oncogenic Ras mutations is still an ongoing investigation. KRas is a small GTPase found in either a GDP-bound inactive form or a GTP-loaded activated form. The activated form of KRas localizes on the membrane where it binds and activates downstream effector proteins such as Raf kinases. GDP-bound Ras can be activated by nucleotide exchange of GTP for GDP, a reaction that is catalyzed by guanine nucleotide exchange factors (GEFs). Ras is inactivated by hydrolysis of GTP, which is assisted by GTPase activating proteins (GAPs). It was recently reported that Ras can be tyrosyl phosphorylated by Src and dephosphorylated by SHP2 (PNAS 2014;111(36):E3785-94; Nat Commun 2015;6:8859). Here we have characterized the structural and functional alterations of Src-phosphorylated KRas to mechanistically explain the impact of tyrosyl phosphorylation on the GTPase cycle. Our NMR and MS analyses show that Src phosphorylates KRas at Tyr32 and Tyr64, which perturbs the chemical shifts of several residues in each of the two "switch" regions that mediate interactions with effectors and regulators. Using real-time NMR and biolayer interferometry (Octet) assays, we demonstrated the negative impact of KRas phosphorylation on the GTPase cycle as well as BRAF binding. Conversely, the SH2 domain containing inositol 5-phosphatase 2 (SHP2) dephosphorylates KRAS and reverses Src-induced phosphorylation. In vivo, either the pharmacologic inhibition or genetic ablation of SHP2 promotes cell death in several KRAS mutant cancers. Our findings reveal that altering the KRas GTPase cycle regulation via the balance of Src and SHIP2 activities may create a therapeutic vulnerability for pancreatic cancer.
Citation Format: Teklab Gebregiworgis, Christopher B. Marshall, Yoshihito Kano, Nikolina Radulovich, Ming-Sound Tsao, Michael Ohh, Mitsuhiko Ikura. Altering the regulation of KRAS GTPase cycle via Src and SHP2 creates a potential therapeutic vulnerability for pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4360.
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Affiliation(s)
| | | | | | | | | | - Michael Ohh
- 2University of Toronto, Toronto, Ontario, Canada
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30
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Novello MJ, Zhu J, Feng Q, Ikura M, Stathopulos PB. Structural elements of stromal interaction molecule function. Cell Calcium 2018; 73:88-94. [PMID: 29698850 DOI: 10.1016/j.ceca.2018.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/13/2018] [Indexed: 02/02/2023]
Abstract
Stromal interaction molecule (STIM)-1 and -2 are multi-domain, single-pass transmembrane proteins involved in sensing changes in compartmentalized calcium (Ca2+) levels and transducing this cellular signal to Orai1 channel proteins. Our understanding of the molecular mechanisms underlying STIM signaling has been dramatically improved through available X-ray crystal and solution NMR structures. This high-resolution structural data has revealed that intricate intramolecular and intermolecular protein-protein interactions are involved in converting STIMs from the quiescent to activation-competent states. This review article summarizes the current high resolution structural data on specific EF-hand, sterile α motif and coiled-coil interactions which drive STIM function in the activation of Orai1 channels. Further, the work discusses the effects of post-translational modifications on the structure and function of STIMs. Future structural studies on larger STIM:Orai complexes will be critical to fully defining the molecular bases for STIM function and how post-translational modifications influence these mechanisms.
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Affiliation(s)
- Matthew J Novello
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada
| | - Jinhui Zhu
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada
| | - Qingping Feng
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.
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31
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Gebregiworgis T, Marshall CB, Nishikawa T, Radulovich N, Sandí MJ, Fang Z, Rottapel R, Tsao MS, Ikura M. Multiplexed Real-Time NMR GTPase Assay for Simultaneous Monitoring of Multiple Guanine Nucleotide Exchange Factor Activities from Human Cancer Cells and Organoids. J Am Chem Soc 2018. [PMID: 29543440 DOI: 10.1021/jacs.7b13703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Small GTPases (sGTPases) are critical switch-like regulators that mediate several important cellular functions and are often mutated in human cancers. They are activated by guanine nucleotide exchange factors (GEFs), which specifically catalyze the exchange of GTP for GDP. GEFs coordinate signaling networks in normal cells, and are frequently deregulated in cancers. sGTPase signaling pathways are complex and interconnected; however, most GEF assays do not reveal such complexity. In this Communication, we describe the development of a unique real-time NMR-based multiplexed GEF assay that employs distinct isotopic labeling schemes for each sGTPase protein to enable simultaneous observation of six proteins of interest. We monitor nucleotide exchange of KRas, Rheb, RalB, RhoA, Cdc42 and Rac1 in a single system, and assayed the activities of GEFs in lysates of cultured human cells and 3D organoids derived from pancreatic cancer patients. We observed potent activation of RhoA by lysates of HEK293a cells transfected with GEF-H1, along with weak stimulation of Rac1, which we showed is indirect. Our functional analyses of pancreatic cancer-derived organoids revealed higher GEF activity for RhoA than other sGTPases, in line with RNA-seq data indicating high expression of RhoA-specific GEFs.
