A Genome-wide Ras-Effector Interaction Network

Journal of Molecular Biology

Volumn 370, Issue 5, 2007, Pages 1020-1032

  Kiel, Christina ^a,b   Foglierini, Mathilde ^a   Kuemmerer, Nico ^a   Beltrao, Pedro ^a   Serrano, Luis ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

FoldX; homology modelling; protein interactions; Ras binding domains; Ras proteins

Indexed keywords

RAS PROTEIN;

ARTICLE; BIOINFORMATICS; GENOME ANALYSIS; MOLECULAR CLONING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 34250186793     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.05.015     Document Type: Article

References (50)

1. Aloy P., Pichaud M., and Russell R.B. Protein complexes: structure prediction challenges for the 21st century. Curr. Opin. Struct. Biol. 1 (2005) 15-22
2. Aloy P., and Russell R.B. Structural systems biology: modelling protein interactions. Nature Rev. Mol. Cell. Biol. 3 (2006) 188-197
3. Kiel C., Wohlgemuth S., Rousseau F., Schymkowitz J., Ferkinghoff-Borg J., Wittinghofer F., et al. Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. J. Mol. Biol. 348 (2005) 759-775
4. Nassar N., Horn G., Herrmann C., Scherer A., McCormick F., and Wittinghofer A. The 2.2 Å crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Nature 375 (1995) 554-560
5. Nassar N., Horn G., Herrmann C., Block C., Janknecht R., and Wittinghofer A. Ras/Rap effector specificity determined by charge reversal. Nature Struct. Biol. 3 (1996) 723-729
6. Huang L., Hofer F., Martin G.S., and Kim S.H. Structural basis for the interaction of Ras with RalGDS. Nature Struct. Biol. 5 (1998) 422-426
7. Vetter I.R., Linnemann T., Wohlgemuth S., Geyer M., Kalbitzer H.R., Herrmann C., et al. Structural and biochemical analysis of Ras-effector signaling via RalGDS. FEBS Letters 451 (1999) 175-180
8. Pacold M.E., Suire S., Perisic O., Lara-Gonzalez S., Davis C.T., Walker E.H., et al. Crystal structure and functional analysis of Ras binding to its effector phosphoinoside 3-kinase gamma. Cell 103 (2000) 931-943
9. Scheffzek K., Grünewald P., Wohlgemuth S., Kabsch W., Tu H., Wigler M., et al. The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast. Structure 9 (2001) 1043-1050
10. Bunney T.D., Harris R., Gandarillas N.L., Josephs M.B., Roe S.M., Sorli S.C., et al. Structural and mechanistic insights into ras association domains of phospholipase C epsilon. Mol. Cell 21 (2006) 495-507
11. Vetter I.R., and Wittinghofer A. Signal transduction - the guanine nucleotide-binding switch in three dimensions. Science 294 (2001) 1299-1304
12. Takai Y., Sasaki T., and Matozaki T. Small GTP binding proteins. Physiol. Rev. 81 (2001) 153-208
13. Colicelli J. Human RAS superfamily proteins and related GTPases. Sci. STKE 250 (2004) RE13-RE31
14. Bourne H.R., Sanders D.A., and McCormick F. The GTPase superfamily: a conserved switch for diverse cell functions. Nature 348 (1990) 125-132
15. Bourne H.R., Sanders D.A., and McCormick F. The GTPase superfamily: conserved structure and molecular mechanism. Nature 349 (1991) 117-127
16. Milburn M.V., Tong L., de Vos A.M., Brünger A., Yamaizumi Z., Nishimura S., et al. Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. Science 247 (1990) 939-945
17. Rapp U.R., Goldsborough M.D., Mark G.E., Bonner T.I., Groffen J., Reynolds Jr. F.H., et al. Structure and biological activity of v-raf, a unique oncogene transduced by a retrovirus. Proc. Natl Acad. Sci. USA 80 (1983) 4218-4222
18. Vojtek A.B., Hollenberg S.M., and Cooper J.A. Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell 74 (1993) 205-214
19. Rodriguez-Viciana P., Warne P.H., Dhand R., Van Haesebroeck B., Gout I., Fry M.J., et al. Phosphatidylinositol-3-OH kinase as a direct target of Ras. Nature 370 (1994) 527-532
20. Hofer F., Fields S., Schneider C., and Martin G.S. Activated Ras interacts with the Ral guanine nucleotide dissociation stimulator. Proc. Natl Acad. Sci. USA 91 (1994) 11089-11093
21. Kikuchi A., Demo S.D., Ye Z.-H., Chen Y.-W., and Williams L.T. RalGDS family members interact with the effector loop of ras p21. Mol. Cell. Biol. 14 (1994) 7483-7491
22. Kuriyama M., Harada N., Kuroda S., Yamamoto T., Nakafuku M., Iwamatsu A., et al. Identification of AF-6 and Canoe as putative targets for Ras. J. Biol. Chem. 271 (1996) 607-610
23. Lambert J.M., Lambert Q.T., Reuther G.W., Malliri A., Siderovski D.P., Sondek J., et al. Tiam1 mediates Ras activation of Rac by a PI(3)K-independent mechanism. Nature Cell. Biol. 4 (2002) 621-625
