Recognizing and defining true ras binding domains II: In Silico prediction based on homology modelling and energy calculations

Journal of Molecular Biology

Volumn 348, Issue 3, 2005, Pages 759-775

  Kiel, Christina ^a   Wohlgemuth, Sabine ^b   Rousseau, Frederic ^c   Schymkowitz, Joost ^c   Ferkinghoff Borg, Jesper ^d   Wittinghofer, Fred ^b   Serrano, Luis ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

^c VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Homology modelling; In silico protein interaction; Protein protein interaction; Stability; Structural genomics

Indexed keywords

RAS PROTEIN; UBIQUITIN;

ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; ENERGY; GENOME; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; SEQUENCE HOMOLOGY; STRUCTURAL GENOMICS; STRUCTURAL HOMOLOGY; VALIDATION PROCESS;

EID: 13844293072     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.02.046     Document Type: Article

References (54)

1. Y. Takai, T. Sasaki, and T. Matozaki Small GTP binding proteins Physiol. Rev. 81 2001 153 208
2. H.R. Bourne, D.A. Sanders, and F. McCormick The GTPase superfamily: a conserved switch for diverse cell functions Nature 348 1990 125 132
3. H.R. Bourne, D.A. Sanders, and F. McCormick The GTPase superfamily: conserved structure and molecular mechanism Nature 349 1991 117 127
4. U.R. Rapp, M.D. Goldsborough, G.E. Mark, T.I. Bonner, J. Groffen, F.H. Reynolds Jr, and J. Stephenson Structure and biological activity of v-raf, a unique oncogene transduced by a retrovirus Proc. Natl Acad. Sci. USA 80 1983 4218 4222
5. A.B. Vojtek, S.M. Hollenberg, and J.A. Cooper Mammalian Ras interacts directly with the serine/threonine kinase Raf Cell 74 1993 205 214
6. P. Rodriguez-Viciana, P.H. Warne, R. Dhand, B. Van Haesebroeck, I. Gout, and M.J. Fry Phosphatidylinositol-3-OH kinase as a direct target of Ras Nature 370 1994 527 532
7. F. Hofer, S. Fields, C. Schneider, and G.S. Martin Activated Ras interacts with the Ral guanine nucleotide dissociation stimulator Proc. Natl Acad. Sci. USA 91 1994 11089 11093
8. A. Kikuchi, S.D. Demo, Z.-H. Ye, Y.-W. Chen, and L.T. Williams RalGDS family members interact with the effector loop of ras p21 Mol. Cell. Biol. 14 1994 7483 7491
9. M. Kuriyama, N. Harada, S. Kuroda, T. Yamamoto, M. Nakafuku, and A. Iwamatsu Identification of AF-6 and Canoe as putative targets for Ras J. Biol. Chem. 271 1996 607 610
10. S.D. Emerson, V.S. Madison, R.E. Palermo, D.S. Waugh, J.E. Scheffler, and K.L. Tsao Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction surface Biochemistry 34 1995 6911 6918
11. L. Huang, X. Weng, F. Hofer, G.S. Martin, and S.H. Kim Three-dimensional structure of the Ras-interacting domain of RalGDS Nature Struct. Biol. 4 1997 609 615
12. M. Geyer, C. Herrmann, S. Wohlgemuth, A. Wittinghofer, and H.R. Kalbitzer Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signaling Nature Struct. Biol. 4 1997 694 699
13. E.H. Walker, O. Perisic, C. Ried, L. Stephens, and R.L. Williams Structural insights into phosphoinoside 3-kinase catalysis and signaling Nature 402 1999 313 320
14. G. Steiner, W. Kremer, T. Linnemann, C. Herrmann, M. Geyer, and H.R. Kalbitzer Sequence-specific resonance assignment of the Ras-binding domain of AF6 J. Biomol. NMR 18 2000 73 74
