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Lee KY. Membrane-Driven Dimerization of the Peripheral Membrane Protein KRAS: Implications for Downstream Signaling. Int J Mol Sci 2024; 25:2530. [PMID: 38473778 DOI: 10.3390/ijms25052530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Transient homo-dimerization of the RAS GTPase at the plasma membrane has been shown to promote the mitogen-activated protein kinase (MAPK) signaling pathway essential for cell proliferation and oncogenesis. To date, numerous crystallographic studies have focused on the well-defined GTPase domains of RAS isoforms, which lack the disordered C-terminal membrane anchor, thus providing limited structural insight into membrane-bound RAS molecules. Recently, lipid-bilayer nanodisc platforms and paramagnetic relaxation enhancement (PRE) analyses have revealed several distinct structures of the membrane-anchored homodimers of KRAS, an isoform that is most frequently mutated in human cancers. The KRAS dimerization interface is highly plastic and altered by biologically relevant conditions, including oncogenic mutations, the nucleotide states of the protein, and the lipid composition. Notably, PRE-derived structures of KRAS homodimers on the membrane substantially differ in terms of the relative orientation of the protomers at an "α-α" dimer interface comprising two α4-α5 regions. This interface plasticity along with the altered orientations of KRAS on the membrane impact the accessibility of KRAS to downstream effectors and regulatory proteins. Further, nanodisc platforms used to drive KRAS dimerization can be used to screen potential anticancer drugs that target membrane-bound RAS dimers and probe their structural mechanism of action.
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Affiliation(s)
- Ki-Young Lee
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Gyeonggi-Do, Republic of Korea
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2
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Whaby M, Nair RS, O'Bryan JP. Probing RAS Function Using Monobody and NanoBiT Technologies. Methods Mol Biol 2024; 2797:211-225. [PMID: 38570462 DOI: 10.1007/978-1-0716-3822-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Missense mutations in the RAS family of oncogenes (HRAS, KRAS, and NRAS) are present in approximately 20% of human cancers, making RAS a valuable therapeutic target (Prior et al., Cancer Res 80:2969-2974, 2020). Although decades of research efforts to develop therapeutic inhibitors of RAS were unsuccessful, there has been success in recent years with the entrance of FDA-approved KRASG12C-specific inhibitors to the clinic (Skoulidis et al., N Engl J Med 384:2371-2381, 2021; Jänne et al., N Engl J Med 387:120-131, 2022). Additionally, KRASG12D-specific inhibitors are presently undergoing clinical trials (Wang et al., J Med Chem 65:3123-3133, 2022). The advent of these allele specific inhibitors has disproved the previous notion that RAS is undruggable. Despite these advancements in RAS-targeted therapeutics, several RAS mutants that frequently arise in cancers remain without tractable drugs. Thus, it is critical to further understand the function and biology of RAS in cells and to develop tools to identify novel therapeutic vulnerabilities for development of anti-RAS therapeutics. To do this, we have exploited the use of monobody (Mb) technology to develop specific protein-based inhibitors of selected RAS isoforms and mutants (Spencer-Smith et al., Nat Chem Biol 13:62-68, 2017; Khan et al., Cell Rep 38:110322, 2022; Wallon et al., Proc Natl Acad Sci USA 119:e2204481119, 2022; Khan et al., Small GTPases 13:114-127, 2021; Khan et al., Oncogene 38:2984-2993, 2019). Herein, we describe our combined use of Mbs and NanoLuc Binary Technology (NanoBiT) to analyze RAS protein-protein interactions and to screen for RAS-binding small molecules in live-cell, high-throughput assays.
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Affiliation(s)
- Michael Whaby
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Rakesh Sathish Nair
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA.
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA.
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3
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Saitoh T, Kim HN, Narita R, Ohtsuka I, Mo W, Lee KY, Enomoto M, Gasmi-Seabrook GMC, Marshall CB, Ikura M. Biochemical and biophysical characterization of the RAS family small GTPase protein DiRAS3. Protein Expr Purif 2023; 212:106361. [PMID: 37652393 DOI: 10.1016/j.pep.2023.106361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
DiRAS3, also called ARHI, is a RAS (sub)family small GTPase protein that shares 50-60% sequence identity with H-, K-, and N-RAS, with substitutions in key conserved G-box motifs and a unique 34 amino acid extension at its N-terminus. Unlike the RAS proto-oncogenes, DiRAS3 exhibits tumor suppressor properties. DiRAS3 function has been studied through genetics and cell biology, but there has been a lack of understanding of the biochemical and biophysical properties of the protein, likely due to its instability and poor solubility. To overcome this solubility issue, we engineered a DiRAS3 variant (C75S/C80S), which significantly improved soluble protein expression in E. coli. Recombinant DiRAS3 was purified by Ni-NTA and size exclusion chromatography (SEC). Concentration dependence of the SEC chromatogram indicated that DiRAS3 exists in monomer-dimer equilibrium. We then produced truncations of the N-terminal (ΔN) and both (ΔNC) extensions to the GTPase domain. Unlike full-length DiRAS3, the SEC profiles showed that ΔNC is monomeric while ΔN was monomeric with aggregation, suggesting that the N and/or C-terminal tail(s) contribute to dimerization and aggregation. The 1H-15N HSQC NMR spectrum of ΔNC construct displayed well-dispersed peaks similar to spectra of other GTPase domains, which enabled us to demonstrate that DiRAS3 has a GTPase domain that can bind GDP and GTP. Taken together, we conclude that, despite the substitutions in the G-box motifs, DiRAS3 can switch between nucleotide-bound states and that the N- and C-terminal extensions interact transiently with the GTPase domain in intra- and inter-molecular fashions, mediating weak multimerization of this unique small GTPase.
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Affiliation(s)
- Takashi Saitoh
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.
| | - Ha-Neul Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Riku Narita
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan
| | - Ibuki Ohtsuka
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan
| | - Weiyu Mo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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4
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Brenner RJ, Landgraf AD, Bum-Erdene K, Gonzalez-Gutierrez G, Meroueh SO. Crystal Packing Reveals a Potential Autoinhibited KRAS Dimer Interface and a Strategy for Small-Molecule Inhibition of RAS Signaling. Biochemistry 2023; 62:3206-3213. [PMID: 37938120 PMCID: PMC10904212 DOI: 10.1021/acs.biochem.3c00378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
KRAS GTPases harbor oncogenic mutations in more than 25% of human tumors. KRAS is considered to be largely undruggable due to the lack of a suitable small-molecule binding site. Here, we report a unique crystal structure of His-tagged KRASG12D that reveals a remarkable conformational change. The Switch I loop of one His-KRASG12D structure extends into the Switch I/II pocket of another His-KRASG12D in an adjacent unit cell to create an elaborate interface that is reminiscent of high-affinity protein-protein complexes. We explore the contributions of amino acids at this interface using alanine-scanning studies with alchemical free energy perturbation calculations based on explicit-solvent molecular dynamics simulations. Several interface amino acids were found to be hot spots as they contributed more than 1.5 kcal/mol to the protein-protein interaction. Computational analysis of the complex revealed the presence of two large binding pockets that possess physicochemical features typically found in pockets considered druggable. Small-molecule binding to these pockets may stabilize this autoinhibited structure of KRAS if it exists in cells to provide a new strategy to inhibit RAS signaling.
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Affiliation(s)
- Robert J. Brenner
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Alexander D. Landgraf
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Khuchtumur Bum-Erdene
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Samy O. Meroueh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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Simão S, Agostinho RR, Martínez-Ruiz A, Araújo IM. Regulation of Ras Signaling by S-Nitrosylation. Antioxidants (Basel) 2023; 12:1562. [PMID: 37627556 PMCID: PMC10451275 DOI: 10.3390/antiox12081562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Ras are a family of small GTPases that function as signal transduction mediators and are involved in cell proliferation, migration, differentiation and survival. The significance of Ras is further evidenced by the fact that Ras genes are among the most mutated oncogenes in different types of cancers. After translation, Ras proteins can be targets of post-translational modifications (PTM), which can alter the intracellular dynamics of the protein. In this review, we will focus on how S-nitrosylation of Ras affects the way these proteins interact with membranes, its cellular localization, and its activity. S-Nitrosylation occurs when a nitrosyl moiety of nitric oxide (NO) is covalently attached to a thiol group of a cysteine residue in a target protein. In Ras, the conserved Cys118 is the most surface-exposed Cys and the preferable residue for NO action, leading to the initiation of transduction events. Ras transduces the mitogen-activated protein kinases (MAPK), the phosphoinositide-3 kinase (PI3K) and the RalGEF cellular pathways. S-Nitrosylation of elements of the RalGEF cascade remains to be identified. On the contrary, it is well established that several components of the MAPK and PI3K pathways, as well as different proteins associated with these cascades, can be modified by S-nitrosylation. Overall, this review presents a better understanding of Ras S-nitrosylation, increasing the knowledge on the dynamics of these proteins in the presence of NO and the underlying implications in cellular signaling.
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Affiliation(s)
- Sónia Simão
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Rafaela Ribeiro Agostinho
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Antonio Martínez-Ruiz
- Unidad de Investigación, Hospital Universitario Santa Cristina, Instituto de Investigación Sanitaria Princesa, 28009 Madrid, Spain;
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Inês Maria Araújo
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, 1400-038 Lisbon, Portugal
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6
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Liu C, Ye D, Yang H, Chen X, Su Z, Li X, Ding M, Liu Y. RAS-targeted cancer therapy: Advances in drugging specific mutations. MedComm (Beijing) 2023; 4:e285. [PMID: 37250144 PMCID: PMC10225044 DOI: 10.1002/mco2.285] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/06/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Rat sarcoma (RAS), as a frequently mutated oncogene, has been studied as an attractive target for treating RAS-driven cancers for over four decades. However, it is until the recent success of kirsten-RAS (KRAS)G12C inhibitor that RAS gets rid of the title "undruggable". It is worth noting that the therapeutic effect of KRASG12C inhibitors on different RAS allelic mutations or even different cancers with KRASG12C varies significantly. Thus, deep understanding of the characteristics of each allelic RAS mutation will be a prerequisite for developing new RAS inhibitors. In this review, the structural and biochemical features of different RAS mutations are summarized and compared. Besides, the pathological characteristics and treatment responses of different cancers carrying RAS mutations are listed based on clinical reports. In addition, the development of RAS inhibitors, either direct or indirect, that target the downstream components in RAS pathway is summarized as well. Hopefully, this review will broaden our knowledge on RAS-targeting strategies and trigger more intensive studies on exploiting new RAS allele-specific inhibitors.
