1
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Girard E, Lopes P, Spoerner M, Dhaussy AC, Prangé T, Kalbitzer HR, Colloc'h N. High Pressure Promotes Binding of the Allosteric Inhibitor Zn 2+-Cyclen in Crystals of Activated H-Ras. Chemistry 2024:e202400304. [PMID: 38647362 DOI: 10.1002/chem.202400304] [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: 01/24/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
In this work, we experimentally investigate the potency of high pressure to drive a protein toward an excited state where an inhibitor targeted for this state can bind. Ras proteins are small GTPases cycling between active GTP-bound and inactive GDP-bound states. Various states of GTP-bound Ras in active conformation coexist in solution, amongst them, state 2 which binds to effectors, and state 1, weakly populated at ambient conditions, which has a low affinity for effectors. Zn2+-cyclen is an allosteric inhibitor of Ras protein, designed to bind specifically to the state 1. In H-Ras(wt).Mg2+.GppNHp crystals soaked with Zn2+-cyclen, no binding could be observed, as expected in the state 2 conformation which is the dominant state at ambient pressure. Interestingly, Zn2+-cyclen binding is observed at 500 MPa pressure, close to the nucleotide, in Ras protein that is driven by pressure to a state 1 conformer. The unknown binding mode of Zn2+-cyclen to H-Ras can thus be fully characterized in atomic details. As a more general conjunction from our study, high pressure x-ray crystallography turns out to be a powerful method to induce transitions allowing drug binding in proteins that are in low-populated conformations at ambient conditions, enabling the design of specific inhibitors.
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Affiliation(s)
- Eric Girard
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Pedro Lopes
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Spoerner
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | | | - Thierry Prangé
- CiTCoM, CNRS, Faculté de Pharmacie, Université de Paris-Cité, Paris, France
| | - Hans Robert Kalbitzer
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Nathalie Colloc'h
- ISTCT UMR6030, Centre Cyceron, CNRS - Université de Caen Normandie - Normandie Université, Caen, France
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2
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Gebregiworgis T, Chan JYL, Kuntz DA, Privé GG, Marshall CB, Ikura M. Crystal structure of NRAS Q61K with a ligand-induced pocket near switch II. Eur J Cell Biol 2024; 103:151414. [PMID: 38640594 DOI: 10.1016/j.ejcb.2024.151414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024] Open
Abstract
The RAS isoforms (KRAS, HRAS and NRAS) have distinct cancer type-specific profiles. NRAS mutations are the second most prevalent RAS mutations in skin and hematological malignancies. Although RAS proteins were considered undruggable for decades, isoform and mutation-specific investigations have produced successful RAS inhibitors that are either specific to certain mutants, isoforms (pan-KRAS) or target all RAS proteins (pan-RAS). While extensive structural and biochemical investigations have focused mainly on K- and H-RAS mutations, NRAS mutations have received less attention, and the most prevalent NRAS mutations in human cancers, Q61K and Q61R, are rare in K- and H-RAS. This manuscript presents a crystal structure of the NRAS Q61K mutant in the GTP-bound form. Our structure reveals a previously unseen pocket near switch II induced by the binding of a ligand to the active form of the protein. This observation reveals a binding site that can potentially be exploited for development of inhibitors against mutant NRAS. Furthermore, the well-resolved catalytic site of this GTPase bound to native GTP provides insight into the stalled GTP hydrolysis observed for NRAS-Q61K.
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Affiliation(s)
- Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5W9, Canada.
| | - Jonathan Yui-Lai Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Douglas A Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada; Department of Biochemistry, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada.
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3
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Hu F, Wang Y, Zeng J, Deng X, Xia F, Xu X. Unveiling the State Transition Mechanisms of Ras Proteins through Enhanced Sampling and QM/MM Simulations. J Phys Chem B 2024; 128:1418-1427. [PMID: 38323538 DOI: 10.1021/acs.jpcb.3c07666] [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: 02/08/2024]
Abstract
In cells, wild-type RasGTP complexes exist in two distinct states: active State 2 and inactive State 1. These complexes regulate their functions by transitioning between the two states. However, the mechanisms underlying this state transition have not been clearly elucidated. To address this, we conducted a detailed simulation study to characterize the energetics of the stable states involved in the state transitions of the HRasGTP complex, specifically from State 2 to State 1. This was achieved by employing multiscale quantum mechanics/molecular mechanics and enhanced sampling molecular dynamics methods. Based on the simulation results, we constructed the two-dimensional free energy landscapes that provide crucial information about the conformational changes of the HRasGTP complex from State 2 to State 1. Furthermore, we also explored the conformational changes from the intermediate state to the product state during guanosine triphosphate hydrolysis. This study on the conformational changes involved in the HRas state transitions serves as a valuable reference for understanding the corresponding events of both KRas and NRas as well.
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Affiliation(s)
- Fangchen Hu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yiqiu Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan 523808, China
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, 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, Department of Chemistry, Fudan University, Shanghai 200433, China
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4
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Baumann P, Jin Y. Far-reaching effects of tyrosine64 phosphorylation on Ras revealed with BeF 3- complexes. Commun Chem 2024; 7:19. [PMID: 38297137 PMCID: PMC10830474 DOI: 10.1038/s42004-024-01105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Tyrosine phosphorylation on Ras by Src kinase is known to uncouple Ras from upstream regulation and downstream communication. However, the mechanisms by which phosphorylation modulates these interactions have not been detailed. Here, the major mono-phosphorylation level on tyrosine64 is quantified by 31P NMR and mutagenesis. Crystal structures of unphosphorylated and tyrosine64-phosphorylated Ras in complex with a BeF3- ground state analogue reveal "closed" Ras conformations very different from those of the "open" conformations previously observed for non-hydrolysable GTP analogue structures of Ras. They deliver new mechanistic and conformational insights into intrinsic GTP hydrolysis. Phosphorylation of tyrosine64 delivers conformational changes distant from the active site, showing why phosphorylated Ras has reduced affinity to its downstream effector Raf. 19F NMR provides evidence for changes in the intrinsic GTPase and nucleotide exchange rate and identifies the concurrent presence of a major "closed" conformation alongside a minor yet functionally important "open" conformation at the ground state of Ras. This study expands the application of metal fluoride complexes in revealing major and minor conformational changes of dynamic and modified Ras proteins.
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Affiliation(s)
- Patrick Baumann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yi Jin
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK.
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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5
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Johnson CW, Fetics SK, Davis KP, Rodrigues JA, Mattos C. Allosteric site variants affect GTP hydrolysis on Ras. Protein Sci 2023; 32:e4767. [PMID: 37615343 PMCID: PMC10510474 DOI: 10.1002/pro.4767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 08/25/2023]
Abstract
RAS GTPases are proto-oncoproteins that regulate cell growth, proliferation, and differentiation in response to extracellular signals. The signaling functions of RAS, and other small GTPases, are dependent on their ability to cycle between GDP-bound and GTP-bound states. Structural analyses suggest that GTP hydrolysis catalyzed by HRAS can be regulated by an allosteric site located between helices 3, 4, and loop 7. Here we explore the relationship between intrinsic GTP hydrolysis on HRAS and the position of helix 3 and loop 7 through manipulation of the allosteric site, showing that the two sites are functionally connected. We generated several hydrophobic mutations in the allosteric site of HRAS to promote shifts in helix 3 relative to helix 4. By combining crystallography and enzymology to study these mutants, we show that closure of the allosteric site correlates with increased hydrolysis of GTP on HRAS in solution. Interestingly, binding to the RAS binding domain of RAF kinase (RAF-RBD) inhibits GTP hydrolysis in the mutants. This behavior may be representative of a cluster of mutations found in human tumors, which potentially cooperate with RAF complex formation to stabilize the GTP-bound state of RAS.
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Affiliation(s)
- Christian W. Johnson
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Susan K. Fetics
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kathleen P. Davis
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Jose A. Rodrigues
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Carla Mattos
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
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6
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Lv X, Lu X, Cao J, Luo Q, Ding Y, Peng F, Pataer A, Lu D, Han D, Malmberg E, Chan DW, Wang X, Savage SR, Mao S, Yu J, Peng F, Yan L, Meng H, Maneix L, Han Y, Chen Y, Yao W, Chang EC, Catic A, Lin X, Miles G, Huang P, Sun Z, Burt B, Wang H, Wang J, Yao QC, Zhang B, Roth JA, O’Malley BW, Ellis MJ, Rimawi MF, Ying H, Chen X. Modulation of the proteostasis network promotes tumor resistance to oncogenic KRAS inhibitors. Science 2023; 381:eabn4180. [PMID: 37676964 PMCID: PMC10720158 DOI: 10.1126/science.abn4180] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 07/28/2023] [Indexed: 09/09/2023]
Abstract
Despite substantial advances in targeting mutant KRAS, tumor resistance to KRAS inhibitors (KRASi) remains a major barrier to progress. Here, we report proteostasis reprogramming as a key convergence point of multiple KRASi-resistance mechanisms. Inactivation of oncogenic KRAS down-regulated both the heat shock response and the inositol-requiring enzyme 1α (IRE1α) branch of the unfolded protein response, causing severe proteostasis disturbances. However, IRE1α was selectively reactivated in an ER stress-independent manner in acquired KRASi-resistant tumors, restoring proteostasis. Oncogenic KRAS promoted IRE1α protein stability through extracellular signal-regulated kinase (ERK)-dependent phosphorylation of IRE1α, leading to IRE1α disassociation from 3-hydroxy-3-methylglutaryl reductase degradation (HRD1) E3-ligase. In KRASi-resistant tumors, both reactivated ERK and hyperactivated AKT restored IRE1α phosphorylation and stability. Suppression of IRE1α overcame resistance to KRASi. This study reveals a druggable mechanism that leads to proteostasis reprogramming and facilitates KRASi resistance.
