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Liu NF, Enomoto M, Marshall CB, Ikura M. Reconstitution and characterization of BRAF in complex with 14-3-3 and KRAS4B on nanodiscs. Protein Sci 2024; 33:e5016. [PMID: 38747381 PMCID: PMC11094772 DOI: 10.1002/pro.5016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
RAF kinases are key components of the RAS-MAPK signaling pathway, which drives cell growth and is frequently overactivated in cancer. Upstream signaling activates the small GTPase RAS, which recruits RAF to the cell membrane, driving a transition of the latter from an auto-inhibited monomeric conformation to an active dimer. Despite recent progress, mechanistic details underlying RAF activation remain unclear, particularly the role of RAS and the membrane in mediating this conformational rearrangement of RAF together with 14-3-3 to permit RAF kinase domain dimerization. Here, we reconstituted an active complex of dimeric BRAF, a 14-3-3 dimer and two KRAS4B on a nanodisc bilayer and verified that its assembly is GTP-dependent. Biolayer interferometry (BLI) was used to compare the binding affinities of monomeric versus dimeric full-length BRAF:14-3-3 complexes for KRAS4B-conjugated nanodiscs (RAS-ND) and to investigate the effects of membrane lipid composition and spatial density of KRAS4B on binding. 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) and higher KRAS4B density enhanced the interaction of BRAF:14-3-3 with RAS-ND to different degrees depending on BRAF oligomeric state. We utilized our reconstituted system to dissect the effects of KRAS4B and the membrane on the kinase activity of monomeric and dimeric BRAF:14-3-3 complexes, finding that KRAS4B or nanodiscs alone were insufficient to stimulate activity, whereas RAS-ND increased activity of both states of BRAF. The reconstituted assembly of full-length BRAF with 14-3-3 and KRAS on a cell-free, defined lipid bilayer offers a more holistic biophysical perspective to probe regulation of this multimeric signaling complex at the membrane surface.
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Affiliation(s)
- Ningdi F. Liu
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
| | - Masahiro Enomoto
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
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2
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Trebino TE, Markusic B, Nan H, Banerjee S, Wang Z. Unveiling the domain-specific and RAS isoform-specific details of BRAF kinase regulation. eLife 2023; 12:RP88836. [PMID: 38150000 PMCID: PMC10752582 DOI: 10.7554/elife.88836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
BRAF is a key member in the MAPK signaling pathway essential for cell growth, proliferation, and differentiation. Mutant BRAF is often the underlying cause of various types of cancer and mutant RAS, the upstream regulator of BRAF, is a driver of up to one-third of all cancers. BRAF interacts with RAS and undergoes a conformational change from an inactive, autoinhibited monomer to an active dimer, which propagates downstream signaling. Because of BRAF's complex regulation mechanism, the exact order and magnitude of its activation steps have yet to be confirmed experimentally. By studying the inter- and intramolecular interactions of BRAF, we unveil the domain-specific and isoform-specific details of BRAF regulation through pulldown assays, open surface plasmon resonance (OpenSPR), and hydrogen-deuterium exchange mass spectrometry (HDX-MS). We demonstrate that the BRAF specific region (BSR) and cysteine rich domain (CRD) play a crucial role in regulating the activation of BRAF in a RAS isoform-specific manner. Moreover, we quantified the binding affinities between BRAF N-terminal and kinase domains (KD) to reveal their individual roles in autoinhibition. Our findings also indicate that oncogenic BRAF-KDD594G mutant has a lower affinity for the N-terminal domains, implicating that pathogenic BRAF acts through decreased propensity for autoinhibition. Collectively, our study provides valuable insight into the activation mechanism of BRAF kinase to guide the development of new therapeutic strategies for cancer treatment.
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Affiliation(s)
| | - Borna Markusic
- Rowan UniversityGlassboroUnited States
- Max Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Haihan Nan
- Rowan UniversityGlassboroUnited States
- School of Laboratory Medicine and Life Science, Wenzhou Medical UniversityWenzhouChina
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3
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Martin-Vega A, Cobb MH. Navigating the ERK1/2 MAPK Cascade. Biomolecules 2023; 13:1555. [PMID: 37892237 PMCID: PMC10605237 DOI: 10.3390/biom13101555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field.
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Affiliation(s)
- Ana Martin-Vega
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
| | - Melanie H. Cobb
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA
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4
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Trebino T, Markusic B, Nan H, Banerjee S, Wang Z. Unveiling the Domain-Specific and RAS Isoform-Specific Details of BRAF Regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538112. [PMID: 37163002 PMCID: PMC10168249 DOI: 10.1101/2023.04.24.538112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BRAF is a key member in the MAPK signaling pathway essential for cell growth, proliferation, and differentiation. Dysregulation or mutation of BRAF is often the underlying cause of various types of cancer. RAS, a small GTPase protein that acts upstream of BRAF, has been identified as a driver of up to one-third of all cancers. When BRAF interacts with RAS via the RAS binding domain (RBD) and membrane recruitment, BRAF undergoes a conformational change from an inactive, autoinhibited monomer to an active dimer and subsequently phosphorylates MEK to propagate the signal. Despite the central role of BRAF in cellular signaling, the exact order and magnitude of its activation steps has yet to be confirmed experimentally. By studying the inter- and intramolecular interactions of BRAF, we unveil the domain-specific and isoform-specific details of BRAF regulation. We employed pulldown assays, open surface plasmon resonance (OpenSPR), and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate the roles of the regulatory regions in BRAF activation and autoinhibition. Our results demonstrate that the BRAF specific region (BSR) and cysteine rich domain (CRD) play a crucial role in regulating the activity of BRAF. Moreover, we quantified the autoinhibitory binding affinities between the N-terminal domains and the kinase domain (KD) of BRAF and revealed the individual roles of the BRAF regulatory domains. Additionally, our findings provide evidence that the BSR negatively regulates BRAF activation in a RAS isoform-specific manner. Our findings also indicate that oncogenic BRAF-KDD594G mutant has a lower affinity for the regulatory domains, implicating that pathogenic BRAF acts through decreased propensity for autoinhibition. Collectively, our study provides valuable insights into the activation mechanism of BRAF kinase and may help to guide the development of new therapeutic strategies for cancer treatment.
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Affiliation(s)
- Tarah Trebino
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Borna Markusic
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
- Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Haihan Nan
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shrhea Banerjee
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Zhihong Wang
- Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
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5
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Park E, Rawson S, Schmoker A, Kim BW, Oh S, Song K, Jeon H, Eck MJ. Cryo-EM structure of a RAS/RAF recruitment complex. Nat Commun 2023; 14:4580. [PMID: 37516774 PMCID: PMC10387098 DOI: 10.1038/s41467-023-40299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/19/2023] [Indexed: 07/31/2023] Open
Abstract
RAF-family kinases are activated by recruitment to the plasma membrane by GTP-bound RAS, whereupon they initiate signaling through the MAP kinase cascade. Prior structural studies of KRAS with RAF have focused on the isolated RAS-binding and cysteine-rich domains of RAF (RBD and CRD, respectively), which interact directly with RAS. Here we describe cryo-EM structures of a KRAS bound to intact BRAF in an autoinhibited state with MEK1 and a 14-3-3 dimer. Analysis of this KRAS/BRAF/MEK1/14-3-3 complex reveals KRAS bound to the RAS-binding domain of BRAF, captured in two orientations. Core autoinhibitory interactions in the complex are unperturbed by binding of KRAS and in vitro activation studies confirm that KRAS binding is insufficient to activate BRAF, absent membrane recruitment. These structures illustrate the separability of binding and activation of BRAF by RAS and suggest stabilization of this pre-activation intermediate as an alternative therapeutic strategy to blocking binding of KRAS.
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Affiliation(s)
- Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Pfizer R&D Center, 3200 Walnut St, Boulder, CO, 80301, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anna Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Byeong-Won Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk, 28160, Republic of Korea
| | - Sehee Oh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA, 01605, USA
| | - Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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6
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Cluet D, Vergier B, Levy NP, Dehau L, Thurman A, Amri I, Spichty M. Titration of apparent in-cellula affinities of protein-protein interactions. Chembiochem 2021; 23:e202100640. [PMID: 34932835 DOI: 10.1002/cbic.202100640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/21/2021] [Indexed: 11/07/2022]
Abstract
A genetic assay permits simultaneous quantification of two interacting proteins and their bound fraction at the single-cell level using flow cytometry. Apparent in-cellula affinities of protein-protein interactions can be extracted from the acquired data through a titration-like analysis. The applicability of this approach is demonstrated on a diverse set of interactions with proteins from different families and organisms and with in-vitro dissociation constants ranging from picomolar to micromolar.