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Affiliation(s)
- Cen Liu
- Beijing University of Chinese MedicineBeijingChina
| | - Danyang Ye
- Beijing University of Chinese MedicineBeijingChina
| | - Hongliu Yang
- Beijing University of Chinese MedicineBeijingChina
| | - Xu Chen
- Beijing University of Chinese MedicineBeijingChina
| | - Zhijun Su
- Beijing University of Chinese MedicineBeijingChina
| | - Xia Li
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Mei Ding
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yonggang Liu
- Beijing University of Chinese MedicineBeijingChina
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7
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Tang X, Xue D, Zhang T, Nilsson-Payant BE, Carrau L, Duan X, Gordillo M, Tan AY, Qiu Y, Xiang J, Schwartz RE, tenOever BR, Evans T, Chen S. A multi-organoid platform identifies CIART as a key factor for SARS-CoV-2 infection. Nat Cell Biol 2023; 25:381-389. [PMID: 36918693 PMCID: PMC10014579 DOI: 10.1038/s41556-023-01095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 01/25/2023] [Indexed: 03/16/2023]
Abstract
COVID-19 is a systemic disease involving multiple organs. We previously established a platform to derive organoids and cells from human pluripotent stem cells to model SARS-CoV-2 infection and perform drug screens1,2. This provided insight into cellular tropism and the host response, yet the molecular mechanisms regulating SARS-CoV-2 infection remain poorly defined. Here we systematically examined changes in transcript profiles caused by SARS-CoV-2 infection at different multiplicities of infection for lung airway organoids, lung alveolar organoids and cardiomyocytes, and identified several genes that are generally implicated in controlling SARS-CoV-2 infection, including CIART, the circadian-associated repressor of transcription. Lung airway organoids, lung alveolar organoids and cardiomyocytes derived from isogenic CIART-/- human pluripotent stem cells were significantly resistant to SARS-CoV-2 infection, independently of viral entry. Single-cell RNA-sequencing analysis further validated the decreased levels of SARS-CoV-2 infection in ciliated-like cells of lung airway organoids. CUT&RUN, ATAC-seq and RNA-sequencing analyses showed that CIART controls SARS-CoV-2 infection at least in part through the regulation of NR4A1, a gene also identified from the multi-organoid analysis. Finally, transcriptional profiling and pharmacological inhibition led to the discovery that the Retinoid X Receptor pathway regulates SARS-CoV-2 infection downstream of CIART and NR4A1. The multi-organoid platform identified the role of circadian-clock regulation in SARS-CoV-2 infection, which provides potential therapeutic targets for protection against COVID-19 across organ systems.
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Affiliation(s)
- Xuming Tang
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin E Nilsson-Payant
- Department of Microbiology, New York University, New York, NY, USA
- TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Lucia Carrau
- Department of Microbiology, New York University, New York, NY, USA
| | - Xiaohua Duan
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Miriam Gordillo
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Adrian Y Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Yunping Qiu
- Stable Isotope and Metabolomics Core Facility, The Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | | | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA.
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8
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Dynamic regulation of RAS and RAS signaling. Biochem J 2023; 480:1-23. [PMID: 36607281 PMCID: PMC9988006 DOI: 10.1042/bcj20220234] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
RAS proteins regulate most aspects of cellular physiology. They are mutated in 30% of human cancers and 4% of developmental disorders termed Rasopathies. They cycle between active GTP-bound and inactive GDP-bound states. When active, they can interact with a wide range of effectors that control fundamental biochemical and biological processes. Emerging evidence suggests that RAS proteins are not simple on/off switches but sophisticated information processing devices that compute cell fate decisions by integrating external and internal cues. A critical component of this compute function is the dynamic regulation of RAS activation and downstream signaling that allows RAS to produce a rich and nuanced spectrum of biological outputs. We discuss recent findings how the dynamics of RAS and its downstream signaling is regulated. Starting from the structural and biochemical properties of wild-type and mutant RAS proteins and their activation cycle, we examine higher molecular assemblies, effector interactions and downstream signaling outputs, all under the aspect of dynamic regulation. We also consider how computational and mathematical modeling approaches contribute to analyze and understand the pleiotropic functions of RAS in health and disease.
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Tang R, Shuldiner EG, Kelly M, Murray CW, Hebert JD, Andrejka L, Tsai MK, Hughes NW, Parker MI, Cai H, Li YC, Wahl GM, Dunbrack RL, Jackson PK, Petrov DA, Winslow MM. Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth. Nat Cell Biol 2023; 25:159-169. [PMID: 36635501 PMCID: PMC10521195 DOI: 10.1038/s41556-022-01049-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/09/2022] [Indexed: 01/13/2023]
Abstract
Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signalling is incomplete. Here to uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumour barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRASG12D-driven tumour growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogues interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signalling. Furthermore, HRAS and NRAS mutations identified in oncogenic KRAS-driven human tumours partially abolished this effect. By comparing the tumour-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogues are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role RAS paralogue imbalance in oncogenic KRAS-driven lung cancer.
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Affiliation(s)
- Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Marcus Kelly
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Baxter Laboratories, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Jess D Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas W Hughes
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mitchell I Parker
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
- Molecular and Cell Biology and Genetics Program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yao-Cheng Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roland L Dunbrack
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter K Jackson
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Baxter Laboratories, Stanford University School of Medicine, Stanford, CA, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- The Chan Zuckerberg BioHub, San Francisco, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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10
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Whaby M, Wallon L, Mazzei M, Khan I, Teng KW, Koide S, O’Bryan JP. Mutations in the α4-α5 allosteric lobe of RAS do not significantly impair RAS signaling or self-association. J Biol Chem 2022; 298:102661. [PMID: 36334633 PMCID: PMC9763690 DOI: 10.1016/j.jbc.2022.102661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
Mutations in one of the three RAS genes (HRAS, KRAS, and NRAS) are present in nearly 20% of all human cancers. These mutations shift RAS to the GTP-loaded active state due to impairment in the intrinsic GTPase activity and disruption of GAP-mediated GTP hydrolysis, resulting in constitutive activation of effectors such as RAF. Because activation of RAF involves dimerization, RAS dimerization has been proposed as an important step in RAS-mediated activation of effectors. The α4-α5 allosteric lobe of RAS has been proposed as a RAS dimerization interface. Indeed, the NS1 monobody, which binds the α4-α5 region within the RAS G domain, inhibits RAS-dependent signaling and transformation as well as RAS nanoclustering at the plasma membrane. Although these results are consistent with a model in which the G domain dimerizes through the α4-α5 region, the isolated G domain of RAS lacks intrinsic dimerization capacity. Furthermore, prior studies analyzing α4-α5 point mutations have reported mixed effects on RAS function. Here, we evaluated the activity of a panel of single amino acid substitutions in the α4-α5 region implicated in RAS dimerization. We found that these proposed "dimerization-disrupting" mutations do not significantly impair self-association, signaling, or transformation of oncogenic RAS. These results are consistent with a model in which activated RAS protomers cluster in close proximity to promote the dimerization of their associated effector proteins (e.g., RAF) without physically associating into dimers mediated by specific molecular interactions. Our findings suggest the need for a nonconventional approach to developing therapeutics targeting the α4-α5 region.
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Affiliation(s)
- Michael Whaby
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lauren Wallon
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Megan Mazzei
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Imran Khan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA,Ralph H. Johnson VA Medical Center, Charleston, South Carolina, USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA,Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA,For correspondence: John P. O’Bryan; Shohei Koide
| | - John P. O’Bryan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA,Ralph H. Johnson VA Medical Center, Charleston, South Carolina, USA,For correspondence: John P. O’Bryan; Shohei Koide
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11
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Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, Burns V, Oppelstrup T, Hengartner N, Simanshu DK, Bremer PT, Chen D, Glosli JN, Shrestha R, Turbyville T, Streitz FH, Nissley DV, Ingólfsson HI, Stephen AG, Lightstone FC, Gnanakaran S. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophys J 2022; 121:3630-3650. [PMID: 35778842 PMCID: PMC9617161 DOI: 10.1016/j.bpj.2022.06.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma membrane. The orientation of RAS at the membrane may be critical for formation of the RAS-RBDCRD complex and subsequent signaling. To explore how RAS membrane orientation relates to the protein dynamics within the RAS-RBDCRD complex, we perform multiscale coarse-grained and all-atom molecular dynamics (MD) simulations of KRAS4b bound to the RBD and CRD domains of RAF-1, both in solution and anchored to a model plasma membrane. Solution MD simulations describe dynamic KRAS4b-CRD conformations, suggesting that the CRD has sufficient flexibility in this environment to substantially change its binding interface with KRAS4b. In contrast, when the ternary complex is anchored to the membrane, the mobility of the CRD relative to KRAS4b is restricted, resulting in fewer distinct KRAS4b-CRD conformations. These simulations implicate membrane orientations of the ternary complex that are consistent with NMR measurements. While a crystal structure-like conformation is observed in both solution and membrane simulations, a particular intermolecular rearrangement of the ternary complex is observed only when it is anchored to the membrane. This configuration emerges when the CRD hydrophobic loops are inserted into the membrane and helices α3-5 of KRAS4b are solvent exposed. This membrane-specific configuration is stabilized by KRAS4b-CRD contacts that are not observed in the crystal structure. These results suggest modulatory interplay between the CRD and plasma membrane that correlate with RAS/RAF complex structure and dynamics, and potentially influence subsequent steps in the activation of MAPK signaling.