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Affiliation(s)
- Xiangdong Lv
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xuan Lu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jin Cao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Qin Luo
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yao Ding
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Fanglue Peng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Apar Pataer
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, USA
| | - Dong Lu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, USA
- Center for Drug Discovery, Baylor College of Medicine, USA
| | - Dong Han
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Eric Malmberg
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Doug W. Chan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaoran Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sara R. Savage
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - Sufeng Mao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jingjing Yu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Fei Peng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, USA
| | - Liang Yan
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, USA
| | - Huan Meng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Laure Maneix
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, USA
| | - Yumin Han
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, USA
| | - Wantong Yao
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, USA
| | - Eric C. Chang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Andre Catic
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, USA
| | - Xia Lin
- Division of Surgical Oncology, Michael E. DeBakey Department of Surgery
| | - George Miles
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - Pengxiang Huang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zheng Sun
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, USA
| | - Bryan Burt
- Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, USA
| | - Huamin Wang
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jin Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, USA
- Center for Drug Discovery, Baylor College of Medicine, USA
| | - Qizhi Cathy Yao
- Division of Surgical Oncology, Michael E. DeBakey Department of Surgery
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - Jack A. Roth
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, USA
| | - Bert W. O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew J. Ellis
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Early Oncology, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mothaffar F. Rimawi
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Lester and Sue Smith Breast Center and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
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7
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Thompson MC. Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods. Methods Enzymol 2023; 688:255-305. [PMID: 37748829 DOI: 10.1016/bs.mie.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Temperature is an important state variable that governs the behavior of microscopic systems, yet crystallographers rarely exploit temperature changes to study the structure and dynamics of biological macromolecules. In fact, approximately 90% of crystal structures in the Protein Data Bank were determined under cryogenic conditions, because sample cryocooling makes crystals robust to X-ray radiation damage and facilitates data collection. On the other hand, cryocooling can introduce artifacts into macromolecular structures, and can suppress conformational dynamics that are critical for function. Fortunately, recent advances in X-ray detector technology, X-ray sources, and computational data processing algorithms make non-cryogenic X-ray crystallography easier and more broadly applicable than ever before. Without the reliance on cryocooling, high-resolution crystallography can be combined with various temperature perturbations to gain deep insight into the conformational landscapes of macromolecules. This Chapter reviews the historical reasons for the prevalence of cryocooling in macromolecular crystallography, and discusses its potential drawbacks. Next, the Chapter summarizes technological developments and methodologies that facilitate non-cryogenic crystallography experiments. Finally, the chapter discusses the theoretical underpinnings and practical aspects of multi-temperature and temperature-jump crystallography experiments, which are powerful tools for understanding the relationship between the structure, dynamics, and function of proteins and other biological macromolecules.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, United States.
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8
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Clavaín L, Fernández-Pisonero I, Movilla N, Lorenzo-Martín LF, Nieto B, Abad A, García-Navas R, Llorente-González C, Sánchez-Martín M, Vicente-Manzanares M, Santos E, Alarcón B, García-Aznar JM, Dosil M, Bustelo XR. Characterization of mutant versions of the R-RAS2/TC21 GTPase found in tumors. Oncogene 2023; 42:389-405. [PMID: 36476833 PMCID: PMC9883167 DOI: 10.1038/s41388-022-02563-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
The R-RAS2 GTP hydrolase (GTPase) (also known as TC21) has been traditionally considered quite similar to classical RAS proteins at the regulatory and signaling levels. Recently, a long-tail hotspot mutation targeting the R-RAS2/TC21 Gln72 residue (Q72L) was identified as a potent oncogenic driver. Additional point mutations were also found in other tumors at low frequencies. Despite this, little information is available regarding the transforming role of these mutant versions and their relevance for the tumorigenic properties of already-transformed cancer cells. Here, we report that many of the RRAS2 mutations found in human cancers are highly transforming when expressed in immortalized cell lines. Moreover, the expression of endogenous R-RAS2Q72L is important for maintaining optimal levels of PI3K and ERK activities as well as for the adhesion, invasiveness, proliferation, and mitochondrial respiration of ovarian and breast cancer cell lines. Endogenous R-RAS2Q72L also regulates gene expression programs linked to both cell adhesion and inflammatory/immune-related responses. Endogenous R-RAS2Q72L is also quite relevant for the in vivo tumorigenic activity of these cells. This dependency is observed even though these cancer cell lines bear concurrent gain-of-function mutations in genes encoding RAS signaling elements. Finally, we show that endogenous R-RAS2, unlike the case of classical RAS proteins, specifically localizes in focal adhesions. Collectively, these results indicate that gain-of-function mutations of R-RAS2/TC21 play roles in tumor initiation and maintenance that are not fully redundant with those regulated by classical RAS oncoproteins.
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Affiliation(s)
- Laura Clavaín
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Isabel Fernández-Pisonero
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Nieves Movilla
- grid.11205.370000 0001 2152 8769Aragon Institute of Engineering Research, Department of Mechanical Engineering, University of Zaragoza, 50018 Zaragoza, Spain
| | - L. Francisco Lorenzo-Martín
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Blanca Nieto
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Antonio Abad
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Rósula García-Navas
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Clara Llorente-González
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Manuel Sánchez-Martín
- grid.11762.330000 0001 2180 1817Transgenesis Facility and Nucleus Platform for Research Services, University of Salamanca, 37007 Salamanca, Spain
| | - Miguel Vicente-Manzanares
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Eugenio Santos
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Balbino Alarcón
- grid.5515.40000000119578126Centro de Biología Molecular Severo Ochoa, CSIC and Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José M. García-Aznar
- grid.11205.370000 0001 2152 8769Aragon Institute of Engineering Research, Department of Mechanical Engineering, University of Zaragoza, 50018 Zaragoza, Spain
| | - Mercedes Dosil
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC and University of Salamanca, 37007 Salamanca, Spain
| | - Xosé R. Bustelo
- grid.11762.330000 0001 2180 1817Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, 37007 Salamanca, Spain ,grid.11762.330000 0001 2180 1817Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC and University of Salamanca, 37007 Salamanca, Spain
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9
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Abstract
A variety of cellular functions are driven by actin, which undergoes cyclic transitions between the monomeric G-form and the filamentous F-form. To gain insights into actin dynamics, the mechanism by which the energy is supplied by the ATP hydrolysis reaction in the F-form actin must be elucidated. This has been hampered by the lack of actin filament structures at atomic resolutions. Here, we have crystallized actin molecules trapped in the F-form without forming filaments, and based upon these structures we determined the reaction path by quantum mechanics calculations. The results are consistent with previous biochemical data. Remarkably, the hydrolysis reaction mechanism is essentially identical to those of motor proteins, while the process of Pi release is distinct. The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and the filamentous F-form, which drive organelle transport and cell motility. This mechanical work is driven by the ATPase activity at the catalytic site in the F-form. For deeper understanding of the actin cellular functions, the reaction mechanism must be elucidated. Here, we show that a single actin molecule is trapped in the F-form by fragmin domain-1 binding and present their crystal structures in the ATP analog-, ADP-Pi-, and ADP-bound forms, at 1.15-Å resolutions. The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. The reaction path consists of four steps: 1) W1 and W2 rotations; 2) PG–O3B bond cleavage; 3) four concomitant events: W1–PO3− formation, OH− and proton cleavage, nucleophilic attack by the OH− against PG, and the abstracted proton transfer; and 4) proton relocation that stabilizes the ADP-Pi–bound F-form actin. The mechanism explains the slow rate of ATP hydrolysis by actin and the irreversibility of the hydrolysis reaction. While the catalytic strategy of actin ATP hydrolysis is essentially the same as those of motor proteins like myosin, the process after the hydrolysis is distinct and discussed in terms of Pi release, F-form destabilization, and global conformational changes.
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10
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Volmar AY, Guterres H, Zhou H, Reid D, Pavlopoulos S, Makowski L, Mattos C. Mechanisms of isoform-specific residue influence on GTP-bound HRas, KRas, and NRas. Biophys J 2022; 121:3616-3629. [PMID: 35794829 PMCID: PMC9617160 DOI: 10.1016/j.bpj.2022.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/04/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
HRas, KRas, and NRas are GTPases with a common set of effectors that control many cell-signaling pathways, including proliferation through Raf kinase. Their G-domains are nearly identical in sequence, with a few isoform-specific residues that have an effect on dynamics and biochemical properties. Here, we use accelerated molecular dynamics (aMD) simulations consistent with solution x-ray scattering experiments to elucidate mechanisms through which isoform-specific residues associated with each Ras isoform affects functionally important regions connected to the active site. HRas-specific residues cluster in loop 8 to stabilize the nucleotide-binding pocket, while NRas-specific residues on helix 3 directly affect the conformations of switch I and switch II. KRas, the most globally flexible of the isoforms, shows greatest fluctuations in the switch regions enhanced by a KRas-specific residue in loop 7 and a highly dynamic loop 8 region. The analysis of isoform-specific residue effects on Ras proteins is supported by NMR experiments and is consistent with previously published biochemical data.