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Affiliation(s)
- Teklab Gebregiworgis
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - Tadateru Nishikawa
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - María-José Sandí
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada.,Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada
| | - Robert Rottapel
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada.,Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada.,Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada.,Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A1 , Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada.,Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada
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32
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Sandí MJ, Marshall CB, Balan M, Coyaud É, Zhou M, Monson DM, Ishiyama N, Chandrakumar AA, La Rose J, Couzens AL, Gingras AC, Raught B, Xu W, Ikura M, Morrison DK, Rottapel R. MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity. Sci Signal 2017; 10:10/503/eaan3286. [PMID: 29089450 DOI: 10.1126/scisignal.aan3286] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The PAR-1-MARK pathway controls cell polarity through the phosphorylation of microtubule-associated proteins. Rho-Rac guanine nucleotide exchange factor 2 (ARHGEF2), which activates Ras homolog family member A (RHOA), is anchored to the microtubule network and sequestered in an inhibited state through binding to dynein light chain Tctex-1 type 1 (DYNLT1). We showed in mammalian cells that liver kinase B1 (LKB1) activated the microtubule affinity-regulating kinase 3 (MARK3), which in turn phosphorylated ARHGEF2 at Ser151 This modification disrupted the interaction between ARHGEF2 and DYNLT1 by generating a 14-3-3 binding site in ARHGEF2, thus causing ARHGEF2 to dissociate from microtubules. Phosphorylation of ARHGEF2 by MARK3 stimulated RHOA activation and the formation of stress fibers and focal adhesions, and was required for organized cellular architecture in three-dimensional culture. Protein phosphatase 2A (PP2A) dephosphorylated Ser151 in ARHGEF2 to restore the inhibited state. Thus, we have identified a regulatory switch controlled by MARK3 that couples microtubules to the actin cytoskeleton to establish epithelial cell polarity through ARHGEF2.
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Affiliation(s)
- María-José Sandí
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Marc Balan
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Ming Zhou
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Daniel M Monson
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Arun A Chandrakumar
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - José La Rose
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Amber L Couzens
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Deborah K Morrison
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Robert Rottapel
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada. .,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Division of Rheumatology, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
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33
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Stathopulos PB, Ikura M. Store operated calcium entry: From concept to structural mechanisms. Cell Calcium 2017; 63:3-7. [DOI: 10.1016/j.ceca.2016.11.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 11/24/2016] [Accepted: 11/24/2016] [Indexed: 11/16/2022]
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34
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Nishikawa T, Ishiyama N, Wang F, Ikura M. Backbone resonance assignments of the F-actin binding domain of mouse αN-catenin. Biomol NMR Assign 2017; 11:21-24. [PMID: 27804064 DOI: 10.1007/s12104-016-9713-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
α-Catenin is a filamentous actin (F-actin) binding protein that links the classical cadherin-catenin complex to the actin cytoskeleton at adherens junctions (AJs). Its C-terminal F-actin binding domain is required for regulating the dynamic interaction between AJs and the actin cytoskeleton during tissue development. Thus, obtaining the molecular details of this interaction is a crucial step towards understanding how α-catenin plays critical roles in biological processes, such as morphogenesis, cell polarity, wound healing and tissue maintenance. Here we report the backbone atom (1HN, 15N, 13Cα, 13Cβ and 13C') resonance assignments of the C-terminal F-actin binding domain of αN-catenin.
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Affiliation(s)
- Tadateru Nishikawa
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Feng Wang
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
- Department of Biochemistry, School of Medicine, Vanderbilt University, 2215 Garland Ave., 607 Light Hall, Nashville, TN, 37232-0146, USA
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada.
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35
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Spencer-Smith R, Koide A, Zhou Y, Eguchi RR, Sha F, Gajwani P, Santana D, Gupta A, Jacobs M, Herrero-Garcia E, Cobbert J, Lavoie H, Smith M, Rajakulendran T, Dowdell E, Okur MN, Dementieva I, Sicheri F, Therrien M, Hancock JF, Ikura M, Koide S, O'Bryan JP. Inhibition of RAS function through targeting an allosteric regulatory site. Nat Chem Biol 2016; 13:62-68. [PMID: 27820802 DOI: 10.1038/nchembio.2231] [Citation(s) in RCA: 204] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022]
Abstract
RAS GTPases are important mediators of oncogenesis in humans. However, pharmacological inhibition of RAS has proved challenging. Here we describe a functionally critical region, located outside the effector lobe of RAS, that can be targeted for inhibition. We developed NS1, a synthetic binding protein (monobody) that bound with high affinity to both GTP- and GDP-bound states of H-RAS and K-RAS but not N-RAS. NS1 potently inhibited growth factor signaling and oncogenic H-RAS- and K-RAS-mediated signaling and transformation but did not block oncogenic N-RAS, BRAF or MEK1. NS1 bound the α4-β6-α5 region of RAS, which disrupted RAS dimerization and nanoclustering and led to blocking of CRAF-BRAF heterodimerization and activation. These results establish the importance of the α4-β6-α5 interface in RAS-mediated signaling and define a previously unrecognized site in RAS for inhibiting RAS function.
