Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction

PLoS Computational Biology

Volumn 11, Issue 9, 2015, Pages

  Hu, Jianfei ^a   Neiswinger, Johnathan ^a   Zhang, Jin ^a,b   Zhu, Heng ^a,b   Qian, Jiang ^a,b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGES; PROTEINS; SCAFFOLDS (BIOLOGY);

COMPUTATIONAL PREDICTIONS; DESIGN PRINCIPLES; KINASE SUBSTRATES; PROTEIN KINASE; PROTEIN-PROTEIN INTERACTIONS; RELATIONSHIP NETWORKS; SCAFFOLD PROTEIN; SIGNALING COMPONENTS; SIGNALLING PATHWAYS; SYSTEMATIC ANALYSIS;

SIGNAL TRANSDUCTION;

HETERODIMER; HOMODIMER; PHOSPHOTRANSFERASE; PROTEOME; SCAFFOLD PROTEIN; PROTEIN;

ARTICLE; CONTROLLED STUDY; ENZYME SUBSTRATE; PREDICTION; PROTEIN MICROARRAY; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; VALIDATION PROCESS; BIOLOGICAL MODEL; BIOLOGY; HUMAN; METABOLISM; PHOSPHORYLATION; PHYSIOLOGY; PROCEDURES;

COMPUTATIONAL BIOLOGY; HUMANS; MODELS, BIOLOGICAL; PHOSPHORYLATION; PROTEIN INTERACTION MAPS; PROTEINS; SIGNAL TRANSDUCTION;

EID: 84943538118     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004508     Document Type: Article

References (40)

1. Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jorgensen C, et al. (2007) Systematic discovery of in vivo phosphorylation networks. Cell 129: 1415–1426. 17570479
2. Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, et al. (2009) Functional organization of the S. cerevisiae phosphorylation network. Cell 136: 952–963. doi: 10.1016/j.cell.2008.12.039 19269370
3. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, et al. (2013) Construction of human activity-based phosphorylation networks. Mol Syst Biol 9: 655. doi: 10.1038/msb.2013.12 23549483
4. Hu J, Rho HS, Newman RH, Hwang W, Neiswinger J, et al. (2014) Global analysis of phosphorylation networks in humans. Biochim Biophys Acta 1844: 224–231. doi: 10.1016/j.bbapap.2013.03.009 23524292
5. Hu J, Rho HS, Newman RH, Zhang J, Zhu H, et al. (2014) PhosphoNetworks: a database for human phosphorylation networks. Bioinformatics 30: 141–142. doi: 10.1093/bioinformatics/btt627 24227675
6. Barford D, Das AK, Egloff MP, (1998) The structure and mechanism of protein phosphatases: insights into catalysis and regulation. Annu Rev Biophys Biomol Struct 27: 133–164. 9646865
7. Cole PA, Shen K, Qiao Y, Wang D, (2003) Protein tyrosine kinases Src and Csk: a tail's tale. Curr Opin Chem Biol 7: 580–585. 14580561
8. Shaw AS, Filbert EL, (2009) Scaffold proteins and immune-cell signalling. Nat Rev Immunol 9: 47–56. doi: 10.1038/nri2473 19104498
9. Bhattacharyya RP, Remenyi A, Yeh BJ, Lim WA, (2006) Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 75: 655–680. 16756506
10. Burack WR, Shaw AS, (2000) Signal transduction: hanging on a scaffold. Curr Opin Cell Biol 12: 211–216. 10712921
11. Ferrell JE, Jr. (2000) What do scaffold proteins really do? Sci STKE 2000: pe1.
12. Good MC, Zalatan JG, Lim WA, (2011) Scaffold proteins: hubs for controlling the flow of cellular information. Science 332: 680–686. doi: 10.1126/science.1198701 21551057
13. Zeke A, Lukacs M, Lim WA, Remenyi A, (2009) Scaffolds: interaction platforms for cellular signalling circuits. Trends Cell Biol 19: 364–374. doi: 10.1016/j.tcb.2009.05.007 19651513
14. Levchenko A, Bruck J, Sternberg PW, (2000) Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc Natl Acad Sci U S A 97: 5818–5823. 10823939
15. Bhattacharyya RP, Remenyi A, Good MC, Bashor CJ, Falick AM, et al. (2006) The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway. Science 311: 822–826. 16424299
16. Choi KY, Satterberg B, Lyons DM, Elion EA, (1994) Ste5 tethers multiple protein kinases in the MAP kinase cascade required for mating in S. cerevisiae. Cell 78: 499–512. 8062390
17. Hu J, Wan J, Hackler L, JrZack DJ, Qian J, (2010) Computational analysis of tissue-specific gene networks: application to murine retinal functional studies. Bioinformatics 26: 2289–2297. doi: 10.1093/bioinformatics/btq408 20616386
18. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824–827. 12399590
19. Alon U, (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450–461. 17510665
20. Buday L, Tompa P, (2010) Functional classification of scaffold proteins and related molecules. FEBS J 277: 4348–4355. doi: 10.1111/j.1742-4658.2010.07864.x 20883491
21. Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, et al. (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 36: W423–426. doi: 10.1093/nar/gkn282 18477636
22. Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, et al. (2012) Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics 11: O111 016253. doi: 10.1074/mcp.O111.016253 22307071
23. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, et al. (2014) Pfam: the protein families database. Nucleic Acids Res 42: D222–230. doi: 10.1093/nar/gkt1223 24288371
24. Songyang Z, Shoelson SE, Chaudhuri M, Gish G, Pawson T, et al. (1993) SH2 domains recognize specific phosphopeptide sequences. Cell 72: 767–778. 7680959
25. Marshall CJ, (1995) Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80: 179–185. 7834738
26. Posas F, Takekawa M, Saito H, (1998) Signal transduction by MAP kinase cascades in budding yeast. Curr Opin Microbiol 1: 175–182. 10066475
27. Karandikar M, Xu S, Cobb MH, (2000) MEKK1 binds raf-1 and the ERK2 cascade components. J Biol Chem 275: 40120–40127. 10969079
28. Chandramouli K, Unciuleac MC, Naik S, Dean DR, Huynh BH, et al. (2007) Formation and properties of [4Fe-4S] clusters on the IscU scaffold protein. Biochemistry 46: 6804–6811. 17506525
29. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, et al. (2012) Landscape of transcription in human cells. Nature 489: 101–108. doi: 10.1038/nature11233 22955620
30. Jones DH, Ley S, Aitken A, (1995) Isoforms of 14-3-3 protein can form homo- and heterodimers in vivo and in vitro: implications for function as adapter proteins. FEBS Lett 368: 55–58. 7615088
31. Yablonski D, Marbach I, Levitzki A, (1996) Dimerization of Ste5, a mitogen-activated protein kinase cascade scaffold protein, is required for signal transduction. Proc Natl Acad Sci U S A 93: 13864–13869. 8943027
32. Latour S, Veillette A, (2001) Proximal protein tyrosine kinases in immunoreceptor signaling. Curr Opin Immunol 13: 299–306. 11406361
33. Soriano P, (1994) Abnormal kidney development and hematological disorders in PDGF beta-receptor mutant mice. Genes Dev 8: 1888–1896. 7958864
34. Heinrich MC, Corless CL, Duensing A, McGreevey L, Chen CJ, et al. (2003) PDGFRA activating mutations in gastrointestinal stromal tumors. Science 299: 708–710. 12522257
35. Hoch RV, Soriano P, (2003) Roles of PDGF in animal development. Development 130: 4769–4784. 12952899
36. Dowler S, Montalvo L, Cantrell D, Morrice N, Alessi DR, (2000) Phosphoinositide 3-kinase-dependent phosphorylation of the dual adaptor for phosphotyrosine and 3-phosphoinositides by the Src family of tyrosine kinase. Biochem J 349: 605–610. 10880360
37. Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, et al. (2010) A human MAP kinase interactome. Nat Methods 7: 801–805. 20936779
38. Franciosa PG, Frigioni D, Giaccio R, (2001) Semi-dynamic breadth-first search in digraphs. Theoretical Computer Science 250: 201–217.
39. Robert T, (1972) Depth-First Search and Linear Graph Algorithms. SIAM Journal on Computing 1: 146–160.
40. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. JR Statist Soc B 57: 289–300.