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Parise A, Cresca S, Magistrato A. Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins. Expert Opin Drug Discov 2024:1-21. [PMID: 39105536 DOI: 10.1080/17460441.2024.2387856] [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: 04/18/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
INTRODUCTION Molecular Dynamics (MD) simulations can support mechanism-based drug design. Indeed, MD simulations by capturing biomolecule motions at finite temperatures can reveal hidden binding sites, accurately predict drug-binding poses, and estimate the thermodynamics and kinetics, crucial information for drug discovery campaigns. Small-Guanosine Triphosphate Phosphohydrolases (GTPases) regulate a cascade of signaling events, that affect most cellular processes. Their deregulation is linked to several diseases, making them appealing drug targets. The broad roles of small-GTPases in cellular processes and the recent approval of a covalent KRas inhibitor as an anticancer agent renewed the interest in targeting small-GTPase with small molecules. AREA COVERED This review emphasizes the role of MD simulations in elucidating small-GTPase mechanisms, assessing the impact of cancer-related variants, and discovering novel inhibitors. EXPERT OPINION The application of MD simulations to small-GTPases exemplifies the role of MD simulations in the structure-based drug design process for challenging biomolecular targets. Furthermore, AI and machine learning-enhanced MD simulations, coupled with the upcoming power of quantum computing, are promising instruments to target elusive small-GTPases mutations and splice variants. This powerful synergy will aid in developing innovative therapeutic strategies associated to small-GTPases deregulation, which could potentially be used for personalized therapies and in a tissue-agnostic manner to treat tumors with mutations in small-GTPases.
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Affiliation(s)
- Angela Parise
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Sofia Cresca
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
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2
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Gookin TE, Chakravorty D, Assmann SM. Influence of expression and purification protocols on Gα biochemical activity: kinetics of plant and mammalian G protein cycles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.10.540258. [PMID: 37214830 PMCID: PMC10197700 DOI: 10.1101/2023.05.10.540258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heterotrimeric G proteins are a class of signal transduction complexes with broad roles in human health and agriculturally important plant traits. In the classic paradigm, guanine nucleotide binding to the Gα subunit regulates the activation status of the complex. Using the Arabidopsis thaliana Gα subunit, GPA1, we developed a rapid StrepII-tag mediated purification method that facilitates isolation of protein with increased enzymatic activities as compared to conventional methods, and is demonstrably also applicable to mammalian Gα subunits. We subsequently utilized domain swaps of GPA1 and human GNAO1 to demonstrate the instability of recombinant GPA1 is a function of the interaction between the Ras and helical domains, and can be partially uncoupled from the rapid nucleotide binding kinetics displayed by GPA1.
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Affiliation(s)
- Timothy E. Gookin
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
- These authors contributed equally to the article
| | - David Chakravorty
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
- These authors contributed equally to the article
| | - Sarah M. Assmann
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
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3
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Foote JB, Mattox TE, Keeton AB, Chen X, Smith F, Berry KL, Holmes T, Wang J, Huang CH, Ward AB, Mitra AK, Ramirez-Alcantara V, Hardy C, Fleten KG, Flatmark K, Yoon KJ, Sarvesh S, Nagaraju GP, Maxuitenko Y, Valiyaveettil J, Carstens JL, Buchsbaum DJ, Yang J, Zhou G, Nurmemmedov E, Babic I, Gaponenko V, Abdelkarim H, Boyd MR, Gorman GS, Manne U, Bae S, El-Rayes BF, Piazza GA. A Novel Pan-RAS Inhibitor with a Unique Mechanism of Action Blocks Tumor Growth in Mouse Models of GI Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.17.541233. [PMID: 38328254 PMCID: PMC10849544 DOI: 10.1101/2023.05.17.541233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Here, we describe a novel pan-RAS inhibitor, ADT-007, that potently inhibited the growth of RAS mutant cancer cells irrespective of the RAS mutation or isozyme. RAS WT cancer cells with activated RAS from upstream mutations were equally sensitive. Conversely, cells from normal tissues or RAS WT cancer cells harboring downstream BRAF mutations were insensitive. Insensitivity to ADT-007 was attributed to low activated RAS levels and metabolic deactivation by UDP-glucuronosyltransferases expressed in normal cells but repressed in RAS mutant cancer cells. Cellular, biochemical, and biophysical experiments show ADT-007 binds nucleotide-free RAS to block GTP activation of RAS and MAPK/AKT signaling. Local administration of ADT-007 strongly inhibited tumor growth in syngeneic immune-competent and xenogeneic immune-deficient mouse models of colorectal and pancreatic cancer while activating innate and adaptive immunity in the tumor immune microenvironment. Oral administration of ADT-007 prodrug inhibited tumor growth, supporting further development of this novel class of pan-RAS inhibitors for treating RAS-driven cancers. SIGNIFICANCE ADT-007 is a 1 st -in-class pan-RAS inhibitor with ultra-high potency and unique selectivity for cancer cells with mutant or activated RAS capable of circumventing resistance and activating antitumor immunity. Further development of ADT-007 analogs or prodrugs with oral bioavailability as a generalizable monotherapy or combined with immunotherapy is warranted.
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Tagad A, Patwari GN. Unraveling the Significance of Mg 2+ Dependency and Nucleotide Binding Specificity of H-RAS. J Phys Chem B 2024; 128:1618-1626. [PMID: 38351706 DOI: 10.1021/acs.jpcb.3c06998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
RAS is a small GTPase and acts as a binary molecular switch; the transition from its active to inactive state plays a crucial role in various cell signaling processes. Molecular dynamics simulations at the atomistic level suggest that the absence of cofactor Mg2+ ion generally leads to pronounced structural changes in the Switch-I than Switch-II regions and assists GTP binding. The presence of the Mg2+ ion also restricts the rotation of ϒ phosphate and enhances the hydrolysis rate of GTP. Further, the simulations reveal that the stability of the protein is almost uncompromised when Mg2+ is replaced with Zn2+ and not the Ca2+ ion. The specificity of H-RAS to GTP was evaluated by substituting with ATP and CTP, which indicates that the binding pocket tolerates purine bases over pyrimidine bases. However, the D119 residue specifically interacts with the guanine base and serves as one of the primary interactions that leads to the selectivity of GTP over ATP. The ring displacement of 32Y serves as gate dynamics in H-RAS which are important for its interaction with GAP for the nucleotide exchange and is restricted in the presence of ATP. Finally, the point mutations 61, 16, and 32 influence the structural changes, specifically in the Switch-II region, which are expected to impact the GTP hydrolysis and thus are termed oncogenic mutations.
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Affiliation(s)
- Amol Tagad
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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5
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Structural basis of the oncogenic KRAS mutant and GJ101 complex. Biochem Biophys Res Commun 2023; 641:27-33. [PMID: 36516586 DOI: 10.1016/j.bbrc.2022.12.019] [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: 11/24/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
KRAS mutations occur in a quarter of all human cancers. When activated in its GTP-bound form, RAS stimulates diverse cellular systems, such as cell division, differentiation, growth, and apoptosis through the activations of various signaling pathways, which include mitogen-activated protein kinase (MAPK), phosphoinositide 3 kinases (PI3K), and RAL-GEFs pathways. We found that GJ101 (65LYDVA69) binds directly to the KRAS mutant (G12V) and showed tumor-suppressive activity. In addition, the GJ101 peptide inhibited KRAS mutant as determined by a [α-32P] guanosine triphosphate (GTP) binding assay and suppressed pancreatic cell line in a cell proliferation assay. Herein, the complex structure of KRAS and GJ101 was clarified by X-ray crystallography. Isothermal titration calorimetry showed that GJ101 binds highly with KRAS mutant and the complex structure of KRAS G12V.GJ101 complex presented that the residue of Q61 directly interacted with L65 of GJ101. Overall, the results suggest GJ101 be considered a developmental starting point for KRAS G12V inhibitor.
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Discovering and Targeting Dynamic Drugging Pockets of Oncogenic Proteins: The Role of Magnesium in Conformational Changes of the G12D Mutated Kirsten Rat Sarcoma-Guanosine Diphosphate Complex. Int J Mol Sci 2022; 23:ijms232213865. [PMID: 36430338 PMCID: PMC9692486 DOI: 10.3390/ijms232213865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
KRAS-G12D mutations are the one of most frequent oncogenic drivers in human cancers. Unfortunately, no therapeutic agent directly targeting KRAS-G12D has been clinically approved yet, with such mutated species remaining undrugged. Notably, cofactor Mg2+ is closely related to the function of small GTPases, but no investigation has been conducted yet on Mg2+ when associated with KRAS. Herein, through microsecond scale molecular dynamics simulations, we found that Mg2+ plays a crucial role in the conformational changes of the KRAS-GDP complex. We located two brand new druggable dynamic pockets exclusive to KRAS-G12D. Using the structural characteristics of these two dynamic pockets, we designed in silico the inhibitor DBD15-21-22, which can specifically and tightly target the KRAS-G12D-GDP-Mg2+ ternary complex. Overall, we provide two brand new druggable pockets located on KRAS-G12D and suitable strategies for its inhibition.
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Kozlova MI, Shalaeva DN, Dibrova DV, Mulkidjanian AY. Common Mechanism of Activated Catalysis in P-loop Fold Nucleoside Triphosphatases-United in Diversity. Biomolecules 2022; 12:1346. [PMID: 36291556 PMCID: PMC9599734 DOI: 10.3390/biom12101346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/20/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
To clarify the obscure hydrolysis mechanism of ubiquitous P-loop-fold nucleoside triphosphatases (Walker NTPases), we analysed the structures of 3136 catalytic sites with bound Mg-NTP complexes or their analogues. Our results are presented in two articles; here, in the second of them, we elucidated whether the Walker A and Walker B sequence motifs-common to all P-loop NTPases-could be directly involved in catalysis. We found that the hydrogen bonds (H-bonds) between the strictly conserved, Mg-coordinating Ser/Thr of the Walker A motif ([Ser/Thr]WA) and aspartate of the Walker B motif (AspWB) are particularly short (even as short as 2.4 ångströms) in the structures with bound transition state (TS) analogues. Given that a short H-bond implies parity in the pKa values of the H-bond partners, we suggest that, in response to the interactions of a P-loop NTPase with its cognate activating partner, a proton relocates from [Ser/Thr]WA to AspWB. The resulting anionic [Ser/Thr]WA alkoxide withdraws a proton from the catalytic water molecule, and the nascent hydroxyl attacks the gamma phosphate of NTP. When the gamma-phosphate breaks away, the trapped proton at AspWB passes by the Grotthuss relay via [Ser/Thr]WA to beta-phosphate and compensates for its developing negative charge that is thought to be responsible for the activation barrier of hydrolysis.