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Affiliation(s)
- Russell Spencer-Smith
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA.,Jesse Brown VA Medical Center, Chicago, Illinois, USA
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA.,Department of Medicine, New York University Langone Medical Center, New York, New York, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, USA
| | - Raphael R Eguchi
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Fern Sha
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Priyanka Gajwani
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Dianicha Santana
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA
| | - Miranda Jacobs
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Erika Herrero-Garcia
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA.,Jesse Brown VA Medical Center, Chicago, Illinois, USA
| | - Jacqueline Cobbert
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Hugo Lavoie
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montreal, Quebec, Canada
| | - Matthew Smith
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Thanashan Rajakulendran
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Evan Dowdell
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Mustafa Nazir Okur
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Irina Dementieva
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montreal, Quebec, Canada
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, USA
| | - Mitsuhiko Ikura
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, New York, USA
| | - John P O'Bryan
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA.,Jesse Brown VA Medical Center, Chicago, Illinois, USA
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36
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Ottoni E, Gerby B, Haman A, Ikura M, Hoang T, Smith M. Structural basis for dimerization-mediated MLL leukemogenesis. Exp Hematol 2016. [DOI: 10.1016/j.exphem.2016.06.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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DeFalco TA, Marshall CB, Munro K, Kang HG, Moeder W, Ikura M, Snedden WA, Yoshioka K. Multiple Calmodulin-Binding Sites Positively and Negatively Regulate Arabidopsis CYCLIC NUCLEOTIDE-GATED CHANNEL12. Plant Cell 2016; 28:1738-51. [PMID: 27335451 PMCID: PMC4981125 DOI: 10.1105/tpc.15.00870] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 06/08/2016] [Accepted: 06/21/2016] [Indexed: 05/18/2023]
Abstract
Ca(2+) signaling is critical to plant immunity; however, the channels involved are poorly characterized. Cyclic nucleotide-gated channels (CNGCs) are nonspecific, Ca(2+)-permeable cation channels. Plant CNGCs are hypothesized to be negatively regulated by the Ca(2+) sensor calmodulin (CaM), and previous work has focused on a C-terminal CaM-binding domain (CaMBD) overlapping with the cyclic nucleotide binding domain of plant CNGCs. However, we show that the Arabidopsis thaliana isoform CNGC12 possesses multiple CaMBDs at cytosolic N and C termini, which is reminiscent of animal CNGCs and unlike any plant channel studied to date. Biophysical characterizations of these sites suggest that apoCaM interacts with a conserved isoleucine-glutamine (IQ) motif in the C terminus of the channel, while Ca(2+)/CaM binds additional N- and C-terminal motifs with different affinities. Expression of CNGC12 with a nonfunctional N-terminal CaMBD constitutively induced programmed cell death, providing in planta evidence of allosteric CNGC regulation by CaM. Furthermore, we determined that CaM binding to the IQ motif was required for channel function, indicating that CaM can both positively and negatively regulate CNGC12. These data indicate a complex mode of plant CNGC regulation by CaM, in contrast to the previously proposed competitive ligand model, and suggest exciting parallels between plant and animal channels.
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Affiliation(s)
- Thomas A DeFalco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Christopher B Marshall
- Department of Medical Biophysics, Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Kim Munro
- Protein Function Discovery Facility, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Hong-Gu Kang
- Department of Biology, Texas State University, San Marcos, Texas 78666
| | - Wolfgang Moeder
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Mitsuhiko Ikura
- Department of Medical Biophysics, Campbell Family Cancer Research Institute/Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Wayne A Snedden
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Keiko Yoshioka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada Center for the Analysis of Genome Evolution and Function (CAGEF), University of Toronto, Toronto, Ontario M5S 3B2, Canada
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38
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Ghosh AP, Marshall CB, Coric T, Shim EH, Kirkman R, Ballestas ME, Ikura M, Bjornsti MA, Sudarshan S. Point mutations of the mTOR-RHEB pathway in renal cell carcinoma. Oncotarget 2016; 6:17895-910. [PMID: 26255626 PMCID: PMC4627224 DOI: 10.18632/oncotarget.4963] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/03/2015] [Indexed: 01/21/2023] Open
Abstract
Aberrations in the mTOR (mechanistic target of rapamycin) axis are frequently reported in cancer. Using publicly available tumor genome sequencing data, we identified several point mutations in MTOR and its upstream regulator RHEB (Ras homolog enriched in brain) in patients with clear cell renal cell carcinoma (ccRCC), the most common histology of kidney cancer. Interestingly, we found a prominent cluster of hyperactivating mutations in the FAT (FRAP-ATM-TTRAP) domain of mTOR in renal cell carcinoma that led to an increase in both mTORC1 and mTORC2 activities and led to an increased proliferation of cells. Several of the FAT domain mutants demonstrated a decreased binding of DEPTOR (DEP domain containing mTOR-interacting protein), while a subset of these mutations showed altered binding of the negative regulator PRAS40 (proline rich AKT substrate 40). We also identified a recurrent mutation in RHEB in ccRCC patients that leads to an increase in mTORC1 activity. In vitro characterization of this RHEB mutation revealed that this mutant showed considerable resistance to TSC2 (Tuberous Sclerosis 2) GAP (GTPase activating protein) activity, though its interaction with TSC2 remained unaltered. Mutations in the FAT domain of MTOR and in RHEB remained sensitive to rapamycin, though several of these mutations demonstrated residual mTOR kinase activity after treatment with rapamycin at clinically relevant doses. Overall, our data suggests that point mutations in the mTOR pathway may lead to downstream mTOR hyperactivation through multiple different mechanisms to confer a proliferative advantage to a tumor cell.
