Reverse interactomics: Decoding protein-protein interactions with combinatorial peptide libraries

Molecular BioSystems

Volumn 3, Issue 8, 2007, Pages 536-541

  Pei, Dehua ^a   Wavreille, Anne Sophie ^a,b  

^a OHIO STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34547198426     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/b706041f     Document Type: Article

References (45)

1. T. Ito T. Chiba R. Ozawa M. Yoshida M. Hattori Y. Sakaki A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc. Natl. Acad. Sci. U. S. A. 2001 98 8 4569 74
2. P. Uetz L. Giot G. Cagney T. A. Mansfield R. S. Judson J. R. Knight D. Lockshon V. Narayan M. Srinivasan P. Pochart A. Qureshi-Emili Y. Li B. Godwin D. Conover T. Kalbfleisch G. Vijayadamodar M. Yang M. Johnston S. Fields J. M. Rothberg A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000 403 6770 601 3
3. L. Giot J. S. Bader C. Brouwer A. Chaudhuri B. Kuang Y. Li Y. L. Hao C. E. Ooi B. Godwin E. Vitols G. Vijayadamodar P. Pochart H. Machineni M. Welsh Y. Kong B. Zerhusen R. Malcolm Z. Varrone A. Collis M. Minto S. Burgess L. McDaniel E. Stimpson F. Spriggs J. Williams K. Neurath N. Ioime M. Agee E. Voss K. Furtak R. Renzulli N. Aanensen S. Carrolla E. Bickelhaupt Z. Lazovatsky A. DaSilva J. Zhong C. A. Stanyon R. L. Finley, Jr. K. P. White M. Braverman T. Jarvie S. Gold M. Leach J. Knight R. A. Shimkets M. P. McKenna J. Chant J. M. Rothberg A protein interaction map of Drosophila melanogaster Science 2003 302 5651 1727 36
4. J. F. Rual K. Venkatesan T. Hao T. Hirozane-Kishikawa A. Dricot N. Li G. F. Berriz F. D. Gibbons M. Dreze N. Ayivi-Guedehoussou N. Klitgord C. Simon M. Boxem S. Milstein J. Rosenberg D. S. Goldberg L. V. Zhang S. L. Wong G. Franklin S. Li J. S. Albala J. Lim C. Fraughton E. Llamosas S. Cevik C. Bex P. Lamesch R. S. Sikorski J. Vandenhaute H. Y. Zoghbi A. Smolyar S. Bosak R. Sequerra L. Doucette-Stamm M. E. Cusick D. E. Hill F. P. Roth M. Vidal Towards a proteome-scale map of the human protein-protein interaction network Nature 2005 437 7062 1173 8
5. J. Borch T. J. Jorgensen P. Roepstorff Mass spectrometric analysis of protein interactions Curr. Opin. Chem. Biol. 2005 9 5 509 16
6. S. H. Lo Reverse interactomics: from peptides to proteins and to functions ACS Chem. Biol. 2007 2 2 93 5
7. T. Pawson P. Nash Assembly of cell regulatory systems through protein interaction domains Science 2003 300 5618 445 52
8. Z. Songyang S. E. Shoelson M. Chaudhuri G. Gish T. Pawson W. G. Haser F. King T. Roberts S. Ratnofsky R. J. Lechleider B. G. Neel R. B. Birge J. E. Fajardo M. M. Chou H. Hanafusa B. Schaffhausen L. C. Cantley SH2 domains recognize specific phosphopeptide sequences Cell 1993 72 5 767 78
9. Z. Songyang A. S. Fanning C. Fu J. Xu S. M. Marfatia A. H. Chishti A. Crompton A. C. Chan J. M. Anderson L. C. Cantley Recognition of unique carboxyl-terminal motifs by distinct PDZ domains Science 1997 275 5296 73 7
10. K. Müller F. O. Gombert U. Manning F. Grossmüller P. Graff H. Zaegel J. F. Zuber F. Freuler C. Tschopp G. Baumann Rapid identification of phosphopeptide ligands for SH2 domains. Screening of peptide libraries by fluorescence-activated bead sorting J. Biol. Chem. 1996 271 28 16500 5