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Affiliation(s)
- Maria I. Kozlova
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Daria N. Shalaeva
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Daria V. Dibrova
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Armen Y. Mulkidjanian
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
- Center of Cellular Nanoanalytics, Osnabrueck University, D-49069 Osnabrueck, Germany
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Kopra K, Valtonen S, Mahran R, Kapp JN, Hassan N, Gillette W, Dennis B, Li L, Westover KD, Plückthun A, Härmä H. Thermal Shift Assay for Small GTPase Stability Screening: Evaluation and Suitability. Int J Mol Sci 2022; 23:7095. [PMID: 35806100 PMCID: PMC9266822 DOI: 10.3390/ijms23137095] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Thermal unfolding methods are commonly used as a predictive technique by tracking the protein's physical properties. Inherent protein thermal stability and unfolding profiles of biotherapeutics can help to screen or study potential drugs and to find stabilizing or destabilizing conditions. Differential scanning calorimetry (DSC) is a 'Gold Standard' for thermal stability assays (TSA), but there are also a multitude of other methodologies, such as differential scanning fluorimetry (DSF). The use of an external probe increases the assay throughput, making it more suitable for screening studies, but the current methodologies suffer from relatively low sensitivity. While DSF is an effective tool for screening, interpretation and comparison of the results is often complicated. To overcome these challenges, we compared three thermal stability probes in small GTPase stability studies: SYPRO Orange, 8-anilino-1-naphthalenesulfonic acid (ANS), and the Protein-Probe. We studied mainly KRAS, as a proof of principle to obtain biochemical knowledge through TSA profiles. We showed that the Protein-Probe can work at lower concentration than the other dyes, and its sensitivity enables effective studies with non-covalent and covalent drugs at the nanomolar level. Using examples, we describe the parameters, which must be taken into account when characterizing the effect of drug candidates, of both small molecules and Designed Ankyrin Repeat Proteins.
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Affiliation(s)
- Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland; (S.V.); (R.M.); (N.H.); (H.H.)
| | - Salla Valtonen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland; (S.V.); (R.M.); (N.H.); (H.H.)
| | - Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland; (S.V.); (R.M.); (N.H.); (H.H.)
| | - Jonas N. Kapp
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (J.N.K.); (A.P.)
| | - Nazia Hassan
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland; (S.V.); (R.M.); (N.H.); (H.H.)
| | - William Gillette
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, 8560 Progress Dr., Frederick, MD 21702, USA;
| | - Bryce Dennis
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, L4.270, Dallas, TX 75390, USA; (B.D.); (L.L.); (K.D.W.)
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, L4.270, Dallas, TX 75390, USA; (B.D.); (L.L.); (K.D.W.)
| | - Kenneth D. Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, L4.270, Dallas, TX 75390, USA; (B.D.); (L.L.); (K.D.W.)
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (J.N.K.); (A.P.)
| | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland; (S.V.); (R.M.); (N.H.); (H.H.)
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9
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Xiong Y, Zeng J, Xia F, Cui Q, Deng X, Xu X. Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process. J Comput Chem 2022; 43:906-916. [PMID: 35324017 PMCID: PMC9191747 DOI: 10.1002/jcc.26846] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/23/2022]
Abstract
The human Son of Sevenless (SOS) activates the signal-transduction protein Ras by forming the complex SOS·Ras and accelerating the guanosine triphosphate (GTP) exchange in Ras. Inhibition of SOS·Ras could regulate the function of Ras in cells and has emerged as an effective strategy for battling Ras related cancers. A key factor to the success of this approach is to understand the conformational change of Ras during the GTP exchange process. In this study, we perform an extensive molecular dynamics simulation to characterize the specific conformations of Ras without and with guanine nucleotide exchange factors (GEFs) of SOS, especially for the substates of State 1 of HRasGTP∙Mg2+ . The potent binding pockets on the surfaces of the RasGDP∙Mg2+ , the S1.1 and S1.2 substates in State 1 of RasGTP∙Mg2+ and the ternary complexes with SOS are predicted, including the binding sites of other domains of SOS. These findings help to obtain a more thorough understanding of Ras functions in the GTP cycling process and provide a structural foundation for future drug design.
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Affiliation(s)
- Yuqing Xiong
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai, China
| | - Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai, China
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Departments of Chemistry, Fudan University, Shanghai, China
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10
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Ramirez NGP, Lee J, Zheng Y, Li L, Dennis B, Chen D, Challa A, Planelles V, Westover KD, Alto NM, D'Orso I. ADAP1 promotes latent HIV-1 reactivation by selectively tuning KRAS-ERK-AP-1 T cell signaling-transcriptional axis. Nat Commun 2022; 13:1109. [PMID: 35232997 PMCID: PMC8888757 DOI: 10.1038/s41467-022-28772-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 02/11/2022] [Indexed: 12/29/2022] Open
Abstract
Immune stimulation fuels cell signaling-transcriptional programs inducing biological responses to eliminate virus-infected cells. Yet, retroviruses that integrate into host cell chromatin, such as HIV-1, co-opt these programs to switch between latent and reactivated states; however, the regulatory mechanisms are still unfolding. Here, we implemented a functional screen leveraging HIV-1's dependence on CD4+ T cell signaling-transcriptional programs and discovered ADAP1 is an undescribed modulator of HIV-1 proviral fate. Specifically, we report ADAP1 (ArfGAP with dual PH domain-containing protein 1), a previously thought neuronal-restricted factor, is an amplifier of select T cell signaling programs. Using complementary biochemical and cellular assays, we demonstrate ADAP1 inducibly interacts with the immune signalosome to directly stimulate KRAS GTPase activity thereby augmenting T cell signaling through targeted activation of the ERK-AP-1 axis. Single cell transcriptomics analysis revealed loss of ADAP1 function blunts gene programs upon T cell stimulation consequently dampening latent HIV-1 reactivation. Our combined experimental approach defines ADAP1 as an unexpected tuner of T cell programs facilitating HIV-1 latency escape.
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Affiliation(s)
- Nora-Guadalupe P Ramirez
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jeon Lee
- Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yue Zheng
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Lianbo Li
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bryce Dennis
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Didi Chen
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Kenneth D Westover
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Neal M Alto
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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Development of a versatile HPLC-based method to evaluate the activation status of small GTPases. J Biol Chem 2021; 297:101428. [PMID: 34801548 PMCID: PMC8668980 DOI: 10.1016/j.jbc.2021.101428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 11/21/2022] Open
Abstract
Small GTPases cycle between an inactive GDP-bound and an active GTP-bound state to control various cellular events, such as cell proliferation, cytoskeleton organization, and membrane trafficking. Clarifying the guanine nucleotide-bound states of small GTPases is vital for understanding the regulation of small GTPase functions and the subsequent cellular responses. Although several methods have been developed to analyze small GTPase activities, our knowledge of the activities for many small GTPases is limited, partly because of the lack of versatile methods to estimate small GTPase activity without unique probes and specialized equipment. In the present study, we developed a versatile and straightforward HPLC-based assay to analyze the activation status of small GTPases by directly quantifying the amounts of guanine nucleotides bound to them. This assay was validated by analyzing the RAS-subfamily GTPases, including HRAS, which showed that the ratios of GTP-bound forms were comparable with those obtained in previous studies. Furthermore, we applied this assay to the investigation of psychiatric disorder-associated mutations of RHEB (RHEB/P37L and RHEB/S68P), revealing that both mutations cause an increase in the ratio of the GTP-bound form in cells. Mechanistically, loss of sensitivity to TSC2 (a GTPase-activating protein for RHEB) for RHEB/P37L, as well as both decreased sensitivity to TSC2 and accelerated guanine-nucleotide exchange for RHEB/S68P, is involved in the increase of their GTP-bound forms, respectively. In summary, the HPLC-based assay developed in this study provides a valuable tool for analyzing small GTPases for which the activities and regulatory mechanisms are less well understood.
