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The structural basis for the transition from Ras-GTP to Ras-GDP.

Hall BE, Bar-Sagi D, Nassar N
Proc Natl Acad Sci U S A 99 12138-42 (2002)
Cited: 90 times
EuropePMC logo PMID: 12213964

Abstract

The conformational changes in Ras that accompany the hydrolysis of GTP are critical to its function as a molecular switch in signaling pathways. Understanding how GTP is hydrolyzed by revealing the sequence of intermediary structures in the reaction is essential for understanding Ras signaling. Until now, no structure of an intermediate in GTP hydrolysis has been experimentally determined for Ras alone. We have solved the crystal structure of the Ala-59 to Gly mutant of Ras, (RasA59G), bound to guanosine 5'-imidotriphosphate or GDP to 1.7-A resolution. In the guanosine 5'-imidotriphosphate-bound form, this mutant adopts a conformation that is intermediate between the GTP- and GDP-bound forms of wild-type Ras and that is similar to what has been predicted by molecular dynamics simulation [Ma, J. P. & Karplus, M. (1997) Proc. Natl. Acad. Sci. USA 94, 11905-11910]. This conformation is stabilized by direct and water-mediated interactions between the switch 1 and switch 2 regions and is characterized by an increase in the binding affinity for GTP. We propose that the structural changes promoted by the Ala-59 to Gly mutation exhibit a discrete conformational state assumed by wild-type Ras during GTP hydrolysis.

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  1. Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution. Nguyen THD, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SHW, Nagai K. Nature 530 298-302 (2016)
  2. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. Grant BJ, Gorfe AA, McCammon JA. PLoS Comput Biol 5 e1000325 (2009)
  3. The distinct conformational dynamics of K-Ras and H-Ras A59G. Lukman S, Grant BJ, Gorfe AA, Grant GH, McCammon JA. PLoS Comput Biol 6 e1000922 (2010)
  4. A structural model of a Ras-Raf signalosome. Mysore VP, Zhou ZW, Ambrogio C, Li L, Kapp JN, Lu C, Wang Q, Tucker MR, Okoro JJ, Nagy-Davidescu G, Bai X, Plückthun A, Jänne PA, Westover KD, Shan Y, Shaw DE. Nat Struct Mol Biol 28 847-857 (2021)
  5. KRAS Switch Mutants D33E and A59G Crystallize in the State 1 Conformation. Lu J, Bera AK, Gondi S, Westover KD. Biochemistry 57 324-333 (2018)
  6. Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. Clausen R, Ma B, Nussinov R, Shehu A. PLoS Comput Biol 11 e1004470 (2015)
  7. Computing energy landscape maps and structural excursions of proteins. Sapin E, Carr DB, De Jong KA, Shehu A. BMC Genomics 17 Suppl 4 546 (2016)
  8. Comparative MD simulations and advanced analytics based studies on wild-type and hot-spot mutant A59G HRas. Sharma N, Sonavane U, Joshi R. PLoS One 15 e0234836 (2020)


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  1. CHARMM: the biomolecular simulation program. Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. J Comput Chem 30 1545-1614 (2009)
  2. Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view. Lu S, Jang H, Gu S, Zhang J, Nussinov R. Chem Soc Rev 45 4929-4952 (2016)
  3. Structural Insights into the Mechanism of Dynamin Superfamily Proteins. Jimah JR, Hinshaw JE. Trends Cell Biol 29 257-273 (2019)
  4. Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. Nussinov R, Jang H, Tsai CJ, Cheng F. PLoS Comput Biol 15 e1006658 (2019)
  5. Invited review: Activation of G proteins by GTP and the mechanism of Gα-catalyzed GTP hydrolysis. Sprang SR. Biopolymers 105 449-462 (2016)