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Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Francesco Di Natale
- Applications, Simulations, and Quality, Lawrence Livermore National Laboratory, Livermore, California
| | | | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Albert H Chan
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Harsh Bhatia
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Gulcin Gulten
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Tyler Reddy
- CCS-7, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Violetta Burns
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Tomas Oppelstrup
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Nick Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Peer-Timo Bremer
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - De Chen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - James N Glosli
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Rebika Shrestha
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Thomas Turbyville
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
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12
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Erman B. Gaussian network model revisited: Effects of mutation and ligand binding on protein behavior. Phys Biol 2022; 19. [PMID: 35105836 DOI: 10.1088/1478-3975/ac50ba] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/01/2022] [Indexed: 11/12/2022]
Abstract
The coarse-grained Gaussian Network model, GNM, considers only the alpha carbons of the folded protein. Therefore it is not directly applicable to the study of mutation or ligand binding problems where atomic detail is required. This shortcoming is improved by including all atom pairs within the coordination shell of each other into the Kirchoff Adjacency Matrix. Counting all contacts rather than only alpha carbon contacts diminishes the magnitude of fluctuations in the system. But more importantly, it changes the graph-like connectivity structure, i.e., the Kirchoff Adjacency Matrix of the protein. This change depends on amino acid type which introduces amino acid specific and position specific information into the classical coarse-grained GNM which was originally modelled in analogy with the phantom network model of rubber elasticity. With this modification, it is now possible to explain the consequences of mutation and ligand binding on residue fluctuations, their pair-correlations and mutual information (MI) shared by each pair. We refer to the new model as 'all-atom GNM'. Using examples from published data we show that the all-atom GNM gives B-factors that are in better agreement with experiment, can explain effects of mutation on long range communication in PDZ domains and can predict effects of GDP and GTP binding on the dimerization of KRAS.
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Affiliation(s)
- Burak Erman
- Department of Chemical and Biological Engineering, Koc University, Rumeifeneri Yolu, Istanbul, Istanbul, 34450, TURKEY
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13
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the 'old' field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
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14
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Shrestha R, Chen D, Frank P, Nissley DV, Turbyville TJ. Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes. iScience 2022; 25:103608. [PMID: 35106460 PMCID: PMC8786645 DOI: 10.1016/j.isci.2021.103608] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/30/2021] [Accepted: 12/08/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the spatiotemporal distribution and dynamics of RAS on the plasma membrane (PM) is the key for elucidating the molecular mechanisms of the RAS signaling pathway. Single particle tracking (SPT) experiments show that in cells, KRAS diffuses in at least three interchanging states on the cellular PM; however, KRAS remains monomeric and always shows homogeneous diffusion on artificial membranes. Here, we show for the first time on a supported lipid bilayer composed of heterogeneous lipid components that we can recapitulate the three-state diffusion of KRAS seen in cells. The use of a biologically relevant eight-lipid system opens a new frontier in the biophysical studies of RAS and other membrane associated proteins on a biomimetic system that recapitulates the complexity of a cellular PM. KRAS4b shows homogeneous diffusion on simple 2-lipids bilayer KRAS4b shows a cell-like, three-state diffusion on a complex 8-lipid bilayer Phase separation in lipids favors the multi-state diffusion of KRAS4b The complex lipid composition favors RAS nanoclustering irrespective of nucleotide state
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Affiliation(s)
- Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Peter Frank
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
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15
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Ingólfsson HI, Neale C, Carpenter TS, Shrestha R, López CA, Tran TH, Oppelstrup T, Bhatia H, Stanton LG, Zhang X, Sundram S, Di Natale F, Agarwal A, Dharuman G, Kokkila Schumacher SIL, Turbyville T, Gulten G, Van QN, Goswami D, Jean-Francois F, Agamasu C, Chen D, Hettige JJ, Travers T, Sarkar S, Surh MP, Yang Y, Moody A, Liu S, Van Essen BC, Voter AF, Ramanathan A, Hengartner NW, Simanshu DK, Stephen AG, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, McCormick F, Nissley DV, Streitz FH. Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins. Proc Natl Acad Sci U S A 2022; 119:e2113297119. [PMID: 34983849 PMCID: PMC8740753 DOI: 10.1073/pnas.2113297119] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/17/2023] Open
Abstract
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.
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Affiliation(s)
- Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Rebika Shrestha
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Timothy H Tran
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Tomas Oppelstrup
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Liam G Stanton
- Department of Mathematics and Statistics, San José State University, San José, CA 95192
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Shiv Sundram
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Animesh Agarwal
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Gautham Dharuman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | | | - Thomas Turbyville
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Gulcin Gulten
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Que N Van
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Debanjan Goswami
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Frantz Jean-Francois
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Constance Agamasu
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - De Chen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Jeevapani J Hettige
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Sumantra Sarkar
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Michael P Surh
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Yue Yang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Adam Moody
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Shusen Liu
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Brian C Van Essen
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Arthur F Voter
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Arvind Ramanathan
- Computing, Environment & Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Dhirendra K Simanshu
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Andrew G Stephen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Peer-Timo Bremer
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - James N Glosli
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Frank McCormick
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701;
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94115
| | - Dwight V Nissley
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701;
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550;
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16
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Nahar R, Iwata S, Morita D, Tahara Y, Sugimoto Y, Miyata M, Maruta S. Multimerization of Small G-protein H-Ras Induced by Chemical Modification at Hyper Variable Region with Caged Compound. J Biochem 2021; 171:215-225. [PMID: 34738101 DOI: 10.1093/jb/mvab120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/29/2021] [Indexed: 11/15/2022] Open
Abstract
The lipid-anchored small G protein Ras is a central regulator of cellular signal transduction processes, thereby functioning as a molecular switch. Ras forms a nanocluster on the plasma membrane by modifying lipids in the hypervariable region (HVR) at the C-terminus to exhibit physiological functions. In this study, we demonstrated that chemical modification of cysteine residues in HVR with caged compounds (instead of lipidation) induces multimerization of H-Ras. The sulfhydryl-reactive caged compound, 2-nitrobenzyl bromide (NBB), was stoichiometrically incorporated into the cysteine residue of HVR and induced the formation of the Ras multimer. Light irradiation induced the elimination of the 2-nitrobenzyl group, resulting in the conversion of the multimer to a monomer. SEC-HPLC and small-angle X-ray scattering (SAXS) analysis revealed that H-Ras forms a pentamer. Electron microscopic observation of the multimer showed a circular ring shape, which is consistent with the structure estimated from X-ray scattering. The shape of the multimer may reflect the physiological state of Ras. It was suggested that the multimerization and monomerization of H-Ras were controlled by modification with a caged compound in HVR under light irradiation.
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Affiliation(s)
- Rufiat Nahar
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Seigo Iwata
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Daiki Morita
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603
| | - Yuhei Tahara
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yasunobu Sugimoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603.,Nagoya University Synchrotron Radiation Research Center, Furo-cho Chikusa-ku, Nagoya 464-8603, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Shinsaku Maruta
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
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17
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Mysore VP, Zhou ZW, Ambrogio C, Li L, Kapp JN, Lu C, Wang Q, Tucker MR, Okoro JJ, Nagy-Davidescu G, Bai X, Plückthun A, Jänne PA, Westover KD, Shan Y, Shaw DE. A structural model of a Ras-Raf signalosome. Nat Struct Mol Biol 2021; 28:847-857. [PMID: 34625747 PMCID: PMC8643099 DOI: 10.1038/s41594-021-00667-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/25/2021] [Indexed: 01/29/2023]
Abstract
The protein K-Ras functions as a molecular switch in signaling pathways regulating cell growth. In the human mitogen-activated protein kinase (MAPK) pathway, which is implicated in many cancers, multiple K-Ras proteins are thought to assemble at the cell membrane with Ras effector proteins from the Raf family. Here we propose an atomistic structural model for such an assembly. Our starting point was an asymmetric guanosine triphosphate-mediated K-Ras dimer model, which we generated using unbiased molecular dynamics simulations and verified with mutagenesis experiments. Adding further K-Ras monomers in a head-to-tail fashion led to a compact helical assembly, a model we validated using electron microscopy and cell-based experiments. This assembly stabilizes K-Ras in its active state and presents composite interfaces to facilitate Raf binding. Guided by existing experimental data, we then positioned C-Raf, the downstream kinase MEK1 and accessory proteins (Galectin-3 and 14-3-3σ) on and around the helical assembly. The resulting Ras-Raf signalosome model offers an explanation for a large body of data on MAPK signaling.
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Affiliation(s)
| | - Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin, Italy
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonas N Kapp
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Chunya Lu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi Wang
- D. E. Shaw Research, New York, NY, USA
| | | | - Jeffrey J Okoro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Xiaochen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - David E Shaw
- D. E. Shaw Research, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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18
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RAS Dimers: The Novice Couple at the RAS-ERK Pathway Ball. Genes (Basel) 2021; 12:genes12101556. [PMID: 34680951 PMCID: PMC8535645 DOI: 10.3390/genes12101556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
Signals conveyed through the RAS-ERK pathway constitute a pivotal regulatory element in cancer-related cellular processes. Recently, RAS dimerization has been proposed as a key step in the relay of RAS signals, critically contributing to RAF activation. RAS clustering at plasma membrane microdomains and endomembranes facilitates RAS dimerization in response to stimulation, promoting RAF dimerization and subsequent activation. Remarkably, inhibiting RAS dimerization forestalls tumorigenesis in cellular and animal models. Thus, the pharmacological disruption of RAS dimers has emerged as an additional target for cancer researchers in the quest for a means to curtail aberrant RAS activity.