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12
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Weber SM, Brossier NM, Prechtl A, Barnes S, Wilson LS, Brosius SN, Longo JF, Carroll SL. R-Ras subfamily proteins elicit distinct physiologic effects and phosphoproteome alterations in neurofibromin-null MPNST cells. Cell Commun Signal 2021; 19:95. [PMID: 34530870 PMCID: PMC8447793 DOI: 10.1186/s12964-021-00773-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/31/2021] [Indexed: 12/31/2022] Open
Abstract
Background Loss of the Ras GTPase-activating protein neurofibromin promotes nervous system tumor pathogenesis in patients with neurofibromatosis type 1 (NF1). Neurofibromin loss potentially hyperactivates classic Ras (H-Ras, N-Ras, K-Ras), M-Ras, and R-Ras (R-Ras, R-Ras2/TC21) subfamily proteins. We have shown that classic Ras proteins promote proliferation and survival, but not migration, in malignant peripheral nerve sheath tumor (MPNST) cells. However, it is unclear whether R-Ras, R-Ras2 and M-Ras are expressed and hyperactivated in MPNSTs and, if so, whether they contribute to MPNST pathogenesis. We assessed the expression and activation of these proteins in MPNST cells and inhibited them to determine the effect this had on proliferation, migration, invasion, survival and the phosphoproteome. Methods NF1-associated (ST88-14, 90-8, NMS2, NMS-PC, S462, T265-2c) and sporadic (STS-26T, YST-1) MPNST lines were used. Cells were transfected with doxycycline-inducible vectors expressing either a pan-inhibitor of the R-Ras subfamily [dominant negative (DN) R-Ras] or enhanced green fluorescent protein (eGFP). Methodologies used included immunoblotting, immunocytochemistry, PCR, Transwell migration, 3H-thymidine incorporation, calcein cleavage assays and shRNA knockdowns. Proteins in cells with or without DN R-Ras expression were differentially labeled with SILAC and mass spectrometry was used to identify phosphoproteins and determine their relative quantities in the presence and absence of DN R-Ras. Validation of R-Ras and R-Ras2 action and R-Ras regulated networks was performed using genetic and/or pharmacologic approaches. Results R-Ras2 was uniformly expressed in MPNST cells, with R-Ras present in a major subset. Both proteins were activated in neurofibromin-null MPNST cells. Consistent with classical Ras inhibition, DN R-Ras and R-Ras2 knockdown inhibited proliferation. However, DN R-Ras inhibition impaired migration and invasion but not survival. Mass spectrometry-based phosphoproteomics identified thirteen protein networks distinctly regulated by DN R-Ras, including multiple networks regulating cellular movement and morphology. ROCK1 was a prominent mediator in these networks. DN R-Ras expression and RRAS and RRAS2 knockdown inhibited migration and ROCK1 phosphorylation; ROCK1 inhibition similarly impaired migration and invasion, altered cellular morphology and triggered the accumulation of large intracellular vesicles. Conclusions R-Ras proteins function distinctly from classic Ras proteins by regulating distinct signaling pathways that promote MPNST tumorigenesis by mediating migration and invasion. Plain English Summary Mutations of the NF1 gene potentially results in the activation of multiple Ras proteins, which are key regulators of many biologic effects. The protein encoded by the NF1 gene, neurofibromin, acts as an inhibitor of both classic Ras and R-Ras proteins; loss of neurofibromin could cause these Ras proteins to become persistently active, leading to the development of cancer. We have previously shown that three related Ras proteins (the classic Ras proteins) are highly activated in malignant peripheral nerve sheath tumor (MPNST) cells with neurofibromin loss and that they drive cancer cell proliferation and survival by activating multiple cellular signaling pathways. Here, we examined the expression, activation and action of R-Ras proteins in MPNST cells that have lost neurofibromin. Both R-Ras and R-Ras2 are expressed in MPNST cells and activated. Inhibition of R-Ras action inhibited proliferation, migration and invasion but not survival. We examined the activation of cytoplasmic signaling pathways in the presence and absence of R-Ras signaling and found that R-Ras proteins regulated 13 signaling pathways distinct from those regulated by classic Ras proteins. Closer study of an R-Ras regulated pathway containing the signaling protein ROCK1 showed that inhibition of either R-Ras, R-Ras2 or ROCK1 similarly impaired cellular migration and invasion and altered cellular morphology. Inhibition of R-Ras/R-Ras2 and ROCK1 signaling also triggered the accumulation of abnormal intracellular vesicles, indicating that these signaling molecules regulate the movement of proteins and other molecules in the cellular interior. Video Abstract
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Supplementary Information The online version contains supplementary material available at 10.1186/s12964-021-00773-4.
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Affiliation(s)
- Shannon M Weber
- Department of Pathology and Laboratory Medicine (SMW, AP, JFL, SLC), MUSC Medical Scientist Training Program (SMW), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Departments of Pathology (NMB, SNB, SLC), Pharmacology and Toxicology (SB, LSW), UAB Medical Scientist Training Program (NMB, SNB), Birmingham, USA.,The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Nicole M Brossier
- Department of Pathology and Laboratory Medicine (SMW, AP, JFL, SLC), MUSC Medical Scientist Training Program (SMW), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Departments of Pathology (NMB, SNB, SLC), Pharmacology and Toxicology (SB, LSW), UAB Medical Scientist Training Program (NMB, SNB), Birmingham, USA.,The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Pediatrics, St. Louis Children's Hospital, St. Louis, USA
| | - Amanda Prechtl
- Department of Pathology and Laboratory Medicine (SMW, AP, JFL, SLC), MUSC Medical Scientist Training Program (SMW), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Departments of Pathology (NMB, SNB, SLC), Pharmacology and Toxicology (SB, LSW), UAB Medical Scientist Training Program (NMB, SNB), Birmingham, USA.,The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Stephen Barnes
- Department of Pathology and Laboratory Medicine (SMW, AP, JFL, SLC), MUSC Medical Scientist Training Program (SMW), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Departments of Pathology (NMB, SNB, SLC), Pharmacology and Toxicology (SB, LSW), UAB Medical Scientist Training Program (NMB, SNB), Birmingham, USA.,The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Landon S Wilson
- Department of Pathology and Laboratory Medicine (SMW, AP, JFL, SLC), MUSC Medical Scientist Training Program (SMW), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Departments of Pathology (NMB, SNB, SLC), Pharmacology and Toxicology (SB, LSW), UAB Medical Scientist Training Program (NMB, SNB), Birmingham, USA.,The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Stephanie N Brosius
- Department of Pathology and Laboratory Medicine (SMW, AP, JFL, SLC), MUSC Medical Scientist Training Program (SMW), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Departments of Pathology (NMB, SNB, SLC), Pharmacology and Toxicology (SB, LSW), UAB Medical Scientist Training Program (NMB, SNB), Birmingham, USA.,The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Departments of Neurology and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.,Division of Child Neurology, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Jody Fromm Longo
- Department of Pathology and Laboratory Medicine (SMW, AP, JFL, SLC), MUSC Medical Scientist Training Program (SMW), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Departments of Pathology (NMB, SNB, SLC), Pharmacology and Toxicology (SB, LSW), UAB Medical Scientist Training Program (NMB, SNB), Birmingham, USA.,The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Steven L Carroll
- Department of Pathology and Laboratory Medicine (SMW, AP, JFL, SLC), MUSC Medical Scientist Training Program (SMW), Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA. .,Departments of Pathology (NMB, SNB, SLC), Pharmacology and Toxicology (SB, LSW), UAB Medical Scientist Training Program (NMB, SNB), Birmingham, USA. .,The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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13
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Osaka N, Hirota Y, Ito D, Ikeda Y, Kamata R, Fujii Y, Chirasani VR, Campbell SL, Takeuchi K, Senda T, Sasaki AT. Divergent Mechanisms Activating RAS and Small GTPases Through Post-translational Modification. Front Mol Biosci 2021; 8:707439. [PMID: 34307463 PMCID: PMC8295990 DOI: 10.3389/fmolb.2021.707439] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022] Open
Abstract
RAS is a founding member of the RAS superfamily of GTPases. These small 21 kDa proteins function as molecular switches to initialize signaling cascades involved in various cellular processes, including gene expression, cell growth, and differentiation. RAS is activated by GTP loading and deactivated upon GTP hydrolysis to GDP. Guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) accelerate GTP loading and hydrolysis, respectively. These accessory proteins play a fundamental role in regulating activities of RAS superfamily small GTPase via a conserved guanine binding (G)-domain, which consists of five G motifs. The Switch regions lie within or proximal to the G2 and G3 motifs, and undergo dynamic conformational changes between the GDP-bound "OFF" state and GTP-bound "ON" state. They play an important role in the recognition of regulatory factors (GEFs and GAPs) and effectors. The G4 and G5 motifs are the focus of the present work and lie outside Switch regions. These motifs are responsible for the recognition of the guanine moiety in GTP and GDP, and contain residues that undergo post-translational modifications that underlie new mechanisms of RAS regulation. Post-translational modification within the G4 and G5 motifs activates RAS by populating the GTP-bound "ON" state, either through enhancement of intrinsic guanine nucleotide exchange or impairing GAP-mediated down-regulation. Here, we provide a comprehensive review of post-translational modifications in the RAS G4 and G5 motifs, and describe the role of these modifications in RAS activation as well as potential applications for cancer therapy.
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Affiliation(s)
- Natsuki Osaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Yoshihisa Hirota
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
| | - Doshun Ito
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Yoshiki Ikeda
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Ryo Kamata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Yuki Fujii
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Graduate School of Science, Osaka City University, Osaka, Japan
| | - Venkat R. Chirasani
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Tokyo, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
- Department of Accelerator Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), Tsukuba, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Atsuo T. Sasaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Department of Cancer Biology, University of Cincinnati College of Medicine, Columbus, OH, United States
- Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH, United States
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14
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Killoran RC, Smith MJ. NMR Detection Methods for Profiling RAS Nucleotide Cycling. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:169-182. [PMID: 33977476 DOI: 10.1007/978-1-0716-1190-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RAS oncoproteins exhibit a switch-like behavior to drive diverse signaling cascades. In the active GTP-bound state, a conformational change occurs in these enzymes that enables interaction with downstream effectors. Nucleotide-dependent conformational exchange is easily detected with real-time NMR (RT-NMR) spectroscopy. RT-NMR has been firmly established as an effective assay to measure RAS oncoprotein nucleotide exchange and GTP hydrolysis kinetics and can further determine the regulatory activity of guanine exchange factors (GEFs) and GTPase activating proteins (GAPs). It is now possible to multiplex these assays, allowing for the precise monitoring of activation states for mixtures of RAS oncoproteins or other RAS superfamily GTPases. Here, we describe the protocols necessary to express and purify isotopically labeled RAS and detail how to carry out an RT-NMR assay on a singular RAS protein or on a mixture of small GTPases.