  6. Direct Modulation of Small GTPase Activity and Function. Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Angew Chem Int Ed Engl 54 13516-13537 (2015)
  7. Direct inhibition of RAS: Quest for the Holy Grail? Spencer-Smith R, O'Bryan JP. Semin Cancer Biol 54 138-148 (2019)
  8. Lessons from computer simulations of Ras proteins in solution and in membrane. Prakash P, Gorfe AA. Biochim Biophys Acta 1830 5211-5218 (2013)
  9. Ras Dimer Formation as a New Signaling Mechanism and Potential Cancer Therapeutic Target. Chen M, Peters A, Huang T, Nan X. Mini Rev Med Chem 16 391-403 (2016)
  10. Receptor Tyrosine Kinase Signaling and Targeting in Glioblastoma Multiforme. Tilak M, Holborn J, New LA, Lalonde J, Jones N. Int J Mol Sci 22 1831 (2021)
  11. The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Brown SL, Kendrick S. Pharmaceuticals (Basel) 14 96 (2021)
  12. Regulators of the RAS-ERK pathway as therapeutic targets in thyroid cancer. Zaballos MA, Acuña-Ruiz A, Morante M, Crespo P, Santisteban P. Endocr Relat Cancer 26 R319-R344 (2019)
  13. Crucial Role of Oncogenic KRAS Mutations in Apoptosis and Autophagy Regulation: Therapeutic Implications. Ferreira A, Pereira F, Reis C, Oliveira MJ, Sousa MJ, Preto A. Cells 11 2183 (2022)
  14. RAS Dimers: The Novice Couple at the RAS-ERK Pathway Ball. Herrero A, Crespo P. Genes (Basel) 12 1556 (2021)
  15. Review: Ras GTPases and myosin: Qualitative conservation and quantitative diversification in signal and energy transduction. Mueller MP, Goody RS. Biopolymers 105 422-430 (2016)
  16. Treatment Strategies for KRAS-Mutated Non-Small-Cell Lung Cancer. O'Sullivan É, Keogh A, Henderson B, Finn SP, Gray SG, Gately K. Cancers (Basel) 15 1635 (2023)
  17. Targeting the RAS/RAF/MAPK pathway for cancer therapy: from mechanism to clinical studies. Bahar ME, Kim HJ, Kim DR. Signal Transduct Target Ther 8 455 (2023)
  18. Multiple Strategies to Develop Small Molecular KRAS Directly Bound Inhibitors. Zhou X, Ji Y, Zhou J. Molecules 28 3615 (2023)
  19. Navigating the ERK1/2 MAPK Cascade. Martin-Vega A, Cobb MH. Biomolecules 13 1555 (2023)
  20. RAS and Other Molecular Targets in Pancreatic Cancer: The Next Wave Is Coming. Miller-Phillips L, Collisson EA. Curr Treat Options Oncol 24 1088-1101 (2023)
  21. Nucleic Acid-Based Approaches to Tackle KRAS Mutant Cancers. Kim J. Int J Mol Sci 24 16933 (2023)

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  1. Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism. Lito P, Solomon M, Li LS, Hansen R, Rosen N. Science 351 604-608 (2016)
  2. Inhibition of RAS function through targeting an allosteric regulatory site. Spencer-Smith R, Koide A, Zhou Y, Eguchi RR, Sha F, Gajwani P, Santana D, Gupta A, Jacobs M, Herrero-Garcia E, Cobbert J, Lavoie H, Smith M, Smith M, Rajakulendran T, Dowdell E, Okur MN, Dementieva I, Sicheri F, Therrien M, Hancock JF, Ikura M, Koide S, O'Bryan JP. Nat Chem Biol 13 62-68 (2017)
  3. Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Gorfe AA, Grant BJ, McCammon JA. Structure 16 885-896 (2008)
  4. Multivalent Small-Molecule Pan-RAS Inhibitors. Welsch ME, Kaplan A, Chambers JM, Stokes ME, Bos PH, Zask A, Zhang Y, Sanchez-Martin M, Badgley MA, Huang CS, Tran TH, Akkiraju H, Brown LM, Nandakumar R, Cremers S, Yang WS, Tong L, Olive KP, Ferrando A, Stockwell BR. Cell 168 878-889.e29 (2017)
  5. Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders. Gremer L, Merbitz-Zahradnik T, Dvorsky R, Cirstea IC, Kratz CP, Zenker M, Wittinghofer A, Ahmadian MR. Hum Mutat 32 33-43 (2011)
  6. The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B. Lu S, Jang H, Nussinov R, Zhang J. Sci Rep 6 21949 (2016)