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Affiliation(s)
- Alicia Y Volmar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Hugo Guterres
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Hao Zhou
- Department of Electrical and Computing Engineering, Northeastern University, Boston, Massachusetts
| | - Derion Reid
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Spiro Pavlopoulos
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts
| | - Lee Makowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts; Department of Bioengineering, Northeastern University, Boston, Massachusetts
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.
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11
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Huynh MV, Hobbs GA, Schaefer A, Pierobon M, Carey LM, Diehl JN, DeLiberty JM, Thurman RD, Cooke AR, Goodwin CM, Cook JH, Lin L, Waters AM, Rashid NU, Petricoin EF, Campbell SL, Haigis KM, Simeone DM, Lyssiotis CA, Cox AD, Der CJ. Functional and biological heterogeneity of KRAS Q61 mutations. Sci Signal 2022; 15:eabn2694. [PMID: 35944066 PMCID: PMC9534304 DOI: 10.1126/scisignal.abn2694] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Missense mutations at the three hotspots in the guanosine triphosphatase (GTPase) RAS-Gly12, Gly13, and Gln61 (commonly known as G12, G13, and Q61, respectively)-occur differentially among the three RAS isoforms. Q61 mutations in KRAS are infrequent and differ markedly in occurrence. Q61H is the predominant mutant (at 57%), followed by Q61R/L/K (collectively 40%), and Q61P and Q61E are the rarest (2 and 1%, respectively). Probability analysis suggested that mutational susceptibility to different DNA base changes cannot account for this distribution. Therefore, we investigated whether these frequencies might be explained by differences in the biochemical, structural, and biological properties of KRASQ61 mutants. Expression of KRASQ61 mutants in NIH 3T3 fibroblasts and RIE-1 epithelial cells caused various alterations in morphology, growth transformation, effector signaling, and metabolism. The relatively rare KRASQ61E mutant stimulated actin stress fiber formation, a phenotype distinct from that of KRASQ61H/R/L/P, which disrupted actin cytoskeletal organization. The crystal structure of KRASQ61E was unexpectedly similar to that of wild-type KRAS, a potential basis for its weak oncogenicity. KRASQ61H/L/R-mutant pancreatic ductal adenocarcinoma (PDAC) cell lines exhibited KRAS-dependent growth and, as observed with KRASG12-mutant PDAC, were susceptible to concurrent inhibition of ERK-MAPK signaling and of autophagy. Our results uncover phenotypic heterogeneity among KRASQ61 mutants and support the potential utility of therapeutic strategies that target KRASQ61 mutant-specific signaling and cellular output.
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Affiliation(s)
- Minh V. Huynh
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - G. Aaron Hobbs
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Leiah M. Carey
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M. DeLiberty
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D. Thurman
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adelaide R. Cooke
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua H. Cook
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical
School, Boston, MA 02115, USA
| | - Lin Lin
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Andrew M. Waters
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Naim U. Rashid
- Department of Biostatistics, University of North Carolina
at Chapel Hill, NC 27955, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Sharon L. Campbell
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin M. Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
- Harvard Digestive Disease Center, Harvard Medical School,
Boston, MA 02115, USA
| | - Diane M. Simeone
- Perlmutter Cancer Center, New York University, New York,
NY10016, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of
Gastroenterology, University of Michigan, Ann Arbor, MI 48198, USA
- University of Michigan Comprehensive Cancer Center, Ann
Arbor, MI 48109, USA
| | - Adrienne D. Cox
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North
Carolina at Chapel Hill, Chapel Hill, NC 2799, USA
| | - Channing J. Der
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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12
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Johnson C, Burkhart DL, Haigis KM. Classification of KRAS-Activating Mutations and the Implications for Therapeutic Intervention. Cancer Discov 2022; 12:913-923. [PMID: 35373279 PMCID: PMC8988514 DOI: 10.1158/2159-8290.cd-22-0035] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
Abstract
Members of the family of RAS proto-oncogenes, discovered just over 40 years ago, were among the first cancer-initiating genes to be discovered. Of the three RAS family members, KRAS is the most frequently mutated in human cancers. Despite intensive biological and biochemical study of RAS proteins over the past four decades, we are only now starting to devise therapeutic strategies to target their oncogenic properties. Here, we highlight the distinct biochemical properties of common and rare KRAS alleles, enabling their classification into functional subtypes. We also discuss the implications of this functional classification for potential therapeutic avenues targeting mutant subtypes. SIGNIFICANCE Efforts in the recent past to inhibit KRAS oncogenicity have focused on kinases that function in downstream signal transduction cascades, although preclinical successes have not translated to patients with KRAS-mutant cancer. Recently, clinically effective covalent inhibitors of KRASG12C have been developed, establishing two principles that form a foundation for future efforts. First, KRAS is druggable. Second, each mutant form of KRAS is likely to have properties that make it uniquely druggable.
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Affiliation(s)
- Christian Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Deborah L Burkhart
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
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13
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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: 2] [Impact Index Per Article: 1.0] [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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14
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A hotspot mutation targeting the R-RAS2 GTPase acts as a potent oncogenic driver in a wide spectrum of tumors. Cell Rep 2022; 38:110522. [PMID: 35294890 DOI: 10.1016/j.celrep.2022.110522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/22/2021] [Accepted: 02/20/2022] [Indexed: 12/20/2022] Open
Abstract
A missense change in RRAS2 (Gln72 to Leu), analogous to the Gln61-to-Leu mutation of RAS oncoproteins, has been identified as a long-tail hotspot mutation in cancer and Noonan syndrome. However, the relevance of this mutation for in vivo tumorigenesis remains understudied. Here we show, using an inducible knockin mouse model, that R-Ras2Q72L triggers rapid development of a wide spectrum of tumors when somatically expressed in adult tissues. These tumors show limited overlap with those originated by classical Ras oncogenes. R-Ras2Q72L-driven tumors can be classified into different subtypes according to therapeutic susceptibility. Importantly, the most relevant R-Ras2Q72L-driven tumors are dependent on mTORC1 but independent of phosphatidylinositol 3-kinase-, MEK-, and Ral guanosine diphosphate (GDP) dissociation stimulator. This pharmacological vulnerability is due to the extensive rewiring by R-Ras2Q72L of pathways that orthogonally stimulate mTORC1 signaling. These findings demonstrate that RRAS2Q72L is a bona fide oncogenic driver and unveil therapeutic strategies for patients with cancer and Noonan syndrome bearing RRAS2 mutations.
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15
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姚 燕, 王 西, 赵 雪, 李 帅, 周 玉, 徐 一. Detection of RAS gene mutation and its clinical significance in children with acute lymphoblastic leukemia. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:309-313. [PMID: 35351263 PMCID: PMC8974658 DOI: 10.7499/j.issn.1008-8830.2109141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVES To investigate the mutation rate of the RAS gene and its clinical significance in children with acute lymphoblastic leukemia. METHODS A retrospective analysis was performed on the medical data of 120 children with newly diagnosed acute lymphoblastic leukemia, who were admitted to the Third Affiliated Hospital of Zhengzhou University from January 2015 to January 2020 and underwent next-generation sequencing. The clinical and molecular features were analyzed. The impact of RAS gene mutation on the overall survival rate was evaluated in these children. RESULTS Among the 120 children, 35 (29.2%) had RAS gene mutation, 30 (25.0%) had KRAS gene mutation, and 5 (4.2%) had both NRAS and KRAS gene mutations. All NRAS mutations and 71% (25/35) of KRAS mutations were located at the 12th and 13th codons. RAS gene mutation was detected in 35 (33.3%) out of 105 children with B-lineage acute lymphoblastic leukemia, but it was not detected in those with acute T lymphocyte leukemia. Of all the children, 11 (9.2%) were lost to follow-up, and among the 109 children followed up, 16 (14.7%) died. The children with RAS gene mutation had a significantly lower 2-year overall survival rate than those without RAS gene mutation (P<0.05). The prognosis of children with RAS gene mutation combined with WT1 overexpression and WBC>50×109/L at diagnosis was worse (P<0.05). CONCLUSIONS RAS gene mutation is commonly observed in children with B-lineage acute lymphoblastic leukemia and may have an adverse effect on prognosis.
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16
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Johnson CW, Seo HS, Terrell EM, Yang MH, KleinJan F, Gebregiworgis T, Gasmi-Seabrook GMC, Geffken EA, Lakhani J, Song K, Bashyal P, Popow O, Paulo JA, Liu A, Mattos C, Marshall CB, Ikura M, Morrison DK, Dhe-Paganon S, Haigis KM. Regulation of GTPase function by autophosphorylation. Mol Cell 2022; 82:950-968.e14. [PMID: 35202574 PMCID: PMC8986090 DOI: 10.1016/j.molcel.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/29/2021] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
Abstract
A unifying feature of the RAS superfamily is a conserved GTPase cycle by which these proteins transition between active and inactive states. We demonstrate that autophosphorylation of some GTPases is an intrinsic regulatory mechanism that reduces nucleotide hydrolysis and enhances nucleotide exchange, altering the on/off switch that forms the basis for their signaling functions. Using X-ray crystallography, nuclear magnetic resonance spectroscopy, binding assays, and molecular dynamics on autophosphorylated mutants of H-RAS and K-RAS, we show that phosphoryl transfer from GTP requires dynamic movement of the switch II region and that autophosphorylation promotes nucleotide exchange by opening the active site and extracting the stabilizing Mg2+. Finally, we demonstrate that autophosphorylated K-RAS exhibits altered effector interactions, including a reduced affinity for RAF proteins in mammalian cells. Thus, autophosphorylation leads to altered active site dynamics and effector interaction properties, creating a pool of GTPases that are functionally distinct from their non-phosphorylated counterparts.