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Affiliation(s)
- Ryan C Killoran
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada. .,Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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15
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Progress in the therapeutic inhibition of Cdc42 signalling. Biochem Soc Trans 2021; 49:1443-1456. [PMID: 34100887 PMCID: PMC8286826 DOI: 10.1042/bst20210112] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Cdc42 is a member of the Rho family of small GTPases and a key regulator of the actin cytoskeleton, controlling cell motility, polarity and cell cycle progression. It signals downstream of the master regulator Ras and is essential for cell transformation by this potent oncogene. Overexpression of Cdc42 is observed in several cancers, where it is linked to poor prognosis. As a regulator of both cell architecture and motility, deregulation of Cdc42 is also linked to tumour metastasis. Like Ras, Cdc42 and other components of the signalling pathways it controls represent important potential targets for cancer therapeutics. In this review, we consider the progress that has been made targeting Cdc42, its regulators and effectors, including new modalities and new approaches to inhibition. Strategies under consideration include inhibition of lipid modification, modulation of Cdc42-GEF, Cdc42-GDI and Cdc42-effector interactions, and direct inhibition of downstream effectors.
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16
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Guo W, Wang Q, Pan S, Li J, Wang Y, Shu Y, Chen J, Wang Q, Zhang S, Zhang X, Yue J. The ERK1/2-ATG13-FIP200 signaling cascade is required for autophagy induction to protect renal cells from hypoglycemia-induced cell death. J Cell Physiol 2021; 236:6932-6947. [PMID: 33682133 DOI: 10.1002/jcp.30354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 11/08/2022]
Abstract
Autophagy, an evolutionarily conserved lysosomal degradation pathway, is known to regulate a variety of physiological and pathological processes. At present, the function and the precise mechanism of autophagy regulation in kidney and renal cells remain elusive. Here, we explored the role of ERK1 and ERK2 (referred as ERK1/2 hereafter) in autophagy regulation in renal cells in response to hypoglycemia. Glucose starvation potently and transiently activated ERK1/2 in renal cells, and this was concomitant with an increase in autophagic flux. Perturbing ERK1/2 activation by treatment with inhibitors of RAF or MEK1/2, via the expression of a dominant-negative mutant form of MEK1/2 or RAS, blocked hypoglycemia-mediated ERK1/2 activation and autophagy induction in renal cells. Glucose starvation also induced the accumulation of reactive oxygen species in renal cells, which was involved in the activation of the ERK1/2 cascade and the induction of autophagy in renal cells. Interestingly, ATG13 and FIP200, the members of the ULK1 complex, contain the ERK consensus phosphorylation sites, and glucose starvation induced an association between ATG13 or FIP200 and ERK1/2. Moreover, the expression of the phospho-defective mutants of ATG13 and FIP200 in renal cells blocked glucose starvation-induced autophagy and rendered cells more susceptible to hypoglycemia-induced cell death. However, the expression of the phospho-mimic mutants of ATG13 and FIP200 induced autophagy and protected renal cells from hypoglycemia-induced cell death. Taken together, our results demonstrate that hypoglycemia activates the ERK1/2 signaling to regulate ATG13 and FIP200, thereby stimulating autophagy to protect the renal cells from hypoglycemia-induced cell death.
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Affiliation(s)
- Wenjing Guo
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Scientific Instruments Center, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Qian Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Shihua Pan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinbing Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yuanhua Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yahai Shu
- Scientific Instruments Center, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Jiaheng Chen
- Scientific Instruments Center, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Qizheng Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Sheng Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jianbo Yue
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, China.,City University of Hong Kong Chengdu Research Institute, Chengdu, China
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17
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Klochkov SG, Neganova ME, Aleksandrova YR. Promising Molecular Targets for Design of Antitumor Drugs Based on Ras Protein Signaling Cascades. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020050118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Johnson CW, Lin YJ, Reid D, Parker J, Pavlopoulos S, Dischinger P, Graveel C, Aguirre AJ, Steensma M, Haigis KM, Mattos C. Isoform-Specific Destabilization of the Active Site Reveals a Molecular Mechanism of Intrinsic Activation of KRas G13D. Cell Rep 2020; 28:1538-1550.e7. [PMID: 31390567 PMCID: PMC6709685 DOI: 10.1016/j.celrep.2019.07.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/28/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022] Open
Abstract
Ras GTPases are mutated at codons 12, 13, and 61, with different frequencies in KRas, HRas, and NRas and in a cancer-specific manner. The G13D mutant appears in 25% of KRas-driven colorectal cancers, while observed only rarely in HRas or NRas. Structures of Ras G13D in the three isoforms show an open active site, with adjustments to the D13 backbone torsion angles and with disconnected switch regions. KRas G13D has unique features that destabilize the nucleotide-binding pocket. In KRas G13D bound to GDP, A59 is placed in the Mg2+ binding site, as in the HRas-SOS complex. Structure and biochemistry are consistent with an intermediate level of KRas G13D bound to GTP, relative to wild-type and KRas G12D, observed in genetically engineered mouse models. The results explain in part the elevated frequency of the G13D mutant in KRas over the other isoforms of Ras.
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Affiliation(s)
- Christian W Johnson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Yi-Jang Lin
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Derion Reid
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jillian Parker
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Spiro Pavlopoulos
- Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | | | - Carrie Graveel
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Andrew J Aguirre
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kevin M Haigis
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Harvard Digestive Disease Center, Boston, MA 02215, USA.
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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19
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Kanade M, Chakraborty S, Shelke SS, Gayathri P. A Distinct Motif in a Prokaryotic Small Ras-Like GTPase Highlights Unifying Features of Walker B Motifs in P-Loop NTPases. J Mol Biol 2020; 432:5544-5564. [PMID: 32750390 DOI: 10.1016/j.jmb.2020.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 01/22/2023]
Abstract
A hallmark of the catalytically essential Walker B motif of P-loop NTPases is the presence of an acidic residue (aspartate/glutamate) for efficient Mg2+ coordination. Although the Walker B motif has been identified in well-studied examples of P-loop NTPases, its identity is ambiguous in many families, for example, in the prokaryotic small Ras-like GTPase family of MglA. MglA, belonging to TRAFAC class of P-loop NTPases, possesses a threonine at the position equivalent to Walker B aspartate in eukaryotic Ras-like GTPases. To resolve the identity of the Walker B residue in MglA, we carried out a comprehensive analysis of Mg2+ coordination on P-loop NTPase structures. Atoms in the octahedral coordination of Mg2+ and their interactions comprise a network including water molecules, Walker A, Walker B and switch motifs of P-loop NTPases. Based on the conserved geometry of Mg2+ coordination, we confirm that a conserved aspartate functions as the Walker B residue of MglA, and validate it through mutagenesis and biochemical characterization. Location of the newly identified aspartate is spatially equivalent to the Walker B residue of the ASCE division of P-loop NTPases. Furthermore, similar to the allosteric regulation of the Walker B aspartate conformation in MglA, we identify protein families in which large conformational changes involving Walker B motif potentially function as allosteric regulators. The study unravels conserved features of Mg2+ coordination among divergent families of P-loop NTPases, especially between ancient Ras-like GTPases and ASCE family of ATPases. The conserved geometric features provide a foundation for design of nucleotide-hydrolyzing enzymes.
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Affiliation(s)
- Manil Kanade
- Indian Institute of Science Education and Research, Pune, India
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20
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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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21
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Han CW, Jeong MS, Ha SC, Jang SB. A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic KRAS Mutants. Cancers (Basel) 2020; 12:cancers12061412. [PMID: 32486141 PMCID: PMC7352977 DOI: 10.3390/cancers12061412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
Kirsten-RAS (KRAS) has been the target of drugs because it is the most mutated gene in human cancers. Because of the low affinity of drugs for KRAS mutations, it was difficult to target these tumor genes directly. We found a direct interaction between KRAS G12V and tumor suppressor novel H-REV107 peptide with high binding affinity. We report the first crystal structure of an oncogenic mutant, KRAS G12V-H-REV107. This peptide was shown to interact with KRAS G12V in the guanosine diphosphate (GDP)-bound inactive state and to form a stable complex, blocking the activation function of KRAS. We showed that the peptide acted as an inhibitor of mutant KRAS targets by [α-32P] guanosine triphosphate (GTP) binding assay. The H-REV107 peptide inhibited pancreatic cancer and colon cancer cell lines in cell proliferation assay. Specially, the H-REV107 peptide can suppress pancreatic tumor growth by reduction of tumor volume and weight in xenotransplantation mouse models. Overall, the results presented herein will facilitate development of novel drugs for inhibition of KRAS mutations in cancer patients.
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Affiliation(s)
- Chang Woo Han
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2, Busandaehak-ro 63 beon-gil, Geumjeong-gu, Busan 46241, Korea;
| | - Mi Suk Jeong
- Korea Nanobiotechnology Center, Pusan National University, 2, Busandaehak-ro 63 beon-gil, Geumjeong-gu, Busan 46241, Korea
- Correspondence: (M.S.J.); (S.B.J.); Tel.: +82-51-510-2523 (S.B.J.); Fax: +82-51-581-2544 (S.B.J.)
| | - Sung Chul Ha
- Pohang Accelarator Laboratory, Pohang University of Science and Technology, 80 Jigok-ro 127 beon-gil, Nam-gu, Gyeongsangbuk-do, Pohang-si 37673, Korea;
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2, Busandaehak-ro 63 beon-gil, Geumjeong-gu, Busan 46241, Korea;
- Correspondence: (M.S.J.); (S.B.J.); Tel.: +82-51-510-2523 (S.B.J.); Fax: +82-51-581-2544 (S.B.J.)
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22
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Laham-Karam N, Pinto GP, Poso A, Kokkonen P. Transcription and Translation Inhibitors in Cancer Treatment. Front Chem 2020; 8:276. [PMID: 32373584 PMCID: PMC7186406 DOI: 10.3389/fchem.2020.00276] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Transcription and translation are fundamental cellular processes that govern the protein production of cells. These processes are generally up regulated in cancer cells, to maintain the enhanced metabolism and proliferative state of these cells. As such cancerous cells can be susceptible to transcription and translation inhibitors. There are numerous druggable proteins involved in transcription and translation which make lucrative targets for cancer drug development. In addition to proteins, recent years have shown that the "undruggable" transcription factors and RNA molecules can also be targeted to hamper the transcription or translation in cancer. In this review, we summarize the properties and function of the transcription and translation inhibitors that have been tested and developed, focusing on the advances of the last 5 years. To complement this, we also discuss some of the recent advances in targeting oncogenes tightly controlling transcription including transcription factors and KRAS. In addition to natural and synthetic compounds, we review DNA and RNA based approaches to develop cancer drugs. Finally, we conclude with the outlook to the future of the development of transcription and translation inhibitors.