  7. Regulation of ras signaling dynamics by Sos-mediated positive feedback. Boykevisch S, Zhao C, Sondermann H, Philippidou P, Halegoua S, Kuriyan J, Bar-Sagi D. Curr Biol 16 2173-2179 (2006)
  8. Transformation efficiency of RasQ61 mutants linked to structural features of the switch regions in the presence of Raf. Buhrman G, Wink G, Mattos C. Structure 15 1618-1629 (2007)
  9. Intersubunit Crosstalk in the Rag GTPase Heterodimer Enables mTORC1 to Respond Rapidly to Amino Acid Availability. Shen K, Choe A, Sabatini DM. Mol Cell 68 552-565.e8 (2017)
  10. Stabilizing a weak binding state for effectors in the human ras protein by cyclen complexes. Rosnizeck IC, Graf T, Spoerner M, Tränkle J, Filchtinski D, Herrmann C, Gremer L, Vetter IR, Wittinghofer A, König B, Kalbitzer HR. Angew Chem Int Ed Engl 49 3830-3833 (2010)
  11. Tyrosyl phosphorylation of KRAS stalls GTPase cycle via alteration of switch I and II conformation. Kano Y, Gebregiworgis T, Marshall CB, Radulovich N, Poon BPK, St-Germain J, Cook JD, Valencia-Sama I, Grant BMM, Herrera SG, Miao J, Raught B, Irwin MS, Lee JE, Yeh JJ, Zhang ZY, Tsao MS, Ikura M, Ohh M. Nat Commun 10 224 (2019)
  12. The crystal structure of YloQ, a circularly permuted GTPase essential for Bacillus subtilis viability. Levdikov VM, Blagova EV, Brannigan JA, Cladière L, Antson AA, Isupov MN, Séror SJ, Wilkinson AJ. J Mol Biol 340 767-782 (2004)
  13. Discovery of High-Affinity Noncovalent Allosteric KRAS Inhibitors That Disrupt Effector Binding. McCarthy MJ, Pagba CV, Prakash P, Naji AK, van der Hoeven D, Liang H, Gupta AK, Zhou Y, Cho KJ, Hancock JF, Gorfe AA. ACS Omega 4 2921-2930 (2019)
  14. Two conformational states of Ras GTPase exhibit differential GTP-binding kinetics. Liao J, Shima F, Araki M, Ye M, Muraoka S, Sugimoto T, Kawamura M, Yamamoto N, Tamura A, Kataoka T. Biochem Biophys Res Commun 369 327-332 (2008)
  15. LRRK2 autophosphorylation enhances its GTPase activity. Liu Z, Mobley JA, DeLucas LJ, Kahn RA, West AB. FASEB J 30 336-347 (2016)
  16. Pan-KRAS inhibitor disables oncogenic signalling and tumour growth. Kim D, Herdeis L, Rudolph D, Zhao Y, Böttcher J, Vides A, Ayala-Santos CI, Pourfarjam Y, Cuevas-Navarro A, Xue JY, Mantoulidis A, Bröker J, Wunberg T, Schaaf O, Popow J, Wolkerstorfer B, Kropatsch KG, Qu R, de Stanchina E, Sang B, Li C, McConnell DB, Kraut N, Lito P. Nature 619 160-166 (2023)
  17. Structure of a transient intermediate for GTP hydrolysis by ras. Ford B, Hornak V, Kleinman H, Nassar N. Structure 14 427-436 (2006)
  18. KRAS(G12D) can be targeted by potent inhibitors via formation of salt bridge. Mao Z, Xiao H, Shen P, Yang Y, Xue J, Yang Y, Shang Y, Zhang L, Li X, Zhang Y, Du Y, Chen CC, Guo RT, Zhang Y. Cell Discov 8 5 (2022)
  19. Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Kondrashov DA, Zhang W, Aranda R, Stec B, Phillips GN. Proteins 70 353-362 (2008)
  20. The role of conserved waters in conformational transitions of Q61H K-ras. Prakash P, Sayyed-Ahmad A, Gorfe AA. PLoS Comput Biol 8 e1002394 (2012)
  21. Molecular dynamics simulations of transducin: interdomain and front to back communication in activation and nucleotide exchange. Ceruso MA, Periole X, Weinstein H. J Mol Biol 338 469-481 (2004)
  22. High-throughput screening identifies small molecules that bind to the RAS:SOS:RAS complex and perturb RAS signaling. Burns MC, Howes JE, Sun Q, Little AJ, Camper DV, Abbott JR, Phan J, Lee T, Waterson AG, Rossanese OW, Fesik SW. Anal Biochem 548 44-52 (2018)
  23. Structure of the dominant negative S17N mutant of Ras. Nassar N, Singh K, Garcia-Diaz M. Biochemistry 49 1970-1974 (2010)