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Affiliation(s)
- David Cluet
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Blandine Vergier
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Nicolas-Pierre Levy
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Lucie Dehau
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Alexandre Thurman
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Ikram Amri
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Martin Spichty
- Laboratoire d'Innovation Moléculaire et Applications, Université de Strasbourg -, Centre National de la Recherche Scientifique, Université de Haute-Alsace, 3 bis rue Alfred Werner, 68057, Mulhouse Cedex, France
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7
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Rezaei Adariani S, Kazemein Jasemi NS, Bazgir F, Wittich C, Amin E, Seidel CAM, Dvorsky R, Ahmadian MR. A comprehensive analysis of RAS-effector interactions reveals interaction hotspots and new binding partners. J Biol Chem 2021; 296:100626. [PMID: 33930461 PMCID: PMC8163975 DOI: 10.1016/j.jbc.2021.100626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
RAS effectors specifically interact with GTP-bound RAS proteins to link extracellular signals to downstream signaling pathways. These interactions rely on two types of domains, called RAS-binding (RB) and RAS association (RA) domains, which share common structural characteristics. Although the molecular nature of RAS-effector interactions is well-studied for some proteins, most of the RA/RB-domain-containing proteins remain largely uncharacterized. Here, we searched through human proteome databases, extracting 41 RA domains in 39 proteins and 16 RB domains in 14 proteins, each of which can specifically select at least one of the 25 members in the RAS family. We next comprehensively investigated the sequence–structure–function relationship between different representatives of the RAS family, including HRAS, RRAS, RALA, RAP1B, RAP2A, RHEB1, and RIT1, with all members of RA domain family proteins (RASSFs) and the RB-domain-containing CRAF. The binding affinity for RAS-effector interactions, determined using fluorescence polarization, broadly ranged between high (0.3 μM) and very low (500 μM) affinities, raising interesting questions about the consequence of these variable binding affinities in the regulation of signaling events. Sequence and structural alignments pointed to two interaction hotspots in the RA/RB domains, consisting of an average of 19 RAS-binding residues. Moreover, we found novel interactions between RRAS1, RIT1, and RALA and RASSF7, RASSF9, and RASSF1, respectively, which were systematically explored in sequence–structure–property relationship analysis, and validated by mutational analysis. These data provide a set of distinct functional properties and putative biological roles that should now be investigated in the cellular context.
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Affiliation(s)
- Soheila Rezaei Adariani
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Farhad Bazgir
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Christoph Wittich
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Ehsan Amin
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany; Medical Faculty, Institute of Neural and Sensory Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Claus A M Seidel
- Chair of Molecular Physical Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Radovan Dvorsky
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany.
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8
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Jurado M, Castaño Ó, Zorzano A. Stochastic modulation evidences a transitory EGF-Ras-ERK MAPK activity induced by PRMT5. Comput Biol Med 2021; 133:104339. [PMID: 33910125 DOI: 10.1016/j.compbiomed.2021.104339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023]
Abstract
The extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) pathway involves a three-step cascade of kinases that transduce signals and promote processes such as cell growth, development, and apoptosis. An aberrant response of this pathway is related to the proliferation of cell diseases and tumors. By using simulation modeling, we document that the protein arginine methyltransferase 5 (PRMT5) modulates the MAPK pathway and thus avoids an aberrant behavior. PRMT5 methylates the Raf kinase, reducing its catalytic activity and thereby, reducing the activation of ERK in time and amplitude. Two minimal computational models of the epidermal growth factor (EGF)-Ras-ERK MAPK pathway influenced by PRMT5 were proposed: a first model in which PRMT5 is activated by EGF and a second one in which PRMT5 is stimulated by the cascade response. The reported results show that PRMT5 reduces the time duration and the expression of the activated ERK in both cases, but only in the first model PRMT5 limits the EGF range that generates an ERK activation. Based on our data, we propose the protein PRMT5 as a regulatory factor to develop strategies to fight against an excessive activity of the MAPK pathway, which could be of use in chronic diseases and cancer.
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Affiliation(s)
- Manuel Jurado
- Biotechnology Ph.D. Programme, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Óscar Castaño
- Electronics and Biomedical Engineering, University of Barcelona, Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain; CIBER in Bioengineering, Biomaterials and Nanomedicine, CIBER-BBN, Madrid, Spain; Bioelectronics Unit and Nanobioengineering Lab., Institute for Nanoscience and Nanotechnology of the University of Barcelona (IN2UB), Barcelona, Spain.
| | - Antonio Zorzano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; CIBER of Diabetes and Associated Metabolic Diseases, Barcelona, Spain; Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
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9
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Cui Y, Ma L, Schacke S, Yin JC, Hsueh YP, Jin H, Morrison H. Merlin cooperates with neurofibromin and Spred1 to suppress the Ras-Erk pathway. Hum Mol Genet 2020; 29:3793-3806. [PMID: 33331896 DOI: 10.1093/hmg/ddaa263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
The Ras-Erk pathway is frequently overactivated in human tumors. Neurofibromatosis types 1 and 2 (NF1, NF2) are characterized by multiple tumors of Schwann cell origin. The NF1 tumor suppressor neurofibromin is a principal Ras-GAP accelerating Ras inactivation, whereas the NF2 tumor suppressor merlin is a scaffold protein coordinating multiple signaling pathways. We have previously reported that merlin interacts with Ras and p120RasGAP. Here, we show that merlin can also interact with the neurofibromin/Spred1 complex via merlin-binding sites present on both proteins. Further, merlin can directly bind to the Ras-binding domain (RBD) and the kinase domain (KiD) of Raf1. As the third component of the neurofibromin/Spred1 complex, merlin cannot increase the Ras-GAP activity; rather, it blocks Ras binding to Raf1 by functioning as a 'selective Ras barrier'. Merlin-deficient Schwann cells require the Ras-Erk pathway activity for proliferation. Accordingly, suppression of the Ras-Erk pathway likely contributes to merlin's tumor suppressor activity. Taken together, our results, and studies by others, support targeting or co-targeting of this pathway as a therapy for NF2 inactivation-related tumors.
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Affiliation(s)
- Yan Cui
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Lin Ma
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.,College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Stephan Schacke
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Jiani C Yin
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou 310016, China
| | - Helen Morrison
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Germany
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10
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Yuan J, Dong X, Yap J, Hu J. The MAPK and AMPK signalings: interplay and implication in targeted cancer therapy. J Hematol Oncol 2020; 13:113. [PMID: 32807225 PMCID: PMC7433213 DOI: 10.1186/s13045-020-00949-4] [Citation(s) in RCA: 235] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer is characterized as a complex disease caused by coordinated alterations of multiple signaling pathways. The Ras/RAF/MEK/ERK (MAPK) signaling is one of the best-defined pathways in cancer biology, and its hyperactivation is responsible for over 40% human cancer cases. To drive carcinogenesis, this signaling promotes cellular overgrowth by turning on proliferative genes, and simultaneously enables cells to overcome metabolic stress by inhibiting AMPK signaling, a key singular node of cellular metabolism. Recent studies have shown that AMPK signaling can also reversibly regulate hyperactive MAPK signaling in cancer cells by phosphorylating its key components, RAF/KSR family kinases, which affects not only carcinogenesis but also the outcomes of targeted cancer therapies against the MAPK signaling. In this review, we will summarize the current proceedings of how MAPK-AMPK signalings interplay with each other in cancer biology, as well as its implications in clinic cancer treatment with MAPK inhibition and AMPK modulators, and discuss the exploitation of combinatory therapies targeting both MAPK and AMPK as a novel therapeutic intervention.
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Affiliation(s)
- Jimin Yuan
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
- Geriatric Department, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
| | - Xiaoduo Dong
- Shenzhen People's Hospital, 1017 Dongmen North Road, Shenzhen, 518020, China
| | - Jiajun Yap
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Jiancheng Hu
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.
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11
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Travers T, López CA, Agamasu C, Hettige JJ, Messing S, García AE, Stephen AG, Gnanakaran S. Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD. Biophys J 2020; 119:525-538. [PMID: 32649863 PMCID: PMC7399501 DOI: 10.1016/j.bpj.2020.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 11/25/2022] Open
Abstract
CRAF activation requires binding to membrane-anchored and active GTP-bound RAS. Whereas its RAS-binding domain (RBD) contains the main binding interface to the RAS G domain, its cysteine-rich domain (CRD) is responsible for association to anionic lipid-rich membranes. Both RAF domains are connected by a short linker, and it remains unclear if the two domains act independently or if one domain can impact the function of the other. Here, we used a combination of coarse-grained and all-atom molecular dynamics simulations of a CRAF RBD-CRD construct to investigate the dynamics of the RBD when it is tethered to CRD that is anchored to a POPC:POPS model membrane. First, we show that the RBD positioning is very dynamic with a preferential localization near the membrane surface. Next, we show that membrane-localized RBD has its RAS-binding interface mostly inaccessible because of its proximity to the membrane. Several positively charged residues in this interface were identified from simulations as important for driving RBD association to the membrane. Surface plasmon resonance (SPR) measurements confirmed that mutations of these RBD residues reduced the liposome partitioning of RBD-CRD. Last, simulations indicated that the presence of RBD near the membrane led to a local enrichment of anionic lipids that could potentially enhance the membrane affinity of the entire RBD-CRD construct. This was supported by SPR measurements that showed stronger liposome partitioning of RBD-CRD relative to CRD alone. These findings thus suggest that the RBD and CRD have synergistic effects on their membrane dynamics, with CRD bringing RBD closer to the membrane that impacts its accessibility to RAS and with RBD causing local anionic lipid enrichment that enhances the overall affinity between the membrane and RBD-CRD. These mechanisms have potential implications on the order of events of the interactions between RAS and CRAF at the membrane.
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Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico
| | - Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | | | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico.
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12
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Cooley R, Kara N, Hui NS, Tart J, Roustan C, George R, Hancock DC, Binkowski BF, Wood KV, Ismail M, Downward J. Development of a cell-free split-luciferase biochemical assay as a tool for screening for inhibitors of challenging protein-protein interaction targets. Wellcome Open Res 2020. [DOI: 10.12688/wellcomeopenres.15675.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Targeting the interaction of proteins with weak binding affinities or low solubility represents a particular challenge for drug screening. The NanoLuc ® Binary Technology (NanoBiT ®) was originally developed to detect protein-protein interactions in live mammalian cells. Here we report the successful translation of the NanoBit cellular assay into a biochemical, cell-free format using mammalian cell lysates. We show that the assay is suitable for the detection of both strong and weak protein interactions such as those involving the binding of RAS oncoproteins to either RAF or phosphoinositide 3-kinase (PI3K) effectors respectively, and that it is also effective for the study of poorly soluble protein domains such as the RAS binding domain of PI3K. Furthermore, the RAS interaction assay is sensitive and responds to both strong and weak RAS inhibitors. Our data show that the assay is robust, reproducible, cost-effective, and can be adapted for small and large-scale screening approaches. The NanoBit Biochemical Assay offers an attractive tool for drug screening against challenging protein-protein interaction targets, including the interaction of RAS with PI3K.