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Affiliation(s)
- Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Gaspar P. Pinto
- International Clinical Research Center, St. Anne University Hospital, Brno, Czechia
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- University Hospital Tübingen, Department of Internal Medicine VIII, University of Tübingen, Tübingen, Germany
| | - Piia Kokkonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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23
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Abstract
Posttranslational modifications (PTMs) are important physiological means to regulate the activities and structures of central regulatory proteins in health and disease. Small GTPases have been recognized as important molecules that are targeted by PTMs during infections of mammalian cells by bacterial pathogens. The enzymes DrrA/SidM and AnkX from Legionella pneumophila AMPylate and phosphocholinate Rab1b during infection, respectively. Cdc42 is AMPylated by IbpA from Histophilus somni at tyrosine 32 or by VopS from Vibrio parahaemolyticus at threonine 35. These modifications take place in the important regulatory switch I or switch II regions of the GTPases. Since Rab1b and Cdc42 are central regulators of intracellular vesicular trafficking and of the actin cytoskeleton, their modifications by bacterial pathogens have a profound impact on the course of infection. Here, we addressed the biochemical and structural consequences of GTPase AMPylation and phosphocholination. By combining biochemical experiments and NMR analysis, we demonstrate that AMPylation can overrule the activity state of Rab1b that is commonly dictated by binding to guanosine diphosphate or guanosine triphosphate. Thus, PTMs may exert conformational control over small GTPases and may add another previously unrecognized layer of activity control to this important regulatory protein family.
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24
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Dharmaiah S, Tran TH, Messing S, Agamasu C, Gillette WK, Yan W, Waybright T, Alexander P, Esposito D, Nissley DV, McCormick F, Stephen AG, Simanshu DK. Structures of N-terminally processed KRAS provide insight into the role of N-acetylation. Sci Rep 2019; 9:10512. [PMID: 31324887 PMCID: PMC6642148 DOI: 10.1038/s41598-019-46846-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 07/04/2019] [Indexed: 01/19/2023] Open
Abstract
Although post-translational modification of the C-terminus of RAS has been studied extensively, little is known about N-terminal processing. Mass spectrometric characterization of KRAS expressed in mammalian cells showed cleavage of the initiator methionine (iMet) and N-acetylation of the nascent N-terminus. Interestingly, structural studies on GDP- and GMPPNP-bound KRAS lacking the iMet and N-acetylation resulted in Mg2+-free structures of KRAS with flexible N-termini. In the Mg2+-free KRAS-GDP structure, the flexible N-terminus causes conformational changes in the interswitch region resulting in a fully open conformation of switch I. In the Mg2+-free KRAS-GMPPNP structure, the flexible N-terminus causes conformational changes around residue A59 resulting in the loss of Mg2+ and switch I in the inactive state 1 conformation. Structural studies on N-acetylated KRAS-GDP lacking the iMet revealed the presence of Mg2+ and a conformation of switch regions also observed in the structure of GDP-bound unprocessed KRAS with the iMet. In the absence of the iMet, the N-acetyl group interacts with the central beta-sheet and stabilizes the N-terminus and the switch regions. These results suggest there is crosstalk between the N-terminus and the Mg2+ binding site, and that N-acetylation plays an important role by stabilizing the N-terminus of RAS upon excision of the iMet.
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Affiliation(s)
- Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - William K Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Wupeng Yan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Patrick Alexander
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
- Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA.
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25
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Gillingham AK, Bertram J, Begum F, Munro S. In vivo identification of GTPase interactors by mitochondrial relocalization and proximity biotinylation. eLife 2019; 8:45916. [PMID: 31294692 PMCID: PMC6639074 DOI: 10.7554/elife.45916] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
The GTPases of the Ras superfamily regulate cell growth, membrane traffic and the cytoskeleton, and a wide range of diseases are caused by mutations in particular members. They function as switchable landmarks with the active GTP-bound form recruiting to the membrane a specific set of effector proteins. The GTPases are precisely controlled by regulators that promote acquisition of GTP (GEFs) or its hydrolysis to GDP (GAPs). We report here MitoID, a method for identifying effectors and regulators by performing in vivo proximity biotinylation with mitochondrially-localized forms of the GTPases. Applying this to 11 human Rab GTPases identified many known effectors and GAPs, as well as putative novel effectors, with examples of the latter validated for Rab2, Rab5, Rab9 and Rab11. MitoID can also efficiently identify effectors and GAPs of Rho and Ras family GTPases such as Cdc42, RhoA, Rheb, and N-Ras, and can identify GEFs by use of GDP-bound forms.
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Affiliation(s)
| | - Jessie Bertram
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Farida Begum
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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26
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Klochkov SG, Neganova ME, Yarla NS, Parvathaneni M, Sharma B, Tarasov VV, Barreto G, Bachurin SO, Ashraf GM, Aliev G. Implications of farnesyltransferase and its inhibitors as a promising strategy for cancer therapy. Semin Cancer Biol 2019; 56:128-134. [DOI: 10.1016/j.semcancer.2017.10.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/14/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
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27
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Killoran RC, Smith MJ. Conformational resolution of nucleotide cycling and effector interactions for multiple small GTPases determined in parallel. J Biol Chem 2019; 294:9937-9948. [PMID: 31088913 DOI: 10.1074/jbc.ra119.008653] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/09/2019] [Indexed: 12/31/2022] Open
Abstract
Small GTPases alternatively bind GDP/GTP guanine nucleotides to gate signaling pathways that direct most cellular processes. Numerous GTPases are implicated in oncogenesis, particularly the three RAS isoforms HRAS, KRAS, and NRAS and the RHO family GTPase RAC1. Signaling networks comprising small GTPases are highly connected, and there is some evidence of direct biochemical cross-talk between their functional G-domains. The activation potential of a given GTPase is contingent on a codependent interaction with the nucleotide and a Mg2+ ion, which bind to individual variants with distinct affinities coordinated by residues in the GTPase nucleotide-binding pocket. Here, we utilized a selective-labeling strategy coupled with real-time NMR spectroscopy to monitor nucleotide exchange, GTP hydrolysis, and effector interactions of multiple small GTPases in a single complex system. We provide insight into nucleotide preference and the role of Mg2+ in activating both WT and oncogenic mutant enzymes. Multiplexing revealed guanine nucleotide exchange factor (GEF), GTPase-activating protein (GAP), and effector-binding specificities in mixtures of GTPases and resolved that the three related RAS isoforms are biochemically equivalent. This work establishes that direct quantitation of the nucleotide-bound conformation is required to accurately determine an activation potential for any given GTPase, as small GTPases such as RAS-like proto-oncogene A (RALA) or the G12C mutant of KRAS display fast exchange kinetics but have a high affinity for GDP. Furthermore, we propose that the G-domains of small GTPases behave autonomously in solution and that nucleotide cycling proceeds independently of protein concentration but is highly impacted by Mg2+ abundance.
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Affiliation(s)
- Ryan C Killoran
- From the Institute for Research in Immunology and Cancer and
| | - Matthew J Smith
- From the Institute for Research in Immunology and Cancer and .,Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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28
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Sugawara R, Ueda H, Honda R. Structural and functional characterization of fast-cycling RhoF GTPase. Biochem Biophys Res Commun 2019; 513:522-527. [PMID: 30981505 DOI: 10.1016/j.bbrc.2019.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/03/2019] [Indexed: 11/18/2022]
Abstract
Ras superfamily GTPases are molecular switches that cycle between GDP-bound inactive state and GTP-bound active state to control many signaling pathways. Emerging evidence suggests that several Ras superfamily GTPases, including RhoF, do not follow the classical GDP/GTP exchange cycle; they act as constitutively active GTP-bound proteins due to their fast activities of GDP/GTP exchange (termed as 'fast-cycling' GTPases). To understand the molecular basis of the fast-cycling GTPases, we generated a GTPase active recombinant RhoF and examined its function and structure. Two point mutations in the switch I/II regions (Q77L and P45S, corresponding to Q61L and P29S of Rac1) significantly reduced the GTPase activity of RhoF, suggesting a conserved mechanism of GTP hydrolysis between RhoF and other RAS superfamily GTPases. However, in contrary to the previous evidence, RhoF represented a slow GDP/GTP exchange activity that dissociates GDP very slowly on a day-to-week time scale, in our experiment using fluorescently labeled GDP. The slow GDP dissociation was accelerated by Mg2+ chelation and canonical fast-cycling mutations, F44L (corresponding to F28L of Rac1) and P45S. NMR and dynamic light scattering data revealed a multimeric structure of RhoF that can switch between different conformations depending on the GTP/GDP-bound state. Overall, our study suggests that (1) RhoF shares a conserved mechanism of GTP hydrolysis with other RAS superfamily GTPases, but (2) RhoF adopts a unique multimeric structure. Our study also argues that (3) the emerging concept of the fast-cycling GTPases for RhoF should be validated using an alternative assay that does not rely on fluorescently labeled GDP (251 words).
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Affiliation(s)
- Ryota Sugawara
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan
| | - Hiroshi Ueda
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan.
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan.