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Affiliation(s)
- Arindam P Ghosh
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher B Marshall
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Tatjana Coric
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eun-Hee Shim
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Richard Kirkman
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mary E Ballestas
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mitsuhiko Ikura
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Mary-Ann Bjornsti
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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39
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Fang Z, Marshall CB, Yin JC, Mazhab-Jafari MT, Gasmi-Seabrook GMC, Smith MJ, Nishikawa T, Xu Y, Neel BG, Ikura M. Biochemical Classification of Disease-associated Mutants of RAS-like Protein Expressed in Many Tissues (RIT1). J Biol Chem 2016; 291:15641-52. [PMID: 27226556 DOI: 10.1074/jbc.m116.714196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 01/09/2023] Open
Abstract
RAS-like protein expressed in many tissues 1 (RIT1) is a disease-associated RAS subfamily small guanosine triphosphatase (GTPase). Recent studies revealed that germ-line and somatic RIT1 mutations can cause Noonan syndrome (NS), and drive proliferation of lung adenocarcinomas, respectively, akin to RAS mutations in these diseases. However, the locations of these RIT1 mutations differ significantly from those found in RAS, and do not affect the three mutational "hot spots" of RAS. Moreover, few studies have characterized the GTPase cycle of RIT1 and its disease-associated mutants. Here we developed a real-time NMR-based GTPase assay for RIT1 and investigated the effect of disease-associated mutations on GTPase cycle. RIT1 exhibits an intrinsic GTP hydrolysis rate similar to that of H-RAS, but its intrinsic nucleotide exchange rate is ∼4-fold faster, likely as a result of divergent residues near the nucleotide binding site. All of the disease-associated mutations investigated increased the GTP-loaded, activated state of RIT1 in vitro, but they could be classified into two groups with different intrinsic GTPase properties. The S35T, A57G, and Y89H mutants exhibited more rapid nucleotide exchange, whereas F82V and T83P impaired GTP hydrolysis. A RAS-binding domain pulldown assay indicated that RIT1 A57G and Y89H were highly activated in HEK293T cells, whereas T83P and F82V exhibited more modest activation. All five mutations are associated with NS, whereas two (A57G and F82V) have also been identified in urinary tract cancers and myeloid malignancies. Characterization of the effects on the GTPase cycle of RIT1 disease-associated mutations should enable better understanding of their role in disease processes.
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Affiliation(s)
- Zhenhao Fang
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Christopher B Marshall
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Jiani C Yin
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Mohammad T Mazhab-Jafari
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Geneviève M C Gasmi-Seabrook
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Matthew J Smith
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Tadateru Nishikawa
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Yang Xu
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Benjamin G Neel
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Mitsuhiko Ikura
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
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40
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Park S, Bin NR, Rajah M, Kim B, Chou TC, Kang SYA, Sugita K, Parsaud L, Smith M, Monnier PP, Ikura M, Zhen M, Sugita S. Conformational states of syntaxin-1 govern the necessity of N-peptide binding in exocytosis of PC12 cells and Caenorhabditis elegans. Mol Biol Cell 2015; 27:669-85. [PMID: 26700321 PMCID: PMC4750926 DOI: 10.1091/mbc.e15-09-0638] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/18/2015] [Indexed: 11/11/2022] Open
Abstract
Syntaxin-1 is the central SNARE protein for neuronal exocytosis. It interacts with Munc18-1 through its cytoplasmic domains, including the N-terminal peptide (N-peptide). Here we examine the role of the N-peptide binding in two conformational states ("closed" vs. "open") of syntaxin-1 using PC12 cells and Caenorhabditis elegans. We show that expression of "closed" syntaxin-1A carrying N-terminal single point mutations (D3R, L8A) that perturb interaction with the hydrophobic pocket of Munc18-1 rescues impaired secretion in syntaxin-1-depleted PC12 cells and the lethality and lethargy of unc-64 (C. elegans orthologue of syntaxin-1)-null mutants. Conversely, expression of the "open" syntaxin-1A harboring the same mutations fails to rescue the impairments. Biochemically, the L8A mutation alone slightly weakens the binding between "closed" syntaxin-1A and Munc18-1, whereas the same mutation in the "open" syntaxin-1A disrupts it. Our results reveal a striking interplay between the syntaxin-1 N-peptide and the conformational state of the protein. We propose that the N-peptide plays a critical role in intracellular trafficking of syntaxin-1, which is dependent on the conformational state of this protein. Surprisingly, however, the N-peptide binding mode seems dispensable for SNARE-mediated exocytosis per se, as long as the protein is trafficked to the plasma membrane.