11. M. Rodriguez S. S. Li J. W. Harper Z. Songyang An oriented peptide array library (OPAL) strategy to study protein-protein interactions J. Biol. Chem. 2004 279 10 8802 7
12. A. N. Bullock J. Debreczeni A. L. Amos S. Knapp B. E. Turk Structure and substrate specificity of the Pim-1 kinase J. Biol. Chem. 2005 280 50 41675 482
13. Y. Hu E. Webb J. Singh B. A. Morgan J. A. Gainor T. D. Gordon T. J. Siahaan Rapid determination of substrate specificity of Clostridium histolyticum beta-collagenase using an immobilized peptide library J. Biol. Chem. 2002 277 10 8366 71
14. U. Reineke R. Volkmer-Engert J. Schneider-Mergener Applications of peptide arrays prepared by the SPOT-technology Curr. Opin. Biotechnol. 2001 12 1 59 64
15. U. Hoffmüller M. Russwurm F. Kleinjung J. Ashurst H. Oschkinat R. Volkmer-Engert D. Koesling J. Schneider-Mergener Interaction of a PDZ protein domain with a synthetic library of all human protein C termini Angew. Chem., Int. Ed. 1999 38 13/14 2000 4
16. P. Boisguerin R. Leben B. Ay G. Radziwill K. Moelling L. Dong R. Volkmer-Engert An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for PDZ domain binding studies Chem. Biol. 2004 11 4 449 59
17. C. M. Salisbury D. J. Maly J. A. Ellman Peptide microarrays for the determination of protease substrate specificity J. Am. Chem. Soc. 2002 124 50 14868 70
18. N. Dekker R. C. Cox R. A. Kramer M. R. Egmond Substrate specificity of the integral membrane protease OmpT determined by spatially addressed peptide libraries Biochemistry 2001 40 6 1694 701
19. M. Kaup K. Dassler U. Reineke C. Weise R. Tauber H. Fuchs Processing of the human transferrin receptor at distinct positions within the stalk region by neutrophil elastase and cathepsin G Biol. Chem. 2002 383 6 1011 20
20. G. P. Smith Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface Science 1985 228 4705 1315 17
21. S. S. Sidhu W. J. Fairbrother K. Deshayes Exploring protein-protein interactions with phage display ChemBioChem 2003 4 1 14 25
22. H. Gram R. Schmitz J. F. Zuber G. Baumann Identification of phosphopeptide ligands for the Src-homology 2 (SH2) domain of Grb2 by phage display Eur. J. Biochem. 1997 246 3 633 37
23. X. You A. W. Nguyen A. Jabaiah M. A. Sheff K. S. Thorn P. S. Daugherty Intracellular protein interaction mapping with FRET hybrids Proc. Natl. Acad. Sci. U. S. A. 2006 103 49 18458 63
24. R. B. Jones A. Gordus J. A. Krall G. MacBeath A quantitative protein interaction network for ErbB receptors using protein microarrays Nature 2006 439 168 174
25. K. S. Lam S. E. Salmon E. M. Hersh V. J. Hruby W. M. Kazmierski R. J. Knapp A new type of synthetic peptide library for identifying ligand-binding activity Nature 1991 354 6348 82 4
26. J. K. Chen W. S. Lane A. W. Brauer A. Tanaka S. L. Schreiber Biased combinatorial libraries: novel ligands for the SH3 domain of phosphatidylinositol 3-kinase J. Am. Chem. Soc. 1993 115 26 12591 2
27. P. Wang G. Arabaci D. Pei Rapid sequencing of library derived peptides by partial Edman degradation and mass spectrometry J. Comb. Chem. 2001 3 3 251 4
28. M. C. Sweeney D. Pei An improved method for rapid sequencing of support-bound peptides by partial Edman degradation and mass spectrometry J. Comb. Chem. 2003 5 3 218 22