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29
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Nikonov O, Kravchenko O, Nevskaya N, Stolboushkina E, Garber M, Nikonov S. The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:392-399. [PMID: 30988256 DOI: 10.1107/s2059798319002304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/12/2019] [Indexed: 11/10/2022]
Abstract
The structure of the γ subunit of archaeal translation initiation factor 2 (aIF2) from Sulfolobus solfataricus (SsoIF2γ) was determined in complex with GDPCP (a GTP analog). Crystals were obtained in the absence of magnesium ions in the crystallization solution. They belonged to space group P1, with five molecules in the unit cell. Four of these molecules are related in pairs by a common noncrystallographic twofold symmetry axis, while the fifth has no symmetry equivalent. Analysis of the structure and its comparison with other known aIF2 γ-subunit structures in the GTP-bound state show that (i) the magnesium ion is necessary for the formation and the maintenance of the active form of SsoIF2γ and (ii) in addition to the two previously known structural switches 1 and 2, eukaryotic translation initiation factor 2 (eIF2) and aIF2 molecules have another flexible region (switch 3), the function of which may consist of initiation of the hydrolysis of GTP and the removal of e/aIF2 from the ribosome after codon-anticodon recognition.
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Affiliation(s)
- Oleg Nikonov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russian Federation
| | - Olesya Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russian Federation
| | - Natalia Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russian Federation
| | - Elena Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russian Federation
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russian Federation
| | - Stanislav Nikonov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russian Federation
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30
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31
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Jeganathan S, Müller MP, Ali I, Goody RS. Assays for Nucleotide Competitive Reversible and Irreversible Inhibitors of Ras GTPases. Biochemistry 2018; 57:4690-4699. [PMID: 29791793 DOI: 10.1021/acs.biochem.8b00234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the Ras protein has been seen as a potential target for cancer therapy for the past 30 years, there was a tendency to consider it undruggable until recently. This has changed with the demonstration that small molecules with a specificity for (disease related mutants of) Ras can indeed be found, and some of these molecules form covalent adducts. A subgroup of these molecules can be characterized as competing with binding of the natural ligands GTP and GDP. Because of the distinct properties of Ras and related GTPases, in particular the very high nucleotide affinities and associated very low dissociation rates, assays for characterizing such molecules are not trivial. This is compounded by the fact that Ras family GTPases tend to be thermally unstable in the absence of a bound nucleotide. Here, we show that instead of using the unstable nucleotide-free Ras, the protein can be isolated as a 1:1 complex with a modified nucleotide (GDP-β-methyl ester) with low affinity to Ras. With this nucleotide analogue bound to the protein, testing of inhibitors is made experimentally more convenient and we present assays that allow the rapid assessment of the kinetic constants describing the inhibition process.
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Affiliation(s)
- Sadasivam Jeganathan
- Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Otto-Hahn-Straße 11 , 44227 , Dortmund , Germany
| | - Matthias P Müller
- Faculty of Chemistry and Chemical Biology , Dortmund University of Technology , Otto-Hahn-Straße 4a , 44227 , Dortmund , Germany
| | - Imtiaz Ali
- Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Otto-Hahn-Straße 11 , 44227 , Dortmund , Germany
| | - Roger S Goody
- Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Otto-Hahn-Straße 11 , 44227 , Dortmund , Germany
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32
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Shah S, Brock EJ, Ji K, Mattingly RR. Ras and Rap1: A tale of two GTPases. Semin Cancer Biol 2018; 54:29-39. [PMID: 29621614 DOI: 10.1016/j.semcancer.2018.03.005] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 02/07/2023]
Abstract
Ras oncoproteins play pivotal roles in both the development and maintenance of many tumor types. Unfortunately, these proteins are difficult to directly target using traditional pharmacological strategies, in part due to their lack of obvious binding pockets or allosteric sites. This obstacle has driven a considerable amount of research into pursuing alternative ways to effectively inhibit Ras, examples of which include inducing mislocalization to prevent Ras maturation and inactivating downstream proteins in Ras-driven signaling pathways. Ras proteins are archetypes of a superfamily of small GTPases that play specific roles in the regulation of many cellular processes, including vesicle trafficking, nuclear transport, cytoskeletal rearrangement, and cell cycle progression. Several other superfamily members have also been linked to the control of normal and cancer cell growth and survival. For example, Rap1 has high sequence similarity to Ras, has overlapping binding partners, and has been demonstrated to both oppose and mimic Ras-driven cancer phenotypes. Rap1 plays an important role in cell adhesion and integrin function in a variety of cell types. Mechanistically, Ras and Rap1 cooperate to initiate and sustain ERK signaling, which is activated in many malignancies and is the target of successful therapeutics. Here we review the role activated Rap1 in ERK signaling and other downstream pathways to promote invasion and cell migration and metastasis in various cancer types.
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Affiliation(s)
- Seema Shah
- Program in Cancer Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Ethan J Brock
- Program in Cancer Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Kyungmin Ji
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Raymond R Mattingly
- Program in Cancer Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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33
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De Cicco M, Kiss L, Dames SA. NMR analysis of the backbone dynamics of the small GTPase Rheb and its interaction with the regulatory protein FKBP38. FEBS Lett 2017; 592:130-146. [PMID: 29194576 DOI: 10.1002/1873-3468.12925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 10/06/2017] [Accepted: 11/17/2017] [Indexed: 12/19/2022]
Abstract
Ras homolog enriched in brain (Rheb) is a small GTPase that regulates mammalian/mechanistic target of rapamycin complex 1 (mTORC1) and, thereby, cell growth and metabolism. Here we show that cycling between the inactive GDP- and the active GTP-bound state modulates the backbone dynamics of a C-terminal truncated form, RhebΔCT, which is suggested to influence its interactions. We further investigated the interactions between RhebΔCT and the proposed Rheb-binding domain of the regulatory protein FKBP38. The observed weak interactions with the GTP-analogue- (GppNHp-) but not the GDP-bound state, appear to accelerate the GDP to GTP exchange, but only very weakly compared to a genuine GEF. Thus, FKBP38 is most likely not a GEF but a Rheb effector that may function in membrane targeting of Rheb.
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Affiliation(s)
- Maristella De Cicco
- Technische Universität München, Department of Chemistry, Biomolecular NMR Spectroscopy, Garching, Germany
| | - Leo Kiss
- Technische Universität München, Department of Chemistry, Biomolecular NMR Spectroscopy, Garching, Germany
| | - Sonja A Dames
- Technische Universität München, Department of Chemistry, Biomolecular NMR Spectroscopy, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
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34
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Kotyada C, Maulik A, Srivastava A, Singh M. Mechanistic Insights into the Differential Catalysis by RheB and Its Mutants: Y35A and Y35A-D65A. ACS OMEGA 2017; 2:6691-6702. [PMID: 29750207 PMCID: PMC5937686 DOI: 10.1021/acsomega.7b01025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/28/2017] [Indexed: 06/08/2023]
Abstract
RheB GTPase is a Ras-related molecular switch, which regulates the mTOR signaling pathway by cycling between the active [guanosine triphosphate (GTP)] state and inactive [guanine diphosphate (GDP)] state. Impairment of GTPase activity because of mutations in several small GTPases is known to be associated with several cancers. The conventional GTPase mechanism such as in H-Ras requires a conserved glutamine (Q64) in the switch-II region of RheB to align the catalytic water molecule for efficient GTP hydrolysis. The conformation of this conserved glutamine is different in RheB, resulting in an altered conformation of the entire switch-II region. Studies on the atypical switch-II conformation in RheB revealed a distinct, noncanonical mode of GTP hydrolysis. An RheB mutant Y35A was previously shown to exclusively enhance the intrinsic GTPase activity of RheB, whereas the Y35A-D65A double mutant was shown to reduce the elevated GTPase activity. Here, we have used all-atom molecular dynamics (MD) simulations for comprehensive understanding of the conformational dynamics associated with the fast (Y35A) and slow (Y35A-D65A) hydrolyzing mutants of RheB. Using a combination of starting models from PDB structures and in-silico generated mutant structures, we discuss the observed conformational deviations in wild type (WT) versus mutants. Our results show that a number of interactions of RheB with phosphates of GTP as well as Mg2+ are destabilized in Y35A mutant in the switch-I region. We report distinct water dynamics at the active site of WT and mutants. Furthermore, principal component analysis showed significant differences in the conformational space sampled by the WT and mutants. Our observations provide improved understanding of the noncanonical GTP hydrolysis mechanism adopted by RheB and its modulation by Y35A and Y35A-D65A mutants.
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Affiliation(s)
- Chaithanya Kotyada
- Molecular
Biophysics Unit and NMR Research Centre, Indian Institute of
Science, Bengaluru 560012, India
| | - Aditi Maulik
- Molecular
Biophysics Unit and NMR Research Centre, Indian Institute of
Science, Bengaluru 560012, India
| | - Anand Srivastava
- Molecular
Biophysics Unit and NMR Research Centre, Indian Institute of
Science, Bengaluru 560012, India
| | - Mahavir Singh
- Molecular
Biophysics Unit and NMR Research Centre, Indian Institute of
Science, Bengaluru 560012, India
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35
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Johnson CW, Reid D, Parker JA, Salter S, Knihtila R, Kuzmic P, Mattos C. The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects. J Biol Chem 2017; 292:12981-12993. [PMID: 28630043 PMCID: PMC5546037 DOI: 10.1074/jbc.m117.778886] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/09/2017] [Indexed: 11/06/2022] Open
Abstract
H-Ras, K-Ras, and N-Ras are small GTPases that are important in the control of cell proliferation, differentiation, and survival, and their mutants occur frequently in human cancers. The G-domain, which catalyzes GTP hydrolysis and mediates downstream signaling, is 95% conserved between the Ras isoforms. Because of their very high sequence identity, biochemical studies done on H-Ras have been considered representative of all three Ras proteins. We show here that this is not a valid assumption. Using enzyme kinetic assays under identical conditions, we observed clear differences between the three isoforms in intrinsic catalysis of GTP by Ras in the absence and presence of the Ras-binding domain (RBD) of the c-Raf kinase protein (Raf-RBD). Given their identical active sites, isoform G-domain differences must be allosteric in origin, due to remote isoform-specific residues that affect conformational states. We present the crystal structure of N-Ras bound to a GTP analogue and interpret the kinetic data in terms of structural features specific for H-, K-, and N-Ras.
