Systematic characterization of the specificity of the SH2 domains of cytoplasmic tyrosine kinases

Journal of Proteomics

Volumn 81, Issue , 2013, Pages 56-69

  Zhao, Bing ^a   Tan, Pauline H ^b   Li, Shawn S C ^a   Pei, Dehua ^b  

^a WESTERN UNIVERSITY   (Canada)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Cytoplasmic tyrosine kinase (CTK); OBOC; Peptide binding; Protein kinase; Src homology 2 (SH2) domain; Support vector machine (SVM)

Indexed keywords

PHOSPHOTYROSINE; PROTEIN TYROSINE KINASE;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; LIGAND BINDING; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PHOSPHORYLATION; SRC HOMOLOGY DOMAIN;

CATALYSIS; CYTOPLASM; HUMANS; MODELS, MOLECULAR; PROTEIN-TYROSINE KINASES; SRC HOMOLOGY DOMAINS; SUBSTRATE SPECIFICITY;

EID: 84877817038     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.12.021     Document Type: Article

References (65)

1. Anderson D., Koch C.A., Grey L., Ellis C., Moran M.F., Pawson T. Binding of SH2 domains of phospholipase C gamma 1, GAP, and Src to activated growth factor receptors. Science 1990, 250:979-982.
2. Fantl W.J., Johnson D.E., Williams L.T. Signalling by receptor tyrosine kinases. Annu Rev Biochem 1993, 62:453-481.
3. Manning G., Whyte D.B., Martinez R., Hunter T., Sudarsanam S. The protein kinase complement of the human genome. Science 2002, 298:1912-1934.
4. Robinson D.R., Wu Y.M., Lin S.F. The protein tyrosine kinase family of the human genome. Oncogene 2000, 19:5548-5557.
5. Lemmon M.A., Schlessinger J. Cell signaling by receptor tyrosine kinases. Cell 2010, 141:1117-1134.
6. Tsygankov A.Y. Non-receptor protein tyrosine kinases. Front Biosci 2003, 8:s595-s635.
7. Yamanashi Y., Tezuka T., Yokoyama K. Activation of receptor protein-tyrosine kinases from the cytoplasmic compartment. J Biochem 2012, 151:353-359.
8. Pawson T., Gish G.D., Nash P. SH2 domains, interaction modules and cellular wiring. Trends Cell Biol 2001, 11:504-511.
9. Liu B.A., Jablonowski K., Raina M., Arce M., Pawson T., Nash P.D. The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling. Mol Cell 2006, 22:851-868.
10. Waksman G., Kuriyan J. Structure and specificity of the SH2 domain. Cell 2004, 116:S45-S48. [3 p following S8].
11. Filippakopoulos P., Muller S., Knapp S. SH2 domains: modulators of nonreceptor tyrosine kinase activity. Curr Opin Struct Biol 2009, 19:643-649.
12. Pawson T. Protein modules and signalling networks. Nature 1995, 373:573-580.
13. Young M.A., Gonfloni S., Superti-Furga G., Roux B., Kuriyan J. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 2001, 105:115-126.
14. Sicheri F., Moarefi I., Kuriyan J. Crystal structure of the Src family tyrosine kinase Hck. Nature 1997, 385:602-609.
15. Sicheri F., Kuriyan J. Structures of Src-family tyrosine kinases. Curr Opin Struct Biol 1997, 7:777-785.
16. Moarefi I., LaFevreBernt M., Sicheri F., Huse M., Lee C.H., Kuriyan J., et al. Activation of the Src-family tyrosine kinase Hck by SH3 domain displacement. Nature 1997, 385:650-653.
17. Levinson N.M., Seeliger M.A., Cole P.A., Kuriyan J. Structural basis for the recognition of c-Src by its inactivator Csk. Cell 2008, 134:124-134.
18. Roskoski R. Src protein-tyrosine kinase structure and regulation. Biochem Biophys Res Commun 2004, 324:1155-1164.
19. Huang H., Li L., Wu C., Schibli D., Colwill K., Ma S., et al. Defining the specificity space of the human SRC homology 2 domain. Mol Cell Proteomics 2008, 7:768-784.
