Synthetic peptide arrays for investigating protein interaction domains

FEBS Letters

Volumn 586, Issue 17, 2012, Pages 2780-2786

  Volkmer, Rudolf ^a   Tapia, Victor ^a   Landgraf, Christiane ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

PDZ domains; Peptide arrays; Protein interaction domains; SH3 domains; SPOT synthesis; WW domains

Indexed keywords

CELLULOSE;

BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; EUKARYOTE; NONHUMAN; PDZ DOMAIN; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MICROARRAY; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REVIEW; SH3 DOMAIN; STRUCTURE ANALYSIS; WW DOMAIN; YEAST;

ANIMALS; BIOCHEMISTRY; CELLULOSE; EQUIPMENT DESIGN; FUNGAL PROTEINS; HUMANS; PEPTIDE LIBRARY; PEPTIDES; PROTEIN ARRAY ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY;

EUKARYOTA;

EID: 84864628803     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.04.028     Document Type: Review

References (83)

1. M. Sudol From Src Homology domains to other signaling modules: proposal of the protein recognition code Oncogene 17 1998 1469 1474
2. D.B. Searls Linguistic approaches to biological sequences Comput. Appl. Biosci. 13 1997 333 344
3. D.B. Searls The language of genes Nature 420 2002 211 217
4. E. Phizicky, P.I.H. Bastiaens, H. Zhu, M. Snyder, and S. Fields Protein analysis on a proteomic scale Nature 422 2003 208 215
5. J.M. Smith Natural selection and the concept of a protein space Nature 225 1970 563 564
6. F. Jacob The Possible and the Actual (Jessie and John Danz Lectures) 1994 University of Washington Press Washington
7. O. Lichtarge, H.R. Bourne, and F.E. Cohen An evolutionary trace method defines binding surfaces common to protein families J. Mol. Biol. 257 1996 342 358
8. M. Gimona Protein linguistics - a grammar for modular protein assembly? Nat. Rev. Mol. Cell Biol. 7 2006 68 73
9. S. Fields, and O. Song A novel genetic system to detect protein-protein interactions Nature 340 1989 245 246
10. P. Uetz A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 403 2000 623 627
11. T. Ito A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc. Natl. Acad. Sci. USA 98 2001 4569 4574
12. A.C. Gavin Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 415 2002 141 147
13. Y. Ho Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 415 2002 180 183
14. E. Santonico, L. Castagnoli, and G. Cesareni Methods to reveal domain networks Drug Discov. Today 10 2005 1111 1117
15. S.H. Yook Functional and topological characterization of protein interaction networks Proteomics 4 2004 928 942
16. S. Das, and T.F. Smith Identifying nature's protein Lego set Adv. Protein Chem. 54 2000 159 183
17. L. Holm, and C. Sander Dictionary of recurrent domains in protein structures Proteins 33 1998 88 96
18. T. Pawson, and P. Nash Assembly of cell regulatory systems through protein interaction domains Science 300 2003 445 452
19. P. Bork, J. Schultz, and C.P. Ponting Cytoplasmic signalling domains: the next generation Trends Biochem. Sci. 22 1997 296 298
20. G. Cesareni Modular Protein Domains 2004 Wiley-VCH Verlags GmbH & KGaA Weinheim
21. S. Jones, and J.M. Thorton Principles of protein-protein interactions Proc. Natl. Acad. Sci. USA 93 1996 13 20
22. B. Ma, T. Elkayam, H. Wolfson, and R. Nussinov Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces Proc. Natl. Acad. Sci. USA 100 2003 5772 5777
23. U. Reineke, A. Kramer, and J. Schneider-Mergener Antigen sequence- and library-based mapping of linear and discontinuous protein-protein-interaction sites by spot synthesis Curr. Top. Microbiol. Immunol. 243 1999 23 36
24. A.A. Bogan, and K.S. Thorn Anatomy of hot spots in protein interfaces J. Mol. Biol. 280 1998 1 9
25. T. Clackson, and J.A. Wells A hot spot of binding energy in a hormone-receptor interface Science 267 1995 383 386
26. M. Sudol, H.I. Chen, C. Bougeret, A. Einbond, and P. Bork Characterization of a novel protein-binding module - the WW domain FEBS Lett. 369 1995 67 71
27. Z. Fidan, A. Younis, P. Schmieder, and R. Volkmer Chemical synthesis of the third WW domain of TCERG 1 by native chemical ligation J. Pept. Sci. 17 2011 644 649
28. A.B. Sparks, L.A. Quilliam, J.M. Thorn, C.J. Der, and B.K. Kay Identification and characterization of Src SH3 ligands from phage-displayed random peptide libraries J. Biol. Chem. 269 1994 23853 23856