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Affiliation(s)
- Christian W Johnson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Derion Reid
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Jillian A Parker
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Shores Salter
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Ryan Knihtila
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | | | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115.
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36
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The Architecture of the Rag GTPase Signaling Network. Biomolecules 2017; 7:biom7030048. [PMID: 28788436 PMCID: PMC5618229 DOI: 10.3390/biom7030048] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
The evolutionarily conserved target of rapamycin complex 1 (TORC1) couples an array of intra- and extracellular stimuli to cell growth, proliferation and metabolism, and its deregulation is associated with various human pathologies such as immunodeficiency, epilepsy, and cancer. Among the diverse stimuli impinging on TORC1, amino acids represent essential input signals, but how they control TORC1 has long remained a mystery. The recent discovery of the Rag GTPases, which assemble as heterodimeric complexes on vacuolar/lysosomal membranes, as central elements of an amino acid signaling network upstream of TORC1 in yeast, flies, and mammalian cells represented a breakthrough in this field. Here, we review the architecture of the Rag GTPase signaling network with a special focus on structural aspects of the Rag GTPases and their regulators in yeast and highlight both the evolutionary conservation and divergence of the mechanisms that control Rag GTPases.
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Müller MP, Jeganathan S, Heidrich A, Campos J, Goody RS. Nucleotide based covalent inhibitors of KRas can only be efficient in vivo if they bind reversibly with GTP-like affinity. Sci Rep 2017. [PMID: 28623374 PMCID: PMC5473928 DOI: 10.1038/s41598-017-03973-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Simple reversible competitive inhibition of nucleotide binding of GTP to Ras family GTPases has long been recognized as an unlikely approach to manipulating the activity of such proteins for experimental or therapeutic purposes. This is due to the high affinity of GTP to GTPases coupled with high cellular GTP concentrations, but also to problems of specificity for the highly conserved binding sites in GTPases. A recent approach suggested that these problems might be overcome by using GDP derivatives that can undergo a covalent reaction with disease specific mutants, in particular addressing inhibition of KRasG12C using GDP equipped with an electrophilic group at the β-phosphate. We show here that a major drawback to this approach is a loss of reversible affinity of such β-modified derivatives for Ras of at least 104 compared to GTP and GDP. With the help of a thorough kinetic characterization, we show that this leads to covalent reaction times that are too slow to make the compounds attractive for intracellular use, but that generation of a hypothetical reactive GDP derivative that retains the high reversible affinity of GDP/GTP to Ras might be a viable alternative.
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Affiliation(s)
- Matthias P Müller
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, Dortmund University of Technology, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany.
| | - Sadasivam Jeganathan
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Angelika Heidrich
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Jeremy Campos
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Roger S Goody
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany.
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38
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Sautier B, Nising CF, Wortmann L. Fortschritte bei der Ras-Inhibition aus medizinisch-chemischer Perspektive. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brice Sautier
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
| | - Carl F. Nising
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
| | - Lars Wortmann
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
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Sautier B, Nising CF, Wortmann L. Latest Advances Towards Ras Inhibition: A Medicinal Chemistry Perspective. Angew Chem Int Ed Engl 2016; 55:15982-15988. [PMID: 27635522 DOI: 10.1002/anie.201608270] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Indexed: 12/17/2022]
Abstract
Owing to their high occurrence rate across many human cancers and their lack of druggability so far, mutant forms of the signaling protein Ras are currently among the most attractive (and elusive) oncology targets. This strong appeal explains the sustained effort in the field, and the ensuing progress has rekindled optimism regarding the discovery of Ras inhibitors. In this Minireview, we discuss the most recent advances towards irreversible inhibitors, and highlight approaches to inhibitors of Ras-effector interactions that have been overshadowed by the current focus on direct Ras inhibition. At the same time, we provide a critical assessment from a medicinal chemistry perspective.
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Affiliation(s)
- Brice Sautier
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
| | - Carl F Nising
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
| | - Lars Wortmann
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
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Mishra AK, Lambright DG. Invited review: Small GTPases and their GAPs. Biopolymers 2016; 105:431-48. [PMID: 26972107 PMCID: PMC5439442 DOI: 10.1002/bip.22833] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 03/10/2016] [Indexed: 12/11/2022]
Abstract
Widespread utilization of small GTPases as major regulatory hubs in many different biological systems derives from a conserved conformational switch mechanism that facilitates cycling between GTP-bound active and GDP-bound inactive states under control of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which accelerate slow intrinsic rates of activation by nucleotide exchange and deactivation by GTP hydrolysis, respectively. Here we review developments leading to current understanding of intrinsic and GAP catalyzed GTP hydrolytic reactions in small GTPases from structural, molecular and chemical mechanistic perspectives. Despite the apparent simplicity of the GTPase cycle, the structural bases underlying the hallmark hydrolytic reaction and catalytic acceleration by GAPs are considerably more diverse than originally anticipated. Even the most fundamental aspects of the reaction mechanism have been challenging to decipher. Through a combination of experimental and in silico approaches, the outlines of a consensus view have begun to emerge for the best studied paradigms. Nevertheless, recent observations indicate that there is still much to be learned. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 431-448, 2016.
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Affiliation(s)
- Ashwini K Mishra
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - David G Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
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41
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Ostrem JML, Shokat KM. Direct small-molecule inhibitors of KRAS: from structural insights to mechanism-based design. Nat Rev Drug Discov 2016; 15:771-785. [PMID: 27469033 DOI: 10.1038/nrd.2016.139] [Citation(s) in RCA: 400] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
KRAS is the most frequently mutated oncogene in human cancer. In addition to holding this distinction, unsuccessful attempts to target this protein have led to the characterization of RAS as 'undruggable'. However, recent advances in technology and novel approaches to drug discovery have renewed hope that a direct KRAS inhibitor may be on the horizon. In this Review, we provide an in-depth analysis of the structure, dynamics, mutational activation and inactivation, and signalling mechanisms of RAS. From this perspective, we then consider potential mechanisms of action for effective RAS inhibitors. Finally, we examine each of the many recent reports of direct RAS inhibitors and discuss promising avenues for further development.
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Affiliation(s)
- Jonathan M L Ostrem
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA
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Khleborodova A, Pan X, Nagre NN, Ryan K. An investigation into the role of ATP in the mammalian pre-mRNA 3' cleavage reaction. Biochimie 2016; 125:213-22. [PMID: 27060432 DOI: 10.1016/j.biochi.2016.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/04/2016] [Indexed: 01/05/2023]
Abstract
RNA Polymerase II transcribes beyond what later becomes the 3' end of a mature messenger RNA (mRNA). The formation of most mRNA 3' ends results from pre-mRNA cleavage followed by polyadenylation. In vitro studies have shown that low concentrations of ATP stimulate the 3' cleavage reaction while high concentrations inhibit it, but the origin of these ATP effects is unknown. ATP might enable a cleavage factor kinase or activate a cleavage factor directly. To distinguish between these possibilities, we tested several ATP structural analogs in a pre-mRNA 3' cleavage reaction reconstituted from DEAE-fractionated cleavage factors. We found that adenosine 5'-(β,γ-methylene)triphosphate (AMP-PCP) is an effective in vitro 3' cleavage inhibitor with an IC50 of ∼300 μM, but that most other ATP analogs, including adenosine 5'-(β,γ-imido)triphosphate, which cannot serve as a protein kinase substrate, promoted 3' cleavage but less efficiently than ATP. In combination with previous literature data, our results do not support ATP stimulation of 3' cleavage through cleavage factor phosphorylation in vitro. Instead, the more likely mechanism is that ATP stimulates cleavage factor activity through direct cleavage factor binding. The mammalian 3' cleavage factors known to bind ATP include the cleavage factor II (CF IIm) Clp1 subunit, the CF Im25 subunit and poly(A) polymerase alpha (PAP). The yeast homolog of the CF IIm complex also binds ATP through yClp1. To investigate the mammalian complex, we used a cell-line expressing FLAG-tagged Clp1 to co-immunoprecipitate Pcf11 as a function of ATP concentration. FLAG-Clp1 co-precipitated Pcf11 with or without ATP and the complex was not affected by AMP-PCP. Diadenosine tetraphosphate (Ap4A), an ATP analog that binds the Nudix domain of the CF Im25 subunit with higher affinity than ATP, neither stimulated 3' cleavage in place of ATP nor antagonized ATP-stimulated 3' cleavage. The ATP-binding site of PAP was disrupted by site directed mutagenesis but a reconstituted 3' cleavage reaction containing a mutant PAP unable to bind ATP nevertheless underwent ATP-stimulated 3' cleavage. Fluctuating ATP levels might contribute to the regulation of pre-mRNA 3' cleavage, but the three subunits investigated here do not appear to be responsible for the ATP-stimulation of pre-mRNA cleavage.
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Affiliation(s)
- Asya Khleborodova
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA; Biochemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA
| | - Xiaozhou Pan
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA
| | - Nagaraja N Nagre
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA
| | - Kevin Ryan
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA; Biochemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA; Chemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA.
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Quah SY, Tan MS, Teh YH, Stanslas J. Pharmacological modulation of oncogenic Ras by natural products and their derivatives: Renewed hope in the discovery of novel anti-Ras drugs. Pharmacol Ther 2016; 162:35-57. [PMID: 27016467 DOI: 10.1016/j.pharmthera.2016.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Oncogenic rat sarcoma (Ras) is linked to the most fatal cancers such as those of the pancreas, colon, and lung. Decades of research to discover an efficacious drug that can block oncogenic Ras signaling have yielded disappointing results; thus, Ras was considered "undruggable" until recently. Inhibitors that directly target Ras by binding to previously undiscovered pockets have been recently identified. Some of these molecules are either isolated from natural products or derived from natural compounds. In this review, we described the potential of these compounds and other inhibitors of Ras signaling in drugging Ras. We highlighted the modes of action of these compounds in suppressing signaling pathways activated by oncogenic Ras, such as mitogen-activated protein kinase (MAPK) signaling and the phosphoinositide-3-kinase (PI3K) pathways. The anti-Ras strategy of these compounds can be categorized into four main types: inhibition of Ras-effector interaction, interference of Ras membrane association, prevention of Ras-guanosine triphosphate (GTP) formation, and downregulation of Ras proteins. Another promising strategy that must be validated experimentally is enhancement of the intrinsic Ras-guanosine triphosphatase (GTPase) activity by small chemical entities. Among the inhibitors of Ras signaling that were reported thus far, salirasib and TLN-4601 have been tested for their clinical efficacy. Although both compounds passed phase I trials, they failed in their respective phase II trials. Therefore, new compounds of natural origin with relevant clinical activity against Ras-driven malignancies are urgently needed. Apart from salirasib and TLN-4601, some other compounds with a proven inhibitory effect on Ras signaling include derivatives of salirasib, sulindac, polyamine, andrographolide, lipstatin, levoglucosenone, rasfonin, and quercetin.