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Affiliation(s)
- Seungmee Park
- Division of Fundamental Neurobiology, University Health Network, Toronto, ON M5T 2S8, Canada Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Na-Ryum Bin
- Division of Fundamental Neurobiology, University Health Network, Toronto, ON M5T 2S8, Canada Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Maaran Rajah
- Division of Fundamental Neurobiology, University Health Network, Toronto, ON M5T 2S8, Canada
| | - Byungjin Kim
- Division of Fundamental Neurobiology, University Health Network, Toronto, ON M5T 2S8, Canada
| | - Ting-Chieh Chou
- Division of Fundamental Neurobiology, University Health Network, Toronto, ON M5T 2S8, Canada Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Soo-Young Ann Kang
- Division of Fundamental Neurobiology, University Health Network, Toronto, ON M5T 2S8, Canada
| | - Kyoko Sugita
- Division of Genetics and Development, Krembil Discovery Tower, University Health Network, Toronto, ON M5T 2S8, Canada
| | - Leon Parsaud
- Division of Fundamental Neurobiology, University Health Network, Toronto, ON M5T 2S8, Canada Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew Smith
- Division of Signaling Biology, MaRS Toronto Medical Discovery Tower, Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Philippe P Monnier
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada Division of Genetics and Development, Krembil Discovery Tower, University Health Network, Toronto, ON M5T 2S8, Canada
| | - Mitsuhiko Ikura
- Division of Genetics and Development, Krembil Discovery Tower, University Health Network, Toronto, ON M5T 2S8, Canada Division of Signaling Biology, MaRS Toronto Medical Discovery Tower, Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuzo Sugita
- Division of Fundamental Neurobiology, University Health Network, Toronto, ON M5T 2S8, Canada Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
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41
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Marshall CB, Nishikawa T, Osawa M, Stathopulos PB, Ikura M. Calmodulin and STIM proteins: Two major calcium sensors in the cytoplasm and endoplasmic reticulum. Biochem Biophys Res Commun 2015; 460:5-21. [PMID: 25998729 DOI: 10.1016/j.bbrc.2015.01.106] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/22/2015] [Indexed: 01/22/2023]
Abstract
The calcium (Ca(2+)) ion is a universal signalling messenger which plays vital physiological roles in all eukaryotes. To decode highly regulated intracellular Ca(2+) signals, cells have evolved a number of sensor proteins that are ideally adapted to respond to a specific range of Ca(2+) levels. Among many such proteins, calmodulin (CaM) is a multi-functional cytoplasmic Ca(2+) sensor with a remarkable ability to interact with and regulate a plethora of structurally diverse target proteins. CaM achieves this 'multi-talented' functionality through two EF-hand domains, each with an independent capacity to bind targets, and an adaptable flexible linker. By contrast, stromal interaction molecule-1 and -2 (STIMs) have evolved for a specific role in endoplasmic reticulum (ER) Ca(2+) sensing using EF-hand machinery analogous to CaM; however, whereas CaM structurally adjusts to dissimilar binding partners, STIMs use the EF-hand machinery to self-regulate the stability of the Ca(2+) sensing domain. The molecular mechanisms underlying the Ca(2+)-dependent signal transduction by CaM and STIMs have revealed a remarkable repertoire of actions and underscore the flexibility of nature in molecular evolution and adaption to discrete Ca(2+) levels. Recent genomic sequencing efforts have uncovered a number of disease-associated mutations in both CaM and STIM1. This article aims to highlight the most recent key structural and functional findings in the CaM and STIM fields, and discusses how these two Ca(2+) sensor proteins execute their biological functions.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Tadateru Nishikawa
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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42
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Li J, Newhall J, Ishiyama N, Gottardi C, Ikura M, Leckband DE, Tajkhorshid E. Structural Determinants of the Mechanical Stability of α-Catenin. J Biol Chem 2015; 290:18890-903. [PMID: 26070562 DOI: 10.1074/jbc.m115.647941] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 11/06/2022] Open
Abstract
α-Catenin plays a crucial role in cadherin-mediated adhesion by binding to β-catenin, F-actin, and vinculin, and its dysfunction is linked to a variety of cancers and developmental disorders. As a mechanotransducer in the cadherin complex at intercellular adhesions, mechanical and force-sensing properties of α-catenin are critical to its proper function. Biochemical data suggest that α-catenin adopts an autoinhibitory conformation, in the absence of junctional tension, and biophysical studies have shown that α-catenin is activated in a tension-dependent manner that in turn results in the recruitment of vinculin to strengthen the cadherin complex/F-actin linkage. However, the molecular switch mechanism from autoinhibited to the activated state remains unknown for α-catenin. Here, based on the results of an aggregate of 3 μs of molecular dynamics simulations, we have identified a dynamic salt-bridge network within the core M region of α-catenin that may be the structural determinant of the stability of the autoinhibitory conformation. According to our constant-force steered molecular dynamics simulations, the reorientation of the MII/MIII subdomains under force may constitute an initial step along the transition pathway. The simulations also suggest that the vinculin-binding domain (subdomain MI) is intrinsically much less stable than the other two subdomains in the M region (MII and MIII). Our findings reveal several key insights toward a complete understanding of the multistaged, force-induced conformational transition of α-catenin to the activated conformation.
