Prediction of binding sites of peptide recognition domains: An application on Grb2 and SAP SH2 domains

Journal of Molecular Biology

Volumn 357, Issue 4, 2006, Pages 1322-1334

  McLaughlin, William A ^a   Hou, Tingjun ^a   Wang, Wei ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Binding site motif; MM PBSA; Protein protein interactions; SH2 domain

Indexed keywords

PROTEIN GRB2; PROTEIN SH2; PROTEOME; SIGNALING LYMPHOCYTE ACTIVATION MOLECULE ASSOCIATED PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN INTERACTION; SEQUENCE ANALYSIS;

EID: 33644828578     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.01.005     Document Type: Article

References (59)

1. T. Pawson Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems Cell 116 2004 191 203
2. J. Schlessinger, and M.A. Lemmon SH2 and PTB domains in tyrosine kinase signaling Sci. STKE 2003 RE12
3. M.B. Yaffe Phosphotyrosine-binding domains in signal transduction Nature Rev. Mol. Cell. Biol. 3 2002 177 186
4. J. Schlessinger, and A. Ullrich Growth factor signaling by receptor tyrosine kinases Neuron 9 1992 383 391
5. S.E. Shoelson SH2 and PTB domain interactions in tyrosine kinase signal transduction Curr. Opin. Chem. Biol. 1 1997 227 234
6. J. Kuriyan, and D. Cowburn Modular peptide recognition domains in eukaryotic signaling Annu. Rev. Biophys. Biomol. Struct. 26 1997 259 288
7. T. Pawson, G.D. Gish, and P. Nash SH2 domains, interaction modules and cellular wiring Trends Cell Biol. 11 2001 504 511
8. K. Machida, and B.J. Mayer The SH2 domain: versatile signaling module and pharmaceutical target Biochim. Biophys. Acta 1747 2005 1 25
9. E.J. Lowenstein, R.J. Daly, A.G. Batzer, W. Li, B. Margolis, and R. Lammers The SH2 and SH3 domain-containing protein GRB2 links receptor tyrosine kinases to ras signaling Cell 70 1992 431 442
10. J. Schlessinger How receptor tyrosine kinases activate Ras Trends Biochem. Sci. 18 1993 273 275
11. J. Sayos, C. Wu, M. Morra, N. Wang, X. Zhang, and D. Allen The X-linked lymphoproliferative-disease gene product SAP regulates signals induced through the co-receptor SLAM Nature 395 1998 462 469
12. M. Morra, D. Howie, M.S. Grande, J. Sayos, N. Wang, and C. Wu X-linked lymphoproliferative disease: a progressive immunodeficiency Annu. Rev. Immunol. 19 2001 657 682
13. B. Chan, A. Lanyi, H.K. Song, J. Griesbach, M. Simarro-Grande, and F. Poy SAP couples Fyn to SLAM immune receptors Nature Cell Biol. 5 2003 155 160
14. A.J. Coffey, R.A. Brooksbank, O. Brandau, T. Oohashi, G.R. Howell, and J.M. Bye Host response to EBV infection in X-linked lymphoproliferative disease results from mutations in an SH2-domain encoding gene Nature Genet. 20 1998 129 135
15. B.J. Mayer, and D. Baltimore Signalling through SH2 and SH3 domains Trends Cell Biol. 3 1993 8 13
16. A. Nantel, K. Mohammad-Ali, J. Sherk, B.I. Posner, and D.Y. Thomas Interaction of the Grb10 adapter protein with the Raf1 and MEK1 kinases J. Biol. Chem. 273 1998 10475 10484
17. Z. Songyang, S.E. Shoelson, M. Chaudhuri, G. Gish, T. Pawson, and W.G. Haser SH2 domains recognize specific phosphopeptide sequences Cell 72 1993 767 778
18. Z. Songyang, S.E. Shoelson, J. McGlade, P. Olivier, T. Pawson, and X.R. Bustelo Specific motifs recognized by the SH2 domains of Csk, 3BP2, fps/fes, GRB-2, HCP, SHC, Syk, and Vav Mol. Cell. Biol. 14 1994 2777 2785
19. M. Morra, J. Lu, F. Poy, M. Martin, J. Sayos, and S. Calpe Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells EMBO J. 20 2001 5840 5852