29. R.J. Rickles Identification of Src, Fyn, Lyn, PI3K and Abl SH3 domain ligands using phage display libraries EMBO J. 13 1994 5598 5604
30. H. Huang, and S.S. Sidhu Studying binding specificities of peptide recognition modules by high-throughput phage display selections Methods Mol. Biol. 781 2011 87 97
31. R. Tonikian A specificity map for the PDZ domain family PLoS Biol. 6 2008 E239
32. A.H. Tong A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules Science 295 2002 321 324
33. C. Landgraf Protein interaction networks by proteome peptide scanning PLoS Biol. 2 2004 E14
34. G. MacBeath, and S.L. Schreiber Printing proteins as microarrays for high-throughput function determination Science 289 2000 1760 1763
35. H. Zhu Global analysis of protein activities using proteome chips Science 293 2001 2101 2105
36. R. Frank SPOT-synthesis: an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support Tetrahedron 48 1992 9217 9232
37. S.P. Fodor, J.L. Read, M.C. Pirrung, L. Stryer, A.T. Lu, and D. Solas Light-directed, spatially addressable parallel chemical synthesis Science 251 1991 767 773
38. Frank, R. and Schneider-Mergener, J. (2002) in: Peptide arrays on membrane supports - synthesis and applications. (Koch, J. and Mahler, M., Eds.), pp. 1-22. Springer Verlag, Heidelberg.
39. R. Volkmer Synthesis and application of peptide arrays: Quo vadis SPOT technology ChemBioChem 10 2009 1431 1442
40. V. Tapia, B. Ay, J. Triebus, E. Wolter, P. Boisguerin, and R. Volkmer Evaluating the coupling efficiency of phosphorylated amino acids for SPOT synthesis J. Pept. Sci. 14 2008 1309 1314
41. P. Rathert Protein lysine methyltransferase G9a acts on non-histone targets Nat. Chem. Biol. 6 2008 344 346
42. P. Filippakopoulos Histone recognition and large-scale structural analysis of the human bromodomain family Cell 149 2012 214 231
43. B. Hoffmann, T. Ast, T. Polakowski, U. Reineke, and R. Volkmer Transformation of a biologically active peptide into peptoid analogs while retaining biological activity Protein Pept. Lett. 13 2006 829 833
44. N. Heine Synthesis and screening of peptoid arrays on cellulose membranes Tetrahedron 59 2003 9919 9930
45. D. Scharn, H. Wenschuh, U. Reineke, J. Schneider-Mergener, and L. Germeroth Spatially addressed synthesis of amino- and amino-oxy-substituted 1,3,5-triazine arrays on polymeric membranes J. Comb. Chem. 2 2000 361 369
46. C.C. Mahrenholz, V. Tapia, R.D. Stigler, and R. Volkmer A study to assess the cross-reactivity of cellulose membrane-bound peptides with detection systems: an analysis at the amino acid level J. Pept. Sci. 16 2010 297 302
47. D.F. Winkler, and P.L. McGeer Protein labeling and biotinylation of peptides during spot synthesis using biotin p-nitrophenyl ester (biotin-ONp) Proteomics 8 2008 961 967
48. B. Ay Sorting and pooling strategy: a novel tool to map a virus proteome for CD8 T-cell epitopes Biopolymers 88 2007 64 75
49. T. Kamradt, and R. Volkmer-Engert Cross-reactivity of T lymphocytes in infection and autoimmunity Mol. Divers. 8 2004 271 280
50. V.E. Tapia Y65C missense mutation in the WW domain of the Golabi-Ito-Hall syndrome protein PQBP1 affects its binding activity and deregulates pre-mRNA splicing J. Biol. Chem. 285 2010 19391 19401
51. H. Hu A map of WW domain family interactions Proteomics 4 2004 643 655
52. P. Boisguerin An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for PDZ domain binding studies Chem. Biol. 11 2004 449 459
53. H.M. Geysen, R.H. Meloen, and S.J. Barteling Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid Proc. Natl. Acad. Sci. USA 81 1984 3998 4002
54. H. Rottensteiner Peroxisomal membrane proteins contain common Pex19p-binding sites that are an integral part of their targeting signals Mol. Biol. Cell 15 2004 3406 3417
55. B.C. Cunningham, and J.A. Wells High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis Science 244 1989 1081 1085
56. G.B. Bolger Scanning peptide array analyses identify overlapping binding sites for the signalling scaffold proteins, beta-arrestin and RACK1, in cAMP-specific phosphodiesterase PDE4D5 Biochemical J. 398 2006 23 36