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Affiliation(s)
- Christian W Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Moon-Hee Yang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Ezekiel A Geffken
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jimit Lakhani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Puspalata Bashyal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Olesja Popow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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17
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Girard E, Lopes P, Spoerner M, Dhaussy AC, Prangé T, Kalbitzer HR, Colloc'h N. Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography. Chem Sci 2022; 13:2001-2010. [PMID: 35308861 PMCID: PMC8848853 DOI: 10.1039/d1sc05488k] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/12/2022] [Indexed: 01/04/2023] Open
Abstract
In this work, we experimentally investigate the allosteric transitions between conformational states on the Ras oncogene protein using high pressure crystallography. Ras protein is a small GTPase involved in central regulatory processes occurring in multiple conformational states. Ras acts as a molecular switch between active GTP-bound, and inactive GDP-bound states, controlling essential signal transduction pathways. An allosteric network of interactions between the effector binding regions and the membrane interacting regions is involved in Ras cycling. The conformational states which coexist simultaneously in solution possess higher Gibbs free energy than the ground state. Equilibria between these states can be shifted by applying pressure favouring conformations with lower partial molar volume, and has been previously analyzed by high-pressure NMR spectroscopy. High-pressure macromolecular crystallography (HPMX) is a powerful tool perfectly complementary to high-pressure NMR, allowing characterization at the molecular level with a high resolution the different allosteric states involved in the Ras cycling. We observe a transition above 300 MPa in the crystal leading to more stable conformers. Thus, we compare the crystallographic structures of Ras(wt)·Mg2+·GppNHp and Ras(D33K)·Mg2+·GppNHp at various high hydrostatic pressures. This gives insight into per-residue descriptions of the structural plasticity involved in allosteric equilibria between conformers. We have mapped out at atomic resolution the different segments of Ras protein which remain in the ground-state conformation or undergo structural changes, adopting excited-energy conformations corresponding to transient intermediate states. Such in crystallo phase transitions induced by pressure open the possibility to finely explore the structural determinants related to switching between Ras allosteric sub-states without any mutations nor exogenous partners. The equilibria between structural states induced by pressure within the crystal structure of Ras are illustrated with different colors corresponding to different Ras substates.![]()
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Affiliation(s)
- Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pedro Lopes
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | - Michael Spoerner
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | | | - Thierry Prangé
- CiTCoM UMR 8038, CNRS Université de Paris, Faculté de Pharmacie, Paris, France
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | - Nathalie Colloc'h
- ISTCT UMR 6030, CNRS, Université de Caen Normandie, CERVOxy Group, Centre Cyceron, Caen, France
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18
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Hannan JP, Swisher GH, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. HPLC method to resolve, identify and quantify guanine nucleotides bound to recombinant ras GTPase. Anal Biochem 2021; 631:114338. [PMID: 34433016 PMCID: PMC8511091 DOI: 10.1016/j.ab.2021.114338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/31/2022]
Abstract
The Ras superfamily of small G proteins play central roles in diverse signaling pathways. Superfamily members act as molecular on-off switches defined by their occupancy with GTP or GDP, respectively. In vitro functional studies require loading with a hydrolysis-resistant GTP analogue to increase the on-state lifetime, as well as knowledge of fractional loading with activating and inactivating nucleotides. The present study describes a method combining elements of previous approaches with new, optimized features to analyze the bound nucleotide composition of a G protein loaded with activating (GMPPNP) or inactivating (GDP) nucleotide. After nucleotide loading, the complex is washed to remove unbound nucleotides then bound nucleotides are heat-extracted and subjected to ion-paired, reverse-phase HPLC-UV to resolve, identify and quantify the individual nucleotide components. These data enable back-calculation to the nucleotide composition and fractional activation of the original, washed G protein population prior to heat extraction. The method is highly reproducible. Application to multiple HRas preparations and mutants confirms its ability to fully extract and analyze bound nucleotides, and to resolve the fractional on- and off-state populations. Furthermore, the findings yield a novel hypothesis for the molecular disease mechanism of Ras mutations at the E63 and Y64 positions.
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Affiliation(s)
- Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Justin G Martyr
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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19
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Zeng J, Weng J, Zhang Y, Xia F, Cui Q, Xu X. Conformational Features of Ras: Key Hydrogen-Bonding Interactions of Gln61 in the Intermediate State during GTP Hydrolysis. J Phys Chem B 2021; 125:8805-8813. [PMID: 34324329 DOI: 10.1021/acs.jpcb.1c04679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Ras protein is one of the most important drug targets for battling cancers. To effectively design novel drugs of Ras, we characterize here its conformational ensembles for the hydrolysis intermediate state RasGDP·Pi and the product state RasGDP by extensive replica-exchange molecular dynamics simulations. Several substates for RasGDP·Pi have been identified, while structural analyses have revealed an unrecognized hydrogen-bonding network that stabilizes the hydrolysis intermediate state. More interestingly, Gln61, which is involved in numerous oncogenic mutations, was found to be engaged in this hydrogen-bonding network, adopting a specific conformation that always points to Pi in contrast to that in the RasGTP state. The simulations also reveal that RasGDP has more than one substate, suggesting a conformational selection mechanism for the interaction between Ras and the guanine nucleotide exchange factors (GEFs). These findings offer new opportunities for the drug design of Ras by stabilizing the hydrolysis intermediate or disrupting its interaction with the GEFs.
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Affiliation(s)
- Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan 523808, China
| | - Jingwei Weng
- 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 200433, China
| | - Yuwei Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - 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 200433, China
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20
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Zhao J, Zhang T, Liang Y, Zou H, Zhang J. Inhibitory activities of 20(R, S)-protopanaxatriol against epidermal growth factor receptor tyrosine kinase. Food Chem Toxicol 2021; 155:112411. [PMID: 34271119 DOI: 10.1016/j.fct.2021.112411] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
As major metabolites of protopanaxatriol-type ginsenosides, 20(R, S)-protopanaxatriol [20(R, S)-PPT] display multiple bioactivities. This work aimed to investigate the inhibitory activities of 20(R, S)-PPT against epidermal growth factor receptor tyrosine kinase and the potential mechanism. 20(R, S)-PPT inhibited the proliferation of HepG2 cells in a dose-dependent manner and blocked cell cycle progression at G1/G0 phase. Then 20(R, S)-PPT were found to influence the protein expressions involved in epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) signaling pathway. Molecular docking suggested that 20(R, S)-PPT could bind to the active sites of all target proteins in EGFR-MAPK pathway. It is worth noting that 20(R, S)-PPT showed stronger binding capacities with EGFR, compared with other proteins. Hence, this work further investigated the binding interactions and binding stabilities between 20(R, S)-PPT and EGFR. Both hydrophobic interactions and hydrogen bonds contributed to the 20(R, S)-PPT-EGFR binding. In addition, the in vitro inhibitory activities of 20(R, S)-PPT against EGFR tyrosine kinase were observed in a homogeneous time-resolved fluorescence assay, with the IC50 values of 24.10 ± 0.17 and 33.19 ± 0.19 μM respectively. Taken together with the above results, both of 20(R)-PPT and 20(S)-PPT might serve as potential EGFR tyrosine kinase inhibitors.
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Affiliation(s)
- Jingqi Zhao
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Haoyang Zou
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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21
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Kumar SU, Priya Doss CG. Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop. Comput Biol Med 2021; 135:104597. [PMID: 34237589 DOI: 10.1016/j.compbiomed.2021.104597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023]
Abstract
The mutant K-Ras with aberrant signaling is the primary cause of several cancers. The proposed study investigated the influence of water molecules in K-Ras crystal structure, where they have a significant function by understanding their residue interaction networks (RINs). We analyzed the RINs of K-Ras with and without water molecules and determined their interaction properties. RINs were developed with the help of StructureViz2 and RINspector; further, the changes in K-Ras backbone flexibility were predicted with the DynaMine. We found that the residues K42, I142, and L159 are the hotspots from water, including the K-Ras-GTP complex with the highest residue centrality analysis (RCA) Z-score. The DynaMine prediction calculated the NMR S2 value for the frequently mutated positions G12, G13, and Q61 showing a minor shift in flexibility, which make up the P-Loop and switch II of the K-Ras protein. This flexibility shift can account for changes in conformational activity and the protein's GTPase activity, making it difficult to recognize by the effectors and exchange factors. Taken together, our study helps in understanding the functional importance of the water molecules in K-Ras protein and the impact of mutation that modulate the conformational state of the protein.