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19
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Raf promotes dimerization of the Ras G-domain with increased allosteric connections. Proc Natl Acad Sci U S A 2021; 118:2015648118. [PMID: 33653954 DOI: 10.1073/pnas.2015648118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ras dimerization is critical for Raf activation. Here we show that the Ras binding domain of Raf (Raf-RBD) induces robust Ras dimerization at low surface densities on supported lipid bilayers and, to a lesser extent, in solution as observed by size exclusion chromatography and confirmed by SAXS. Community network analysis based on molecular dynamics simulations shows robust allosteric connections linking the two Raf-RBD D113 residues located in the Galectin scaffold protein binding site of each Raf-RBD molecule and 85 Å apart on opposite ends of the dimer complex. Our results suggest that Raf-RBD binding and Ras dimerization are concerted events that lead to a high-affinity signaling complex at the membrane that we propose is an essential unit in the macromolecular assembly of higher order Ras/Raf/Galectin complexes important for signaling through the Ras/Raf/MEK/ERK pathway.
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20
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Inhibition of RAS: proven and potential vulnerabilities. Biochem Soc Trans 2021; 48:1831-1841. [PMID: 32869838 DOI: 10.1042/bst20190023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023]
Abstract
RAS is a membrane localized small GTPase frequently mutated in human cancer. As such, RAS has been a focal target for developing cancer therapeutics since its discovery nearly four decades ago. However, efforts to directly target RAS have been challenging due to the apparent lack of readily discernable deep pockets for binding small molecule inhibitors leading many to consider RAS as undruggable. An important milestone in direct RAS inhibition was achieved recently with the groundbreaking discovery of covalent inhibitors that target the mutant Cys residue in KRAS(G12C). Surprisingly, these G12C-reactive compounds only target mutant RAS in the GDP-bound state thereby locking it in the inactive conformation and blocking its ability to couple with downstream effector pathways. Building on this success, several groups have developed similar compounds that selectively target KRAS(G12C), with AMG510 and MRTX849 the first to advance to clinical trials. Both have shown early promising results. Though the success with these compounds has reignited the possibility of direct pharmacological inhibition of RAS, these covalent inhibitors are limited to treating KRAS(G12C) tumors which account for <15% of all RAS mutants in human tumors. Thus, there remains an unmet need to identify more broadly efficacious RAS inhibitors. Here, we will discuss the current state of RAS(G12C) inhibitors and the potential for inhibiting additional RAS mutants through targeting RAS dimerization which has emerged as an important step in the allosteric regulation of RAS function.
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21
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Cookis T, Mattos C. Crystal Structure Reveals the Full Ras-Raf Interface and Advances Mechanistic Understanding of Raf Activation. Biomolecules 2021; 11:996. [PMID: 34356620 PMCID: PMC8301913 DOI: 10.3390/biom11070996] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 01/17/2023] Open
Abstract
Ras and Raf-kinase interact through the Ras-binding (RBD) and cysteine-rich domains (CRD) of Raf to signal through the mitogen-activated protein kinase pathway, yet the molecular mechanism leading to Raf activation has remained elusive. We present the 2.8 Å crystal structure of the HRas-CRaf-RBD_CRD complex showing the Ras-Raf interface as a continuous surface on Ras, as seen in the KRas-CRaf-RBD_CRD structure. In molecular dynamics simulations of a Ras dimer model formed through the α4-α5 interface, the CRD is dynamic and located between the two Ras protomers, poised for direct or allosteric modulation of functionally relevant regions of Ras and Raf. We propose a molecular model in which Ras binding is involved in the release of Raf autoinhibition while the Ras-Raf complex dimerizes to promote a platform for signal amplification, with Raf-CRD centrally located to impact regulation and function.
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Affiliation(s)
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA;
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22
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Ras Variant Biology and Contributions to Human Disease. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:3-18. [PMID: 33977468 DOI: 10.1007/978-1-0716-1190-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of cancer and RASopathy genetic databases reveals that ~19% of all cancer cases and ~4% of developmental disorders contain Ras mutations. Ras isoform and mutation variants differentially contribute to these diseases and provide an opportunity for deeper understanding of Ras function. The putative mechanisms underpinning these differences, new approaches that are being applied, and some of the key questions and challenges that remain are discussed.
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23
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Rudack T, Teuber C, Scherlo M, Güldenhaupt J, Schartner J, Lübben M, Klare J, Gerwert K, Kötting C. The Ras dimer structure. Chem Sci 2021; 12:8178-8189. [PMID: 34194708 PMCID: PMC8208300 DOI: 10.1039/d1sc00957e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/29/2021] [Indexed: 12/31/2022] Open
Abstract
Oncogenic mutated Ras is a key player in cancer, but despite intense and expensive approaches its catalytic center seems undruggable. The Ras dimer interface is a possible alternative drug target. Dimerization at the membrane affects cell growth signal transduction. In vivo studies indicate that preventing dimerization of oncogenic mutated Ras inhibits uncontrolled cell growth. Conventional computational drug-screening approaches require a precise atomic dimer model as input to successfully access drug candidates. However, the proposed dimer structural models are controversial. Here, we provide a clear-cut experimentally validated N-Ras dimer structural model. We incorporated unnatural amino acids into Ras to enable the binding of labels at multiple positions via click chemistry. This labeling allowed the determination of multiple distances of the membrane-bound Ras-dimer measured by fluorescence and electron paramagnetic resonance spectroscopy. In combination with protein-protein docking and biomolecular simulations, we identified key residues for dimerization. Site-directed mutations of these residues prevent dimer formation in our experiments, proving our dimer model to be correct. The presented dimer structure enables computational drug-screening studies exploiting the Ras dimer interface as an alternative drug target.
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Affiliation(s)
- Till Rudack
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum 44801 Bochum Germany
- Department of Biophysics, Ruhr University Bochum 44801 Bochum Germany
| | - Christian Teuber
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum 44801 Bochum Germany
- Department of Biophysics, Ruhr University Bochum 44801 Bochum Germany
| | - Marvin Scherlo
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum 44801 Bochum Germany
- Department of Biophysics, Ruhr University Bochum 44801 Bochum Germany
| | - Jörn Güldenhaupt
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum 44801 Bochum Germany
- Department of Biophysics, Ruhr University Bochum 44801 Bochum Germany
| | - Jonas Schartner
- Department of Biophysics, Ruhr University Bochum 44801 Bochum Germany
| | - Mathias Lübben
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum 44801 Bochum Germany
- Department of Biophysics, Ruhr University Bochum 44801 Bochum Germany
| | - Johann Klare
- Department of Physics, Osnabrück University 49074 Osnabrück Germany
| | - Klaus Gerwert
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum 44801 Bochum Germany
- Department of Biophysics, Ruhr University Bochum 44801 Bochum Germany
| | - Carsten Kötting
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum 44801 Bochum Germany
- Department of Biophysics, Ruhr University Bochum 44801 Bochum Germany
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24
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Koyama-Honda I, Fujiwara TK, Kasai RS, Suzuki KGN, Kajikawa E, Tsuboi H, Tsunoyama TA, Kusumi A. High-speed single-molecule imaging reveals signal transduction by induced transbilayer raft phases. J Cell Biol 2021; 219:211461. [PMID: 33053147 PMCID: PMC7563750 DOI: 10.1083/jcb.202006125] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/09/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
Using single-molecule imaging with enhanced time resolutions down to 5 ms, we found that CD59 cluster rafts and GM1 cluster rafts were stably induced in the outer leaflet of the plasma membrane (PM), which triggered the activation of Lyn, H-Ras, and ERK and continually recruited Lyn and H-Ras right beneath them in the inner leaflet with dwell lifetimes <0.1 s. The detection was possible due to the enhanced time resolutions employed here. The recruitment depended on the PM cholesterol and saturated alkyl chains of Lyn and H-Ras, whereas it was blocked by the nonraftophilic transmembrane protein moiety and unsaturated alkyl chains linked to the inner-leaflet molecules. Because GM1 cluster rafts recruited Lyn and H-Ras as efficiently as CD59 cluster rafts, and because the protein moieties of Lyn and H-Ras were not required for the recruitment, we conclude that the transbilayer raft phases induced by the outer-leaflet stabilized rafts recruit lipid-anchored signaling molecules by lateral raft-lipid interactions and thus serve as a key signal transduction platform.
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Affiliation(s)
- Ikuko Koyama-Honda
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, University of Tokyo, Tokyo, Japan
| | - Takahiro K Fujiwara
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Rinshi S Kasai
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kenichi G N Suzuki
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.,Institute for Glyco-core Research, Gifu University, Nagoya, Japan.,Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University, Gifu, Japan
| | - Eriko Kajikawa
- Laboratory for Organismal Patterning, Center for Biosystems Dynamics Research, RIKEN Kobe, Kobe, Japan
| | - Hisae Tsuboi
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Taka A Tsunoyama
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Akihiro Kusumi
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
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25
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Van QN, Prakash P, Shrestha R, Balius TE, Turbyville TJ, Stephen AG. RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention. Biomolecules 2021; 11:377. [PMID: 33802474 PMCID: PMC8000715 DOI: 10.3390/biom11030377] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 01/18/2023] Open
Abstract
RAS proteins are mutated in approximately 20% of all cancers and are generally associated with poor clinical outcomes. RAS proteins are localized to the plasma membrane and function as molecular switches, turned on by partners that receive extracellular mitogenic signals. In the on-state, they activate intracellular signal transduction cascades. Membrane-bound RAS molecules segregate into multimers, known as nanoclusters. These nanoclusters, held together through weak protein-protein and protein-lipid associations, are highly dynamic and respond to cellular input signals and fluctuations in the local lipid environment. Disruption of RAS nanoclusters results in downregulation of RAS-mediated mitogenic signaling. In this review, we discuss the propensity of RAS proteins to display clustering behavior and the interfaces that are associated with these assemblies. Strategies to therapeutically disrupt nanocluster formation or the stabilization of signaling incompetent RAS complexes are discussed.
