Probing the chemical basis of binding activity in an SH3 domain by protein signature analysis

Chemistry and Biology

Volumn 3, Issue 10, 1996, Pages 817-825

  Muir, Tom W ^a,b   Dawson, Philip E ^a   Fitzgerald, Michael C ^a   Kent, Stephen B H ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

Author keywords

combinatorial protein chemistry; protein array; protein signature analysis

Indexed keywords

EID: 0030267666     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(96)90067-8     Document Type: Article

References (39)

1. Smith, M. (1994), Synthetic DNA and biology. (Nobel lecture). Angew. Chem. Int. Ed. Engl. 33, 1214-1221.
2. Mendel, D., Ellman, JA, Chang, Z., Veenstra, D.L., Kollman P.A. & Schultz, P.G. (1992). Probing protein stability with unnatural amino acids. Science 256, 1798-1802.
3. Cornish, V.W., Mendel, D. & Schultz, P.G. (1995). Probing protein structure and function with an expanded genetic code. Angew. Chem. Int. Ed. Engl. 34, 621-633.
4. Schnölzer, M., Alewood, P., Jones, A., Alewood D. & Kent, S.B.H. (1992). In situ neutralization in Boc-chemistry solid phase peptide synthesis: rapid, high yield assembly of difficult sequences. Int. J. Pept. Protein Res. 40, 180-193.
5. Schnölzer, M. & Kent, S.B.H. (1992). Constructing proteins by dovetailing unprotected synthetic peptides: backbone-engineered HIV protease. Science 256, 221-225.
6. Gaertner, H.F., Rose, K., Cotton, R., Timms, D., Gamble R. & Offord, R.E. (1992). Construction of protein analogues by site-specific condensation of unprotected peptides. Bioconjugate Chem. 3, 262-268.
7. Dawson, P.E., Muir, T.W., dark-Lewis I. & Kent, S.B.H. (1994). Synthesis of proteins by native chemical ligation. Science 266, 776-779.
8. Kemp, D.S. & Carey, R.I. (1993). Synthesis of a 39-peptide and a 25-peptide by thiol-capture ligations: observation of a 40-fold rate acceleration of the intramolecular O,N-acyl transfer reaction between peptide fragments bearing only cysteine protecting groups. J. Org. Chem. 58, 2216-2222.
9. Liu, C.-F. & Tarn, J.P. (1994). Peptide segment ligation strategy without use of protecting groups. Proc. Natl. Acad. Sci. USA 91, 6584-6588.
10. Nefzi, A., Sun X. & Mutter, M. (1995). Chemoselective ligation of multifunctional peptides to topological templates via thioether formation for TASP synthesis. Tetrahedron Lett. 36, 229-230.
11. Cunningham, B.C. & Wells, J.A. (1989). High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 244, 1081-1085.
12. Blaber, M., Baase, W.A., Gassner N. & Matthews, B.W. (1995). Alanine-scanning mutagenesis of the a-helix 115-123 of phage T4 lysoyme: effect on structure, stability and binding of solvent. J. Mol. Biol. 246, 317-330.
13. Tarn, J.P. & Ke, X.-H., et al., (1989). Systematic approach to study the structure-activity of transforming growth factor a. In Peptides: chemistry and biology [Proceedings of the 11 th American Peptide Symposium.] pp. 75-77, ESCOM, Leiden.
14. Gibbs, C.S. & Leung, L.L.K., et al., (1995). Conversion of thrombin into an anticoagulant by protein engineering. Nature 378, 413-416.
15. Reidhaar-Olsen, J.F. & Sauer, R.T. (1988). Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science 241, 53-57.
16. Scott, J.K. & Smith, G.P. (1990). Searching for peptide ligands using an epitope ligand. Science 249, 386-390.
17. Davidson, A.R., Lumb K.L. & Sauer, R.T. (1995). Cooperative folding proteins in random sequence libraries. Nat. Struct. Biol. 2, 856-864.