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Affiliation(s)
- S Udhaya Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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22
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Avery JT, Zhang R, Boohaker RJ. GLI1: A Therapeutic Target for Cancer. Front Oncol 2021; 11:673154. [PMID: 34113570 PMCID: PMC8186314 DOI: 10.3389/fonc.2021.673154] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
GLI1 is a transcriptional effector at the terminal end of the Hedgehog signaling (Hh) pathway and is tightly regulated during embryonic development and tissue patterning/differentiation. GLI1 has low-level expression in differentiated tissues, however, in certain cancers, aberrant activation of GLI1 has been linked to the promotion of numerous hallmarks of cancer, such as proliferation, survival, angiogenesis, metastasis, metabolic rewiring, and chemotherapeutic resistance. All of these are driven, in part, by GLI1’s role in regulating cell cycle, DNA replication and DNA damage repair processes. The consequences of GLI1 oncogenic activity, specifically the activity surrounding DNA damage repair proteins, such as NBS1, and cell cycle proteins, such as CDK1, can be linked to tumorigenesis and chemoresistance. Therefore, understanding the underlying mechanisms driving GLI1 dysregulation can provide prognostic and diagnostic biomarkers to identify a patient population that would derive therapeutic benefit from either direct inhibition of GLI1 or targeted therapy towards proteins downstream of GLI1 regulation.
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Affiliation(s)
- Justin T Avery
- Oncology Department, Drug Discovery Division, Southern Research, Birmingham, AL, United States
| | - Ruowen Zhang
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Rebecca J Boohaker
- Oncology Department, Drug Discovery Division, Southern Research, Birmingham, AL, United States
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23
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Bryant N, Malpeli N, Ziaee J, Blauwendraat C, Liu Z, West AB. Identification of LRRK2 missense variants in the accelerating medicines partnership Parkinson's disease cohort. Hum Mol Genet 2021; 30:454-466. [PMID: 33640967 PMCID: PMC8101351 DOI: 10.1093/hmg/ddab058] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/31/2021] [Accepted: 02/16/2021] [Indexed: 12/19/2022] Open
Abstract
Pathogenic missense variants in the leucine-rich repeat kinase 2 (LRRK2) gene have been identified through linkage analysis in familial Parkinson disease (PD). Subsequently, other missense variants with lower effect sizes on PD risk have emerged, as well as non-coding polymorphisms (e.g. rs76904798) enriched in PD cases in genome-wide association studies. Here we leverage recent whole-genome sequences from the Accelerating Medicines Partnership-Parkinson's Disease (AMP-PD) and the Genome Aggregation (gnomAD) databases to characterize novel missense variants in LRRK2 and explore their relationships with known pathogenic and PD-linked missense variants. Using a computational prediction tool that successfully classifies known pathogenic LRRK2 missense variants, we describe an online web-based resource that catalogs characteristics of over 1200 LRRK2 missense variants of unknown significance. Novel high-pathogenicity scoring variants, some identified exclusively in PD cases, tightly cluster within the ROC-COR-Kinase domains. Structure-function predictions support that some of these variants exert gain-of-function effects with respect to LRRK2 kinase activity. In AMP-PD participants, all p.R1441G carriers (N = 89) are also carriers of the more common PD-linked variant p.M1646T. In addition, nearly all carriers of the PD-linked p.N2081D missense variant are also carriers of the LRRK2 PD-risk variant rs76904798. These results provide a compendium of LRRK2 missense variants and how they associate with one another. While the pathogenic p.G2019S variant is by far the most frequent high-pathogenicity scoring variant, our results suggest that ultra-rare missense variants may have an important cumulative impact in increasing the number of individuals with LRRK2-linked PD.
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Affiliation(s)
- Nicole Bryant
- Duke Center for Neurodegeneration and Neurotherapeutics Research, Departments of Pharmacology and Cancer Biology, and Neurology, Duke University, Durham, NC 27710 USA
| | - Nicole Malpeli
- Duke Center for Neurodegeneration and Neurotherapeutics Research, Departments of Pharmacology and Cancer Biology, and Neurology, Duke University, Durham, NC 27710 USA
| | - Julia Ziaee
- Duke Center for Neurodegeneration and Neurotherapeutics Research, Departments of Pharmacology and Cancer Biology, and Neurology, Duke University, Durham, NC 27710 USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhiyong Liu
- Duke Center for Neurodegeneration and Neurotherapeutics Research, Departments of Pharmacology and Cancer Biology, and Neurology, Duke University, Durham, NC 27710 USA
| | | | - Andrew B West
- Duke Center for Neurodegeneration and Neurotherapeutics Research, Departments of Pharmacology and Cancer Biology, and Neurology, Duke University, Durham, NC 27710 USA
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24
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Wang Y, Ji D, Lei C, Chen Y, Qiu Y, Li X, Li M, Ni D, Pu J, Zhang J, Fu Q, Liu Y, Lu S. Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins. Comput Struct Biotechnol J 2021; 19:1184-1199. [PMID: 33680360 PMCID: PMC7902900 DOI: 10.1016/j.csbj.2021.01.044] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ras undergoes interconversion between the active GTP-bound state and the inactive GDP-bound state. This GTPase cycle, which controls the activities of Ras, is accelerated by Ras GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (SOS). Oncogenic Ras mutations could affect the GTPase cycle and impair Ras functions. Additionally, Src-induced K-Ras Y32/64 dual phosphorylation has been reported to disrupt GTPase cycle and hinder Ras downstream signaling. However, the underlying mechanisms remain unclear. To address this, we performed molecular dynamics simulations (~30 μs in total) on unphosphorylated and phosphorylated K-Ras4B in GTP- and GDP-bound states, and on their complexes with GTPase cycle regulators (GAP and SOS) and the effector protein Raf. We found that K-Ras4B dual phosphorylation mainly alters the conformation at the nucleotide binding site and creates disorder at the catalytic site, resulting in the enlargement of GDP binding pocket and the retard of Ras-GTP intrinsic hydrolysis. We observed phosphorylation-induced shift in the distribution of Ras-GTP inactive-active sub-states and recognized potential druggable pockets in the phosphorylated Ras-GTP. Moreover, decreased catalytic competence or signal delivery abilities due to reduced binding affinities and/or distorted catalytic conformations of GAP, SOS and Raf were observed. In addition, the allosteric pathway from Ras/Raf interface to the distal Raf L4 loop was compromised by Ras phosphorylation. These results reveal the mechanisms by which phosphorylation influences the intrinsic or GAP/SOS catalyzed transformations between GTP- and GDP-bound states of Ras and its signal transduction to Raf. Our findings project Ras phosphorylation as a target for cancer drug discovery.
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Affiliation(s)
- Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China
| | - Chaoyu Lei
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yingfei Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yuran Qiu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xinyi Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- The Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Jun Pu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200120, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Qiang Fu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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25
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Lin Y, Lu S, Zhang J, Zheng Y. Structure of an inactive conformation of GTP-bound RhoA GTPase. Structure 2021; 29:553-563.e5. [PMID: 33497604 DOI: 10.1016/j.str.2020.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/22/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022]
Abstract
By using 31P NMR, we present evidence that the Rho family GTPase RhoA, similar to Ras GTPases, exists in an equilibrium of conformations when bound to GTP. High-resolution crystal structures of RhoA bound to the GTP analog GMPPNP and to GDP show that they display a similar overall inactive conformation. In contrast to the previously reported crystal structures of GTP analog-bound forms of two RhoA dominantly active mutants (G14V and Q63L), GMPPNP-bound RhoA assumes an open conformation in the Switch I loop with a previously unseen interaction between the γ-phosphate and Pro36, instead of the canonical Thr37. Molecular dynamics simulations found that the oncogenic RhoAG14V mutant displays a reduced flexibility in the Switch regions, consistent with a crystal structure of GDP-bound RhoAG14V. Thus, GDP- and GTP-bound RhoA can present similar inactive conformations, and the molecular dynamics in the Switch regions are likely to have a role in RhoA activation.
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Affiliation(s)
- Yuan Lin
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 280 Chongqing South Road, Shanghai 200025, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 280 Chongqing South Road, Shanghai 200025, China
| | - Yi Zheng
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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26
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Swisher GH, Hannan JP, Cordaro NJ, Erbse AH, Falke JJ. Ras-guanine nucleotide complexes: A UV spectral deconvolution method to analyze protein concentration, nucleotide stoichiometry, and purity. Anal Biochem 2021; 618:114066. [PMID: 33485819 DOI: 10.1016/j.ab.2020.114066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/31/2022]
Abstract
The many members of the Ras superfamily are small GTPases that serve as molecular switches. These proteins bind the guanine nucleotides GTP and GDP with picomolar affinities, thereby stabilizing on- and off-signaling states, respectively. Quantitative in vitro Ras studies require accurate determination of total protein, its fractional occupancy with guanine nucleotide, and spectroscopic purity. Yet the high nucleotide affinity of Ras and the overlapping UV spectra of the protein and bound nucleotide make such determinations challenging. Here we describe a generalizable UV spectral deconvolution method to analyze the total protein concentration, total nucleotide stoichiometry, and purity of Ras complexes.
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Affiliation(s)
- G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States.