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13
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Li L, Möbitz S, Winter R. Characterization of the Spatial Organization of Raf Isoforms Interacting with K-Ras4B in the Lipid Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5944-5953. [PMID: 32390436 DOI: 10.1021/acs.langmuir.0c00770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Activation of Raf kinases by the membrane-anchored protein K-Ras4B is a key step of cellular signal regulation. As a predominant variant of the Ras family, K-Ras4B has been considered to be a major drug target in cancer therapy. Therefore, an integrated study of Raf interaction with membrane-associated K-Ras4B is essential. While the Ras-binding domain (RBD) of Raf contains the main binding interface to K-Ras4B, its cysteine-rich domain (CRD) is thought to be responsible for its association with the membrane interface. We applied time-lapse tapping-mode atomic force microscopy to visualize and characterize the interaction of these binding motifs of A-, B-, and C-Raf isoforms with K-Ras4B in a raft-like anionic model biomembrane. However, we found that the RBDs of the Raf isomers are readily recruited to K-Ras4B nanoclusters in the lipid membrane, with different efficiencies. Unexpectedly and different from A-Raf-RBD, B- and C-Raf-RBD are able to bind markedly also directly to the lipid membrane. We also found that Raf-RBD-CRD is readily recruited to the K-Ras4B forming nanoclusters in the fluid membrane phase, with the CRD domains binding to the lipid interface. The K-Ras4B-nanoclusters are likely to enhance Raf binding and activate signaling by enriching the Raf proteins and facilitating formation of Raf dimers. Interestingly, A-, B-, and C-Raf-RBD-CRD are also able to bind directly to the heterogeneous membrane surrounding the K-Ras4B nanoclusters, which could potentially enhance the overall affinity to K-Ras4B in a Raf-isoform-dependent manner. Overall, these results provide new insights into the spatial organization of the membrane-associated Raf-Ras signaling module for the various Raf isoforms, which is important for understanding the activation of Raf kinases and required for the development of drugs against cancers through targeting Raf-Ras interactions.
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Affiliation(s)
- Lei Li
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Simone Möbitz
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
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14
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Nussinov R, Jang H, Zhang M, Tsai CJ, Sablina AA. The Mystery of Rap1 Suppression of Oncogenic Ras. Trends Cancer 2020; 6:369-379. [PMID: 32249186 PMCID: PMC7211489 DOI: 10.1016/j.trecan.2020.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
Abstract
Decades ago, Rap1, a small GTPase very similar to Ras, was observed to suppress oncogenic Ras phenotype, reverting its transformation. The proposed reason, persisting since, has been competition between Ras and Rap1 for a common target. Yet, none was found. There was also Rap1's puzzling suppression of Raf-1 versus activation of BRAF. Reemerging interest in Rap1 envisages capturing its Ras suppression action by inhibitors. Here, we review the literature and resolve the enigma. In vivo oncogenic Ras exists in isoform-distinct nanoclusters. The presence of Rap1 within the nanoclusters reduces the number of the clustered oncogenic Ras molecules, thus suppressing Raf-1 activation and mitogen-activated protein kinase (MAPK) signaling. Nanoclustering suggests that Rap1 suppression is Ras isoform dependent. Altogether, a potent Rap1-like inhibitor appears unlikely.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Anna A Sablina
- VIB Center for the Biology of Disease and KU Leuven Department of Oncology, Leuven Cancer Institute, Leuven, Belgium
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15
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Cluet D, Amri I, Vergier B, Léault J, Audibert A, Grosjean C, Calabrési D, Spichty M. A Quantitative Tri-fluorescent Yeast Two-hybrid System: From Flow Cytometry to In cellula Affinities. Mol Cell Proteomics 2020; 19:701-715. [PMID: 32015065 PMCID: PMC7124468 DOI: 10.1074/mcp.tir119.001692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/31/2020] [Indexed: 12/14/2022] Open
Abstract
We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pm to 17 μm After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.
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Affiliation(s)
- David Cluet
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Ikram Amri
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Blandine Vergier
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Jérémie Léault
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Astrid Audibert
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Clémence Grosjean
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Dylan Calabrési
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Martin Spichty
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France.
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16
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Cooley R, Kara N, Hui NS, Tart J, Roustan C, George R, Hancock DC, Binkowski BF, Wood KV, Ismail M, Downward J. Development of a cell-free split-luciferase biochemical assay as a tool for screening for inhibitors of challenging protein-protein interaction targets. Wellcome Open Res 2020; 5:20. [PMID: 32587898 PMCID: PMC7308888 DOI: 10.12688/wellcomeopenres.15675.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2020] [Indexed: 12/14/2022] Open
Abstract
Targeting the interaction of proteins with weak binding affinities or low solubility represents a particular challenge for drug screening. The NanoLuc â ® Binary Technology (NanoBiT â ®) was originally developed to detect protein-protein interactions in live mammalian cells. Here we report the successful translation of the NanoBit cellular assay into a biochemical, cell-free format using mammalian cell lysates. We show that the assay is suitable for the detection of both strong and weak protein interactions such as those involving the binding of RAS oncoproteins to either RAF or phosphoinositide 3-kinase (PI3K) effectors respectively, and that it is also effective for the study of poorly soluble protein domains such as the RAS binding domain of PI3K. Furthermore, the RAS interaction assay is sensitive and responds to both strong and weak RAS inhibitors. Our data show that the assay is robust, reproducible, cost-effective, and can be adapted for small and large-scale screening approaches. The NanoBit Biochemical Assay offers an attractive tool for drug screening against challenging protein-protein interaction targets, including the interaction of RAS with PI3K.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Julian Downward
- Francis Crick Institute, London, UK
- Institute of Cancer Research, UK, London, UK
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17
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Degirmenci U, Wang M, Hu J. Targeting Aberrant RAS/RAF/MEK/ERK Signaling for Cancer Therapy. Cells 2020; 9:E198. [PMID: 31941155 PMCID: PMC7017232 DOI: 10.3390/cells9010198] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/29/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
The RAS/RAF/MEK/ERK (MAPK) signaling cascade is essential for cell inter- and intra-cellular communication, which regulates fundamental cell functions such as growth, survival, and differentiation. The MAPK pathway also integrates signals from complex intracellular networks in performing cellular functions. Despite the initial discovery of the core elements of the MAPK pathways nearly four decades ago, additional findings continue to make a thorough understanding of the molecular mechanisms involved in the regulation of this pathway challenging. Considerable effort has been focused on the regulation of RAF, especially after the discovery of drug resistance and paradoxical activation upon inhibitor binding to the kinase. RAF activity is regulated by phosphorylation and conformation-dependent regulation, including auto-inhibition and dimerization. In this review, we summarize the recent major findings in the study of the RAS/RAF/MEK/ERK signaling cascade, particularly with respect to the impact on clinical cancer therapy.
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Affiliation(s)
- Ufuk Degirmenci
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Mei Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
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18
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Terrell EM, Durrant DE, Ritt DA, Sealover NE, Sheffels E, Spencer-Smith R, Esposito D, Zhou Y, Hancock JF, Kortum RL, Morrison DK. Distinct Binding Preferences between Ras and Raf Family Members and the Impact on Oncogenic Ras Signaling. Mol Cell 2019; 76:872-884.e5. [PMID: 31606273 PMCID: PMC7001861 DOI: 10.1016/j.molcel.2019.09.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 07/22/2019] [Accepted: 09/05/2019] [Indexed: 12/17/2022]
Abstract
The Ras GTPases are frequently mutated in human cancer, and, although the Raf kinases are essential effectors of Ras signaling, the tumorigenic properties of specific Ras-Raf complexes are not well characterized. Here, we examine the ability of individual Ras and Raf proteins to interact in live cells using bioluminescence resonance energy transfer (BRET) technology. We find that C-Raf binds all mutant Ras proteins with high affinity, whereas B-Raf exhibits a striking preference for mutant K-Ras. This selectivity is mediated by the acidic, N-terminal segment of B-Raf and requires the K-Ras polybasic region for high-affinity binding. In addition, we find that C-Raf is critical for mutant H-Ras-driven signaling and that events stabilizing B-Raf/C-Raf dimerization, such as Raf inhibitor treatment or certain B-Raf mutations, can allow mutant H-Ras to engage B-Raf with increased affinity to promote tumorigenesis, thus revealing a previously unappreciated role for C-Raf in potentiating B-Raf function.
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Affiliation(s)
- Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - David E Durrant
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Daniel A Ritt
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Nancy E Sealover
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Erin Sheffels
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Russell Spencer-Smith
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Dominic Esposito
- NCI-Ras Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Robert L Kortum
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA.