18. Kamteker, S., Schiffer, J.M., Xiong, H., Babik, J.M. & Hecht, M.H. (1993). Protein design by binary patterning of polar and non-polar amino acids. Science 262, 1680-1685.
19. Hayashibara, K.C. & Verdine, G.L. (1991). Template-directed interference footprinting of protein-guanine contacts in DNA. J. Am. Chem. Soc. 113, 5104-5106.
20. Hayashibara, K.C. & Verdine, G.L. (1992). Template-directed interference footprinting of cytosine contacts in a protein-DNA complex: potent interference of 5-aza-2′-deoxycytidine. Biochemistry 31, 11265-11273.
21. Mascarenas, J.L., Hayashibara, K.C. & Verdine, G.L. (1993). Template-directed interference footprinting of protein-thymidine contact. J. Am. Chem. Soc. 115, 373-374.
22. Min, C., Gushing, T.D. & Verdine, G.L. (1996). Template-directed Interference footprinting of protein-adenine contacts. J. Am. Chem. Soc. 118, 6116-6120.
23. Pawson, T. & Sohlessinger, J. (1993). SH2 and SH3 domains. Curr. Biol. 3, 434-442.
24. Kuriyan, J. & Cowburn, D. (1993). Structures of SH2 and SH3 domains. Curr. Opin. Struct. Biol. 3, 828-837.
25. Feng, S., Chen, J.K., Yu, H., Simon J.A. & Schreiber, S.A. (1994). Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science 266, 1241-1247.
26. Knudsen, B.S., Feller S.M. & Hanafusa, H. (1994). Four proline-rich sequences of the guanine-nucleotide exchange factor, C3G, bind with unique specificity to the first Src homology 3 domain of Crk. J. Biol. Chem. 269, 32781-32787.
27. Shortle, D. & Sondek, J. (1995). The emerging role of insertions and deletions in protein engineering. Curr. Opin. Biotechnol. 6, 387-393.
28. Chait, B.T. & Kent, S.B.H. (1992). Weighing naked proteins: practical high accuracy mass measurement of peptides and proteins. Science 257, 1885-1894.
29. Chait, B.T., Wang, R., Beavis R.C. & Kent, S.B.H. (1993). Protein ladder sequencing. Science 262, 89-92.
30. Zhao, Y., Muir, T.W., Kent, S.B.H., Tischer, E., Scardina, J.M. & Chait, B.T. (1996). Mapping protein-protein interactions by affinity-directed mass spectrometry. Proc. Natl. Acad. Sci. USA 93, 4020-4024.
31. Mayer, B.J. & Hanafusa, H. (1993). Mutagenic analysis of the v-crk oncogene: requirement for the SH2 and SH3 domains and correlation between increased cellular phosphotyrosine and transformation. J. Virol. 64,3581-3589.
32. Wu, X. & Kuriyan, J., et al., (1995). Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. Structure 3, 215-226.
33. Muir, T.W. & Kent, S.B.H. (1993). The chemical synthesis of proteins. Curr. Opin. Biotechnol. 4, 420-427.
34. Muir, T.W. (1995). A chemical approach to the construction of multimeric protein assemblies. Structure 3, 649-652.
35. Baca, M., Alewood, P.P. & Kent, S.B.H. (1993). Structural engineering of the HIV-1 protease molecule with a β-turn mimic of fixed geometry. Prot. Sci. 2, 1085-1091.
36. Baca, M. & Kent, S.B.H. (1993). Catalytic contribution of flapsubstrate hydrogen bonds in HIV-1 protease explored by chemical synthesis. Proc. Natl. Acad. Sci. USA 90, 11638-11642.
37. Canne, LE., Ferre-D'Amare, A.R., Burley, S.K. & Kent, S.B.H. (1995). Total chemical synthesis of a unique transcription factor-related protein: c-Myc-Max. J. Am. Chem. Soc. 117, 2998-3007.
38. Baca, M., Muir, T.W, Schnolzer, M. & Kent, S.B.H. (1995). Chemical ligation of cysteine-containing peptides: synthesis of a 22-kDa tethered dimer HIV-1 protease. J. Am. Chem. Soc. 117, 1881-1887.
39. 2. Bull. Chem. Soc. Jpn. 64, 111-117.