20. Kreegipuu A., Blom N., Brunak S., Jarv J. Statistical analysis of protein kinase specificity determinants. FEBS Lett 1998, 430:45-50.
21. Jin J., Xie X.Y., Chen C., Park J.G., Stark C., James D.A., et al. Eukaryotic protein domains as functional units of cellular evolution. Sci Signal 2009, 2.
22. Songyang Z., Cantley L.C. Recognition and specificity in protein tyrosine kinase-mediated signalling. Trends Biochem Sci 1995, 20:470-475.
23. Filippakopoulos P., Kofler M., Hantschel O., Gish G.D., Grebien F., Salah E., et al. Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation. Cell 2008, 134:793-803.
24. Nagar B., Hantschel O., Seeliger M., Davies J.M., Weis W.I., Superti-Furga G., et al. Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase. Mol Cell 2006, 21:787-798.
25. Zhu G., Liu Y., Shaw S. Protein kinase specificity. A strategic collaboration between kinase peptide specificity and substrate recruitment. Cell Cycle 2005, 4:52-56.
26. Wojcik J., Hantschel O., Grebien F., Kaupe I., Bennett K.L., Barkinge J., et al. A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nat Struct Mol Biol 2010, 17:519-527.
27. Thakkar A., Cohen A.S., Connolly M.D., Zuckermann R.N., Pei D. High-throughput sequencing of peptoids and peptide-peptoid hybrids by partial edman degradation and mass spectrometry. J Comb Chem 2009, 11:294-302.
28. Liu T., Qian Z., Xiao Q., Pei D. High-throughput screening of one-bead-one-compound libraries: identification of cyclic peptidyl inhibitors against calcineurin/NFAT interaction. ACS Comb Sci 2011, 13:537-546.
29. Wavreille A.S., Garaud M., Zhang Y., Pei D. Defining SH2 domain and PTP specificity by screening combinatorial peptide libraries. Methods 2007, 42:207-219.
30. Thakkar A., Wavreille A.S., Pei D. Traceless capping agent for peptide sequencing by partial edman degradation and mass spectrometry. Anal Chem 2006, 78:5935-5939.
31. Ren L., Chen X., Luechapanichkul R., Selner N.G., Meyer T.M., Wavreille A.S., et al. Substrate specificity of protein tyrosine phosphatases 1B, RPTPalpha, SHP-1, and SHP-2. Biochemistry 2011, 50:2339-2356.
32. Cristianini N., Shawe-Taylor J. An introduction to support vector machines: and other kernel-based learning methods 2000, Cambridge University Press, Cambridge; New York.
33. Cortes C., Vapnik V. Support-vector networks. Mach Learn 1995, 20:273-297.
34. Zhao Y., Pinilla C., Valmori D., Martin R., Simon R. Application of support vector machines for T-cell epitopes prediction. Bioinformatics 2003, 19:1978-1984.
35. Siepen J.A., Radford S.E., Westhead D.R. Beta edge strands in protein structure prediction and aggregation. Protein Sci 2003, 12:2348-2359.
36. Qian J., Lin J., Luscombe N.M., Yu H., Gerstein M. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics 2003, 19:1917-1926.
37. Brown M.P., Grundy W.N., Lin D., Cristianini N., Sugnet C.W., Furey T.S., et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A 2000, 97:262-267.
38. Xu H., Lemischka I.R., Ma'ayan A. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol 2010, 4:173.
39. Hornbeck P.V., Chabra I., Kornhauser J.M., Skrzypek E., Zhang B. PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 2004, 4:1551-1561.
40. Hornbeck P.V., Kornhauser J.M., Tkachev S., Zhang B., Skrzypek E., Murray B., et al. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res 2012, 40:D261-D270.
41. Dinkel H., Chica C., Via A., Gould C.M., Jensen L.J., Gibson T.J., et al. Phospho.ELM: a database of phosphorylation sites - update 2011. Nucleic Acids Res Jan. 2011, 39(Database issue):D261-D267.