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19
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Che Y, Siprashvili Z, Kovalski JR, Jiang T, Wozniak G, Elcavage L, Khavari PA. KRAS regulation by small non-coding RNAs and SNARE proteins. Nat Commun 2019; 10:5118. [PMID: 31712554 PMCID: PMC6848142 DOI: 10.1038/s41467-019-13106-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 10/13/2019] [Indexed: 12/30/2022] Open
Abstract
KRAS receives and relays signals at the plasma membrane (PM) where it transmits extracellular growth factor signals to downstream effectors. SNORD50A/B were recently found to bind KRAS and inhibit its tumorigenic action by unknown mechanisms. KRAS proximity protein labeling was therefore undertaken in SNORD50A/B wild-type and knockout cells, revealing that SNORD50A/B RNAs shape the composition of proteins proximal to KRAS, notably by inhibiting KRAS proximity to the SNARE vesicular transport proteins SNAP23, SNAP29, and VAMP3. To remain enriched on the PM, KRAS undergoes cycles of endocytosis, solubilization, and vesicular transport to the PM. Here we report that SNAREs are essential for the final step of this process, with KRAS localization to the PM facilitated by SNAREs but antagonized by SNORD50A/B. Antagonism between SNORD50A/B RNAs and specific SNARE proteins thus controls KRAS localization, signaling, and tumorigenesis, and disrupting SNARE-enabled KRAS function represents a potential therapeutic opportunity in KRAS-driven cancer.
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Affiliation(s)
- Yonglu Che
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Joanna R Kovalski
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tiffany Jiang
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Glenn Wozniak
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Lara Elcavage
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA.
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA.
- VA Palo Alto Healthcare System, Palo Alto, CA, 94304, USA.
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20
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Surve SV, Myers PJ, Clayton SA, Watkins SC, Lazzara MJ, Sorkin A. Localization dynamics of endogenous fluorescently labeled RAF1 in EGF-stimulated cells. Mol Biol Cell 2019; 30:506-523. [PMID: 30586319 PMCID: PMC6594441 DOI: 10.1091/mbc.e18-08-0512] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Activation of the epidermal growth factor (EGF) receptor (EGFR) at the cell surface initiates signaling through the RAS-RAF-MAPK/ERK1/2 pathway and receptor endocytosis. Whether this signaling continues from endosomes remains unclear, because RAS is predominantly located on the plasma membrane, and the localization of endogenous RAF kinases, downstream effectors of RAS, is not defined. To examine RAF localization, we labeled endogenous RAF1 with mVenus using gene editing. From 10 to 15% of RAF1-mVenus (<2000 molecules/cell), which was initially entirely cytosolic, transiently translocated to the plasma membrane after EGF stimulation. Following an early burst of translocation, the membrane-associated RAF1-mVenus was undetectable by microscopy or subcellular fractionation, and this pool was estimated to be <200 molecules per cell. In contrast, persistent EGF-dependent translocation of RAF1-mVenus to the plasma membrane was driven by the RAF inhibitor sorafenib, which increases the affinity of Ras-GTP:RAF1 interactions. RAF1-mVenus was not found in EGFR-containing endosomes under any conditions. Computational modeling of RAF1 dynamics revealed that RAF1 membrane abundance is controlled most prominently by association and dissociation rates from RAS-GTP and by RAS-GTP concentration. The model further suggested that the relatively protracted activation of the RAF-MEK1/2-ERK1/2 module, in comparison with RAF1 membrane localization, may involve multiple rounds of cytosolic RAF1 rebinding to active RAS at the membrane.
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Affiliation(s)
- Sachin V Surve
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Paul J Myers
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904
| | - Samantha A Clayton
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Matthew J Lazzara
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904.,Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904
| | - Alexander Sorkin
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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21
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Abstract
Most proteins associate with other proteins to function, forming complexes that are central to almost all physiological processes. Determining the structures of these complexes and understanding how they associate are problems of fundamental importance. Using long-timescale molecular dynamics simulations, some performed using a new enhanced sampling method, we observed spontaneous association and dissociation of five protein–protein systems to and from their experimentally determined native complexes. By analyzing the simulations of these five systems, which include members of diverse structural and functional classes, we are able to draw general mechanistic conclusions about protein association. Despite the biological importance of protein–protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein–protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)–based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein–protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.
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22
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Intensiometric biosensors visualize the activity of multiple small GTPases in vivo. Nat Commun 2019; 10:211. [PMID: 30643148 PMCID: PMC6331645 DOI: 10.1038/s41467-018-08217-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/22/2018] [Indexed: 01/21/2023] Open
Abstract
Ras and Rho small GTPases are critical for numerous cellular processes including cell division, migration, and intercellular communication. Despite extensive efforts to visualize the spatiotemporal activity of these proteins, achieving the sensitivity and dynamic range necessary for in vivo application has been challenging. Here, we present highly sensitive intensiometric small GTPase biosensors visualizing the activity of multiple small GTPases in single cells in vivo. Red-shifted sensors combined with blue light-controllable optogenetic modules achieved simultaneous monitoring and manipulation of protein activities in a highly spatiotemporal manner. Our biosensors revealed spatial dynamics of Cdc42 and Ras activities upon structural plasticity of single dendritic spines, as well as a broad range of subcellular Ras activities in the brains of freely behaving mice. Thus, these intensiometric small GTPase sensors enable the spatiotemporal dissection of complex protein signaling networks in live animals. FRET sensors hardly achieve visualization of spatiotemporal dynamics of protein activity in vivo. Here the authors present intensiometric small GTPase biosensors based on dimerization-dependent fluorescent proteins that enable monitoring of activity of small GTPases in the brains of behaving mice at a single spine resolution.
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23
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Structural snapshots of RAF kinase interactions. Biochem Soc Trans 2018; 46:1393-1406. [PMID: 30381334 DOI: 10.1042/bst20170528] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023]
Abstract
RAF (rapidly accelerated fibrosarcoma) Ser/Thr kinases (ARAF, BRAF, and CRAF) link the RAS (rat sarcoma) protein family with the MAPK (mitogen-activated protein kinase) pathway and control cell growth, differentiation, development, aging, and tumorigenesis. Their activity is specifically modulated by protein-protein interactions, post-translational modifications, and conformational changes in specific spatiotemporal patterns via various upstream regulators, including the kinases, phosphatase, GTPases, and scaffold and modulator proteins. Dephosphorylation of Ser-259 (CRAF numbering) and dissociation of 14-3-3 release the RAF regulatory domains RAS-binding domain and cysteine-rich domain for interaction with RAS-GTP and membrane lipids. This, in turn, results in RAF phosphorylation at Ser-621 and 14-3-3 reassociation, followed by its dimerization and ultimately substrate binding and phosphorylation. This review focuses on structural understanding of how distinct binding partners trigger a cascade of molecular events that induces RAF kinase activation.
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24
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Cope N, Candelora C, Wong K, Kumar S, Nan H, Grasso M, Novak B, Li Y, Marmorstein R, Wang Z. Mechanism of BRAF Activation through Biochemical Characterization of the Recombinant Full-Length Protein. Chembiochem 2018; 19:1988-1997. [PMID: 29992710 DOI: 10.1002/cbic.201800359] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Indexed: 12/17/2022]
Abstract
BRAF kinase plays an important role in mitogen-activated protein kinase (MAPK) signaling and harbors activating mutations in about half of melanomas and in a smaller percentage in many other cancers. Despite its importance, few in vitro studies have been performed to characterize the biochemical properties of full-length BRAF. Herein, a strategy to generate an active, intact form of BRAF protein suitable for in vitro enzyme kinetics is described. It is shown that purified, intact BRAF protein autophosphorylates the kinase activation loop and this can be enhanced by binding the MEK protein substrate through an allosteric mechanism. These studies provide in vitro evidence that BRAF selectively binds to active RAS and that the BRAF/CRAF heterodimer is the most active form, relative to their respective homodimers. Full-length BRAF analysis with small-molecule BRAF inhibitors shows that two drugs, dabrafenib and vemurafenib, can modestly enhance kinase activity of BRAF at low concentration. Taken together, this characterization of intact BRAF contributes to a framework for understanding its role in cell signaling.
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Affiliation(s)
- Nicholas Cope
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Christine Candelora
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Kenneth Wong
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Sujeet Kumar
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Haihan Nan
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Michael Grasso
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Borna Novak
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
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25
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Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling. Cell Syst 2018; 7:161-179.e14. [PMID: 30007540 DOI: 10.1016/j.cels.2018.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/09/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022]
Abstract
Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can be chosen. We built a next-generation mechanistic dynamic model to analyze combinations of structurally different RAF inhibitors, which can efficiently suppress MEK/ERK signaling. This rule-based model of the RAS/ERK pathway integrates thermodynamics and kinetics of drug-protein interactions, structural elements, posttranslational modifications, and cell mutational status as model rules to predict RAF inhibitor combinations for inhibiting ERK activity in oncogenic RAS and/or BRAFV600E backgrounds. Predicted synergistic inhibition of ERK signaling was corroborated by experiments in mutant NRAS, HRAS, and BRAFV600E cells, and inhibition of oncogenic RAS signaling was associated with reduced cell proliferation and colony formation.
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26
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Travers T, López CA, Van QN, Neale C, Tonelli M, Stephen AG, Gnanakaran S. Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain. Sci Rep 2018; 8:8461. [PMID: 29855542 PMCID: PMC5981303 DOI: 10.1038/s41598-018-26832-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/18/2018] [Indexed: 01/14/2023] Open
Abstract
Activation of RAF kinase involves the association of its RAS-binding domain (RBD) and cysteine-rich domain (CRD) with membrane-anchored RAS. However, the overall architecture of the RAS/RBD/CRD ternary complex and the orientations of its constituent domains at the membrane remain unclear. Here, we have combined all-atom and coarse-grained molecular dynamics (MD) simulations with experimental data to construct and validate a model of membrane-anchored CRD, and used this as a basis to explore models of membrane-anchored RAS/RBD/CRD complex. First, simulations of the CRD revealed that it anchors to the membrane via insertion of its two hydrophobic loops, which is consistent with our NMR measurements of CRD bound to nanodiscs. Simulations of the CRD in the context of membrane-anchored RAS/RBD then show how CRD association with either RAS or RBD could play an unexpected role in guiding the membrane orientations of RAS/RBD. This finding has implications for the formation of RAS-RAS dimers, as different membrane orientations of RAS expose distinct putative dimerization interfaces.