15. W. Gronwald, F. Huber, P. Grünewald, M. Spörner, S. Wohlgemuth, C. Herrmann, and H.R. Kalbitzer Solution structure of the Ras-binding domain of the protein kinase Byr2 from Schizosaccharomyces pombe Structure 9 2001 1029 1041
16. N. Nassar, G. Horn, C. Herrmann, A. Scherer, F. McCormick, and A. Wittinghofer 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
17. N. Nassar, G. Horn, C. Herrmann, C. Block, R. Janknecht, and A. Wittinghofer Ras/Rap effector specificity determined by charge reversal Nature Struct. Biol. 3 1996 723 729
18. L. Huang, F. Hofer, G.S. Martin, and S.H. Kim Structural basis for the interaction of Ras with RalGDS Nature Struct. Biol. 5 1998 422 426
19. I.R. Vetter, T. Linnemann, S. Wohlgemuth, M. Geyer, H.R. Kalbitzer, C. Herrmann, and A. Wittinghofer Structural and biochemical analysis of Ras-effector signaling via RalGDS FEBS Letters 451 1999 175 180
20. M.E. Pacold, S. Suire, O. Perisic, S. Lara-Gonzalez, C.T. Davis, and E.H. Walker Crystal structure and functional analysis of Ras binding to its effector phosphoinoside 3-kinase gamma Cell 103 2000 931 943
21. K. Scheffzek, P. Grünewald, S. Wohlgemuth, W. Kabsch, H. Tu, and M. Wigler The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast Structure 9 2001 1043 1050
22. C. Herrmann, G. Horn, M. Spaargaren, and A. Wittinghofer Differential interaction of the ras family GTP-binding proteins H-Ras, Rap1A and R-Ras with the putative effector molecules raf kinase and ral-guanine nucleotide exchange factor J. Biol. Chem. 271 1996 6794 6800
23. M.G. Rudolph, T. Linnemann, P. Grünewald, A. Wittinghofer, I.R. Vetter, and C. Herrmann Thermodynamics of Ras/effector interactions probed by isothermal titration calorimetry J. Biol. Chem. 276 2001 23914 23921
24. Wohlgemuth, S., Kiel, C., Kraemer, A., Serrano, L., Wittinghofer, F. & Herrmann, C. (2005). Recognizing and defining true Ras binding domains I: biochemical analysis. J. Mol. Biol. (this issue).
25. C.A. Orengo, D.T. Jones, and J.M. Thornton Protein superfamilies and domain superfolds Nature 372 1994 631 634
26. J. Schultz, F. Milpetz, P. Bork, and C.P. Ponting Smart, a simple modular architecture research tool - identification of signalling domains Proc. Natl Acad. Sci. USA 95 1998 5857 5864
27. I. Letunic, L. Goodstadt, N.J. Dickens, T. Doerks, J. Schultz, and R. Mott Recent improvements to the SMART domain-based sequence annotation resource Nucl. Acids Res. 30 2002 242 244
28. C.P. Ponting, and D.R. Benjamin A novel family of ras-binding domains Trends Biochem. Sci. 21 1996 422 425
29. P. Rodriguez-Viciana, C. Sabatier, and F. McCormick Signaling specificity by Ras family GTPases is determined by the full spectrum of effectors they regulate Mol. Cell. Biol. 24 2004 4943 4954
30. R. Guerois, J.E. Nielsen, and L. Serrano Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations J. Mol. Biol. 320 2002 369 387
31. W.J. Cook, L.C. Jeffrey, M. Carson, Z. Chen, and C.M. Pickart Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme J. Biol. Chem. 267 1992 16467 16471
32. C. Kiel, L. Serrano, and C. Herrmann A detailed thermodynamic analysis of Ras/effector complex interfaces J. Mol. Biol. 340 2004 1039 1058
33. C. Kiel, T. Selzer, Y. Shaul, G. Schreiber, and C. Herrmann Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex Proc. Natl Acad. Sci. USA 101 2004 9223 9228