24. Malliri A., van der Kammen R.A., Clark K., van der Valk M., Michiels F., and Collard J.G. Mice deficient in the Rac activator Tiam1 are resistant to Ras-induced skin tumours. Nature 417 (2002) 867-871
25. Han L., Wong D., Dhaka A., Afar D., White M., Xie W., et al. Protein binding and signaling properties of RIN1 suggest a unique effector function. Proc. Natl Acad. Sci. USA 94 (1997) 4954-4959
26. Tall G.G., Barbieri M.A., Stahl P.D., and Horazdovsky B.F. Ras-activated endocytosis is mediated by the Rab5 guanine nucleotide exchange activity of RIN1. Dev. Cell 1 (2001) 73-82
27. Wang Y., Waldron R.T., Dhaka A., Patel A., Riley M.M., Rozengurt E., et al. The RAS effector RIN1 directly competes with RAF and is regulated by 14-3-3 proteins. Mol. Cell. Biol. 22 (2002) 916-926
28. Kelley G.G., Reks S.E., Ondrako J.M., and Smrcka A. V. Phospholipase C (epsilon): a novel Ras effector. EMBO J. 20 (2001) 743-754
29. Khokhlatchev A., Rabizadeh S., Xavier R., Nedwidek M., Chen T., Zhang X.F., et al. Identification of a novel Ras-regulated proapoptotic pathway. Curr. Biol. 12 (2002) 253-265
30. Orengo C.A., Jones D.T., and Thornton J.M. Protein superfamilies and domain superfolds. Nature 372 (1994) 631-634
31. Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., et al. Recent improvements to the SMART domain-based sequence annotation resource. Nucl. Acids Res. 30 (2002) 242-244
32. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., et al. The Pfam protein families database. Nucl. Acids Res. 32 (2004) D138-D141
33. Ponting C.P., and Benjamin D.R. A novel family of ras-binding domains. Trends Biochem. Sci. 21 (1996) 422-425
34. Wohlgemuth S., Kiel C., Kraemer A., Serrano L., Wittinghofer F., and Herrmann C. Recognizing and defining true Ras binding domains I: biochemical analysis. J. Mol. Biol. 348 (2005) 741-758
35. Rodriguez-Viciana P., Sabatier C., and McCormick F. Signaling specificity by Ras family GTPases is determined by the full spectrum of effectors they regulate. Mol. Cell. Biol. 24 (2004) 4943-4954
36. Guerois R., Nielsen J.E., and Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320 (2002) 369-387
37. Schymkowitz J., Borg J., Stricher F., Nys R., Rousseau F., and Serrano L. The FoldX web server: an online force field. Nucl. Acids Res. 33 (2005) W382-W388
38. Schymkowitz J.W.H., Rousseau F., Martins I.C., Ferkinghoff-Borg J., Stricher F., and Serrano L. Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc. Natl Acad. Sci. USA 102 (2005) 10147-10152
39. Wallace I.M., Blackshields G., and Higgins D.G. Multiple sequence alignments. Curr. Opin. Struct. Biol. 15 (2005) 261-266
40. O'Sullivan O., Suhre K., Abergel C., Higgins D.G., and Notredame C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 340 (2004) 385-395
41. Kiel C., and Serrano L. The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes. J. Mol. Biol. 355 (2006) 821-844
42. Ye M., Shima F., Muraoka S., Liao J., Okamoto H., Yamamoto M., et al. Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases. J. Biol. Chem. 280 (2005) 31267-31275
43. Yu Y., Li S., Xu X., Li Y., Guan K., Arnold E., et al. Structural basis for the unique biological function of small GTPase RHEB. J. Biol. Chem. 280 (2005) 17093-17100
44. Vriend G. WHAT IF: a molecular modelling and drug design program. J. Mol. Graph. 8 (1990) 52-56
45. Rhodes D.R., Tomlins S.A., Varambally S., Mahavisno V., Barrette T., Kalyana-Sundaram S., et al. Probabilistic model of the human protein-protein interaction network. Nature Biotech. 23 (2005) 951-959
46. Feig L.A. Ral-GTPases: approaching their 15 minutes of fame. Trends Cell Biol. 13 (2003) 419-425
47. Fukai S., Matern H.T., Jagath J.R., Scheller R.H., and Brunger A.T. Structural basis of the interaction between RalA and Sec5, a subunit of the sec6/8 complex. EMBO J. 22 (2003) 3267-3278
48. Hoshino M., and Nakamura S. Small GTPase Rin induces neurite outgrowth through Rac/Cdc42 and calmodulin in PC12 cells. J. Cell. Biol. 163 (2003) 1067-1076
49. Lee C.H., Della N.G., Chew C.E., and Zack D.J. Rin, a neuron-specific and calmodulin-binding small G-protein, and Rit define a novel subfamily of ras proteins. J. Neurosci. 16 (1996) 6784-6794
50. Shao H., Kadono-Okuda K., Finlin B.S., and Andres D.A. Biochemical characterization of the Ras-related GTPases Rit and Rin. Arch. Biochem. Biophys. 371 (1999) 207-219