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Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, United States
| | - Chris Neale
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Marco Tonelli
- National Magnetic Resource Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.
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27
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Kauke MJ, Tisdale AW, Kelly RL, Braun CJ, Hemann MT, Wittrup KD. A Raf-Competitive K-Ras Binder Can Fail to Functionally Antagonize Signaling. Mol Cancer Ther 2018; 17:1773-1780. [PMID: 29720559 DOI: 10.1158/1535-7163.mct-17-0645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 11/15/2017] [Accepted: 04/23/2018] [Indexed: 11/16/2022]
Abstract
Mutated in approximately 30% of human cancers, Ras GTPases are the most common drivers of oncogenesis and render tumors unresponsive to many standard therapies. Despite decades of research, no drugs directly targeting Ras are currently available. We have previously characterized a small protein antagonist of K-Ras, R11.1.6, and demonstrated its direct competition with Raf for Ras binding. Here we evaluate the effects of R11.1.6 on Ras signaling and cellular proliferation in a panel of human cancer cell lines. Through lentiviral transduction, we generated cell lines that constitutively or through induction with doxycycline express R11.1.6 or a control protein YW1 and show specific binding by R11.1.6 to endogenous Ras through microscopy and co-immunoprecipitation experiments. Genetically encoded intracellular expression of this high-affinity Ras antagonist, however, fails to measurably disrupt signaling through either the MAPK or PI3K pathway. Consistently, cellular proliferation was unaffected as well. To understand this lack of signaling inhibition, we quantified the number of molecules of R11.1.6 expressed by the inducible cell lines and developed a simple mathematical model describing the competitive binding of Ras by R11.1.6 and Raf. This model supports a potential mechanism for the lack of biological effects that we observed, suggesting stoichiometric and thermodynamic barriers that should be overcome in pharmacologic efforts to directly compete with downstream effector proteins localized to membranes at very high effective concentrations. Mol Cancer Ther; 17(8); 1773-80. ©2018 AACR.
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Affiliation(s)
- Monique J Kauke
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Alison W Tisdale
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ryan L Kelly
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christian J Braun
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael T Hemann
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - K Dane Wittrup
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. .,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
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28
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Pfeiffer V, Götz R, Camarero G, Heinsen H, Blum R, Rapp UR. Impaired neuronal maturation of hippocampal neural progenitor cells in mice lacking CRAF. PLoS One 2018; 13:e0192067. [PMID: 29590115 PMCID: PMC5873938 DOI: 10.1371/journal.pone.0192067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 01/16/2018] [Indexed: 11/19/2022] Open
Abstract
RAF kinases are major constituents of the mitogen activated signaling pathway, regulating cell proliferation, differentiation and cell survival of many cell types, including neurons. In mammals, the family of RAF proteins consists of three members, ARAF, BRAF, and CRAF. Ablation of CRAF kinase in inbred mouse strains causes major developmental defects during fetal growth and embryonic or perinatal lethality. Heterozygous germline mutations in CRAF result in Noonan syndrome, which is characterized by neurocognitive impairment that may involve hippocampal physiology. The role of CRAF signaling during hippocampal development and generation of new postnatal hippocampal granule neurons has not been examined and may provide novel insight into the cause of hippocampal dysfunction in Noonan syndrome. In this study, by crossing CRAF-deficiency to CD-1 outbred mice, a CRAF mouse model was established which enabled us to investigate the interplay of neural progenitor proliferation and postmitotic differentiation during adult neurogenesis in the hippocampus. Albeit the general morphology of the hippocampus was unchanged, CRAF-deficient mice displayed smaller granule cell layer (GCL) volume at postnatal day 30 (P30). In CRAF-deficient mice a substantial number of abnormal, chromophilic, fast dividing cells were found in the subgranular zone (SGZ) and hilus of the dentate gyrus (DG), indicating that CRAF signaling contributes to hippocampal neural progenitor proliferation. CRAF-deficient neural progenitor cells showed an increased cell death rate and reduced neuronal maturation. These results indicate that CRAF function affects postmitotic neural cell differentiation and points to a critical role of CRAF-dependent growth factor signaling pathway in the postmitotic development of adult-born neurons.
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Affiliation(s)
- Verena Pfeiffer
- University of Würzburg, Institute of Anatomy and Cell Biology, Koellikerstraße 6, Würzburg, Germany
- University of Würzburg, Institute for Medical Radiation and Cell Research (MSZ), Versbacher Strasse 5, Würzburg, Germany
- * E-mail:
| | - Rudolf Götz
- University of Würzburg, Institute for Medical Radiation and Cell Research (MSZ), Versbacher Strasse 5, Würzburg, Germany
- Institute for Clinical Neurobiology, University Hospital Würzburg, Versbacher Strasse 5, Würzburg, Germany
| | - Guadelupe Camarero
- University of Würzburg, Institute for Medical Radiation and Cell Research (MSZ), Versbacher Strasse 5, Würzburg, Germany
| | - Helmut Heinsen
- University of Würzburg, Department of Psychiatry, Psychosomatics and Psychotherapy, Margarethe-Höppel-Platz 1, Würzburg, Germany
- Universidade de Sao Paulo Faculdade de Medicina, Pathology—LIM 44 Sao Paulo, SP, Brazil
| | - Robert Blum
- Institute for Clinical Neurobiology, University Hospital Würzburg, Versbacher Strasse 5, Würzburg, Germany
| | - Ulf Rüdiger Rapp
- University of Würzburg, Institute for Medical Radiation and Cell Research (MSZ), Versbacher Strasse 5, Würzburg, Germany
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Parkstr.1, Bad Nauheim, Germany
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29
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Heard JJ, Phung I, Potes MI, Tamanoi F. An oncogenic mutant of RHEB, RHEB Y35N, exhibits an altered interaction with BRAF resulting in cancer transformation. BMC Cancer 2018; 18:69. [PMID: 29320991 PMCID: PMC5763582 DOI: 10.1186/s12885-017-3938-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022] Open
Abstract
Background RHEB is a unique member of the RAS superfamily of small GTPases expressed in all tissues and conserved from yeast to humans. Early studies on RHEB indicated a possible RHEB-RAF interaction, but this has not been fully explored. Recent work on cancer genome databases has revealed a reoccurring mutation in RHEB at the Tyr35 position, and a recent study points to the oncogenic potential of this mutant that involves activation of RAF/MEK/ERK signaling. These developments prompted us to reassess the significance of RHEB effect on RAF, and to compare mutant and wild type RHEB. Methods To study RHEB-RAF interaction, and the effect of the Y35N mutation on this interaction, we used transfection, immunoprecipitation, and Western blotting techniques. We generated cell lines stably expressing RHEB WT, RHEB Y35N, and KRAS G12V, and monitored cellular transforming properties through cell proliferation, anchorage independent growth, cell cycle analysis, and foci formation assays. Results We observe a strong interaction between RHEB and BRAF, but not with CRAF. This interaction is dependent on an intact RHEB effector domain and RHEB-GTP loading status. RHEB overexpression decreases RAF activation of the RAF/MEK/ERK pathway and RHEB knockdown results in an increase in RAF/MEK/ERK activation. RHEB Y35N mutation has decreased interaction with BRAF, and RHEB Y35N cells exhibit greater BRAF/CRAF heterodimerization resulting in increased RAF/MEK/ERK signaling. This leads to cancer transformation of RHEB Y35N stably expressing cell lines, similar to KRAS G12 V expressing cell lines. Conclusions RHEB interaction with BRAF is crucial for inhibiting RAF/MEK/ERK signaling. The RHEB Y35N mutant sustains RAF/MEK/ERK signaling due to a decreased interaction with BRAF, leading to increased BRAF/CRAF heterodimerization. RHEB Y35N expressing cells undergo cancer transformation due to decreased interaction between RHEB and BRAF resulting in overactive RAF/MEK/ERK signaling. Taken together with the previously established function of RHEB to activate mTORC1 signaling, it appears that RHEB performs a dual function; one is to suppress the RAF/MEK/ERK signaling and the other is to activate mTORC1 signaling. Electronic supplementary material The online version of this article (10.1186/s12885-017-3938-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeffrey J Heard
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Sciences Bldg, 609 Charles E. Young Dr. East, Los Angeles, CA, 90095-1489, USA
| | - Ivy Phung
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Sciences Bldg, 609 Charles E. Young Dr. East, Los Angeles, CA, 90095-1489, USA
| | - Mark I Potes
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Sciences Bldg, 609 Charles E. Young Dr. East, Los Angeles, CA, 90095-1489, USA
| | - Fuyuhiko Tamanoi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Sciences Bldg, 609 Charles E. Young Dr. East, Los Angeles, CA, 90095-1489, USA. .,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.