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Affiliation(s)
| | | | | | | | | | - Andrew G. Stephen
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, National Cancer Institute RAS Initiative, Inc., Frederick, MD 21702, USA; (Q.N.V.); (P.P.); (R.S.); (T.E.B.); (T.J.T.)
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26
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Liu Y, Gao GF, Minna JD, Williams NS, Westover KD. Loss of wild type KRAS in KRAS MUT lung adenocarcinoma is associated with cancer mortality and confers sensitivity to FASN inhibitors. Lung Cancer 2021; 153:73-80. [PMID: 33465697 DOI: 10.1016/j.lungcan.2020.12.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 12/04/2020] [Accepted: 12/22/2020] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Wild type RAS (RASWT) suppresses the function of oncogenic RAS mutants (RASMUT) in laboratory models. Loss of RASWT, which we termed loss of heterozygosity (LOH) for any RAS (LAR) or LAKR in the context of KRAS (LOH at KRAS), is found in patients with RASMUT cancers. However, the incidence and prognostic significance of LAR has not been studied in modern patient cohorts. LAR or LAKR in RASMUT cancers is attractive as a potential biomarker for targeted therapy. MATERIALS AND METHODS We evaluated for associations between LAKR and cancer mortality in patients with KRASMUT lung adenocarcinoma (LUAD). We also evaluated for associations between LAKR and the metabolic state of cancer cell lines, given that KRAS has been shown to regulate fatty acid synthesis. In line with this, we investigated fatty acid synthase (FASN) inhibitors as potential therapies for KRASMUT LAKR, including combination strategies involving clinical KRASG12C and FASN inhibitors. RESULTS 24 % of patients with KRASMUT LUAD showed LAKR. KRASMUT LAKR cases had a median survival of 16 vs. 30 months in KRASMUT non-LAKR (p = 0.017) and LAKR was independently associated with death in this cohort (p = 0.011). We also found that KRASMUT LUAD cell lines with LAKR contained elevated levels of FASN and fatty acids relative to non-LAKR cell lines. KRASMUT LUAD cells with LAKR showed higher sensitivity to treatment with FASN inhibitors than those without. FASN inhibitors such as TVB-3664 showed synergistic effects with the KRASG12C inhibitor MRTX849 in LUAD cells with KRASG12C and LAKR, including an in vivo trial using a xenograft model. CONCLUSIONS LAKR in KRASMUT cancers may represent an independent negative prognostic factor for patients with KRASMUT LUAD. It also predicts for response to treatment with FASN inhibitors. Prospective testing of combination therapies including KRASG12C and FASN inhibitors in patients with KRASG12C LAKR is warranted.
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Affiliation(s)
- Yan Liu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, United States
| | - Galen F Gao
- School of Medicine, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, United States
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, Departments of Internal Medicine and Pharmacology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, 75390-8593, United States
| | - Noelle S Williams
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, United States
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, United States.
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27
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Natural Products Attenuating Biosynthesis, Processing, and Activity of Ras Oncoproteins: State of the Art and Future Perspectives. Biomolecules 2020; 10:biom10111535. [PMID: 33182807 PMCID: PMC7698260 DOI: 10.3390/biom10111535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/08/2020] [Indexed: 02/07/2023] Open
Abstract
RAS genes encode signaling proteins, which, in mammalian cells, act as molecular switches regulating critical cellular processes as proliferation, growth, differentiation, survival, motility, and metabolism in response to specific stimuli. Deregulation of Ras functions has a high impact on human health: gain-of-function point mutations in RAS genes are found in some developmental disorders and thirty percent of all human cancers, including the deadliest. For this reason, the pathogenic Ras variants represent important clinical targets against which to develop novel, effective, and possibly selective pharmacological inhibitors. Natural products represent a virtually unlimited resource of structurally different compounds from which one could draw on for this purpose, given the improvements in isolation and screening of active molecules from complex sources. After a summary of Ras proteins molecular and regulatory features and Ras-dependent pathways relevant for drug development, we point out the most promising inhibitory approaches, the known druggable sites of wild-type and oncogenic Ras mutants, and describe the known natural compounds capable of attenuating Ras signaling. Finally, we highlight critical issues and perspectives for the future selection of potential Ras inhibitors from natural sources.
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28
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Shevchenko E, Poso A, Pantsar T. The autoinhibited state of MKK4: Phosphorylation, putative dimerization and R134W mutant studied by molecular dynamics simulations. Comput Struct Biotechnol J 2020; 18:2687-2698. [PMID: 33101607 PMCID: PMC7550801 DOI: 10.1016/j.csbj.2020.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/19/2022] Open
Abstract
Protein kinases are crucial components of the cell-signalling machinery that orchestrate and convey messages to their downstream targets. Most often, kinases are activated upon a phosphorylation to their activation loop, which will shift the kinase into the active conformation. The Dual specificity mitogen-activated protein kinase kinase 4 (MKK4) exists in a unique conformation in its inactive unphosphorylated state, where its activation segment appears in a stable α-helical conformation. However, the precise role of this unique conformational state of MKK4 is unknown. Here, by all-atom molecular dynamics simulations (MD simulations), we show that this inactive state is unstable as monomer even when unphosphorylated and that the phosphorylation of the activation segment further destabilizes the autoinhibited α-helix. The specific phosphorylation pattern of the activation segment has also a unique influence on MKK4 dynamics. Furthermore, we observed that this specific inactive state is stable as a dimer, which becomes destabilized upon phosphorylation. Finally, we noticed that the most frequent MKK4 mutation observed in cancer, R134W, which role has not been disclosed to date, contributes to the dimer stability. Based on these data we postulate that MKK4 occurs as a dimer in its inactive autoinhibited state, providing an additional layer for its activity regulation.
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Affiliation(s)
- Ekaterina Shevchenko
- Dept of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Antti Poso
- Dept of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, 70210 Kuopio, Finland
| | - Tatu Pantsar
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1C, 70210 Kuopio, Finland
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Corresponding author.
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29
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Lamas I, Weber N, Martin SG. Activation of Cdc42 GTPase upon CRY2-Induced Cortical Recruitment Is Antagonized by GAPs in Fission Yeast. Cells 2020; 9:E2089. [PMID: 32932721 PMCID: PMC7565336 DOI: 10.3390/cells9092089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
The small GTPase Cdc42 is critical for cell polarization in eukaryotic cells. In rod-shaped fission yeast Schizosaccharomyces pombe cells, active GTP-bound Cdc42 promotes polarized growth at cell poles, while inactive Cdc42-GDP localizes ubiquitously also along cell sides. Zones of Cdc42 activity are maintained by positive feedback amplification involving the formation of a complex between Cdc42-GTP, the scaffold Scd2, and the guanine nucleotide exchange factor (GEF) Scd1, which promotes the activation of more Cdc42. Here, we use the CRY2-CIB1 optogenetic system to recruit and cluster a cytosolic Cdc42 variant at the plasma membrane and show that this leads to its moderate activation also on cell sides. Surprisingly, Scd2, which binds Cdc42-GTP, is still recruited to CRY2-Cdc42 clusters at cell sides in individual deletion of the GEFs Scd1 or Gef1. We show that activated Cdc42 clusters at cell sides are able to recruit Scd1, dependent on the scaffold Scd2. However, Cdc42 activity is not amplified by positive feedback and does not lead to morphogenetic changes, due to antagonistic activity of the GTPase activating protein Rga4. Thus, the cell architecture is robust to moderate activation of Cdc42 at cell sides.
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Affiliation(s)
| | | | - Sophie G. Martin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore building, 1015 Lausanne, Switzerland; (I.L.); (N.W.)
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30
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Dudas B, Merzel F, Jang H, Nussinov R, Perahia D, Balog E. Nucleotide-Specific Autoinhibition of Full-Length K-Ras4B Identified by Extensive Conformational Sampling. Front Mol Biosci 2020; 7:145. [PMID: 32754617 PMCID: PMC7366858 DOI: 10.3389/fmolb.2020.00145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
K-Ras is one of the most frequently mutated oncogenes in human tumor cells. It consists of a well-conserved globular catalytic domain and a flexible tail-like hypervariable region (HVR) at its C-terminal end. It plays a key role in signaling networks in proliferation, differentiation, and survival, undergoing a conformational switch between the active and inactive states. It is regulated through the GDP-GTP cycle of the inactive GDP-bound and active GTP-bound states. Here, without imposing any prior constraints, we mapped the interaction pattern between the catalytic domain and the HVR using Molecular Dynamics with excited Normal Modes (MDeNM) starting from an initially extended HVR conformation for both states. Our sampling captured similar interaction patterns in both GDP- and GTP-bound states with shifted populations depending on the bound nucleotide. In the GDP-bound state, the conformations where the HVR interacts with the effector lobe are more populated than in the GTP-bound state, forming a buried thus autoinhibited catalytic site; in the GTP-bound state conformations where the HVR interacts with the allosteric lobe are more populated, overlapping the α3/α4 dimerization interface. The interaction of the GTP with Switch I and Switch II is stronger than that of the GDP in line with a decrease in the fluctuation upon GTP binding.
