Yeast two-hybrid junk sequences contain selected linear motifs

Nucleic Acids Research

Volumn 39, Issue 19, 2011, Pages

  Liu, Yun ^a   Woods, Nicholas T ^b   Kim, Dewey ^a   Sweet, Michael ^b   Monteiro, Alvaro N A ^b   Karchin, Rachel ^a  

^a Johns Hopkins University   (United States)

^b H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 ASSOCIATED RING DOMAIN PROTEIN 1; BRCA1 PROTEIN; ECT2 PROTEIN; GENE PRODUCT; LIG4 PROTEIN; MDC1 PROTEIN; PA2G4 PROTEIN; PAXIP1 PROTEIN; RNA BINDING PROTEIN; TP53BP1 PROTEIN; UNCLASSIFIED DRUG; PEPTIDE;

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CLONE; HUMAN; MATHEMATICAL MODEL; MONTE CARLO METHOD; OUT OF FRAME CLONE; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; SCREENING; SHORT LINEAR MOTIF; TEIRESIAS METHOD; TWO HYBRID SYSTEM; YEAST; CHEMISTRY; COMPUTER PROGRAM; GENETICS; PROTEIN DOMAIN; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; VALIDATION STUDY;

AMINO ACID MOTIFS; HUMANS; PEPTIDES; PROTEIN INTERACTION DOMAINS AND MOTIFS; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 80455129692     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr600     Document Type: Article

References (32)

1. Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature, 340, 245-246.
2. Vidalain, P.-O., Boxem, M., Ge, H., Li, S. and Vidal, M. (2004) Increasing specificity in high-throughput yeast two-hybrid experiments. Methods, 32, 363-370.
3. Pawson, T. and Nash, P. (2003) Assembly of cell regulatory systems through protein interaction domains. Science, 300, 445-452.
4. Pawson, T. (1995) Protein modules and signalling networks. Nature, 373, 573-580.
5. Yaffe, M.B., Leparc, G.G., Lai, J., Obata, T., Volinia, S. and Cantley, L.C. (2001) A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nat. Biotechnol., 19, 348-353.
6. Neduva, V., Linding, R., Su-Angrand, I., Stark, A., de Masi, F., Gibson, T.J., Lewis, J., Serrano, L. and Russell, R.B. (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol., 3, e405.
7. Neduva, V. and Russell, R.B. (2005) Linear motifs: evolutionary interaction switches. FEBS Lett., 579, 3342-3345.
8. Zarrinpar, A., Park, S.-H. and Lim, W.A. (2003) Optimization of specificity in a cellular protein interaction network by negative selection. Nature, 426, 676-680.
9. Fuxreiter, M., Tompa, P. and Simon, I. (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics, 23, 950-956.
10. Hugo, W., Song, F., Aung, Z., Ng, S.-K. and Sung, W.-K. (2010) SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank. Bioinformatics, 26, 1036-1042.
11. Rigoutsos, I. and Floratos, A. (1998) Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics, 14, 55-67.
12. Edwards, R.J., Davey, N.E. and Shields, D.C. (2007) SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE, 2, e967.
13. Frith, M.C., Saunders, N.F.W., Kobe, B. and Bailey, T.L. (2008) Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol., 4, e1000071.
14. La, D. and Livesay, D.R. (2005) MINER: software for phylogenetic motif identification. Nucleic Acids Res., 33, W267-W270.
15. Tan, S.-H., Hugo, W., Sung, W.-K. and Ng, S.-K. (2006) A correlated motif approach for finding short linear motifs from protein interaction networks. BMC Bioinformatics, 7, 502.
16. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
17. Rodriguez, M., Yu, X., Chen, J. and Songyang, Z. (2003) Phosphopeptide binding specificities of BRCA1 COOH-terminal (BRCT) domains. J. Biol. Chem., 278, 52914-52918.
18. Burkard, M.E., Maciejowski, J., Rodriguez-Bravo, V., Repka, M., Lowery, D.M., Clauser, K.R., Zhang, C., Shokat, K.M., Carr, S.A., Yaffe, M.B. et al. (2009) Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells. PLoS Biol., 7, e1000111.
19. Manke, I.A., Lowery, D.M., Nguyen, A. and Yaffe, M.B. (2003) BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science, 302, 636-639.
20. Altschul, S.F., Madden, T.L., Schiffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
21. Squatrito, M., Mancino, M., Donzelli, M., Areces, L.B. and Draetta, G.F. (2004) EBP1 is a nucleolar growth-regulating protein that is part of pre-ribosomal ribonucleoprotein complexes. Oncogene, 23, 4454-4465.
22. Zhang, Y. and Hamburger, A.W. (2005) Specificity and heregulin regulation of Ebp1 (ErbB3 binding protein 1) mediated repression of androgen receptor signalling. Br. J. Cancer, 92, 140-146.
23. Kowalinski, E., Bange, G., Bradatsch, B., Hurt, E., Wild, K. and Sinning, I. (2007) The crystal structure of Ebp1 reveals a methionine aminopeptidase fold as binding platform for multiple interactions. FEBS Lett., 581, 4450-4454.
24. Wu, P.-Y., Frit, P., Meesala, S., Dauvillier, S., Modesti, M., Andres, S.N., Huang, Y., Sekiguchi, J., Calsou, P., Salles, B. et al. (2009) Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4. Mol. Cell. Biol., 29, 3163-3172.
25. Modesti, M., Junop, M.S., Ghirlando, R., van deRakt, M., Gellert, M., Yang, W. and Kanaar, R. (2003) Tetramerization and DNA ligase IV interaction of the DNA double-strand break repair protein XRCC4 are mutually exclusive. J. Mol. Biol., 334, 215-228.
26. Ohren, J.F., Chen, H., Pavlovsky, A., Whitehead, C., Zhang, E., Kuffa, P., Yan, C., McConnell, P., Spessard, C., Banotai, C. et al. (2004) Structures of human MAPKK1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition. Nat. Struct. Mol. Biol., 11, 1192-1197.
27. Liepinsh, E., Banyai, L., Pintacuda, G., Trexler, M., Patthy, L. and Otting, G. (2003) NMR structure of the netrin-like domain (NTR) of human type I procollagen C-proteinase enhancer defines structural consensus of NTR domains and assesses potential proteinase inhibitory activity and ligand binding. J. Biol. Chem., 278, 25982-25989.
28. Sim, L., Willemsma, C., Mohan, S., Naim, H.Y., Pinto, B.M. and Rose, D.R. (2010) Structural basis for substrate selectivity in human maltase-glucoamylase and sucrase-isomaltase N-terminal domains. J. Biol. Chem., 285, 17763-17770.
29. Karlin, S. and Altschul, S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
30. Coleman, T. and Li, Y. (1994) On the convergence of reflective newton methods for large-scale nonlinear minimization subject to bounds. Math. Progr., 67, 189-224.
31. Coleman, T. and Li, Y. (1996) An interior, trust region approach for nonlinear minimization subject to bounds. SIAM J. Optimiz., 6, 418-445.
32. Gould, C.M., Diella, F., Via, A., Puntervoll, P., Gemnd, C., Chabanis-Davidson, S., Michael, S., Sayadi, A., Bryne, J.C., Chica, C. et al. (2010) ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res., 38, D167-D180.