20. F. Poy, M.B. Yaffe, J. Sayos, K. Saxena, M. Morra, and J. Sumegi Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition Mol. Cell 4 1999 555 561
21. J.C. Obenauer, L.C. Cantley, and M.B. Yaffe Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs Nucl. Acids Res. 31 2003 3635 3641
22. M.B. Yaffe, G.G. Leparc, J. Lai, T. Obata, S. Volinia, and L.C. Cantley A motif-based profile scanning approach for genome-wide prediction of signaling pathways Nature Biotechnol. 19 2001 348 353
23. A.M. Wollacott, and J.R. Desjarlais Virtual interaction profiles of proteins J. Mol. Biol. 313 2001 317 342
24. P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, and L. Chong Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Accts Chem. Res. 33 2000 889 897
25. W. Wang, O. Donini, C.M. Reyes, and P.A. Kollman Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions Annu. Rev. Biophys. Biomol. Struct. 30 2001 211 243
26. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids 1998 Cambridge University Press Cambridge, UK
27. B. Boeckmann, A. Bairoch, R. Apweiler, M.C. Blatter, A. Estreicher, and E. Gasteiger The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucl. Acids Res. 31 2003 365 370
28. O. Schueler-Furman, Y. Altuvia, A. Sette, and H. Margalit Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles Protein Sci. 9 2000 1838 1846
29. P.M. Hwang, C. Li, M. Morra, J. Lillywhite, D.R. Muhandiram, and F. Gertler A "three-pronged" binding mechanism for the SAP/SH2D1A SH2 domain: structural basis and relevance to the XLP syndrome EMBO J. 21 2002 314 323
30. G.D. Bader, D. Betel, and C.W. Hogue BIND: the Biomolecular Interaction Network Database Nucl. Acids Res. 31 2003 248 250
31. A. Zanzoni, L. Montecchi-Palazzi, M. Quondam, G. Ausiello, M. Helmer-Citterich, and G. Cesareni MINT: a Molecular INTeraction database FEBS Letters 513 2002 135 140
32. J. Braunger, L. Schleithoff, A.S. Schulz, H. Kessler, R. Lammers, and A. Ullrich Intracellular signaling of the Ufo/Axl receptor tyrosine kinase is mediated mainly by a multi-substrate docking-site Oncogene 14 1997 2619 2631
33. F. Diella, S. Cameron, C. Gemund, R. Linding, A. Via, and B. Kuster Phospho. ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins BMC Bioinformatics 5 2004 79
34. J.W. Janssen, A.S. Schulz, A.C. Steenvoorden, M. Schmidberger, S. Strehl, P.F. Ambros, and C.R. Bartram A novel putative tyrosine kinase receptor with oncogenic potential Oncogene 6 1991 2113 2120
35. C. Rochlitz, A. Lohri, M. Bacchi, M. Schmidt, S. Nagel, and M. Fopp Axl expression is associated with adverse prognosis and with expression of Bcl-2 and CD34 in de novo acute myeloid leukemia (AML): results from a multicenter trial of the Swiss Group for Clinical Cancer Research (SAKK) Leukemia 13 1999 1352 1358
36. T.N. Stitt, G. Conn, M. Gore, C. Lai, J. Bruno, and C. Radziejewski The anticoagulation factor protein S and its relative, Gas6, are ligands for the Tyro 3/Axl family of receptor tyrosine kinases Cell 80 1995 661 670
37. L.R. Rohrschneider, R.P. Bourette, M.N. Lioubin, P.A. Algate, G.M. Myles, and K. Carlberg Growth and differentiation signals regulated by the M-CSF receptor Mol. Reprod. Dev. 46 1997 96 103
38. M.N. Lioubin, G.M. Myles, K. Carlberg, D. Bowtell, and L.R. Rohrschneider Shc, Grb2, Sos1, and a 150-kilodalton tyrosine-phosphorylated protein form complexes with Fms in hematopoietic cells Mol. Cell. Biol. 14 1994 5682 5691