29. A. Thakkar A.-S. Wavreille D. Pei Traceless capping agent for peptide sequencing by partial Edman degradation and mass spectrometry Anal. Chem. 2006 78 16 5935 9
30. M. C. Sweeney A.-S. Wavreille J. Park J. Butchar S. Tridandapani D. Pei Decoding protein-protein interactions through combinatorial chemistry: sequence specificity of SHP-1, SHP-2, and SHIP SH2 domains Biochemistry 2005 44 45 14932 47
31. D. Imhof A.-S. Wavreille A. May M. Zacharias S. Tridandapani D. Pei Sequence specificity of SHP-1 and SHP-2 Src homology 2 domains. Critical roles of residues beyond the pY + 3 position J. Biol. Chem. 2006 281 29 20271 82
32. A.-S. Wavreille D. Pei A chemical approach to the identification of tensin-binding proteins ACS Chem. Biol. 2007 2 2 109 18
33. P. Wang I. J. Byeon H. Liao K. D. Beebe S. Yongkiettrakul D. Pei M. D. Tsai Structure and specificity of the interaction between the FHA2 domain of Rad53 and phosphotyrosyl peptides J. Mol. Biol. 2000 302 4 927 40
34. M. C. Sweeney X. Wang J. Park Y. Liu D. Pei Determination of the sequence specificity of XIAP BIR domains by screening a combinatorial peptide library Biochemistry 2006 45 49 14740 8
35. Y.-J. Hu Y. Wei Y. Zhou P. T. R. Rajagopalan D. Pei determination of substrate specificity for peptide deformylase through the screening of a combinatorial peptide library Biochemistry 1999 38 2 643 50
36. M. Garaud D. Pei Substrate profiling of protein tyrosine phosphatase PTP1B by screening a combinatorial peptide library J. Am. Chem. Soc. 2007 129 5366 5367
37. E. de Castro C. J. A. Sigrist A. Gattiker V. Bulliard P. S. Langendijk-Genevaux E. Gasteiger A. Bairoch N. Hulo ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins Nucleic Acids Res. 2006 34 W362 W365
38. M. Yaffe G. G. Leparc J. Lai T. Obata S. Volinia L. C. Cantley A motif-based profile scanning approach for genome-wide prediction of signalling pathways Nat. Biotechnol. 2001 19 4 348 53
39. J. A. Wilkins M. A. Risinger S. Lin Studies on proteins that co-purify with smooth muscle vinculin: identification of immunologically related species in focal adhesions of non-muscle and Z-lines of muscle cells J. Cell Biol. 1986 103 1483 1494
40. S. H. Lo E. Weisberg L. B. Chen Tensin: a potential link between the cytoskeleton and signal transduction Bioessays 1994 16 11 817 23
41. R. Salgia B. Brunkhorst E. Pisick J. L. Li S. H. Lo L. B. Chen J. D. Griffin Increased tyrosine phosphorylation of focal adhesion proteins in myeloid cell lines expressing p210BCR/ABL Oncogene 1995 11 6 1149 55
42. A. H. Tong B. Drees G. Nardelli G. D. Bader B. Brannetti L. Castagnoli M. Evangelista S. Ferracuti B. Nelson S. Paoluzi M. Quondam A. Zucconi C. W. Hogue S. Fields C. Boone G. Cesareni A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules Science 2002 295 5553 321 4
43. A. E. Elia L. C. Cantley M. B. Yaffe Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates Science 2003 299 5610 1228 31
44. R. P. Laura A. S. Witt H. A. Held R. Gerstner K. Deshayes M. F. Koehler K. S. Kosik S. S. Sidhu L. A. Lasky The Erbin PDZ domain binds with high affinity and specificity to the carboxyl termini of delta-catenin and ARVCF J. Biol. Chem. 2002 277 15 12906 14
45. J. Wu Q. N. Ma K. S. Lam Identifying substrate motifs of protein kinases by a random library approach Biochemistry 1994 33 49 14825 14833