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27
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Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
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28
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Savitskiy S, Wachtel R, Pourjafar-Dehkordi D, Kang HS, Trauschke V, Lamb DC, Sattler M, Zacharias M, Itzen A. Proteolysis of Rab32 by Salmonella GtgE induces an inactive GTPase conformation. iScience 2020; 24:101940. [PMID: 33426511 PMCID: PMC7779776 DOI: 10.1016/j.isci.2020.101940] [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: 09/09/2020] [Revised: 11/18/2020] [Accepted: 12/10/2020] [Indexed: 12/26/2022] Open
Abstract
Rab GTPases are central regulators of intracellular vesicular trafficking. They are frequently targeted by bacterial pathogens through post-translational modifications. Salmonella typhimurium secretes the cysteine protease GtgE during infection, leading to a regioselective proteolytic cleavage of the regulatory switch I loop in the small GTPases of the Rab32 subfamily. Here, using a combination of biochemical methods, molecular dynamics simulations, NMR spectroscopy, and single-pair Förster resonance energy transfer, we demonstrate that the cleavage of Rab32 causes a local increase of conformational flexibility in both switch regions. Cleaved Rab32 maintains its ability to interact with the GDP dissociation inhibitor (GDI). Interestingly, the Rab32 cleavage enables GDI binding also with an active GTP-bound Rab32 in vitro. Furthermore, the Rab32 proteolysis provokes disturbance in the interaction with its downstream effector VARP. Thus, the proteolysis of Rab32 is not a globally degradative mechanism but affects various biochemical and structural properties of the GTPase in a diverse manner.
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Affiliation(s)
- Sergey Savitskiy
- Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Rudolf Wachtel
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Danial Pourjafar-Dehkordi
- Physics Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, 85748 Garching, Germany
| | - Vanessa Trauschke
- Department of Chemistry, Center for Nanoscience (CeNS), NanoSystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians-Universität München, Munich Germany
| | - Don C Lamb
- Department of Chemistry, Center for Nanoscience (CeNS), NanoSystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians-Universität München, Munich Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Aymelt Itzen
- Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.,Centre for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
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29
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Kim D, Xue JY, Lito P. Targeting KRAS(G12C): From Inhibitory Mechanism to Modulation of Antitumor Effects in Patients. Cell 2020; 183:850-859. [PMID: 33065029 PMCID: PMC7669705 DOI: 10.1016/j.cell.2020.09.044] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/24/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023]
Abstract
KRAS mutations are among the most common genetic alterations in lung, colorectal, and pancreatic cancers. Direct inhibition of KRAS oncoproteins has been a long-standing pursuit in precision oncology, one established shortly after the discovery of RAS mutations in human cancer cells nearly 40 years ago. Recent advances in medicinal chemistry have established inhibitors targeting KRAS(G12C), a mutation found in ∼13% of lung adenocarcinomas and, at a lower frequency, in other cancers. Preclinical studies describing their discovery and mechanism of action, coupled with emerging clinical data from patients treated with these drugs, have sparked a renewed enthusiasm in the study of KRAS and its therapeutic potential. Here, we discuss how these advances are reshaping the fundamental aspects of KRAS oncoprotein biology and the strides being made toward improving patient outcomes in the clinic.
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Affiliation(s)
- Dongsung Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, USA
| | - Jenny Yaohua Xue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Piro Lito
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer, New York, NY, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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30
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Sharma N, Sonavane U, Joshi R. Comparative MD simulations and advanced analytics based studies on wild-type and hot-spot mutant A59G HRas. PLoS One 2020; 15:e0234836. [PMID: 33064725 PMCID: PMC7567374 DOI: 10.1371/journal.pone.0234836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022] Open
Abstract
The Ras family of proteins is known to play an important role in cellular signal transduction. The oncoprotein Ras is also found to be mutated in ~90% of the pancreatic cancers, of which G12V, G13V, A59G and Q61L are the known hot-spot mutants. These ubiquitous proteins fall in the family of G-proteins, and hence switches between active GTP bound and inactive GDP bound states, which is hindered in most of its oncogenic mutant counterparts. Moreover, Ras being a GTPase has an intrinsic property to hydrolyze GTP to GDP, which is obstructed due to mutations and lends the mutants stuck in constitutively active state leading to oncogenic behavior. In this regard, the present study aims to understand the dynamics involved in the hot-spot mutant A59G-Ras using long 10μs classical MD simulations (5μs for each of the wild-type and mutant systems) and comparing the same with its wild-type counterpart. Advanced analytics using Markov State Model (MSM) based approach has been deployed to comparatively understand the transition path for the wild-type and mutant systems. Roles of crucial residues like Tyr32, Gln61 and Tyr64 have also been established using multivariate PCA analyses. Furthermore, this multivariate PCA analysis also provides crucial features which may be used as reaction coordinates for biased simulations for further studies. The absence of formation of pre-hydrolysis network is also reported for the mutant conformation, using the distance-based analyses (between crucial residues) of the conserved regions. The implications of this study strengthen the hypothesis that the disruption of the pre-hydrolysis network in the mutant A59G ensemble might lead to permanently active oncogenic conformation in the mutant conformers.
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Affiliation(s)
- Neeru Sharma
- HPC-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, India
| | - Uddhavesh Sonavane
- HPC-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, India
| | - Rajendra Joshi
- HPC-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, India
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31
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Gasper R, Wittinghofer F. The Ras switch in structural and historical perspective. Biol Chem 2020; 401:143-163. [PMID: 31600136 DOI: 10.1515/hsz-2019-0330] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022]
Abstract
Since its discovery as an oncogene more than 40 years ago, Ras has been and still is in the focus of many academic and pharmaceutical labs around the world. A huge amount of work has accumulated on its biology. However, many questions about the role of the different Ras isoforms in health and disease still exist and a full understanding will require more intensive work in the future. Here we try to survey some of the structural findings in a historical perspective and how it has influenced our understanding of structure-function and mechanistic relationships of Ras and its interactions. The structures show that Ras is a stable molecular machine that uses the dynamics of its switch regions for the interaction with all regulators and effectors. This conformational flexibility has been used to create small molecule drug candidates against this important oncoprotein.
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Affiliation(s)
- Raphael Gasper
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
| | - Fred Wittinghofer
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
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32
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Menyhárd DK, Pálfy G, Orgován Z, Vida I, Keserű GM, Perczel A. Structural impact of GTP binding on downstream KRAS signaling. Chem Sci 2020; 11:9272-9289. [PMID: 34094198 PMCID: PMC8161693 DOI: 10.1039/d0sc03441j] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Oncogenic RAS proteins, involved in ∼30% of human tumors, are molecular switches of various signal transduction pathways. Here we apply a new protocol for the NMR study of KRAS in its (inactive) GDP- and (activated) GTP-bound form, allowing a comprehensive analysis of the backbone dynamics of its WT-, G12C- and G12D variants. We found that Tyr32 shows opposite mobility with respect to the backbone of its surroundings: it is more flexible in the GDP-bound form while more rigid in GTP-complexes (especially in WT- and G12D-GTP). Using the G12C/Y32F double mutant, we showed that the presence of the hydroxyl group of Tyr32 has a marked effect on the G12C-KRAS-GTP system as well. Molecular dynamics simulations indicate that Tyr32 is linked to the γ-phosphate of GTP in the activated states – an arrangement shown, using QM/MM calculations, to support catalysis. Anchoring Tyr32 to the γ-phosphate contributes to the capture of the catalytic waters participating in the intrinsic hydrolysis of GTP and supports a simultaneous triple proton transfer step (catalytic water → assisting water → Tyr32 → O1G of the γ-phosphate) leading to straightforward product formation. The coupled flip of negatively charged residues of switch I toward the inside of the effector binding pocket potentiates ligand recognition, while positioning of Thr35 to enter the coordination sphere of the Mg2+ widens the pocket. Position 12 mutations do not disturb the capture of Tyr32 by the γ-phosphate, but (partially) displace Gln61, which opens up the catalytic pocket and destabilizes catalytic water molecules thus impairing intrinsic hydrolysis. Nucleotide exchange to the physiological, activated, GTP-bound form of KRAS results in the anchoring of Tyr32 within the active site.![]()
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Affiliation(s)
- Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - István Vida
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University Pázmány Péter sétány 1/A 1117 Budapest Hungary
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33
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Kattan WE, Hancock JF. RAS Function in cancer cells: translating membrane biology and biochemistry into new therapeutics. Biochem J 2020; 477:2893-2919. [PMID: 32797215 PMCID: PMC7891675 DOI: 10.1042/bcj20190839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
Abstract
The three human RAS proteins are mutated and constitutively activated in ∼20% of cancers leading to cell growth and proliferation. For the past three decades, many attempts have been made to inhibit these proteins with little success. Recently; however, multiple methods have emerged to inhibit KRAS, the most prevalently mutated isoform. These methods and the underlying biology will be discussed in this review with a special focus on KRAS-plasma membrane interactions.
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Affiliation(s)
- Walaa E. Kattan
- Department of Integrative Biology and Pharmacology, McGovern Medical School University of Texas Health Science Center at Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, TX 77030, USA
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School University of Texas Health Science Center at Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, TX 77030, USA
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34
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Sakurai S, Shimizu T, Ohto U. Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases. Acta Crystallogr F Struct Biol Commun 2020; 76:326-333. [PMID: 32744243 PMCID: PMC7397462 DOI: 10.1107/s2053230x20009012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/02/2020] [Indexed: 01/07/2023] Open
Abstract
FYCO1 is a multidomain adaptor protein that plays an important role in autophagy by mediating the kinesin-dependent microtubule plus-end-directed transport of autophagosomes. FYCO1 contains a RUN domain, which is hypothesized to function as a specific effector for members of the Ras superfamily of small GTPases, but its role has not been well characterized and its interaction partner(s) have not been identified. Here, the crystal structure of the FYCO1 RUN domain was determined at 1.3 Å resolution. The overall structure of the FYCO1 RUN domain was similar to those of previously reported RUN domains. Detailed structural comparisons with other RUN domains and docking studies suggested a possible interaction interface of the FYCO1 RUN domain with small GTPases of the Ras superfamily.