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Affiliation(s)
- Jing Li
- From the Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, and
| | - Jillian Newhall
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | | | - Cara Gottardi
- the Department of Acute Pulmonary Care, Feinberg College of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Mitsuhiko Ikura
- the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada, and
| | - Deborah E Leckband
- From the Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, and Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
| | - Emad Tajkhorshid
- From the Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, and
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43
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Wang F, Marshall CB, Ikura M. Forkhead followed by disordered tail: The intrinsically disordered regions of FOXO3a. Intrinsically Disord Proteins 2015; 3:e1056906. [PMID: 28232890 DOI: 10.1080/21690707.2015.1056906] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 12/22/2022]
Abstract
Forkhead box Class O is one of 19 subfamilies of the Forkhead box family, comprising 4 human transcription factors: FOXO1, FOXO3a, FOXO4, and FOXO6, which are involved in many crucial cellular processes. FOXO3a is a tumor suppressor involved in multiple physiological and pathological processes, and plays essential roles in metabolism, cell cycle arrest, DNA repair, and apoptosis. In its role as a transcription factor, the FOXO3a binds a consensus Forkhead response element DNA sequence, and recruits transcriptional coactivators to activate gene transcription. FOXO3a has additional functions, such as regulating p53-mediated apoptosis and activating kinase ATM. With the exception of the structured DNA-binding forkhead domain, most of the FOXO3a sequence comprises intrinsically disordered regions (IDRs), including 3 regions (CR1-3) that are conserved within the FOXO subfamily. Numerous studies have demonstrated that these IDRs directly mediate many of the diverse functions of FOXO3a. These regions contain post-translational modification and protein-protein interaction sites that integrate upstream signals to maintain homeostasis. Thus, the FOXO3a IDRs are emerging as key mediators of diverse regulatory processes, and represent an important target for the future development of therapeutics for FOXO3a-related diseases.
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Affiliation(s)
- Feng Wang
- The Campbell Family Cancer Research Institute, Princess Margaret Cancer Center, Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Present affiliation: Department of Biochemistry; Vanderbilt University School of Medicine; Nashville, TN USA
| | - Christopher B Marshall
- The Campbell Family Cancer Research Institute, Princess Margaret Cancer Center, Department of Medical Biophysics, University of Toronto , Toronto, Ontario, Canada
| | - Mitsuhiko Ikura
- The Campbell Family Cancer Research Institute, Princess Margaret Cancer Center, Department of Medical Biophysics, University of Toronto , Toronto, Ontario, Canada
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44
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Maus M, Jairaman A, Stathopulos PB, Muik M, Fahrner M, Weidinger C, Benson M, Fuchs S, Ehl S, Romanin C, Ikura M, Prakriya M, Feske S. Missense mutation in immunodeficient patients shows the multifunctional roles of coiled-coil domain 3 (CC3) in STIM1 activation. Proc Natl Acad Sci U S A 2015; 112:6206-11. [PMID: 25918394 PMCID: PMC4434767 DOI: 10.1073/pnas.1418852112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Store-operated Ca(2+) entry (SOCE) is a universal Ca(2+) influx pathway that is important for the function of many cell types. SOCE occurs upon depletion of endoplasmic reticulum (ER) Ca(2+) stores and relies on a complex molecular interplay between the plasma membrane (PM) Ca(2+) channel ORAI1 and the ER Ca(2+) sensor stromal interaction molecule (STIM) 1. Patients with null mutations in ORAI1 or STIM1 genes present with severe combined immunodeficiency (SCID)-like disease. Here, we describe the molecular mechanisms by which a loss-of-function STIM1 mutation (R429C) in human patients abolishes SOCE. R429 is located in the third coiled-coil (CC3) domain of the cytoplasmic C terminus of STIM1. Mutation of R429 destabilizes the CC3 structure and alters the conformation of the STIM1 C terminus, thereby releasing a polybasic domain that promotes STIM1 recruitment to ER-PM junctions. However, the mutation also impairs cytoplasmic STIM1 oligomerization and abolishes STIM1-ORAI1 interactions. Thus, despite its constitutive localization at ER-PM junctions, mutant STIM1 fails to activate SOCE. Our results demonstrate multifunctional roles of the CC3 domain in regulating intra- and intermolecular STIM1 interactions that control (i) transition of STIM1 from a quiescent to an active conformational state, (ii) cytoplasmic STIM1 oligomerization, and (iii) STIM1-ORAI1 binding required for ORAI1 activation.
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Affiliation(s)
- Mate Maus
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Amit Jairaman
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Peter B Stathopulos
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada, M5G 1L7; Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Martin Muik
- Institute of Biophysics, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Marc Fahrner
- Institute of Biophysics, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Carl Weidinger
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Melina Benson
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Sebastian Fuchs
- Center for Chronic Immunodeficiency, University Medical Center, University of Freiburg, D-79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany; and
| | - Stephan Ehl
- Center for Chronic Immunodeficiency, University Medical Center, University of Freiburg, D-79106 Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, University of Freiburg, D-79106 Freiburg, Germany
| | - Christoph Romanin
- Institute of Biophysics, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada, M5G 1L7
| | - Murali Prakriya
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Stefan Feske
- Department of Pathology, New York University School of Medicine, New York, NY 10016;
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Smith MJ, Marshall CB, Theillet FX, Binolfi A, Selenko P, Ikura M. Real-time NMR monitoring of biological activities in complex physiological environments. Curr Opin Struct Biol 2015; 32:39-47. [PMID: 25727665 DOI: 10.1016/j.sbi.2015.02.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/03/2015] [Accepted: 02/05/2015] [Indexed: 11/19/2022]
Abstract
Biological reactions occur in a highly organized spatiotemporal context and with kinetics that are modulated by multiple environmental factors. To integrate these variables in our experimental investigations of 'native' biological activities, we require quantitative tools for time-resolved in situ analyses in physiologically relevant settings. Here, we outline the use of high-resolution NMR spectroscopy to directly observe biological reactions in complex environments and in real-time. Specifically, we discuss how real-time NMR (RT-NMR) methods have delineated insights into metabolic processes, post-translational protein modifications, activities of cellular GTPases and their regulators, as well as of protein folding events.