57. Reineke, U., Schneider-Mergener, J. and Schutkowski, M. (2005) Peptide arrays in proteomics and drug discovery in: BioMEMS and Biomedical Nanotechnology, Micro and Nano-technologies for Genomics and Proteomics, vol. II (Ozkan, M. and Heller, M.J., Eds.), pp. 161-282, Springer, New York.
58. M. Portwich A network of coiled-coil associations derived from synthetic GCN4 leucine-zipper arrays Angew. Chem. Int. Ed. 46 2007 1654 1657
59. L. Vouilleme, P.R. Cushing, R. Volkmer, D.R. Madden, and P. Boisguerin Engineering peptide inhibitors to overcome PDZ binding promiscuity Angew. Chem. Int. Ed. 49 2010 9912 9916
60. M. Takahashi, A. Ueno, and H. Mihara Peptide design based on an antibody complementarity determining region (CDR): construction of porphyrin-binding peptides and their affinity maturation by a combinatorial method Chem. Eur. J. 6 2000 3196 3203
61. A. Kramer Spot synthesis: observations and optimizations J. Pept. Res. 54 1999 319 327
62. H. Wenschuh Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides Biopolymers 55 2000 188 206
63. F. Molina, D. Laune, C. Gougat, B. Pau, and C. Granier Improved performances of spot multiple peptide synthesis Peptide Res. 9 1996 151 155
64. J. Przezdziak Probing the ligand binding specificity and analyzing the folding state of SPOT synthesized FBP28 WW domain variants ChemBioChem 7 2006 780 788
65. R. Tonikian Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins PLoS Biol. 7 2009 E1000218
66. A.A. Weiser SPOT synthesis: reliability of array-based measurement of peptide binding affinity Anal. Biochem. 342 2005 300 311
67. R.B. Jones, A. Gordus, J.A. Krall, and G. MacBeath A quantitative protein interaction network for the ErbB receptors using protein microarrays Nature 439 2006 168 174
68. R. Volkmer-Engert, B. Hoffman, and J. Schneider-Mergener Stable attachment of the HMB-linker to continuous cellulose membranes for parallel solid phase spot synthesis Tetrahedron Lett. 38 1997 1029 1032
69. A. Schell-Steven Identification of a novel, intraperoxisomal Pex14-binding bite in Pex13: Association of Pex13 with the docking complex is essential for peroxisomal matrix protein import Mol. Cell. Biol. 25 2005 3007 3018
70. J.R. Pires The ScPex13p SH3 domain exposes two distinct binding sites for Pex5p and Pex14p J. Mol. Biol. 326 2003 1427 1435
71. A. Dürauer Evaluation of a sensitive detection method for peptide arrays prepared by SPOT synthesis J. Biochem. Biophys. Methods 66 2006 45 57
72. R. Gail, R. Frank, and A. Wittinghofer Systematic peptide array-based delineation of the differential beta-catenin interaction with Tcf4, E-cadherin, and adenomatous polyposis coli J. Biol. Chem. 280 2005 7107 7117
73. L. Otvos Jr. In situ stimulation of a T helper cell hybridoma with a cellulose-bound peptide antigen J. Immunol. Methods 233 2000 95 105
74. Q. Lin, J.C. O'Neill, and H.E. Blackwell Small molecule macroarray construction via Ugi four-component reactions Org. Lett. 7 2005 4455 4458
75. P. Boisguerin Characterization of a putative phosphorylation switch: adaptation of SPOT synthesis to analyze PDZ domain regulation mechanisms ChemBioChem 8 2007 2302 2307
76. K. Licha Highly parallel nano-synthesis of cleavable peptide-dye conjugates on cellulose membranes Tetrahedon Lett. 41 2000 1711 1715
77. P.R. Cushing, L. Vouilleme, M. Pellegrini, P. Boisguerin, and D.R. Madden A stabilizing influence: CAL PDZ inhibition extends the half-life of ΔF508-CFTR Angew. Chem. Int. Ed. 49 2010 9907 9911
78. U. Beutling, K. Städing, T. Stradal, and R. Frank Large-scale analysis of protein-protein interactions using cellulose-bound peptide arrays Adv. Biochem. Eng./Biotechnol. 110 2008 115 152
79. G. Henderson, and M. Bradley Functional peptide arrays for high-throughput chemical biology based applications Curr. Opin. Biotechnol. 18 2007 326 330
80. V.E. Tapia, B. Ay, and R. Volkmer Exploring and profiling protein function with peptide arrays Methods Mol. Biol. 570 2009 3 17
81. U. Reimer, U. Reineke, and J. Schneider-Mergener Peptide arrays: from macro to micro Curr. Opin. Biotechnol. 13 2002 315 320
82. M. Carducci The protein interaction network mediated by human SH3 domains Biotechnol. Adv. 30 2012 4 15
83. V. Stadler Combinatorial synthesis of peptide arrays with a laser printer Angew. Chem. Int. Ed. 47 2008 7132 7135