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Affiliation(s)
- Balint Dudas
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.,Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
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31
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Abstract
RAS was identified as a human oncogene in the early 1980s and subsequently found to be mutated in nearly 30% of all human cancers. More importantly, RAS plays a central role in driving tumor development and maintenance. Despite decades of effort, there remain no FDA approved drugs that directly inhibit RAS. The prevalence of RAS mutations in cancer and the lack of effective anti-RAS therapies stem from RAS' core role in growth factor signaling, unique structural features, and biochemistry. However, recent advances have brought promising new drugs to clinical trials and shone a ray of hope in the field. Here, we will exposit the details of RAS biology that illustrate its key role in cell signaling and shed light on the difficulties in therapeutically targeting RAS. Furthermore, past and current efforts to develop RAS inhibitors will be discussed in depth.
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Affiliation(s)
- J Matthew Rhett
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States
| | - Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States.
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32
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Abstract
RAS (KRAS, NRAS and HRAS) is the most frequently mutated gene family in cancers, and, consequently, investigators have sought an effective RAS inhibitor for more than three decades. Even 10 years ago, RAS inhibitors were so elusive that RAS was termed 'undruggable'. Now, with the success of allele-specific covalent inhibitors against the most frequently mutated version of RAS in non-small-cell lung cancer, KRASG12C, we have the opportunity to evaluate the best therapeutic strategies to treat RAS-driven cancers. Mutation-specific biochemical properties, as well as the tissue of origin, are likely to affect the effectiveness of such treatments. Currently, direct inhibition of mutant RAS through allele-specific inhibitors provides the best therapeutic approach. Therapies that target RAS-activating pathways or RAS effector pathways could be combined with these direct RAS inhibitors, immune checkpoint inhibitors or T cell-targeting approaches to treat RAS-mutant tumours. Here we review recent advances in therapies that target mutant RAS proteins and discuss the future challenges of these therapies, including combination strategies.
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33
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Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function. Proc Natl Acad Sci U S A 2020; 117:8563-8572. [PMID: 32220963 DOI: 10.1073/pnas.2000703117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The small GTPase RABL3 is an oncogene of unknown physiological function. Homozygous knockout alleles of mouse Rabl3 were embryonic lethal, but a viable hypomorphic allele (xiamen [xm]) causing in-frame deletion of four amino acids from the interswitch region resulted in profound defects in lymphopoiesis. Impaired lymphoid progenitor development led to deficiencies of B cells, T cells, and natural killer (NK) cells in Rabl3 xm/xm mice. T cells and NK cells exhibited impaired cytolytic activity, and mice infected with mouse cytomegalovirus (MCMV) displayed elevated titers in the spleen. Myeloid cells were normal in number and function. Biophysical and crystallographic studies demonstrated that RABL3 formed a homodimer in solution via interactions between the effector binding surfaces on each subunit; monomers adopted a typical small G protein fold. RABL3xm displayed a large compensatory alteration in switch I, which adopted a β-strand configuration normally provided by the deleted interswitch residues, thereby permitting homodimer formation. Dysregulated effector binding due to conformational changes in the switch I-interswitch-switch II module likely underlies the xm phenotype. One such effector may be GPR89, putatively an ion channel or G protein-coupled receptor (GPCR). RABL3, but not RABL3xm, strongly associated with and stabilized GPR89, and an N-ethyl-N-nitrosourea (ENU)-induced mutation (explorer) in Gpr89 phenocopied Rabl3 xm.
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34
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Sarkar S, García AE. Presence or Absence of Ras Dimerization Shows Distinct Kinetic Signature in Ras-Raf Interaction. Biophys J 2020; 118:1799-1810. [PMID: 32199071 DOI: 10.1016/j.bpj.2020.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/30/2019] [Accepted: 03/02/2020] [Indexed: 02/07/2023] Open
Abstract
Initiations of cell signaling pathways often occur through the formation of multiprotein complexes that form through protein-protein interactions. Therefore, detecting their presence is central to understanding the function of a cell signaling pathway, aberration of which often leads to fatal diseases, including cancers. However, the multiprotein complexes are often difficult to detect using microscopes due to their small sizes. Therefore, currently, their presence can be only detected through indirect means. In this article, we propose to investigate the presence or absence of protein complexes through some easily measurable kinetic parameters, such as activation rates. As a proof of concept, we investigate the Ras-Raf system, a well-characterized cell signaling system. It has been hypothesized that Ras dimerization is necessary to create activated Raf dimers. Although there are circumstantial evidences supporting the Ras dimerization hypothesis, direct proof of Ras dimerization is still inconclusive. In the absence of conclusive direct experimental proof, this hypothesis can only be examined through indirect evidences of Ras dimerization. In this article, using a multiscale simulation technique, we provide multiple criteria that distinguishes an activation mechanism involving Ras dimerization from another mechanism that does not involve Ras dimerization. The provided criteria will be useful in the investigation of not only Ras-Raf interaction but also other two-protein interactions.
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Affiliation(s)
- Sumantra Sarkar
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico.
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35
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Muratcioglu S, Aydin C, Odabasi E, Ozdemir ES, Firat-Karalar EN, Jang H, Tsai CJ, Nussinov R, Kavakli IH, Gursoy A, Keskin O. Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling. J Mol Biol 2020; 432:1199-1215. [PMID: 31931009 PMCID: PMC8533050 DOI: 10.1016/j.jmb.2020.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023]
Abstract
Ras recruits and activates effectors that transmit receptor-initiated signals. Monomeric Ras can bind Raf; however, Raf's activation requires dimerization, which can be facilitated by Ras dimerization. Previously, we showed that active K-Ras4B dimerizes in silico and in vitro through two major interfaces: (i) β-interface, mapped to Switch I and effector-binding regions, (ii) α-interface at the allosteric lobe. Here, we chose constitutively active K-Ras4B as our control and two double mutants (K101D and R102E; and R41E and K42D) in the α- and β-interfaces. Two of the mutations are from The Cancer Genome Atlas (TCGA) and the Catalogue Of Somatic Mutations In Cancer (COSMIC) data sets. R41 and R102 are found in several adenocarcinomas in Ras isoforms. We performed site-directed mutagenesis, cellular localization experiments, and molecular dynamics (MD) simulations to assess the impact of the mutations on K-Ras4B dimerization and function. α-interface K101D/R102E double mutations reduced dimerization but only slightly reduced downstream phosphorylated extracellular signal-regulated kinase (ERK) (pERK) levels. While β-interface R41E/K42D double mutations did not interfere with dimerization, they almost completely blocked K-Ras4B-mediated ERK phosphorylation. Both double mutations increased downstream phosphorylated Akt (pAkt) levels in cells. Changes in pERK and pAkt levels altered ERK- and Akt-regulated gene expressions, such as EGR1, JUN, and BCL2L11. These results underscore the role of the α-interface in K-Ras4B homodimerization and the β-surface in effector binding. MD simulations highlight that the membrane and hypervariable region (HVR) interact with both α- and β-interfaces of K-Ras4B mutants, respectively, inhibiting homodimerization and probably effector binding. Mutations at both interfaces interfered with mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase signaling but in different forms and extents. We conclude that dimerization is not necessary but enhances downstream MAPK signaling.
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Affiliation(s)
- Serena Muratcioglu
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey
| | - Cihan Aydin
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey
| | - Ezgi Odabasi
- Departments of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - E Sila Ozdemir
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey
| | | | - Hyunbum Jang
- 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
| | - 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
| | - Ibrahim Halil Kavakli
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey; Departments of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Attila Gursoy
- Departments of Computer Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey.
| | - Ozlem Keskin
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey.
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36
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Khan I, Rhett JM, O'Bryan JP. Therapeutic targeting of RAS: New hope for drugging the "undruggable". BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118570. [PMID: 31678118 PMCID: PMC6937383 DOI: 10.1016/j.bbamcr.2019.118570] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/01/2019] [Accepted: 10/14/2019] [Indexed: 12/18/2022]
Abstract
RAS is the most frequently mutated oncogene in cancer and a critical driver of oncogenesis. Therapeutic targeting of RAS has been a goal of cancer research for more than 30 years due to its essential role in tumor formation and maintenance. Yet the quest to inhibit this challenging foe has been elusive. Although once considered "undruggable", the struggle to directly inhibit RAS has seen recent success with the development of pharmacological agents that specifically target the KRAS(G12C) mutant protein, which include the first direct RAS inhibitor to gain entry to clinical trials. However, the limited applicability of these inhibitors to G12C-mutant tumors demands further efforts to identify more broadly efficacious RAS inhibitors. Understanding allosteric influences on RAS may open new avenues to inhibit RAS. Here, we provide a brief overview of RAS biology and biochemistry, discuss the allosteric regulation of RAS, and summarize the various approaches to develop RAS inhibitors.
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Affiliation(s)
- Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America
| | - J Matthew Rhett
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America.