39. T. Yin, and K.J. Green Regulation of desmosome assembly and adhesion Semin. Cell Dev. Biol. 15 2004 665 677
40. A.G. Batzer, D. Rotin, J.M. Urena, E.Y. Skolnik, and J. Schlessinger Hierarchy of binding sites for Grb2 and Shc on the epidermal growth factor receptor Mol. Cell. Biol. 14 1994 5192 5201
41. J.H. Lorch, J. Klessner, J.K. Park, S. Getsios, Y.L. Wu, M.S. Stack, and K.J. Green Epidermal growth factor receptor inhibition promotes desmosome assembly and strengthens intercellular adhesion in squamous cell carcinoma cells J. Biol. Chem. 279 2004 37191 37200
42. C. Bottino, M. Falco, S. Parolini, E. Marcenaro, R. Augugliaro, and S. Sivori NTB-A [correction of GNTB-A], a novel SH2D1A-associated surface molecule contributing to the inability of natural killer cells to kill Epstein-Barr virus-infected B cells in X-linked lymphoproliferative disease J. Expt. Med. 194 2001 235 246
43. A.C. Pearce, Y.A. Senis, D.D. Billadeau, M. Turner, S.P. Watson, and E. Vigorito Vav1 and vav3 have critical but redundant roles in mediating platelet activation by collagen J. Biol. Chem. 279 2004 53955 53962
44. A. Aoukaty, and R. Tan Role for glycogen synthase kinase-3 in NK cell cytotoxicity and X-linked lymphoproliferative disease J. Immunol. 174 2005 4551 4558
45. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
46. P. Nioche, W.Q. Liu, I. Broutin, F. Charbonnier, M.T. Latreille, and M. Vidal Crystal structures of the SH2 domain of Grb2: highlight on the binding of a new high-affinity inhibitor J. Mol. Biol. 315 2002 1167 1177
47. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucl. Acids Res. 25 1997 3389 3402
48. R. Apweiler, A. Bairoch, C.H. Wu, W.C. Barker, B. Boeckmann, and S. Ferro UniProt: the Universal Protein knowledgebase Nucl. Acids Res. 32 2004 D115 D119
49. C. Li, C. Iosef, C.Y. Jia, V.K. Han, and S.S. Li Dual functional roles for the X-linked lymphoproliferative syndrome gene product SAP/SH2D1A in signaling through the signaling lymphocyte activation molecule (SLAM) family of immune receptors J. Biol. Chem. 278 2003 3852 3859
50. A.A. Canutescu, A.A. Shelenkov, and R.L. Dunbrack Jr A graph-theory algorithm for rapid protein side-chain prediction Protein Sci. 12 2003 2001 2014
51. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
52. J.M. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 2000 1049 1074
53. A. Suenaga, M. Hatakeyama, M. Ichikawa, X. Yu, N. Futatsugi, and T. Narumi Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides Biochemistry 42 2003 5195 5200
54. J. Hartigan Clustering Algorithms 1975 Wiley New York
55. Witten, I.H. & Frank, F. (2000). Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations, Morgan Kaufmann, San Francisco, CA.
56. A.P. Dempster, N.M. Laird, and D.B. Rubin Maximum likelihood from incomplete data via the em algorithm J. Roy. Stat. Soc. 39 1977 1 38
57. W. Li, L. Jaroszewski, and A. Godzik Clustering of highly homologous sequences to reduce the size of large protein databases Bioinformatics 17 2001 282 283
58. D.L. Wheeler, T. Barrett, D.A. Benson, S.H. Bryant, K. Canese, and D.M. Church Database resources of the National Center for Biotechnology Information Nucl. Acids Res. 33 2005 D39 D45
59. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) Nomenclature and Symbolism for Amino Acids and Peptides Eur. J. Biochem. 138 1984 9 37