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30
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Jing H, Zhang X, Wisner SA, Chen X, Spiegelman NA, Linder ME, Lin H. SIRT2 and lysine fatty acylation regulate the transforming activity of K-Ras4a. eLife 2017; 6:32436. [PMID: 29239724 PMCID: PMC5745086 DOI: 10.7554/elife.32436] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/13/2017] [Indexed: 12/30/2022] Open
Abstract
Ras proteins play vital roles in numerous biological processes and Ras mutations are found in many human tumors. Understanding how Ras proteins are regulated is important for elucidating cell signaling pathways and identifying new targets for treating human diseases. Here we report that one of the K-Ras splice variants, K-Ras4a, is subject to lysine fatty acylation, a previously under-studied protein post-translational modification. Sirtuin 2 (SIRT2), one of the mammalian nicotinamide adenine dinucleotide (NAD)-dependent lysine deacylases, catalyzes the removal of fatty acylation from K-Ras4a. We further demonstrate that SIRT2-mediated lysine defatty-acylation promotes endomembrane localization of K-Ras4a, enhances its interaction with A-Raf, and thus promotes cellular transformation. Our study identifies lysine fatty acylation as a previously unknown regulatory mechanism for the Ras family of GTPases that is distinct from cysteine fatty acylation. These findings highlight the biological significance of lysine fatty acylation and sirtuin-catalyzed protein lysine defatty-acylation.
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Affiliation(s)
- Hui Jing
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Xiaoyu Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Stephanie A Wisner
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Xiao Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Nicole A Spiegelman
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Maurine E Linder
- Department of Molecular Medicine, Cornell University College of Veterinary Medicine, Ithaca, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States.,Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
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31
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Lim CS, Wen C, Sheng Y, Wang G, Zhou Z, Wang S, Zhang H, Ye A, Zhu JJ. Piconewton-Scale Analysis of Ras-BRaf Signal Transduction with Single-Molecule Force Spectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:10.1002/smll.201701972. [PMID: 28809097 PMCID: PMC6272124 DOI: 10.1002/smll.201701972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Intermolecular interactions dominate the behavior of signal transduction in various physiological and pathological cell processes, yet assessing these interactions remains a challenging task. Here, this study reports a single-molecule force spectroscopic method that enables functional delineation of two interaction sites (≈35 pN and ≈90 pN) between signaling effectors Ras and BRaf in the canonical mitogen-activated protein kinase (MAPK) pathway. This analysis reveals mutations on BRaf at Q257 and A246, two sites frequently linked to cardio-faciocutaneous syndrome, result in ≈10-30 pN alterations in RasBRaf intermolecular binding force. The magnitude of changes in RasBRaf binding force correlates with the size of alterations in protein affinity and in α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-sensitive glutamate receptor (-R)-mediated synaptic transmission in neurons expressing replacement BRaf mutants, and predicts the extent of learning impairments in animals expressing replacement BRaf mutants. These results establish single-molecule force spectroscopy as an effective platform for evaluating the piconewton-level interaction of signaling molecules and predicting the behavior outcome of signal transduction.
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Affiliation(s)
- Chae-Seok Lim
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Cheng Wen
- School of Electronic Engineering and Computer Science, Peking University, Beijing, 100871, China
| | - Yanghui Sheng
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Undergraduate Class of 2011, Yuanpei Honors College, Peking University, Beijing, 100871, China
- Institute of Molecular Medicine, Peking University, Beijing, 100871, China
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Guangfu Wang
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Zhuan Zhou
- Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Shiqiang Wang
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Huaye Zhang
- Department of Microbiology and Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Anpei Ye
- School of Electronic Engineering and Computer Science, Peking University, Beijing, 100871, China
| | - J Julius Zhu
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525, EN, Nijmegen, Netherlands
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32
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Nakhaeizadeh H, Amin E, Nakhaei-Rad S, Dvorsky R, Ahmadian MR. The RAS-Effector Interface: Isoform-Specific Differences in the Effector Binding Regions. PLoS One 2016; 11:e0167145. [PMID: 27936046 PMCID: PMC5147862 DOI: 10.1371/journal.pone.0167145] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/09/2016] [Indexed: 12/31/2022] Open
Abstract
RAS effectors specifically interact with the GTP-bound form of RAS in response to extracellular signals and link them to downstream signaling pathways. The molecular nature of effector interaction by RAS is well-studied but yet still incompletely understood in a comprehensive and systematic way. Here, structure-function relationships in the interaction between different RAS proteins and various effectors were investigated in detail by combining our in vitro data with in silico data. Equilibrium dissociation constants were determined for the binding of HRAS, KRAS, NRAS, RRAS1 and RRAS2 to both the RAS binding (RB) domain of CRAF and PI3Kα, and the RAS association (RA) domain of RASSF5, RALGDS and PLCε, respectively, using fluorescence polarization. An interaction matrix, constructed on the basis of available crystal structures, allowed identification of hotspots as critical determinants for RAS-effector interaction. New insights provided by this study are the dissection of the identified hotspots in five distinct regions (R1 to R5) in spite of high sequence variability not only between, but also within, RB/RA domain-containing effectors proteins. Finally, we propose that intermolecular β-sheet interaction in R1 is a central recognition region while R3 may determine specific contacts of RAS versus RRAS isoforms with effectors.
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Affiliation(s)
- Hossein Nakhaeizadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Ehsan Amin
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Saeideh Nakhaei-Rad
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
- * E-mail:
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33
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Sayyed-Ahmad A, Cho KJ, Hancock JF, Gorfe AA. Computational Equilibrium Thermodynamic and Kinetic Analysis of K-Ras Dimerization through an Effector Binding Surface Suggests Limited Functional Role. J Phys Chem B 2016; 120:8547-56. [PMID: 27072779 DOI: 10.1021/acs.jpcb.6b02403] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Dimer formation is believed to have a substantial impact on regulating K-Ras function. However, the evidence for dimerization and the molecular details of the process are scant. In this study, we characterize a K-Ras pseudo-C2-symmetric dimerization interface involving the effector interacting β2-strand. We used structure matching and all-atom molecular dynamics (MD) simulations to predict, refine, and investigate the stability of this interface. Our MD simulation suggested that the β2-dimer is potentially stable and remains relatively close to its initial conformation due to the presence of a number of hydrogen bonds, ionic salt bridges, and other favorable interactions. We carried out potential of mean force calculations to determine the relative binding strength of the interface. The results of these calculations indicated that the β2 dimerization interface provides a weak binding free energy in solution and a dissociation constant that is close to 1 mM. Analyses of Brownian dynamics simulations suggested an association rate kon ≈ 10(5)-10(6) M(-1) s(-1). Combining these observations with available literature data, we propose that formation of auto-inhibited β2 K-Ras dimers is possible but its fraction in cells is likely very small under normal physiologic conditions.
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Affiliation(s)
- Abdallah Sayyed-Ahmad
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
| | - Kwang-Jin Cho
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston , 6431 Fannin Street, Houston, Texas 77030, United States
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34
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35
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Coyle SM, Lim WA. Mapping the functional versatility and fragility of Ras GTPase signaling circuits through in vitro network reconstitution. eLife 2016; 5. [PMID: 26765565 PMCID: PMC4775219 DOI: 10.7554/elife.12435] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/13/2016] [Indexed: 01/06/2023] Open
Abstract
The Ras-superfamily GTPases are central controllers of cell proliferation and morphology. Ras signaling is mediated by a system of interacting molecules: upstream enzymes (GEF/GAP) regulate Ras's ability to recruit multiple competing downstream effectors. We developed a multiplexed, multi-turnover assay for measuring the dynamic signaling behavior of in vitro reconstituted H-Ras signaling systems. By including both upstream regulators and downstream effectors, we can systematically map how different network configurations shape the dynamic system response. The concentration and identity of both upstream and downstream signaling components strongly impacted the timing, duration, shape, and amplitude of effector outputs. The distorted output of oncogenic alleles of Ras was highly dependent on the balance of positive (GAP) and negative (GEF) regulators in the system. We found that different effectors interpreted the same inputs with distinct output dynamics, enabling a Ras system to encode multiple unique temporal outputs in response to a single input. We also found that different Ras-to-GEF positive feedback mechanisms could reshape output dynamics in distinct ways, such as signal amplification or overshoot minimization. Mapping of the space of output behaviors accessible to Ras provides a design manual for programming Ras circuits, and reveals how these systems are readily adapted to produce an array of dynamic signaling behaviors. Nonetheless, this versatility comes with a trade-off of fragility, as there exist numerous paths to altered signaling behaviors that could cause disease.
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Affiliation(s)
- Scott M Coyle
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Program in Biological Sciences, University of California, San Francisco, San Francisco, United States.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, United States
| | - Wendell A Lim
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Program in Biological Sciences, University of California, San Francisco, San Francisco, United States.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, United States
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36
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Aramini JM, Vorobiev SM, Tuberty LM, Janjua H, Campbell ET, Seetharaman J, Su M, Huang YJ, Acton TB, Xiao R, Tong L, Montelione GT. The RAS-Binding Domain of Human BRAF Protein Serine/Threonine Kinase Exhibits Allosteric Conformational Changes upon Binding HRAS. Structure 2015; 23:1382-1393. [PMID: 26165597 DOI: 10.1016/j.str.2015.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/27/2015] [Accepted: 06/04/2015] [Indexed: 02/07/2023]
Abstract
RAS binding is a critical step in the activation of BRAF protein serine/threonine kinase and stimulation of the mitogen-activated protein kinase signaling pathway. Mutations in both RAS and BRAF are associated with many human cancers. Here, we report the solution nuclear magnetic resonance (NMR) and X-ray crystal structures of the RAS-binding domain (RBD) from human BRAF. We further studied the complex between BRAF RBD and the GppNHp bound form of HRAS in solution. Backbone, side-chain, and (19)F NMR chemical shift perturbations reveal unexpected changes distal to the RAS-binding face that extend through the core of the RBD structure. Moreover, backbone amide hydrogen/deuterium exchange NMR data demonstrate conformational ensemble changes in the RBD core structure upon complex formation. These changes in BRAF RBD reveal a basis for allosteric regulation of BRAF structure and function, and suggest a mechanism by which RAS binding can signal the drastic domain rearrangements required for activation of BRAF kinase.