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Affiliation(s)
- Shunya Sakurai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Umeharu Ohto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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35
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Gao Z, Xing K, Zhang C, Qi J, Wang L, Gao S, Lai R. Crystal structure and function of Rbj: A constitutively GTP-bound small G protein with an extra DnaJ domain. Protein Cell 2020; 10:760-763. [PMID: 30945136 PMCID: PMC6776491 DOI: 10.1007/s13238-019-0622-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Zhengrong Gao
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keke Xing
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Chang Zhang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shan Gao
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Ren Lai
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China.
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36
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Liu D, Chen X, Long D. NMR-Derived Conformational Ensemble of State 1 of Activated Ras Reveals Insights into a Druggable Pocket. J Phys Chem Lett 2020; 11:3642-3646. [PMID: 32302142 DOI: 10.1021/acs.jpclett.0c00858] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The lack of apparent pockets in the ground conformation of Ras has long challenged the rational design of inhibitors against this oncogenic protein. The sparsely populated, transiently formed state 1 of activated Ras, on the other hand, shows appreciable surface roughness and is increasingly recognized as a potential target for drug discovery. State 1, however, is extremely flexible, and a static structure cannot fully unveil its conformational space that can be exploited for drug design. Here, we present a conformational ensemble of state 1 that was derived using chemical shift-based modeling. The ensemble reveals the intrinsic plasticity of a druggable pocket in state 1 and demonstrates the mechanism of conformational selection for inhibitor recognition. The large set of structural templates in the ensemble, providing a comprehensive description of thermally accessible pocket conformations, is expected to significantly aid the rational design of anti-Ras drugs.
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Affiliation(s)
- Dan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Xiaomin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, Anhui, China
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37
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Comprehensive characterization of RAS mutations in colon and rectal cancers in old and young patients. Nat Commun 2019; 10:3722. [PMID: 31427573 PMCID: PMC6700103 DOI: 10.1038/s41467-019-11530-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 06/14/2019] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is increasingly appreciated as a heterogeneous disease, with factors such as microsatellite instability (MSI), cancer subsite within the colon versus rectum, and age of diagnosis associated with specific disease course and therapeutic response. Activating oncogenic mutations in KRAS and NRAS are common in CRC, driving tumor progression and influencing efficacy of both cytotoxic and targeted therapies. The RAS mutational spectrum differs substantially between tumors arising from distinct tissues. Structure-function analysis of relatively common somatic RAS mutations in G12, Q61, and other codons is characterized by differing potency and modes of action. Here we show the mutational profile of KRAS, NRAS, and the less common HRAS in 13,336 CRC tumors, comparing the frequency of specific mutations based on age of diagnosis, MSI status, and colon versus rectum subsite. We identify mutation hotspots, and unexpected differences in mutation spectrum, based on these clinical parameters. Activating oncogenic mutations in KRAS and NRAS are common in colorectal cancer, which is a heterogenous disease. Here, the authors show that the RAS mutation spectrum is markedly different between colon and rectal cancer, and also different based on age of diagnosis and microsatellite instability.
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38
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Calixto AR, Moreira C, Pabis A, Kötting C, Gerwert K, Rudack T, Kamerlin SCL. GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases. J Am Chem Soc 2019; 141:10684-10701. [PMID: 31199130 DOI: 10.1021/jacs.9b03193] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the Gαi subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.
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Affiliation(s)
- Ana R Calixto
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Cátia Moreira
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Anna Pabis
- Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 , Uppsala , Sweden
| | - Carsten Kötting
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Klaus Gerwert
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Till Rudack
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Shina C L Kamerlin
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
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39
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Ji J, Yuan J, Guo X, Ji R, Quan Q, Ding M, Li X, Liu Y. Harmine suppresses hyper-activated Ras-MAPK pathway by selectively targeting oncogenic mutated Ras/Raf in Caenorhabditis elegans. Cancer Cell Int 2019; 19:159. [PMID: 31198408 PMCID: PMC6558680 DOI: 10.1186/s12935-019-0880-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 06/03/2019] [Indexed: 11/10/2022] Open
Abstract
Background Mutationally activated Ras proteins are closely linked to a wide variety of human cancers. Hence, there has been an intensive search for anti-Ras therapies for cancer treatment. The sole Ras gene, which encodes LET-60, in Caenorhabditis elegans regulates vulval development. While the loss of let-60 function leads to failure of vulva formation, the let-60(n1046gf) allele, which contains a missense mutation mimicking a Ras codon 13 mutation found in human cancers, results in extra vulval tissue, a phenotype named Muv (multiple vulvas). Methods By taking advantage of the easy-to-score Muv phenotype of let-60(n1046gf), we used a step-by-step screening approach (from crude extract to active fraction to active natural compound) to search for inhibitors of oncogenic Ras. Mutants of other key components in the Ras-mitogen-activated protein kinase (MAPK) pathway were used to identify other candidate targets. Results The natural compound harmine, isolated from the plant Peganum harmala, was found to suppress the Muv phenotype of let-60(n1046gf). In addition, harmine targets the hyper-activation of the Ras/MAPK pathway specifically caused by overexpression or mutated forms of LET-60/Ras and its immediate downstream molecule LIN-45/Raf. Finally, harmine can be absorbed into the worm body and probably functions in its native form, rather than requiring metabolic activation. Conclusion In sum, we have revealed for the first time the anti-Ras activity of harmine in a C. elegans model system. Our results revealed the potential anti-cancer mechanism of harmine, which may be useful for the treatment of specific human cancers that are associated with oncogenic Ras mutations.
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Affiliation(s)
- Jiaojiao Ji
- 1Beijing University of Chinese Medicine, Beijing, China
| | - Jiang Yuan
- 1Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoyu Guo
- 1Beijing University of Chinese Medicine, Beijing, China
| | - Ruifang Ji
- 1Beijing University of Chinese Medicine, Beijing, China
| | - Qinghua Quan
- 1Beijing University of Chinese Medicine, Beijing, China
| | - Mei Ding
- 2State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xia Li
- 2State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yonggang Liu
- 1Beijing University of Chinese Medicine, Beijing, China
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40
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Tichauer RH, Favre G, Cabantous S, Brut M. Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21 N-ras and the Resulting GTP Electronic Density. J Phys Chem B 2019; 123:3935-3944. [PMID: 30991803 DOI: 10.1021/acs.jpcb.9b02660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
p21ras protein activity, regulated by GTP hydrolysis, constitutes an active field of research for the development of cancer targeted therapies that would concern ∼30% of human tumors to which specific mutations have been associated. Indeed, the catalyzing mechanisms provided by the protein environment during GTP hydrolysis and how they are impaired by specific mutations remain to be fully elucidated. In this article, we present results from molecular mechanics (MM) molecular dynamics (MD) simulations and density functional theory (DFT) calculations carried out for wild-type p21 N-ras and six Gln 61 mutants. In the first part, we present the water distribution within the active site of the wild-type protein according to MM MD. Significant differences are observed when comparing the results to the previous distribution assessed through quantum mechanics/molecular mechanics (QM/MM) MD. Such method-dependent results highlight the importance of accounting for the electrostatic coupling between the protein complex and the solvent molecules in identifying hydration sites. In the second part, we present the results from DFT calculations performed to determine the electronic distribution of the GTP ligand, considering the wild-type active site arrangement according to both classical and hybrid approaches. Only in the QM/MM-based configuration is the ligand electronic density similar to that of a GDP-like state observed experimentally. For this reason, in the last set of calculations carried out for p21 N-ras Gln 61 mutants, only the active site structural conformations obtained through hybrid MD are considered. Through the analysis of the GTP electronic density, we conclude that the wild-type active site arrangement according to QM/MM MD is closer to a catalytically efficient conformation of the protein than the arrangement according to MM MD. Hence, water distribution according to the hybrid approach must correspond to the optimal placement of solvent in the active site. Within all of the studied Gln 61 substituted proteins, p21ras major catalyzing effect, which consists of stabilizing a more GDP-like state, is lost.
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Affiliation(s)
- Ruth H Tichauer
- LAAS-CNRS , Université de Toulouse , CNRS, UPS, Toulouse , France
| | - Gilles Favre
- Cancer Research Center of Toulouse , INSERM U1037, Université de Toulouse , 31037 Toulouse , France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse , INSERM U1037, Université de Toulouse , 31037 Toulouse , France
| | - Marie Brut
- LAAS-CNRS , Université de Toulouse , CNRS, UPS, Toulouse , France
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41
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Yaeger R, Corcoran RB. Targeting Alterations in the RAF-MEK Pathway. Cancer Discov 2019; 9:329-341. [PMID: 30770389 PMCID: PMC6397699 DOI: 10.1158/2159-8290.cd-18-1321] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/26/2018] [Accepted: 01/16/2019] [Indexed: 12/13/2022]
Abstract
The MAPK pathway is one of the most commonly mutated oncogenic pathways in cancer. Although RAS mutations are the most frequent MAPK alterations, less frequent alterations in downstream components of the pathway, including the RAF and MEK genes, offer promising therapeutic opportunities. In addition to BRAFV600 mutations, for which several approved therapeutic regimens exist, other alterations in the RAF and MEK genes may provide more rare, but tractable, targets. However, recent studies have illustrated the complexity of MAPK signaling and highlighted that distinct alterations in these genes may have strikingly different properties. Understanding the unique functional characteristics of specific RAF and MEK alterations, reviewed herein, will be critical for developing effective therapeutic approaches for these targets. SIGNIFICANCE: Alterations in the RAF and MEK genes represent promising therapeutic targets in multiple cancer types. However, given the unique and complex signaling biology of the MAPK pathway, the diverse array of RAF and MEK alterations observed in cancer can possess distinct functional characteristics. As outlined in this review, understanding the key functional properties of different RAF and MEK alterations is fundamental to selecting the optimal therapeutic approach.
