Functional genomics of intracellular peptide recognition domains with combinatorial biology methods

Current Opinion in Chemical Biology

Volumn 7, Issue 1, 2003, Pages 97-102

  Sidhu, Sachdev S ^a   Bader, Gary D ^b,c   Boone, Charles ^d  

^a GENENTECH INC   (United States)

^b MOUNT SINAI HOSPITAL   (Canada)

^c MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^d NONE

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN;

BACTERIOPHAGE; BINDING AFFINITY; BIOLOGY; CARBOXY TERMINAL SEQUENCE; GENOMICS; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; REVIEW; YEAST;

EID: 0037305940     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(02)00011-X     Document Type: Review

References (38)

1. Pawson T. Protein modules and signalling networks. Nature. 373:1995;573-580.
2. Pawson T., Scott J.D. Signaling through scaffold, anchoring and adapter proteis. Science. 278:1997;2075-2080.
3. Sudol M. From Src homology domains to other signaling modules: proposal of the 'protein recognition code'. Oncogene. 17:1998;1469-1474.
4. Aasland R., Abrams C., Ampe C., Ball L.J., Bedford M.T., Cesareni G., Gimona M., Hurley J.H., Jarchau T., Lehto V.P.et al. Normalization of nomenclature for peptide motifs as ligands of modular protein domains. FEBS Lett. 513:2002;141-144 The authors propose a general nomenclature for describing residue preferences in peptide motifs recognized by peptide-binding domains. Universal acceptance of the code would greatly reduce the current confusion in the description of binding motifs.
5. Kay B.K., Kasanov J., Knight S., Kurakin A. Convergent evolution with combinatorial libraries. FEBS Lett. 480:2000;55-62.
6. Sidhu S.S. Phage display in pharmaceutical biotechnology. Curr. Opin. Biotechnol. 11:2000;610-616.
7. Sidhu S.S., Lowman H.B., Cunningham B.C., Wells J.A. Phage display for selection of novel binding peptides. Meth. Enzymol. 328:2000;333-363.
8. Craven S.E., Bredt D.S. PDZ proteins organize synaptic signaling pathways. Cell. 93:1998;495-498.
9. Fanning A.S., Anderson J.M. Protein modules as organizers of membrane structure. Curr. Opin. Cell. Biol. 11:1999;432-439.
10. Schultz J., Copley R.R., Doerks T., Ponting C.P., Bork P. SMART: a web-based tool for the study of genetically mobile domains. Nucl. Acid Res. 28:2000;231-234.
11. Doyle D.A., Lee A., Lewis J., Kim E., Sheng M., MacKinnon R. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell. 85:1996;1067-1076.
12. 2 adrenergic and platelet-derived growth factor receptors. J. Biol. Chem. 277:2002;18973-18978.
13. