Reexamination of the recognition preference of the specificity pocket of the Abl SH3 domain

Journal of Molecular Recognition

Volumn 16, Issue 3, 2003, Pages 131-138

  Santamaria, Fanny ^a   Wu, Zhibin ^a   Boulègue, Cyril ^a   Pál, Gábor ^b   Lu, Wuyuan ^a  

^a INSTITUTE OF HUMAN VIROLOGY   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

Chemical protein synthesis; Peptide library; Protein peptide recognition; SH3 domain; Solid phase peptide synthesis; Specificity

Indexed keywords

CHROMATOGRAPHY, AFFINITY; LIGANDS; MODELS, MOLECULAR; PEPTIDE LIBRARY; PROTEIN BINDING; PROTEIN FOLDING; PROTO-ONCOGENE PROTEINS C-ABL; SRC HOMOLOGY DOMAINS; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; TITRIMETRY;

EID: 0038350592     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.620     Document Type: Article

References (34)

1. Alexandropoulos K, Cheng G and Baltimore D. 1995. Proline-rich sequences that bind to Src homology 3 domains with individual specificities. Proc. Natl Acad. Sci. USA 92: 3110-3114.
2. Cicchetti P, Mayer BJ, Thiel G and Baltimore D. 1992. Identification of a protein that binds to the SH3 region of Abl and is similar to Bcr and GAP-rho. Science 257: 803-806.
3. Cohen GB, Ren R and Baltimore D. 1995. Modular binding domains in signal transduction proteins. Cell 80: 237-248.
4. Dalgarno DC, Botfield MC and Rickles RJ. 1997. SH3 domains and drug design: ligands, structure, and biological function. Biopolymers 43: 383-400.
5. Feng S, Chen JK, Yu H, Simon JA and Schreiber SL. 1994. Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science 266: 1241-1247.
6. Feng S, Kasahara C, Rickles RJ and Schreiber SL. 1995. Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands. Proc. Natl Acad. Sci. USA 92: 12408-12415.
7. Feng S, Kapoor TM, Shirai F, Combs AP and Schreiber SL. 1996. Molecular basis for the binding of SH3 ligands with non-peptide elements identified by combinatorial synthesis. Chem. Biol. 3: 661-670.
8. Ghaemmaghami S, Fitzgerald MC and Oas TG. 2000. A quantitative, high-throughput screen for protein stability. Proc. Natl Acad. Sci. USA 97: 8296-8301.
9. Graf L, Hegyi G, Liko I, Hepp J, Medzihradszky K, Craik CS and Rutter WJ. 1988. Structural and functional integrity of specificity and catalytic sites of trypsin. Int. J. Pept. Protein Res. 32: 512-518.
10. Kay BK, Williamson MP and Sudol M. 2000. The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. Faseb J. 14: 231-241.
11. Kuriyan J and Cowburn D. 1997. Modular peptide recognition domains in eukaryotic signaling. A. Rev. Biophys. Biomol. Struct. 26: 259-288.
12. Lakowicz JR. 1999. Principles of Fluorescence Spectroscopy, 2nd edn. Kluwer Academic/Plenum Publishers: New York.
13. Lim WA, Richards FM and Fox RO. 1994. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 372: 375-379.
14. Lu W, Apostol I, Qasim MA, Warne N, Wynn R, Zhang WL, Anderson S, Chiang YW, Ogin E, Rothberg I et al. 1997. Binding of amino acid side-chains to S1 cavities of serine proteinases. J. Mol. Biol. 266: 441-461.
15. Mayer B. 2001. SH3 domains: complexity in moderation. J. Cell Sci. 114: 1253-1263.
16. Nguyen JT, Porter M, Amoui M, Miller WT, Zuckermann RN and Lim WA. 2000. Improving SH3 domain ligand selectivity using a non-natural scaffold. Chem. Biol. 7: 463-473.
17. Pace CN, Vajdos F, Fee L, Grimsley G and Gray T. 1995. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4: 2411-2423.
18. Pawson T. 1995. Protein modules and signalling networks. Nature 373: 573-580.
19. Perona JJ and Craik CS. 1995. Structural basis of substrate specificity in the serine proteases. Protein Sci. 4: 337-360.
20. Pisabarro MT and Serrano L. 1996. Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain. Biochemistry 35: 10634-10640.
21. Pisabarro MT, Serrano L and Wilmanns M. 1998. Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions. J. Mol. Biol. 281: 513-521.
22. Posern G, Zheng J, Knudsen BS, Kardinal C, Muller KB, Voss J, Shishido T, Cowburn D, Cheng G, Wang B et al. 1998. Development of highly selective SH3 binding peptides for Crk and CRKL which disrupt Crk-complexes with DOCK 180, SoS and C3G. Oncogene 16: 1903-1912.
23. Powell KD, Ghaemmaghami S, Wang MZ, Ma L, Oas TG and Fitzgerald MC. 2002. A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution. J. Am. Chem. Soc. 124: 10256-10257.
24. Powell KD and Fitzgerald MC. 2003. Accuracy and precision of a new H/D exchange- and mass spectrometry-based technique for measuring the thermodynamic properties of protein-peptide complexes. Biochemistry 42: 4962-4970.
25. Ren R, Mayer BJ, Cicchetti P and Baltimore D. 1993. Identification of a ten-amino acid proline-rich SH3 binding site. Science 259: 1157-1161.
26. Rickles RJ, Botfield MC, Weng Z, Taylor JA, Green OM, Brugge JS and Zoller MJ. 1994. Identification of Src, Fyn, Lyn, PI3K and Abl SH3 domain ligands using phage display libraries. Embo J. 13: 5598-5604.
27. Scheidig AJ, Hynes TR, Pelletier LA, Wells JA and Kossiakoff AA. 1997. Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities. Protein Sci. 6: 1806-1824.
28. Schnölzer M, Alewood P, Jones A, Alewood D and Kent SB. 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.
29. Sidhu SS, Lowman HB, Cunningham BC and Wells JA. 2000. Phage display for selection of novel binding peptides. Meth. Enzymol. 328: 333-363.
30. Sparks AB, Rider JE, Hoffman NG, Fowlkes DM, Quillam LA and Kay BK. 1996. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2. Proc. Natl Acad. Sci. USA 93: 1540-1544.
31. Tanford C. 1962. J. Am. Chem. Soc. 84: 4240-4247.
32. Viguera AR, Arrondo JL, Musacchio A, Saraste M and Serrano L. 1994. Characterization of the interaction of natural proline-rich peptides with five different SH3 domains. Biochemistry 33: 10925-10933.
33. Weng Z, Rickles RJ, Feng S, Richard S, Shaw AS, Schreiber SL and Brugge JS. 1995. Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions. Mol. Cell Biol. 15: 5627-5634.
34. Yu H, Chen JK, Feng S, Dalgarno DC, Brauer AW and Schreiber SL. 1994. Structural basis for the binding of proline-rich peptides to SH3 domains. Cell 76: 933-945.