42. Lam K.S., Salmon S.E., Hersh E.M., Hruby V.J., Kazmierski W.M., Knapp R.J. A new type of synthetic peptide library for identifying ligand-binding activity. Nature 1991, 354:82-84.
43. Houghten R.A., Pinilla C., Blondelle S.E., Appel J.R., Dooley C.T., Cuervo J.H. Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature 1991, 354:84-86.
44. Chang C.C., Lin C.J. LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol 2011, 2(27):1-27. [27].
45. Sarojini B., Ramaraj N., Nickolas S. Enhancing the performance of LibSVM classifier by kernel F-score feature selection. Commun Comput Inf Sci 2009, 40:533-543.
46. Schones D.E., Sumazin P., Zhang M.Q. Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics 2005, 21:307-313.
47. Kielbasa S.M., Gonze D., Herzel H. Measuring similarities between transcription factor binding sites. BMC Bioinformatics 2005, 6:237.
48. Fleiss J.L., Levin B.A., Paik M.C. Statistical methods for rates and proportions 2003, J. Wiley, Hoboken, N.J. 3rd ed.
49. Magrane M., Consortium U. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011, 2011:bar009.
50. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
51. Lam K.S., Liu R.W., Miyamoto S., Lehman A.L., Tuscano J.M. Applications of one-bead one-compound combinatorial libraries and chemical microarrays in signal transduction research. Acc Chem Res 2003, 36:370-377.
52. Schneider T.D., Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18:6097-6100.
53. Songyang Z., Shoelson S.E., McGlade J., Olivier P., Pawson T., Bustelo X.R., et al. Specific motifs recognized by the SH2 domains of Csk, 3BP2, fps/fes, GRB-2, HCP, SHC, Syk, and Vav. Mol Cell Biol 1994, 14:2777-2785.
54. Li L., Zhao B., Du J., Zhang K., Ling C.X., Li S.S. DomPep - a general method for predicting modular domain-mediated protein-protein interactions. PLoS One 2011, 6:e25528.
55. Malek S.N., Desiderio S. SH2 domains of the protein-tyrosine kinases Blk, Lyn, and Fyn(T) bind distinct sets of phosphoproteins from B lymphocytes. J Biol Chem 1993, 268:22557-22565.
56. Sada K., Takano T., Yanagi S., Yamamura H. Structure and function of Syk protein-tyrosine kinase. J Biochem 2001, 130:177-186.
57. Hubbard S.R., Till J.H. Protein tyrosine kinase structure and function. Annu Rev Biochem 2000, 69:373-398.
58. Musgrave I.F. Structure and function of protein kinases and protein phosphatases. IDrugs 1998, 1:617-619.
59. Bialik S., Kimchi A. The death-associated protein kinases: structure, function, and beyond. Annu Rev Biochem 2006, 75:189-210.
60. Lee C.C., Jia Y., Li N., Sun X., Ng K., Ambing E., et al. Crystal structure of the ALK (anaplastic lymphoma kinase) catalytic domain. Biochem J 2010, 430:425-437.
61. Liu B.A., Jablonowski K., Shah E.E., Engelmann B.W., Jones R.B., Nash P.D. SH2 domains recognize contextual peptide sequence information to determine selectivity. Mol Cell Proteomics 2010, 9:2391-2404.
62. Brinkworth R.I., Breinl R.A., Kobe B. Structural basis and prediction of substrate specificity in protein serine/threonine kinases. Proc Natl Acad Sci U S A 2003, 100:74-79.
63. Eo H.S., Kim S., Koo H., Kim W. A machine learning based method for the prediction of G protein-coupled receptor-binding PDZ domain proteins. Mol Cells 2009, 27:629-634.
64. Hui S., Bader G.D. Proteome scanning to predict PDZ domain interactions using support vector machines. BMC Bioinformatics 2010, 11:507.
65. Lathrop J.T., Hammond D. The Bead blot: a method for selecting small molecule ligands for protein capture and purification. Nat Protoc 2007, 2:3102-3110.