Linear motifs: Evolutionary interaction switches

FEBS Letters

Volumn 579, Issue 15, 2005, Pages 3342-3345

  Neduva, Victor ^a   Russell, Robert B ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Binding motifs; Motif conservation; Protein evolution; Protein ligand interaction

Indexed keywords

AMINO ACID; NUCLEIC ACID;

AMINO ACID SEQUENCE; BINDING AFFINITY; EVOLUTION; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SHORT SURVEY; STRUCTURE ANALYSIS;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACIDS;

EID: 20444414545     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.04.005     Document Type: Short Survey

References (39)

1. A. Bateman The Pfam protein families database Nucleic Acids Res. 30 1 2002 276 280
2. T.J. Gibson, and J. Spring Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins Trends Genet. 14 2 1998 46 49 Discussion 49-50
3. H.J. Dyson, and P.E. Wright Intrinsically unstructured proteins and their functions Nat. Rev. Mol. Cell. Biol. 6 3 2005 197 208
4. P. Puntervoll ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins Nucleic Acids Res. 31 13 2003 3625 3630
5. M.B. Yaffe Phosphotyrosine-binding domains in signal transduction Nat. Rev. Mol. Cell. Biol. 3 3 2002 177 186
6. C. Harter, and F. Wieland The secretory pathway: mechanisms of protein sorting and transport Biochim. Biophys. Acta 1286 2 1996 75 93
7. B. Mayer SH3 domains: complexity in moderation J. Cell Sci. 114 7 2001 1253 1263
8. C.P. Ponting, and R.R Russell The natural history of protein domains Annu. Rev. Biophys. Biomol. Struct. 31 2002 45 71
9. S.F. Altschul Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 17 1997 3389 3402
10. S.R. Eddy Profile hidden Markov models Bioinformatics 14 9 1998 755 763
11. D.G. Higgins, J.D. Thompson, and T.J. Gibson Using CLUSTAL for multiple sequence alignments Meth. Enzymol. 266 1996 383 402
12. R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 5 2004 1792 1797
13. I. Letunic Recent improvements to the SMART domain-based sequence annotation resource Nucleic Acids Res. 30 1 2002 242 244
14. A. Marchler-Bauer CDD: a database of conserved domain alignments with links to domain three-dimensional structure Nucleic Acids Res. 30 1 2002 281 283
15. N.J. Mulder The InterPro Database, 2003 brings increased coverage and new features Nucleic Acids Res. 31 1 2003 315 318
16. D.D. Sabatini Mechanisms for the incorporation of proteins in membranes and organelles J. Cell Biol. 92 1 1982 1 22
17. B.D. Davis, and P.C. Tai The mechanism of protein secretion across membranes Nature 283 5746 1980 433 438
18. C. Dingwall, and R.A. Laskey Nuclear targeting sequences - a consensus? Trends Biochem. Sci. 16 12 1991 478 481
19. J.C. Semenza ERD2, a yeast gene required for the receptor-mediated retrieval of luminal ER proteins from the secretory pathway Cell 61 7 1990 1349 1357
20. C.A. Koch SH2 and SH3 domains: elements that control interactions of cytoplasmic signaling proteins Science 252 5006 1991 668 674
21. R. Ren Identification of a ten-amino acid proline-rich SH3 binding site Science 259 5098 1993 1157 1161
22. H. Yu Solution structure of the SH3 domain of Src and identification of its ligand-binding site Science 258 5088 1992 1665 1668
23. A.H. Tong A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules Science 295 5553 2002 321 324
24. C. Landgraf Protein interaction networks by proteome peptide scanning PLoS Biol. 2 1 2004 E14
25. M. Marti Targeting malaria virulence and remodeling proteins to the host erythrocyte Science 306 5703 2004 1930 1933
26. N.L. Hiller A host-targeting signal in virulence proteins reveals a secretome in malarial infection Science 306 5703 2004 1934 1937
27. J.C. Obenauer, L.C. Cantley, and M.B. Yaffe Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs Nucleic Acids Res. 31 13 2003 3635 3641
28. G. Schreiber Kinetic studies of protein-protein interactions Curr. Opin. Struct. Biol. 12 1 2002 41 47
29. J.E. Ladbury Measurement of the binding of tyrosyl phosphopeptides to SH2 domains: a reappraisal Proc. Natl. Acad. Sci. USA 92 8 1995 3199 3203
30. A. Zarrinpar, S.H. Park, and W.A. Lim Optimization of specificity in a cellular protein interaction network by negative selection Nature 426 6967 2003 676 680
31. B. Brannetti SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family J. Mol. Biol. 298 2 2000 313 328
32. K.W. Lo The 8-kDa dynein light chain binds to its targets via a conserved (K/R)XTQT motif J. Biol. Chem. 276 17 2001 14059 14066
33. J.E. Dueber Reprogramming control of an allosteric signaling switch through modular recombination Science 301 5641 2003 1904 1908
34. S.H. Park, A. Zarrinpar, and W.A. Lim Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms Science 299 5609 2003 1061 1064
35. A. Stark Identification of Drosophila MicroRNA targets PLoS Biol. 1 3 2003 E60
36. C.T. Harbison Transcriptional regulatory code of a eukaryotic genome Nature 431 7004 2004 99 104
37. L.M. Ettwiller, J. Rung, and E. Birney Discovering novel cis-regulatory motifs using functional networks Genome Res. 13 5 2003 883 895
38. B. John Human MicroRNA targets PLoS Biol. 2 11 2004 e363
39. B.P. Lewis, C.B. Burge, and D.P. Bartel Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 120 1 2005 15 20