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Affiliation(s)
- James M Aramini
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Sergey M Vorobiev
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Lynda M Tuberty
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haleema Janjua
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Elliot T Campbell
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jayaraman Seetharaman
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Min Su
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Yuanpeng J Huang
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Thomas B Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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37
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Abstract
RAF family kinases were among the first oncoproteins to be described more than 30 years ago. They primarily act as signalling relays downstream of RAS, and their close ties to cancer have fuelled a large number of studies. However, we still lack a systems-level understanding of their regulation and mode of action. The recent discovery that the catalytic activity of RAF depends on an allosteric mechanism driven by kinase domain dimerization is providing a vital new piece of information towards a comprehensive model of RAF function. The fact that current RAF inhibitors unexpectedly induce ERK signalling by stimulating RAF dimerization also calls for a deeper structural characterization of this family of kinases.
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38
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[Mechanisms of resistance to anti-BRAF treatments]. Ann Dermatol Venereol 2014; 141:671-81. [PMID: 25442471 DOI: 10.1016/j.annder.2014.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 04/30/2014] [Accepted: 06/19/2014] [Indexed: 12/19/2022]
Abstract
CONTEXT In patients with melanoma positive for the BRAF V600 mutation, clinical response to specific BRAF inhibitors is usually rapid and striking, with significant benefits in terms of progression-free survival and overall survival. However, resistance to treatment almost invariably arises, typically within a median timeframe of 6 months. Indeed, very few patients exhibit long-lasting response to these targeted therapies. AIMS It is essential to better understand the mechanisms of resistance to targeted anti-BRAF therapies in order to increase both response rates and the duration of clinical response to treatment. This literature review describes the signaling pathways involving BRAF and presents recent data from clinical trials with these molecules. Furthermore, we aim to describe the main resistance mechanisms linked with targeted anti-BRAF therapies. METHODS The keywords (resistance, BRAF, melanoma, targeted therapy, vemurafenib, and dabrafenib) were used to extract relevant articles in the Medline/Pubmed database published before 31 January 2014. DISCUSSION Improved knowledge and understanding of the mechanisms of resistance to targeted anti-BRAF therapies should enable the development of new therapeutic strategies in order to overcome such resistance and allow more significant and sustained response rates to be achieved among melanoma patients.
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39
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Iversen L, Tu HL, Lin WC, Christensen SM, Abel SM, Iwig J, Wu HJ, Gureasko J, Rhodes C, Petit RS, Hansen SD, Thill P, Yu CH, Stamou D, Chakraborty AK, Kuriyan J, Groves JT. Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics. Science 2014; 345:50-4. [PMID: 24994643 DOI: 10.1126/science.1250373] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.
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Affiliation(s)
- Lars Iversen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hsiung-Lin Tu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wan-Chen Lin
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sune M Christensen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Steven M Abel
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Jeff Iwig
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hung-Jen Wu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jodi Gureasko
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher Rhodes
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca S Petit
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Scott D Hansen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter Thill
- Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Cheng-Han Yu
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Dimitrios Stamou
- Department of Chemistry and Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02139, USA. Department of Biological Engineering, MIT, Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA. Department of Physics, MIT, Cambridge, MA 02139, USA. Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - John Kuriyan
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay T Groves
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Mechanobiology Institute, National University of Singapore, Singapore. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Berkeley Education Alliance for Research in Singapore, 1 Create Way, CREATE tower level 11, University Town, Singapore 138602.
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40
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Quantitative in vivo fluorescence cross-correlation analyses highlight the importance of competitive effects in the regulation of protein-protein interactions. Mol Cell Biol 2014; 34:3272-90. [PMID: 24958104 DOI: 10.1128/mcb.00087-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Computer-assisted simulation is a promising approach for clarifying complicated signaling networks. However, this approach is currently limited by a deficiency of kinetic parameters determined in living cells. To overcome this problem, we applied fluorescence cross-correlation spectrometry (FCCS) to measure dissociation constant (Kd) values of signaling molecule complexes in living cells (in vivo Kd). Among the pairs of fluorescent molecules tested, that of monomerized enhanced green fluorescent protein (mEGFP) and HaloTag-tetramethylrhodamine was most suitable for the measurement of in vivo Kd by FCCS. Using this pair, we determined 22 in vivo Kd values of signaling molecule complexes comprising the epidermal growth factor receptor (EGFR)-Ras-extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase pathway. With these parameters, we developed a kinetic simulation model of the EGFR-Ras-ERK MAP kinase pathway and uncovered a potential role played by stoichiometry in Shc binding to EGFR during the peak activations of Ras, MEK, and ERK. Intriguingly, most of the in vivo Kd values determined in this study were higher than the in vitro Kd values reported previously, suggesting the significance of competitive bindings inside cells. These in vivo Kd values will provide a sound basis for the quantitative understanding of signal transduction.
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41
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Martín-Algarra S, Fernández-Figueras MT, López-Martín JA, Santos-Briz A, Arance A, Lozano MD, Berrocal A, Ríos-Martín JJ, Espinosa E, Rodríguez-Peralto JL. Guidelines for biomarker testing in metastatic melanoma: a National Consensus of the Spanish Society of Pathology and the Spanish Society of Medical Oncology. Clin Transl Oncol 2013; 16:362-73. [DOI: 10.1007/s12094-013-1090-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/16/2013] [Indexed: 12/19/2022]
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42
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Sullivan RJ, Flaherty KT. Resistance to BRAF-targeted therapy in melanoma. Eur J Cancer 2013; 49:1297-304. [DOI: 10.1016/j.ejca.2012.11.019] [Citation(s) in RCA: 272] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 11/11/2012] [Indexed: 12/17/2022]
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43
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Abstract
The mitogen-activated protein kinase (MAPK) pathway is critical to oncogenic signaling in the majority of patients with malignant melanoma. Driver mutations in both NRAS and BRAF have important implications for prognosis and treatment. The development of inhibitors to mediators of the MAPK pathway, including those to CRAF, BRAF, and MEK, has led to major advances in the treatment of patients with melanoma. In particular, the selective BRAF inhibitor vemurafenib has been shown to improve overall survival in patients with tumors harboring BRAF mutations. However, the duration of benefit is limited in many patients and highlights the need for understanding the limitations of therapy in order to devise more effective strategies. MEK inhibitors have proven to particularly active in BRAF mutant melanomas also. Emerging knowledge about mechanisms of resistance as well as a more complete understanding of the biology of MAPK pathway signaling provides insight into rational combination regimens and sequences of molecularly targeted therapies.
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Affiliation(s)
- R J Sullivan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
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44
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Baljuls A, Beck M, Oenel A, Robubi A, Kroschewski R, Hekman M, Rudel T, Rapp UR. The tumor suppressor DiRas3 forms a complex with H-Ras and C-RAF proteins and regulates localization, dimerization, and kinase activity of C-RAF. J Biol Chem 2012; 287:23128-40. [PMID: 22605333 DOI: 10.1074/jbc.m112.343780] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The maternally imprinted Ras-related tumor suppressor gene DiRas3 is lost or down-regulated in more than 60% of ovarian and breast cancers. The anti-tumorigenic effect of DiRas3 is achieved through several mechanisms, including inhibition of cell proliferation, motility, and invasion, as well as induction of apoptosis and autophagy. Re-expression of DiRas3 in cancer cells interferes with the signaling through Ras/MAPK and PI3K. Despite intensive research, the mode of interference of DiRas3 with the Ras/RAF/MEK/ERK signal transduction is still a matter of speculation. In this study, we show that DiRas3 associates with the H-Ras oncogene and that activation of H-Ras enforces this interaction. Furthermore, while associated with DiRas3, H-Ras is able to bind to its effector protein C-RAF. The resulting multimeric complex consisting of DiRas3, C-RAF, and active H-Ras is more stable than the two protein complexes H-Ras·C-RAF or H-Ras·DiRas3, respectively. The consequence of this complex formation is a DiRas3-mediated recruitment and anchorage of C-RAF to components of the membrane skeleton, suppression of C-RAF/B-RAF heterodimerization, and inhibition of C-RAF kinase activity.
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Affiliation(s)
- Angela Baljuls
- Theodor Boveri Institute of Bioscience, Department of Microbiology, University of Wuerzburg, 97074 Wuerzburg, Germany.
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45
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Anderson DJ, Durieux JK, Song K, Alvarado R, Jackson PK, Hatzivassiliou G, Ludlam MJC. Live-cell microscopy reveals small molecule inhibitor effects on MAPK pathway dynamics. PLoS One 2011; 6:e22607. [PMID: 21829637 PMCID: PMC3150364 DOI: 10.1371/journal.pone.0022607] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 06/26/2011] [Indexed: 12/19/2022] Open
Abstract
Oncogenic mutations in the mitogen activated protein kinase (MAPK) pathway are prevalent in human tumors, making this pathway a target of drug development efforts. Recently, ATP-competitive Raf inhibitors were shown to cause MAPK pathway activation via Raf kinase priming in wild-type BRaf cells and tumors, highlighting the need for a thorough understanding of signaling in the context of small molecule kinase inhibitors. Here, we present critical improvements in cell-line engineering and image analysis coupled with automated image acquisition that allow for the simultaneous identification of cellular localization of multiple MAPK pathway components (KRas, CRaf, Mek1 and Erk2). We use these assays in a systematic study of the effect of small molecule inhibitors across the MAPK cascade either as single agents or in combination. Both Raf inhibitor priming as well as the release from negative feedback induced by Mek and Erk inhibitors cause translocation of CRaf to the plasma membrane via mechanisms that are additive in pathway activation. Analysis of Erk activation and sub-cellular localization upon inhibitor treatments reveals differential inhibition and activation with the Raf inhibitors AZD628 and GDC0879 respectively. Since both single agent and combination studies of Raf and Mek inhibitors are currently in the clinic, our assays provide valuable insight into their effects on MAPK signaling in live cells.