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Affiliation(s)
- Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts.
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42
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Tichauer RH, Favre G, Cabantous S, Landa G, Hemeryck A, Brut M. Water Distribution within Wild-Type NRas Protein and Q61 Mutants during Unrestrained QM/MM Dynamics. Biophys J 2018; 115:1417-1430. [PMID: 30224050 DOI: 10.1016/j.bpj.2018.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022] Open
Abstract
Point mutations in p21ras are associated with ∼30% of human tumors by disrupting its GTP hydrolysis cycle, which is critical to its molecular switch function in cellular signaling pathways. In this work, we investigate the impact of Gln 61 substitutions in the structure of the p21N-ras active site and particularly focus on water reorganization around GTP, which appears to be crucial to evaluate favorable and unfavorable hydration sites for hydrolysis. The NRas-GTP complex is analyzed using a hybrid quantum mechanics/molecular mechanics approach, treating for the first time to our knowledge transient water molecules at the ab initio level and leading to results that account for the electrostatic coupling between the protein complex and the solvent. We show that for the wild-type protein, water molecules are found around the GTP γ-phosphate group, forming an arch extended from residues 12 to 35. Two density peaks are observed, supporting previous results that suggest the presence of two water molecules in the active site, one in the vicinity of residue 35 and a second one stabilized by hydrogen bonds formed with nitrogen backbone atoms of residues 12 and 60. The structural changes observed in NRas Gln 61 mutants result in the drastic delocalization of water molecules that we discuss. In mutants Q61H and Q61K, for which water distribution is overlocalized next to residue 60, the second density peak supports the hypothesis of a second water molecule. We also conclude that Gly 60 indirectly participates in GTP hydrolysis by correctly positioning transient water molecules in the protein complex and that Gln 61 has an indirect steric effect in stabilizing the preorganized catalytic site.
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Affiliation(s)
- Ruth H Tichauer
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse, INSERM U1037, Toulouse, France; Université de Toulouse, Toulouse, France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse, INSERM U1037, Toulouse, France; Université de Toulouse, Toulouse, France
| | - Georges Landa
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne Hemeryck
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie Brut
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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43
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Sapin E, De Jong KA, Shehu A. From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:719-731. [PMID: 28113951 DOI: 10.1109/tcbb.2016.2628745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Stochastic search is often the only viable option to address complex optimization problems. Recently, evolutionary algorithms have been shown to handle challenging continuous optimization problems related to protein structure modeling. Building on recent work in our laboratories, we propose an evolutionary algorithm for efficiently mapping the multi-basin energy landscapes of dynamic proteins that switch between thermodynamically stable or semi-stable structural states to regulate their biological activity in the cell. The proposed algorithm balances computational resources between exploration and exploitation of the nonlinear, multimodal landscapes that characterize multi-state proteins via a novel combination of global and local search to generate a dynamically-updated, information-rich map of a protein's energy landscape. This new mapping-oriented EA is applied to several dynamic proteins and their disease-implicated variants to illustrate its ability to map complex energy landscapes in a computationally feasible manner. We further show that, given the availability of such maps, comparison between the maps of wildtype and variants of a protein allows for the formulation of a structural and thermodynamic basis for the impact of sequence mutations on dysfunction that may prove useful in guiding further wet-laboratory investigations of dysfunction and molecular interventions.
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Aggarwal L, Biswas P. Hydration Water Distribution around Intrinsically Disordered Proteins. J Phys Chem B 2018; 122:4206-4218. [DOI: 10.1021/acs.jpcb.7b11091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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Li Y, Zhang Y, Großerüschkamp F, Stephan S, Cui Q, Kötting C, Xia F, Gerwert K. Specific Substates of Ras To Interact with GAPs and Effectors: Revealed by Theoretical Simulations and FTIR Experiments. J Phys Chem Lett 2018; 9:1312-1317. [PMID: 29488771 PMCID: PMC6692134 DOI: 10.1021/acs.jpclett.8b00342] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The oncogenic Ras protein adopts various specific conformational states to execute its function in signal transduction. The large number of Ras structures obtained from X-ray and NMR experiments illustrates the diverse conformations that Ras adopts. It is difficult, however, to connect specific structural features with Ras functions. We report the free-energy landscape of Ras·GTP based on extensive explicit solvent simulations. The free-energy map clearly shows that the functional state 2 of Ras·GTP in fact has two distinct substates, denoted here as "Tyr32in" and "Tyr32out". Unbiased MD simulations show that the two substrates interconvert on the submicrosecond scale in solution, pointing to a novel mechanism for Ras·GTP to selectively interact with GAPs and effectors. This proposal is further supported by time-resolved FTIR experiments, which demonstrate that Tyr32 destabilizes the Ras·GAP complex and facilitates an efficient termination of Ras signaling.
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Affiliation(s)
- Yang Li
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China
- School of Information Science and Engineering , Shandong Agricultural University , Taian 271018 , China
| | - Yuwei Zhang
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China
| | | | - Sara Stephan
- Department of Biophysics , Ruhr-University Bochum , ND 04 North , 44780 Bochum , Germany
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute , University of Wisconsin , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Carsten Kötting
- Department of Biophysics , Ruhr-University Bochum , ND 04 North , 44780 Bochum , Germany
| | - Fei Xia
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062 , China
| | - Klaus Gerwert
- Department of Biophysics , Ruhr-University Bochum , ND 04 North , 44780 Bochum , Germany
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Petrović D, Szeler K, Kamerlin SCL. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chem Commun (Camb) 2018; 54:3077-3089. [PMID: 29412205 DOI: 10.1039/c7cc09504j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.
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Affiliation(s)
- Dušan Petrović
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| | - Klaudia Szeler
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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Mann D, Güldenhaupt J, Schartner J, Gerwert K, Kötting C. The protonation states of GTP and GppNHp in Ras proteins. J Biol Chem 2018; 293:3871-3879. [PMID: 29382720 DOI: 10.1074/jbc.ra117.001110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/29/2018] [Indexed: 01/09/2023] Open
Abstract
The small GTPase Ras transmits signals in a variety of cellular signaling pathways, most prominently in cell proliferation. GTP hydrolysis in the active center of Ras acts as a prototype for many GTPases and is the key to the understanding of several diseases, including cancer. Therefore, Ras has been the focus of intense research over the last decades. A recent neutron diffraction crystal structure of Ras indicated a protonated γ-guanylyl imidodiphosphate (γ-GppNHp) group, which has put the protonation state of GTP in question. A possible protonation of GTP was not considered in previously published mechanistic studies. To determine the detailed prehydrolysis state of Ras, we calculated infrared and NMR spectra from quantum mechanics/molecular mechanics (QM/MM) simulations and compared them with those from previous studies. Furthermore, we measured infrared spectra of GTP and several GTP analogs bound to lipidated Ras on a membrane system under near-native conditions. Our findings unify results from previous studies and indicate a structural model confirming the hypothesis that γ-GTP is fully deprotonated in the prehydrolysis state of Ras.
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Affiliation(s)
- Daniel Mann
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and
| | - Jörn Güldenhaupt
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and
| | - Jonas Schartner
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and
| | - Klaus Gerwert
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and .,Max-Planck-Gesellschaft-Chinese Academy of Sciences (MPG-CAS) Partner Institute for Computational Biology (PICB), Shanghai 200031, China
| | - Carsten Kötting
- From the Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany and
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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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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: 82] [Impact Index Per Article: 11.7] [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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Vetter IR. Interface analysis of small GTP binding protein complexes suggests preferred membrane orientations. Biol Chem 2017; 398:637-651. [PMID: 28002022 DOI: 10.1515/hsz-2016-0287] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/12/2016] [Indexed: 11/15/2022]
Abstract
Crystal structures of small GTP binding protein complexes with their effectors and regulators reveal that one particularly flat side of the G domain that contains helix α4 and the C-terminal helix α5 is practically devoid of contacts. Although this observation seems trivial as the main binding targets are the switch I and II regions opposite of this side, the fact that all interacting proteins, even the largest ones, seem to avoid occupying this area (except for Ran, that does not localize to membranes) is very striking. An orientation with this 'flat' side parallel to the membrane was proposed before and would allow simultaneous interaction of the lipidated C-terminus and positive charges in the α4 helix with the membrane while being bound to effector or regulator molecules. Furthermore, this 'flat' side might be involved in regulatory mechanisms: a Ras dimer that is found in different crystal forms interacts exactly at this side. Additional interface analysis of GTPase complexes nicely confirms the effect of different flexibilities of the GTP and GDP forms. Besides Ran proteins, guanine nucleotide exchange factors (GEFs) bury the largest surface areas to provide the binding energy to open up the switch regions for nucleotide exchange.
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Affiliation(s)
- Ingrid R Vetter
- Max Planck Institute of Molecular Physiology, Department of Mechanistic Cell Biology, Otto-Hahn-Str. 11, D-44227 Dortmund
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