  24. Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants. Sayyed-Ahmad A, Prakash P, Gorfe AA. Proteins 85 1618-1632 (2017)
  25. Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras. Xu S, Long BN, Boris GH, Chen A, Ni S, Kennedy MA. Acta Crystallogr D Struct Biol 73 970-984 (2017)
  26. Structural Dynamics in Ras and Related Proteins upon Nucleotide Switching. Harrison RA, Lu J, Carrasco M, Hunter J, Manandhar A, Gondi S, Westover KD, Engen JR. J Mol Biol 428 4723-4735 (2016)
  27. Characterization of a Ras mutant with identical GDP- and GTP-bound structures . Ford B, Boykevisch S, Zhao C, Kunzelmann S, Bar-Sagi D, Herrmann C, Nassar N. Biochemistry 48 11449-11457 (2009)
  28. The G protein signaling regulator RGS3 enhances the GTPase activity of KRAS. Li C, Vides A, Kim D, Xue JY, Zhao Y, Lito P. Science 374 197-201 (2021)
  29. Differential dynamics of RAS isoforms in GDP- and GTP-bound states. Kapoor A, Travesset A. Proteins 83 1091-1106 (2015)
  30. K-RasG12D Has a Potential Allosteric Small Molecule Binding Site. Feng H, Zhang Y, Bos PH, Chambers JM, Dupont MM, Stockwell BR. Biochemistry 58 2542-2554 (2019)
  31. New Noonan syndrome model mice with RIT1 mutation exhibit cardiac hypertrophy and susceptibility to β-adrenergic stimulation-induced cardiac fibrosis. Takahara S, Inoue SI, Miyagawa-Tomita S, Matsuura K, Nakashima Y, Niihori T, Matsubara Y, Saiki Y, Aoki Y. EBioMedicine 42 43-53 (2019)
  32. Small Molecule KRAS Agonist for Mutant KRAS Cancer Therapy. Xu K, Park D, Magis AT, Zhang J, Zhou W, Sica GL, Ramalingam SS, Curran WJ, Deng X. Mol Cancer 18 85 (2019)
  33. Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bodén M, Bailey TL. Bioinformatics 22 1809-1814 (2006)
  34. Spontaneous nucleotide exchange in low molecular weight GTPases by fluorescently labeled gamma-phosphate-linked GTP analogs. Korlach J, Baird DW, Heikal AA, Gee KR, Hoffman GR, Webb WW. Proc Natl Acad Sci U S A 101 2800-2805 (2004)
  35. Structural basis of the atypical activation mechanism of KRASV14I. Bera AK, Lu J, Wales TE, Gondi S, Gurbani D, Nelson A, Engen JR, Westover KD. J Biol Chem 294 13964-13972 (2019)
  36. Early endosome localization and activity of RasGEF1b, a toll-like receptor-inducible Ras guanine-nucleotide exchange factor. Andrade WA, Silva AM, Alves VS, Salgado AP, Melo MB, Andrade HM, Dall'Orto FV, Garcia SA, Silveira TN, Gazzinelli RT. Genes Immun 11 447-457 (2010)
  37. Structural impact of GTP binding on downstream KRAS signaling. Menyhárd DK, Pálfy G, Orgován Z, Vida I, Keserű GM, Perczel A. Chem Sci 11 9272-9289 (2020)
  38. Conformational and Dynamical Effects of Tyr32 Phosphorylation in K-Ras: Molecular Dynamics Simulation and Markov State Models Analysis. Khaled M, Gorfe A, Sayyed-Ahmad A. J Phys Chem B 123 7667-7675 (2019)
  39. Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation. Ni D, Song K, Zhang J, Lu S. Int J Mol Sci 18 E2249 (2017)
  40. Intragenic suppressor mutations restore GTPase and translation functions of a eukaryotic initiation factor 5B switch II mutant. Shin BS, Acker MG, Maag D, Kim JR, Lorsch JR, Dever TE. Mol Cell Biol 27 1677-1685 (2007)
  41. A small-molecule induces apoptosis and suppresses metastasis in pancreatic cancer cells. Li D, Liu Z, Zhao W, Zheng X, Wang J, Wang E. Eur J Pharm Sci 48 658-667 (2013)
  42. Human Miro Proteins Act as NTP Hydrolases through a Novel, Non-Canonical Catalytic Mechanism. Peters DT, Kay L, Eswaran J, Lakey JH, Soundararajan M. Int J Mol Sci 19 E3839 (2018)
  43. Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions. Kumawat A, Chakrabarty S, Kulkarni K. Sci Rep 7 45829 (2017)