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37
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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: 291] [Impact Index Per Article: 72.8] [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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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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Lee Y, Phelps C, Huang T, Mostofian B, Wu L, Zhang Y, Tao K, Chang YH, Stork PJ, Gray JW, Zuckerman DM, Nan X. High-throughput, single-particle tracking reveals nested membrane domains that dictate KRas G12D diffusion and trafficking. eLife 2019; 8:46393. [PMID: 31674905 PMCID: PMC7060040 DOI: 10.7554/elife.46393] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Membrane nanodomains have been implicated in Ras signaling, but what these domains are and how they interact with Ras remain obscure. Here, using single particle tracking with photoactivated localization microscopy (spt-PALM) and detailed trajectory analysis, we show that distinct membrane domains dictate KRasG12D (an active KRas mutant) diffusion and trafficking in U2OS cells. KRasG12D exhibits an immobile state in ~70 nm domains, each embedded in a larger domain (~200 nm) that confers intermediate mobility, while the rest of the membrane supports fast diffusion. Moreover, KRasG12D is continuously removed from the membrane via the immobile state and replenished to the fast state, reminiscent of Ras internalization and recycling. Importantly, both the diffusion and trafficking properties of KRasG12D remain invariant over a broad range of protein expression levels. Our results reveal how membrane organization dictates membrane diffusion and trafficking of Ras and offer new insight into the spatial regulation of Ras signaling. The Ras family of proteins play an important role in relaying signals from the outside to the inside of the cell. Ras proteins are attached by a fatty tail to the inner surface of the cell membrane. When activated they transmit a burst of signal that controls critical behaviors like growth, survival and movement. It has been suggested that to prevent these signals from being accidently activated, Ras molecules must group together at specialized sites within the membrane before passing on their message. However, visualizing how Ras molecules cluster together at these domains has thus far been challenging. As a result, little is known about where these sites are located and how Ras molecules come to a stop at these domains. Now, Lee et al. have combined two microscopy techniques called ‘single-particle tracking’ and ‘photoactivated localization microscopy' to track how individual molecules of activated Ras move in human cells grown in the lab. This revealed that Ras molecules quickly diffuse along the inside of the membrane until they arrive at certain locations that cause them to halt. However, computer models consisting of just the ‘fast’ and ‘immobile’ state could not correctly re-capture the way Ras molecules moved along the membrane. Lee et al. found that for these models to mimic the movement of Ras, a third ‘intermediate’ state of Ras mobility needed to be included. To investigate this further, Lee et al. created a fluorescent map that overlaid all the individual paths taken by each Ras molecule. The map showed regions in the membrane where the Ras molecules had stopped and possibly clustered together. Each of these ‘immobilization domains’ were then surrounded by an ‘intermediate domain’ where Ras molecules had begun to slow down their movement. Although the intermediate domains did not last long, they seemed to guide Ras molecules into the immobilization domains where they could cluster together with other molecules. From there, the cell constantly removed Ras molecules from these membrane domains and returned them back to their ‘fast’ diffusing state. Mutations in Ras proteins occur in around a third of all cancers, so a better understanding of their dynamics could help with future drug discovery. The methods used here could also be used to investigate the movement of other signaling molecules.
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Affiliation(s)
- Yerim Lee
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Carey Phelps
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Tao Huang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Barmak Mostofian
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Lei Wu
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States.,Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Ying Zhang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Kai Tao
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Philip Js Stork
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States.,Knight Cancer Early Detection Advanced Research (CEDAR) Center, Oregon Health and Science University, Portland, United States
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40
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Mehaffey MR, Schardon CL, Novelli ET, Cammarata MB, Webb LJ, Fast W, Brodbelt JS. Investigation of GTP-dependent dimerization of G12X K-Ras variants using ultraviolet photodissociation mass spectrometry. Chem Sci 2019; 10:8025-8034. [PMID: 31853358 PMCID: PMC6837035 DOI: 10.1039/c9sc01032g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/14/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in the GTPase enzyme K-Ras, specifically at codon G12, remain the most common genetic alterations in human cancers. The mechanisms governing activation of downstream signaling pathways and how they relate back to the identity of the mutation have yet to be completely defined. Here we use native mass spectrometry (MS) combined with ultraviolet photodissociation (UVPD) to investigate the impact of three G12X mutations (G12C, G12V, G12S) on the homodimerization of K-Ras as well as heterodimerization with a downstream effector protein, Raf. Electrospray ionization (ESI) was used to transfer complexes of WT or G12X K-Ras bound to guanosine 5'-diphosphate (GDP) or GppNHp (non-hydrolyzable analogue of GTP) into the gas phase. Relative abundances of homo- or hetero-dimer complexes were estimated from ESI-MS spectra. K-Ras + Raf heterocomplexes were activated with UVPD to probe structural changes responsible for observed differences in the amount of heterocomplex formed for each variant. Holo (ligand-bound) fragment ions resulting from photodissociation suggest the G12X mutants bind Raf along the expected effector binding region (β-interface) but may interact with Raf via an alternative α-interface as well. Variations in backbone cleavage efficiencies during UV photoactivation of each variant were used to relate mutation identity to structural changes that might impact downstream signaling. Specifically, oncogenic upregulation for hydrogen-bonding amino acid substitutions (G12C, G12S) is achieved by stabilizing β-interface interactions with Raf, while a bulkier, hydrophobic G12V substitution leads to destabilization of this interface and instead increases the proximity of residues along the α-helical bundles. This study deciphers new pieces of the complex puzzle of how different K-Ras mutations exert influence in downstream signaling.
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
| | - Christopher L Schardon
- Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy , University of Texas at Austin , Austin , TX 78712 , USA
| | - Elisa T Novelli
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
| | - Michael B Cammarata
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
| | - Lauren J Webb
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy , University of Texas at Austin , Austin , TX 78712 , USA
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
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41
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Barklis E, Stephen AG, Staubus AO, Barklis RL, Alfadhli A. Organization of Farnesylated, Carboxymethylated KRAS4B on Membranes. J Mol Biol 2019; 431:3706-3717. [PMID: 31330153 PMCID: PMC6733658 DOI: 10.1016/j.jmb.2019.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 11/24/2022]
Abstract
Mutations of the Ras proteins HRAS, KRAS4A, KRAS4B, and NRAS are associated with a high percentage of all human cancers. The proteins are composed of highly homologous N-terminal catalytic or globular domains, plus C-terminal hypervariable regions (HVRs). Post-translational modifications of all RAS HVRs helps target RAS proteins to cellular membrane locations where they perform their signaling functions. For the predominant KRAS4 isoform, KRAS4B, post-translational farnesylation and carboxymethylation, along with a patch of HVR basic residues help foster membrane binding. Recent investigations implicate membrane-bound RAS dimers, oligomers, and nanoclusters as landing pads for effector proteins that relay RAS signals. The details of these RAS signaling platforms have not been elucidated completely, in part due to the difficulties in preparing modified proteins. We have employed properly farnesylated and carboxymethylated KRAS4B in lipid monolayer incubations to examine how the proteins assemble on membranes. Our results reveal novel insights into to how KRAS4B may organize on membranes.
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Affiliation(s)
- Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA.
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21072, USA
| | - August O Staubus
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
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42
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Wei X, Zhao T, Zhang Y, Ai K, Li H, Yang J. Involvement of H-Ras in the adaptive immunity of Nile tilapia by regulating lymphocyte activation. FISH & SHELLFISH IMMUNOLOGY 2019; 89:281-289. [PMID: 30953781 DOI: 10.1016/j.fsi.2019.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/24/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
H-Ras is a guanosine triphosphatase (GTPase), which acts as a molecular switch and controls multiple important cellular processes including lymphocyte activation and function. However, regulatory mechanism of adaptive immune response by H-Ras remains unclear in non-mammalian animals. In the present study, we investigated the involvement of H-Ras in lymphocyte activation with a teleost model Oreochromis niloticus. H-Ras from O. niloticus (On-H-Ras) is highly conserved with those from other vertebrates. The mRNA of On-H-Ras showed a wide expression pattern in the lymphoid-tissues and with the highest level in liver. After Aeromonas hydrophila infection, transcription of On-H-Ras was significantly induced on day 8 but came back to basal level on day 16, suggesting that On-H-Ras potentially participated in primary response during the adaptive immunity. Furthermore, On-H-Ras mRNA was obviously up-regulated when leukocytes were activated by T lymphocyte mitogen PHA in vitro. Meanwhile, protein level of H-Ras was also augmented once leukocytes were stimulated with lymphocyte receptor signaling agonist PMA and ionomycin. More importantly, once Ras activity was inhibited by specific inhibitor, the up-regulation of lymphocyte activation marker CD122 was obviously impaired during lymphocyte activation process. Therefore, On-H-Ras regulated lymphocyte activation through both mRNA and protein level. Altogether, our results illustrated the involvement of H-Ras in teleost adaptive immunity via controlling lymphocyte activation, and thus provided a novel perspective to understand evolution of the lymphocyte-mediated adaptive immunity.
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Affiliation(s)
- Xiumei Wei
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Aquatic Comparative Immunology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Tianyu Zhao
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Aquatic Comparative Immunology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yu Zhang
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Aquatic Comparative Immunology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Kete Ai
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Aquatic Comparative Immunology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Huiying Li
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Aquatic Comparative Immunology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jialong Yang
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Aquatic Comparative Immunology, School of Life Sciences, East China Normal University, Shanghai, 200241, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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43
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Cao S, Chung S, Kim S, Li Z, Manor D, Buck M. K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function. J Biol Chem 2019; 294:7068-7084. [PMID: 30792310 DOI: 10.1074/jbc.ra118.004021] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
Ras genes potently drive human cancers, with mutated proto-oncogene GTPase KRAS4B (K-Ras4B) being the most abundant isoform. Targeted inhibition of oncogenic gene products is considered the "holy grail" of present-day cancer therapy, and recent discoveries of small-molecule KRas4B inhibitors were made thanks to a deeper understanding of the structure and dynamics of this GTPase. Because interactions with biological membranes are key for Ras function, Ras-lipid interactions have become a major focus, especially because such interactions evidently involve both the Ras C terminus for lipid anchoring and its G-protein domain. Here, using NMR spectroscopy and molecular dynamics simulations complemented by biophysical- and cell-biology assays, we investigated the interaction between K-Ras4B with the signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2). We discovered that the β2 and β3 strands as well as helices 4 and 5 of the GTPase G-domain bind to PIP2 and identified the specific residues in these structural elements employed in these interactions, likely occurring in two K-Ras4B orientation states relative to the membrane. Importantly, we found that some of these residues known to be oncogenic when mutated (D47K, D92N, K104M, and D126N) are critical for K-Ras-mediated transformation of fibroblast cells, but do not substantially affect basal and assisted nucleotide hydrolysis and exchange. Moreover, the K104M substitution abolished localization of K-Ras to the plasma membrane. The findings suggest that specific G-domain residues can critically regulate Ras function by mediating interactions with membrane-associated PIP2 lipids; these insights that may inform the future design of therapeutic reagents targeting Ras activity.