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Affiliation(s)
- Matthew J Smith
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Christopher B Marshall
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Francois-Xavier Theillet
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany
| | - Andres Binolfi
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany
| | - Philipp Selenko
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany.
| | - Mitsuhiko Ikura
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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46
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Seo MD, Enomoto M, Ishiyama N, Stathopulos PB, Ikura M. Structural insights into endoplasmic reticulum stored calcium regulation by inositol 1,4,5-trisphosphate and ryanodine receptors. Biochim Biophys Acta 2014; 1853:1980-91. [PMID: 25461839 DOI: 10.1016/j.bbamcr.2014.11.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/17/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
Abstract
The two major calcium (Ca²⁺) release channels on the sarco/endoplasmic reticulum (SR/ER) are inositol 1,4,5-trisphosphate and ryanodine receptors (IP3Rs and RyRs). They play versatile roles in essential cell signaling processes, and abnormalities of these channels are associated with a variety of diseases. Structural information on IP3Rs and RyRs determined using multiple techniques including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (EM), has significantly advanced our understanding of the mechanisms by which these Ca²⁺ release channels function under normal and pathophysiological circumstances. In this review, structural advances on the understanding of the mechanisms of IP3R and RyR function and dysfunction are summarized. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.
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Affiliation(s)
- Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 443-749, Republic of Korea; College of Pharmacy, Ajou University, Suwon, Gyeonggi 443-749, Republic of Korea
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada.
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47
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Fahrner M, Muik M, Schindl R, Butorac C, Stathopulos P, Zheng L, Jardin I, Ikura M, Romanin C. A coiled-coil clamp controls both conformation and clustering of stromal interaction molecule 1 (STIM1). J Biol Chem 2014; 289:33231-44. [PMID: 25342749 PMCID: PMC4246082 DOI: 10.1074/jbc.m114.610022] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Store-operated Ca2+ entry, essential for the adaptive immunity, is initiated by the endoplasmic reticulum (ER) Ca2+ sensor STIM1. Ca2+ entry occurs through the plasma membrane resident Ca2+ channel Orai1 that directly interacts with the C-terminal STIM1 domain, named SOAR/CAD. Depletion of the ER Ca2+ store controls this STIM1/Orai1 interaction via transition to an extended STIM1 C-terminal conformation, exposure of the SOAR/CAD domain, and STIM1/Orai1 co-clustering. Here we developed a novel approach termed FRET-derived Interaction in a Restricted Environment (FIRE) in an attempt to dissect the interplay of coiled-coil (CC) interactions in controlling STIM1 quiescent as well as active conformation and cluster formation. We present evidence of a sequential activation mechanism in the STIM1 cytosolic domains where the interaction between CC1 and CC3 segment regulates both SOAR/CAD exposure and CC3-mediated higher-order oligomerization as well as cluster formation. These dual levels of STIM1 auto-inhibition provide efficient control over the coupling to and activation of Orai1 channels.
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Affiliation(s)
- Marc Fahrner
- From the Life Science Center JKU, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Martin Muik
- From the Life Science Center JKU, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Rainer Schindl
- From the Life Science Center JKU, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Carmen Butorac
- From the Life Science Center JKU, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Peter Stathopulos
- Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5C1, Canada, and
| | - Le Zheng
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Isaac Jardin
- From the Life Science Center JKU, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Christoph Romanin
- From the Life Science Center JKU, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria,
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48
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Meiri D, Marshall CB, Mokady D, LaRose J, Mullin M, Gingras AC, Ikura M, Rottapel R. Mechanistic insight into GPCR-mediated activation of the microtubule-associated RhoA exchange factor GEF-H1. Nat Commun 2014; 5:4857. [PMID: 25209408 DOI: 10.1038/ncomms5857] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/31/2014] [Indexed: 12/15/2022] Open
Abstract
The RhoGEF GEF-H1 can be sequestered in an inactive state on polymerized microtubules by the dynein motor light-chain Tctex-1. Phosphorylation of GEF-H1 Ser885 by PKA or PAK kinases creates an inhibitory 14-3-3-binding site. Here we show a new mode of GEF-H1 activation in response to the G-protein-coupled receptor (GPCR) ligands lysophosphatidic acid (LPA) or thrombin that is independent of microtubule depolymerization. LPA/thrombin stimulates disassembly of the GEF-H1:dynein multi-protein complex through the concerted action of Gα and Gβγ. Gα binds directly to GEF-H1 and displaces it from Tctex-1, while Gβγ binds to Tctex-1 and disrupts its interaction with the dynein intermediate chain, resulting in the release of GEF-H1. Full activation of GEF-H1 requires dephosphorylation of Ser885 by PP2A, which is induced by thrombin. The coordinated displacement of GEF-H1 from microtubules by G-proteins and its dephosphorylation by PP2A demonstrate a multistep GEF-H1 activation and present a unique mechanism coupling GPCR signalling to Rho activation.