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Affiliation(s)
- Daniel J. Anderson
- Department of Cell Regulation, Genentech, Inc., South San Francisco, California, United States of America
- * E-mail:
| | - Jenni K. Durieux
- Department of Cell Regulation, Genentech, Inc., South San Francisco, California, United States of America
| | - Kyung Song
- Department of Cancer Signaling, Genentech, Inc., South San Francisco, California, United States of America
| | - Ryan Alvarado
- Department of Cancer Signaling, Genentech, Inc., South San Francisco, California, United States of America
| | - Peter K. Jackson
- Department of Cell Regulation, Genentech, Inc., South San Francisco, California, United States of America
| | - Georgia Hatzivassiliou
- Department of Cancer Signaling, Genentech, Inc., South San Francisco, California, United States of America
| | - Mary J. C. Ludlam
- Department of Cell Regulation, Genentech, Inc., South San Francisco, California, United States of America
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46
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Baljuls A, Mahr R, Schwarzenau I, Müller T, Polzien L, Hekman M, Rapp UR. Single substitution within the RKTR motif impairs kinase activity but promotes dimerization of RAF kinase. J Biol Chem 2011; 286:16491-503. [PMID: 21454547 DOI: 10.1074/jbc.m110.194167] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The serine/threonine kinase RAF is a central component of the MAPK cascade. Regulation of RAF activity is highly complex and involves recruitment to membranes and association with Ras and scaffold proteins as well as multiple phosphorylation and dephosphorylation events. Previously, we identified by molecular modeling an interaction between the N-region and the RKTR motif of the kinase domain in RAF and assigned a new function to this tetrapeptide segment. Here we found that a single substitution of each basic residue within the RKTR motif inhibited catalytic activity of all three RAF isoforms. However, the inhibition and phosphorylation pattern of C-RAF and A-RAF differed from B-RAF. Furthermore, substitution of the first arginine led to hyperphosphorylation and accumulation of A-RAF and C-RAF in plasma membrane fraction, indicating that this residue interferes with the recycling process of A-RAF and C-RAF but not B-RAF. In contrast, all RAF isoforms behave similarly with respect to the RKTR motif-dependent dimerization. The exchange of the second arginine led to exceedingly increased dimerization as long as one of the protomers was not mutated, suggesting that substitution of this residue with alanine may result in similar a structural rearrangement of the RAF kinase domain, as has been found for the C-RAF kinase domain co-crystallized with a dimerization-stabilizing RAF inhibitor. In summary, we provide evidence that each of the basic residues within the RKTR motif is indispensable for correct RAF function.
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Affiliation(s)
- Angela Baljuls
- Theodor-Boveri Institute of Bioscience, Department of Microbiology, University of Wuerzburg, Wuerzburg, Germany.
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47
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Matallanas D, Birtwistle M, Romano D, Zebisch A, Rauch J, von Kriegsheim A, Kolch W. Raf family kinases: old dogs have learned new tricks. Genes Cancer 2011; 2:232-60. [PMID: 21779496 PMCID: PMC3128629 DOI: 10.1177/1947601911407323] [Citation(s) in RCA: 266] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
First identified in the early 1980s as retroviral oncogenes, the Raf proteins have been the objects of intense research. The discoveries 10 years later that the Raf family members (Raf-1, B-Raf, and A-Raf) are bona fide Ras effectors and upstream activators of the ubiquitous ERK pathway increased the interest in these proteins primarily because of the central role that this cascade plays in cancer development. The important role of Raf in cancer was corroborated in 2002 with the discovery of B-Raf genetic mutations in a large number of tumors. This led to intensified drug development efforts to target Raf signaling in cancer. This work yielded not only recent clinical successes but also surprising insights into the regulation of Raf proteins by homodimerization and heterodimerization. Surprising insights also came from the hunt for new Raf targets. Although MEK remains the only widely accepted Raf substrate, new kinase-independent roles for Raf proteins have emerged. These include the regulation of apoptosis by suppressing the activity of the proapoptotic kinases, ASK1 and MST2, and the regulation of cell motility and differentiation by controlling the activity of Rok-α. In this review, we discuss the regulation of Raf proteins and their role in cancer, with special focus on the interacting proteins that modulate Raf signaling. We also describe the new pathways controlled by Raf proteins and summarize the successes and failures in the development of efficient anticancer therapies targeting Raf. Finally, we also argue for the necessity of more systemic approaches to obtain a better understanding of how the Ras-Raf signaling network generates biological specificity.
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Affiliation(s)
- David Matallanas
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
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48
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Udell CM, Rajakulendran T, Sicheri F, Therrien M. Mechanistic principles of RAF kinase signaling. Cell Mol Life Sci 2011; 68:553-65. [PMID: 20820846 PMCID: PMC11114552 DOI: 10.1007/s00018-010-0520-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 08/24/2010] [Accepted: 08/25/2010] [Indexed: 12/19/2022]
Abstract
The RAF family of kinases are key components acting downstream of receptor tyrosine kinases and cells employ several distinct mechanisms to strictly control their activity. RAF transitions from an inactive state, where the N-terminal regulatory region binds intramolecularly to the C-terminal kinase domain, to an open state capable of executing the phosphoryl transfer reaction. This transition involves changes both within and between the protein domains in RAF. Many different proteins regulate the transition between inactive and active states of RAF, including RAS and KSR, which are arguably the two most prominent regulators of RAF function. Recent developments have added several new twists to our understanding of RAF regulation. Among others, dimerization of the RAF kinase domain is emerging as a crucial step in the RAF activation process. The multitude of regulatory protein-protein interactions involving RAF remains a largely untapped area for therapeutic applications.
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Affiliation(s)
- Christian M. Udell
- Laboratory of Intracellular Signaling, Département de pathologie et de biologie cellulaire, Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC H3C 3J7 Canada
| | - Thanashan Rajakulendran
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, ON M5G 1X5 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada
| | - Frank Sicheri
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, ON M5G 1X5 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada
| | - Marc Therrien
- Laboratory of Intracellular Signaling, Département de pathologie et de biologie cellulaire, Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC H3C 3J7 Canada
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49
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Stark F, Pfannstiel J, Klaiber I, Raabe T. Protein kinase CK2 links polyamine metabolism to MAPK signalling in Drosophila. Cell Signal 2011; 23:876-82. [PMID: 21262350 DOI: 10.1016/j.cellsig.2011.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 01/13/2011] [Indexed: 01/22/2023]
Abstract
MAPK signalling is a complex process not only requiring the core components Raf, MEK and Erk, but also many proteins like the scaffold protein KSR and several kinases to specifically localize, modulate and fine-tune the outcome of the pathway in a cell context specific manner. In mammals, protein kinase CK2 was shown to bind to the scaffold protein KSR and to phosphorylate Raf proteins at a conserved serine residue in the negative-charge regulatory (N-) region, thereby facilitating maximal activity of the MAPK signalling pathway. In this work we show that in Drosophila CK2 is also bound to KSR. However, despite the presence of a corresponding serine residue in the N-region of DRaf, CK2-mediated phosphorylation of DRaf takes place on a serine residue at the N-terminus and is required for Erk activation. Previous work identified polyamines as regulators of CK2 kinase activity. The main cellular source of polyamines is the catabolism of amino acids. Evidence is provided that phosphorylation of DRaf by CK2 is modulated by polyamines, with spermine being the most potent inhibitor of the reaction. We suggest that CK2 is able to monitor intracellular polyamine levels and translates this information to modulate MAPK signalling.
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Affiliation(s)
- Felix Stark
- Universität Würzburg, Institut für Medizinische Strahlenkunde und Zellforschung, Versbacherstr. 5, D-97078 Würzburg, Germany
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50
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Calcineurin increases glucose activation of ERK1/2 by reversing negative feedback. Proc Natl Acad Sci U S A 2010; 107:22314-9. [PMID: 21135229 DOI: 10.1073/pnas.1016630108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In pancreatic β cells, ERK1 and ERK2 participate in nutrient sensing, and their activities rise and fall as a function of glucose concentration over the physiologic range. Glucose metabolism triggers calcium influx and release of calcium from intracellular stores to activate ERK1/2. Calcium influx also activates the calcium-dependent phosphatase calcineurin, which is required for maximal ERK1/2 activation by glucose. Calcineurin controls insulin gene expression by ERK1/2-dependent and -independent mechanisms. Here, we show that, in β cells, glucose activates the ERK1/2 cascade primarily through B-Raf. Glucose activation of B-Raf, like that of ERK1/2, is calcineurin-sensitive. Calcineurin binds to B-Raf in both unstimulated and stimulated cells. We show that B-Raf is a calcineurin substrate; among calcineurin target residues on B-Raf is T401, a site of negative feedback phosphorylation by ERK1/2. Blocking calcineurin activity in β cells prevents dephosphorylation of B-Raf T401 and decreases B-Raf and ERK1/2 activities. We conclude that the major calcineurin-dependent event in glucose sensing by ERK1/2 is the activation of B-Raf.
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