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Affiliation(s)
- Shun Ying Quah
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Michelle Siying Tan
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yuan Han Teh
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Johnson Stanslas
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia; Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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44
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Choi JY, Shin YC, Yoon JH, Kim CM, Lee JH, Jeon JH, Park HH. Molecular mechanism of constitutively active Rab11A was revealed by crystal structure of Rab11A S20V. FEBS Lett 2016; 590:819-27. [PMID: 26879265 DOI: 10.1002/1873-3468.12100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/02/2016] [Accepted: 02/05/2016] [Indexed: 11/06/2022]
Abstract
Rab11A is a small GTP-binding protein involved in the regulation of vesicle trafficking during recycling of endosomes. Substitution of S20 to V (S20V) at Rab11A inhibits the GTP hydrolysis activity of Rab11A. This mutation is known to be constitutively in an active form. Here, we report the crystal structure of the human Rab11A S20V mutant form complexed with GTP at a resolution of 2.4 Å. Without adding any substrate, Rab11A contained non-hydrolyzed natural substrate GTP in the nucleotide binding pocket with Mg(2+). In our observations, substituted V20 of Rab11A was found to interfere with proper localization of the water molecule, which mediated GTP hydrolysis, resulting in GTP being locked in an active form of Rab11A S20V.
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Affiliation(s)
- Jae Young Choi
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
| | - Young-Cheul Shin
- Department of Physiology, Department of Biomedical Sciences, and Institute of Dermatological Science, Seoul National University College of Medicine, South Korea
| | - Jong Hwan Yoon
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
| | - Chang Min Kim
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Inchon, South Korea
| | - Ju-Hong Jeon
- Department of Physiology, Department of Biomedical Sciences, and Institute of Dermatological Science, Seoul National University College of Medicine, South Korea
| | - Hyun Ho Park
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
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45
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Koch D, Rai A, Ali I, Bleimling N, Friese T, Brockmeyer A, Janning P, Goud B, Itzen A, Müller MP, Goody RS. A pull-down procedure for the identification of unknown GEFs for small GTPases. Small GTPases 2016; 7:93-106. [PMID: 26918858 PMCID: PMC4905258 DOI: 10.1080/21541248.2016.1156803] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Members of the family of small GTPases regulate a variety of important cellular functions. In order to accomplish this, tight temporal and spatial regulation is absolutely necessary. The two most important factors for this regulation are GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs), the latter being responsible for the activation of the GTPase downstream pathways at the correct location and time. Although a large number of exchange factors have been identified, it is likely that a similarly large number remains unidentified. We have therefore developed a procedure to specifically enrich GEF proteins from biological samples making use of the high affinity binding of GEFs to nucleotide-free GTPases. In order to verify the results of these pull-down experiments, we have additionally developed two simple validation procedures: An in vitro transcription/translation system coupled with a GEF activity assay and a yeast two-hybrid screen for detection of GEFs. Although the procedures were established and tested using the Rab protein Sec4, the similar basic principle of action of all nucleotide exchange factors will allow the method to be used for identification of unknown GEFs of small GTPases in general.
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Affiliation(s)
- Daniel Koch
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Amrita Rai
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Imtiaz Ali
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Nathalie Bleimling
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Timon Friese
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Andreas Brockmeyer
- b Department of Chemical Biology , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Petra Janning
- b Department of Chemical Biology , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Bruno Goud
- c Institut Curie, PSL Research University, CNRS UMR 144 , Paris , France
| | - Aymelt Itzen
- d Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München , Garching , Germany
| | - Matthias P Müller
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Roger S Goody
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
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46
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Morris KM, Henderson R, Suresh Kumar TK, Heyes CD, Adams PD. Intrinsic GTP hydrolysis is observed for a switch 1 variant of Cdc42 in the presence of a specific GTPase inhibitor. Small GTPases 2016; 7:1-11. [PMID: 26828437 DOI: 10.1080/21541248.2015.1123797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The Ras-related protein Cell division cycle 42 (Cdc42) is important in cell-signaling processes. Protein interactions involving Cdc42 occur primarily in flexible "Switch" regions that help regulate effector binding. We studied the kinetics of intrinsic GTP hydrolysis reaction in the absence and presence of a biologically active peptide derivative of a p21-activated kinase effector (PBD46) for wt Cdc42 and compared it to the Switch 1 variant Cdc42(T35A). While the binding of PBD46 to wt Cdc42 results in complete inhibition of GTP hydrolysis, this interaction in Cdc42(T35A) does not. Comparison of the crystal structure of wt Cdc42 in the absence of effector (1AN0.pdb), as well as the NMR structure of wt Cdc42 bound to an effector in the Switch 1 region (1CF4.pdb) ( www.rcsb.org ) suggests that the orientation of T(35) with bound Mg(2+) changes in the presence of effector, resulting in movement of GTP away from the catalytic box leading to the inhibition of GTP hydrolysis. For Cdc42(T35A), molecular dynamics simulations and structural analyses suggest that the nucleotide does not undergo the conformational shift observed for the wt Cdc42-effector interaction. Our data suggest that change in dynamics in the Switch 1 region of Cdc42 caused by the T35A mutation (Chandrashekar, et al. 2011, Biochemistry, 50, p. 6196) fosters a conformation for this Cdc42 variant that allows hydrolysis of GTP in the presence of PBD46, and that alteration of the conformational dynamics could potentially modulate Ras-related over-activity.
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Affiliation(s)
- Kyla M Morris
- a Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Fayetteville , AR , USA
| | - Rory Henderson
- a Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Fayetteville , AR , USA
| | | | - Colin D Heyes
- a Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Fayetteville , AR , USA
| | - Paul D Adams
- a Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Fayetteville , AR , USA
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Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet 2016; 48:183-8. [PMID: 26691987 PMCID: PMC4731318 DOI: 10.1038/ng.3473] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/23/2015] [Indexed: 12/13/2022]
Abstract
Follicular lymphoma is an incurable B cell malignancy characterized by the t(14;18) translocation and mutations affecting the epigenome. Although frequent gene mutations in key signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlaps with that in the closely related diffuse large B cell lymphoma (DLBCL). Using a combination of discovery exome and extended targeted sequencing, we identified recurrent somatic mutations in RRAGC uniquely enriched in patients with follicular lymphoma (17%). More than half of the mutations preferentially co-occurred with mutations in ATP6V1B2 and ATP6AP1, which encode components of the vacuolar H(+)-ATP ATPase (V-ATPase) known to be necessary for amino acid-induced activation of mTORC1. The RagC variants increased raptor binding while rendering mTORC1 signaling resistant to amino acid deprivation. The activating nature of the RRAGC mutations, their existence in the dominant clone and their stability during disease progression support their potential as an excellent candidate for therapeutic targeting.
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Affiliation(s)
- Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jun Wang
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Shamzah Araf
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lucy Wilkins
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Brian M Castellano
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Leire Escudero-Ibarz
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ahad Fahad Al Seraihi
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Julia Richter
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel and Christian Albrechts University Kiel, Kiel, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Alejo Efeyan
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sameena Iqbal
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Janet Matthews
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andrew Clear
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Csaba Bödör
- MTA-SE Lendulet Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Hilmar Quentmeier
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Peter Johnson
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Davies
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jonathan C Strefford
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Graham Packham
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, St. James's Institute of Oncology, Leeds, UK
| | - Andrew Jack
- Haematological Malignancy Diagnostic Service, St. James's Institute of Oncology, Leeds, UK
| | - Ming-Qing Du
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maria Calaminici
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - T Andrew Lister
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rebecca Auer
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Silvia Montoto
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - John G Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel and Christian Albrechts University Kiel, Kiel, Germany
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direkte Modulation von Aktivität und Funktion kleiner GTPasen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direct Modulation of Small GTPase Activity and Function. Angew Chem Int Ed Engl 2015; 54:13516-37. [DOI: 10.1002/anie.201504357] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/19/2022]
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Kim CM, Choi JY, Yoon JH, Park HH. Purification, crystallization and X-ray crystallographic analysis of human RAB11(S20V), a constitutively active GTP-binding form. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1247-50. [PMID: 26457514 DOI: 10.1107/s2053230x15015447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/18/2015] [Indexed: 11/10/2022]
Abstract
RAB11, a member of the Ras superfamily of small G proteins, is involved in the regulation of vesicle trafficking during endosome recycling. Substitution of Ser20 by Val20 in Rab11 [RAB11(S20V)] inhibits its GTP hydrolysis activity and produces a constitutively active GTP-binding form. In this study, the RAB11(S20V) mutant was overexpressed in Escherichia coli with an engineered C-terminal His tag. RAB11(S20V) was then purified to homogeneity and was crystallized at 293 K. X-ray diffraction data were collected to a resolution of 2.4 Å from a crystal belonging to space group I4, with unit-cell parameters a = 74.11, b = 74.11, c = 149.44 Å. The asymmetric unit was estimated to contain two molecules of RAB11(S20V).
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Affiliation(s)
- Chang Min Kim
- Department of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jae Young Choi
- Department of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jong Hwan Yoon
- Department of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Hyun Ho Park
- Department of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
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