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Affiliation(s)
- David Meiri
- Department of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Room 12-704, Toronto Medical Discovery Tower, Toronto, Ontario, Canada M5G 1L7
| | - Daphna Mokady
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Room 12-704, Toronto Medical Discovery Tower, Toronto, Ontario, Canada M5G 1L7
| | - Jose LaRose
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Room 12-704, Toronto Medical Discovery Tower, Toronto, Ontario, Canada M5G 1L7
| | - Michael Mullin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 992A, Toronto, Ontario, Canada M5G 1X5
| | - Anne-Claude Gingras
- 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 992A, Toronto, Ontario, Canada M5G 1X5 [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Mitsuhiko Ikura
- 1] Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Room 12-704, Toronto Medical Discovery Tower, Toronto, Ontario, Canada M5G 1L7 [2] Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Robert Rottapel
- 1] Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Room 12-704, Toronto Medical Discovery Tower, Toronto, Ontario, Canada M5G 1L7 [2] Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8 [3] Department of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8 [4] Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8 [5] Division of Rheumatology, St Michael's Hospital, 30 Bond Street, Toronto, Ontario, Canada M5B 1W8
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Stathopulos PB, Schindl R, Fahrner M, Zheng L, Gasmi-Seabrook GM, Muik M, Romanin C, Ikura M. STIM1/Orai1 coiled-coil interplay in the regulation of store-operated calcium entry. Nat Commun 2014; 4:2963. [PMID: 24351972 PMCID: PMC3927877 DOI: 10.1038/ncomms3963] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 11/20/2013] [Indexed: 12/11/2022] Open
Abstract
Orai1 calcium channels in the plasma membrane are activated by stromal interaction molecule-1 (STIM1), an endoplasmic reticulum calcium sensor, to mediate store-operated calcium entry (SOCE). The cytosolic region of STIM1 contains a long putative coiled-coil (CC)1 segment and shorter CC2 and CC3 domains. Here we present solution nuclear magnetic resonance structures of a trypsin-resistant CC1–CC2 fragment in the apo and Orai1-bound states. Each CC1–CC2 subunit forms a U-shaped structure that homodimerizes through antiparallel interactions between equivalent α-helices. The CC2:CC2′ helix pair clamps two identical acidic Orai1 C-terminal helices at opposite ends of a hydrophobic/basic STIM–Orai association pocket. STIM1 mutants disrupting CC1:CC1′ interactions attenuate, while variants promoting CC1 stability spontaneously activate Orai1 currents. CC2 mutations cause remarkable variability in Orai1 activation because of a dual function in binding Orai1 and autoinhibiting STIM1 oligomerization via interactions with CC3. We conclude that SOCE is activated through dynamic interplay between STIM1 and Orai1 helices. When endoplasmic reticulum calcium levels are low, STIM1 binds to and opens Orai1 channels in the plasma membrane to replenish calcium stores. Stathopulos et al. present solution structures of the STIM1 coiled-coil domain in the presence and absence of Orai1, revealing the structural basis for this interaction.
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Affiliation(s)
- Peter B Stathopulos
- University Health Network and Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, University of Toronto, Room 4-804, MaRS TMDT, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Rainer Schindl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Marc Fahrner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Le Zheng
- University Health Network and Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, University of Toronto, Room 4-804, MaRS TMDT, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Geneviève M Gasmi-Seabrook
- University Health Network and Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, University of Toronto, Room 4-804, MaRS TMDT, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Martin Muik
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Christoph Romanin
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Mitsuhiko Ikura
- University Health Network and Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, University of Toronto, Room 4-804, MaRS TMDT, 101 College Street, Toronto, Ontario, Canada M5G 1L7
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50
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Mazhab-Jafari MT, Marshall CB, Ho J, Ishiyama N, Stambolic V, Ikura M. Structure-guided mutation of the conserved G3-box glycine in Rheb generates a constitutively activated regulator of mammalian target of rapamycin (mTOR). J Biol Chem 2014; 289:12195-201. [PMID: 24648513 DOI: 10.1074/jbc.c113.543736] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Constitutively activated variants of small GTPases, which provide valuable functional probes of their role in cellular signaling pathways, can often be generated by mutating the canonical catalytic residue (e.g. Ras Q61L) to impair GTP hydrolysis. However, this general approach is ineffective for a substantial fraction of the small GTPase family in which this residue is not conserved (e.g. Rap) or not catalytic (e.g. Rheb). Using a novel engineering approach, we have manipulated nucleotide binding through structure-guided substitutions of an ultraconserved glycine residue in the G3-box motif (DXXG). Substitution of Rheb Gly-63 with alanine impaired both intrinsic and TSC2 GTPase-activating protein (GAP)-mediated GTP hydrolysis by displacing the hydrolytic water molecule, whereas introduction of a bulkier valine side chain selectively blocked GTP binding by steric occlusion of the γ-phosphate. Rheb G63A stimulated phosphorylation of the mTORC1 substrate p70S6 kinase more strongly than wild-type, thus offering a new tool for mammalian target of rapamycin (mTOR) signaling.
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Affiliation(s)
- Mohammad T Mazhab-Jafari
- From the Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre and, Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
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