  44. The Roc-COR tandem domain of leucine-rich repeat kinase 2 forms dimers and exhibits conventional Ras-like GTPase properties. Mills RD, Liang LY, Lio DS, Mok YF, Mulhern TD, Cao G, Griffin M, Kenche VB, Culvenor JG, Cheng HC. J Neurochem 147 409-428 (2018)
  45. The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly. Jeganathan A, Razi A, Thurlow B, Ortega J. RNA 21 1203-1216 (2015)
  46. Identification of New KRAS G12D Inhibitors through Computer-Aided Drug Discovery Methods. Kulkarni AM, Kumar V, Parate S, Lee G, Yoon S, Lee KW. Int J Mol Sci 23 1309 (2022)
  47. Interconversion of two GDP-bound conformations and their selection in an Arf-family small G protein. Okamura H, Nishikiori M, Xiang H, Ishikawa M, Katoh E. Structure 19 988-998 (2011)
  48. Engineering subtilisin proteases that specifically degrade active RAS. Chen Y, Toth EA, Ruan B, Choi EJ, Simmerman R, Chen Y, He Y, Wang R, Godoy-Ruiz R, King H, Custer G, Travis Gallagher D, Rozak DA, Solomon M, Muro S, Weber DJ, Orban J, Fuerst TR, Bryan PN. Commun Biol 4 299 (2021)
  49. Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A. Sci Rep 7 7180 (2017)
  50. Mechanism of the exchange reaction in HRAS from multiscale modeling. Kapoor A, Travesset A. PLoS One 9 e108846 (2014)
  51. Electric-Field-Induced Protein Translocation via a Conformational Transition in SecDF: An MD Study. Ficici E, Jeong D, Andricioaei I. Biophys J 112 2520-2528 (2017)
  52. KRAS G12C fragment screening renders new binding pockets. Mathieu M, Steier V, Fassy F, Delorme C, Papin D, Genet B, Duffieux F, Bertrand T, Delarbre L, Le-Borgne H, Parent A, Didier P, Marquette JP, Lowinski M, Houtmann J, Lamberton A, Debussche L, Alexey R. Small GTPases 13 225-238 (2022)
  53. A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions. Miller SP, Maio G, Zhang X, Badillo Soto FS, Zhu J, Ramirez SZ, Lin H. Mol Cell Proteomics 21 100268 (2022)
  54. From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes. Sapin E, De Jong KA, Shehu A. IEEE/ACM Trans Comput Biol Bioinform 15 719-731 (2018)
  55. Lead identification for the K-Ras protein: virtual screening and combinatorial fragment-based approaches. Pathan AA, Panthi B, Khan Z, Koppula PR, Alanazi MS, Sachchidanand, Parine NR, Chourasia M. Onco Targets Ther 9 2575-2584 (2016)
  56. Differentiating the pre-hydrolysis states of wild-type and A59G mutant HRas: An insight through MD simulations. Sharma N, Sonavane U, Joshi R. Comput Biol Chem 69 96-109 (2017)
  57. Discovering and Targeting Dynamic Drugging Pockets of Oncogenic Proteins: The Role of Magnesium in Conformational Changes of the G12D Mutated Kirsten Rat Sarcoma-Guanosine Diphosphate Complex. Hu Z, Marti J. Int J Mol Sci 23 13865 (2022)
  58. HPLC method to resolve, identify and quantify guanine nucleotides bound to recombinant ras GTPase. Hannan JP, Swisher GH, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. Anal Biochem 631 114338 (2021)
  59. Case Reports Identification of Codon 146 KRAS Variants in Isolated Epidermal Nevus and Multiple Lesions in Oculoectodermal Syndrome: Confirmation of the Phenotypic Continuum of Mosaic RASopathies. Beyens A, Dequeker L, Brems H, Janssens S, Syryn H, D'Hooghe A, De Paepe P, Vanwalleghem L, Stockman A, Vankwikelberge E, De Schepper S, Goeteyn M, Delbeke P, Callewaert B. Int J Mol Sci 23 4036 (2022)
  60. Mechanistic Insights into the Differential Catalysis by RheB and Its Mutants: Y35A and Y35A-D65A. Kotyada C, Maulik A, Srivastava A, Singh M. ACS Omega 2 6691-6702 (2017)
  61. NMR resonance assignment of the N-terminal GTPase domain of human Miro2 Bound to GTP. Smith CE, Jones DNM. Biomol NMR Assign 16 349-355 (2022)


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