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Affiliation(s)
- Shufen Cao
- From the Departments of Physiology and Biophysics
| | | | | | - Zhenlu Li
- From the Departments of Physiology and Biophysics
| | - Danny Manor
- Nutrition, .,Pharmacology, and.,the Case Comprehensive Cancer Center and
| | - Matthias Buck
- From the Departments of Physiology and Biophysics, .,the Case Comprehensive Cancer Center and.,Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106 and.,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
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Perspectives of RAS and RHEB GTPase Signaling Pathways in Regenerating Brain Neurons. Int J Mol Sci 2018; 19:ijms19124052. [PMID: 30558189 PMCID: PMC6321366 DOI: 10.3390/ijms19124052] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/29/2022] Open
Abstract
Cellular activation of RAS GTPases into the GTP-binding “ON” state is a key switch for regulating brain functions. Molecular protein structural elements of rat sarcoma (RAS) and RAS homolog protein enriched in brain (RHEB) GTPases involved in this switch are discussed including their subcellular membrane localization for triggering specific signaling pathways resulting in regulation of synaptic connectivity, axonal growth, differentiation, migration, cytoskeletal dynamics, neural protection, and apoptosis. A beneficial role of neuronal H-RAS activity is suggested from cellular and animal models of neurodegenerative diseases. Recent experiments on optogenetic regulation offer insights into the spatiotemporal aspects controlling RAS/mitogen activated protein kinase (MAPK) or phosphoinositide-3 kinase (PI3K) pathways. As optogenetic manipulation of cellular signaling in deep brain regions critically requires penetration of light through large distances of absorbing tissue, we discuss magnetic guidance of re-growing axons as a complementary approach. In Parkinson’s disease, dopaminergic neuronal cell bodies degenerate in the substantia nigra. Current human trials of stem cell-derived dopaminergic neurons must take into account the inability of neuronal axons navigating over a large distance from the grafted site into striatal target regions. Grafting dopaminergic precursor neurons directly into the degenerating substantia nigra is discussed as a novel concept aiming to guide axonal growth by activating GTPase signaling through protein-functionalized intracellular magnetic nanoparticles responding to external magnets.
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O'Bryan JP. Pharmacological targeting of RAS: Recent success with direct inhibitors. Pharmacol Res 2018; 139:503-511. [PMID: 30366101 DOI: 10.1016/j.phrs.2018.10.021] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/19/2018] [Accepted: 10/21/2018] [Indexed: 02/06/2023]
Abstract
RAS has long been viewed as undruggable due to its lack of deep pockets for binding of small molecule inhibitors. However, recent successes in the development of direct RAS inhibitors suggest that the goal of pharmacological inhibition of RAS in patients may soon be realized. This review will discuss the role of RAS in cancer, the approaches used to develop direct RAS inhibitors, and highlight recent successes in the development of novel RAS inhibitory compounds that target different aspects of RAS biochemistry. In particular, this review will discuss the different properties of RAS that have been targeted by various inhibitors including membrane localization, the different activation states of RAS, effector binding, and nucleotide exchange. In addition, this review will highlight the recent success with mutation-specific inhibitors that exploit the unique biochemistry of the RAS(G12C) mutant. Although this mutation in KRAS accounts for 11% of all KRAS mutations in cancer, it is the most prominent KRAS mutant in lung cancer suggesting that G12C-specific inhibitors may provide a new approach for treating the subset of lung cancer patients harboring this mutant allele. Finally, this review will discuss the involvement of dimerization in RAS function and highlight new approaches to inhibit RAS by specifically interfering with RAS:RAS interaction.
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Affiliation(s)
- John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, 29401, United States.
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Spencer-Smith R, O'Bryan JP. Direct inhibition of RAS: Quest for the Holy Grail? Semin Cancer Biol 2017; 54:138-148. [PMID: 29248537 DOI: 10.1016/j.semcancer.2017.12.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/13/2017] [Indexed: 12/25/2022]
Abstract
RAS GTPases (H-, K-, and N-RAS) are the most frequently mutated oncoprotein family in human cancer. However, the relatively smooth surface architecture of RAS and its picomolar affinity for nucleotide have given rise to the assumption that RAS is an "undruggable" target. Recent advancements in drug screening, molecular modeling, and a greater understanding of RAS function have led to a resurgence in efforts to pharmacologically target this challenging foe. This review focuses on the state of the art of RAS inhibition, the approaches taken to achieve this goal, and the challenges of translating these discoveries into viable therapeutics.
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Affiliation(s)
- Russell Spencer-Smith
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA; University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, USA; Jesse Brown VA Medical Center, Chicago, IL, USA
| | - John P O'Bryan
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA; University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, USA; Jesse Brown VA Medical Center, Chicago, IL, USA.
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Sarkar-Banerjee S, Sayyed-Ahmad A, Prakash P, Cho KJ, Waxham MN, Hancock JF, Gorfe AA. Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes. J Am Chem Soc 2017; 139:13466-13475. [PMID: 28863262 PMCID: PMC5663506 DOI: 10.1021/jacs.7b06292] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-assembly of plasma membrane-associated Ras GTPases has major implications to the regulation of cell signaling. However, the structural basis of homo-oligomerization and the fractional distribution of oligomeric states remained undetermined. We have addressed these issues by deciphering the distribution of dimers and higher-order oligomers of K-Ras4B, the most frequently mutated Ras isoform in human cancers. We focused on the constitutively active G12V K-Ras and two of its variants, K101E and K101C/E107C, which respectively destabilize and stabilize oligomers. Using raster image correlation spectroscopy and number and brightness analysis combined with fluorescence recovery after photobleaching, fluorescence correlation spectroscopy and electron microscopy in live cells, we show that G12V K-Ras exists as a mixture of monomers, dimers and larger oligomers, while the K101E mutant is predominantly monomeric and K101C/E107C is dominated by oligomers. This observation demonstrates the ability of K-Ras to exist in multiple oligomeric states whose population can be altered by interfacial mutations. Using molecular modeling and simulations we further show that K-Ras uses two partially overlapping interfaces to form compositionally and topologically diverse oligomers. Our results thus provide the first detailed insight into the multiplicity, structure, and membrane organization of K-Ras homomers.
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Affiliation(s)
- Suparna Sarkar-Banerjee
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | | | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, United States
| | - M. Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
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Vetter IR. Interface analysis of small GTP binding protein complexes suggests preferred membrane orientations. Biol Chem 2017; 398:637-651. [PMID: 28002022 DOI: 10.1515/hsz-2016-0287] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/12/2016] [Indexed: 11/15/2022]
Abstract
Crystal structures of small GTP binding protein complexes with their effectors and regulators reveal that one particularly flat side of the G domain that contains helix α4 and the C-terminal helix α5 is practically devoid of contacts. Although this observation seems trivial as the main binding targets are the switch I and II regions opposite of this side, the fact that all interacting proteins, even the largest ones, seem to avoid occupying this area (except for Ran, that does not localize to membranes) is very striking. An orientation with this 'flat' side parallel to the membrane was proposed before and would allow simultaneous interaction of the lipidated C-terminus and positive charges in the α4 helix with the membrane while being bound to effector or regulator molecules. Furthermore, this 'flat' side might be involved in regulatory mechanisms: a Ras dimer that is found in different crystal forms interacts exactly at this side. Additional interface analysis of GTPase complexes nicely confirms the effect of different flexibilities of the GTP and GDP forms. Besides Ran proteins, guanine nucleotide exchange factors (GEFs) bury the largest surface areas to provide the binding energy to open up the switch regions for nucleotide exchange.
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Affiliation(s)
- Ingrid R Vetter
- Max Planck Institute of Molecular Physiology, Department of Mechanistic Cell Biology, Otto-Hahn-Str. 11, D-44227 Dortmund
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Simanshu DK, Nissley DV, McCormick F. RAS Proteins and Their Regulators in Human Disease. Cell 2017; 170:17-33. [PMID: 28666118 PMCID: PMC5555610 DOI: 10.1016/j.cell.2017.06.009] [Citation(s) in RCA: 1099] [Impact Index Per Article: 157.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/22/2017] [Accepted: 06/07/2017] [Indexed: 02/07/2023]
Abstract
RAS proteins are binary switches, cycling between ON and OFF states during signal transduction. These switches are normally tightly controlled, but in RAS-related diseases, such as cancer, RASopathies, and many psychiatric disorders, mutations in the RAS genes or their regulators render RAS proteins persistently active. The structural basis of the switch and many of the pathways that RAS controls are well known, but the precise mechanisms by which RAS proteins function are less clear. All RAS biology occurs in membranes: a precise understanding of RAS' interaction with membranes is essential to understand RAS action and to intervene in RAS-driven diseases.
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Affiliation(s)
- Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21701, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21701, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3(rd) Street, San Francisco, CA 94158, USA.
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Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers. Sci Rep 2017; 7:40109. [PMID: 28067274 PMCID: PMC5220301 DOI: 10.1038/srep40109] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/01/2016] [Indexed: 02/02/2023] Open
Abstract
Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers. For validation we used mutagenesis, electron microscopy and biochemical assays under non-denaturing conditions. We show that partial disruption of a predicted interface through charge reversal mutation of apposed residues reduces oligomerization while introduction of cysteines at these positions enhanced dimerization likely through the formation of an intermolecular disulfide bond. Free energy calculations indicated that K-Ras dimerization involves direct but weak protein-protein interactions in solution, consistent with the notion that dimerization is facilitated by membrane binding. Taken together, our atomically detailed analyses provide unique mechanistic insights into K-Ras dimer formation and membrane organization as well as the conformational fluctuations and equilibrium thermodynamics underlying these processes.
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