34. N.Y. Mitin, M.B. Ramocki, A.J. Zullo, C.J. Der, S.F. Konieczny, and E.J. Taparowsky Identification and characterization of rain, a novel Ras-interacting protein with a unique subcellular localization J. Biol. Chem. 279 2004 22353 22361
35. J.M. Lambert, Q.T. Lambert, G.W. Reuther, A. Malliri, D.P. Siderovski, and J. Sondek Tiam1 mediates Ras activation of Rac by a PI(3)K-independent mechanism Nature Cell Biol. 4 2002 621 625
36. K.P. Murphy, D. Xie, K.S. Thompson, L.M. Amzel, and E. Freire Entropy in biological binding processes: estimation of translational entropy loss Proteins: Struct. Funct. Genet. 18 1994 63 67
37. J.R. Sydor, M. Engelhard, A. Wittinghofer, R. Goody, and C. Herrmann Transient kinetic studies on the interaction of Ras and the Ras-binding domain of c-Raf-1 reveal rapid equilibrium of the complex Biochemistry 37 1998 14292 14299
38. T. Linnemann, M. Geyer, B.K. Jaitner, C. Block, H.R. Kalbitzer, A. Wittinghofer, and C. Herrmann Thermodynamic and kinetic characterization of the interaction between the Ras binding domain of AF6 and members of the Ras subfamily J. Biol. Chem. 274 1999 13556 13562
39. T. Linnemann, C. Kiel, P. Herter, and C. Herrmann The activation of RalGDS can be achieved independently of its Ras binding domain: implications for an activation mechanism in Ras effector specificity and signal distribution J. Biol. Chem. 10 2002 7831 7837
40. O.G. Berg, and P.H. von Hippel Diffusion-controlled macromolecular interactions Annu. Rev. Biophys. Biophys. Chem. 14 1985 131 160
41. S.H. Northrup, and H.P. Erickson Kinetics of protein-protein association explained by Brownian dynamic computer simulation Proc. Natl Acad. Sci. USA 89 1992 3338 3342
42. M. Vijayakumar, K.-Y. Wong, G. Schreiber, A.R. Fersht, A. Szabo, and H.-X. Zhou Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar J. Mol. Biol. 278 1998 1015 1024
43. T. Selzer, and G. Schreiber New insights into the mechanism of protein-protein association Proteins: Struct. Funct. Genet. 45 2001 190 198
44. D.C. Han, T.-L. Shen, and J.-L. Guan The Grb7 family proteins: structure, interactions with other signaling molecules and potential cellular functions Oncogene 20 2001 6315 6321
45. K.M. Druey Bridging with GAPs: receptor communication through RGS proteins Sci. STKE 104 2001 RE14
46. R.J. Kimple, L. De Vries, H. Tronchere, C.I. Behe, R.A. Morris, M. Gist Farquhar, and D.P. Siderovski RGS12 and RGS14 GoLoco motifs are G alpha (i) interaction sites with guanine nucleotide dissociation inhibitor activity J. Biol. Chem. 276 2001 29275 29281
47. 0 Biochem. J. 350 2000 19 29
48. F.J.T. Zwartkruis, and J.L. Bos Ras and Rap1: two highly related small GTPases with distinct function Expt. Cell Res. 253 1999 157 165
49. B. Boettner, C. Herrmann, and L. Van Aelst Ras and Rap1 interaction with AF-6 effector target Methods Enzymol. 332 2001 151 168
50. R. Abagyan, and M. Totrov Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins J. Mol. Biol. 235 1994 983 1002
51. M. Petukhov, D. Cregut, C.M. Soares, and L. Serrano Local water bridges and protein conformational stability Protein Sci. 8 1999 1982 1989
52. V. Munoz, and L. Serrano Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales Proteins: Struct. Funct. Genet. 20 1994 301 311
53. M.M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye binding Anal. Biochem. 72 1976 248 253
54. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723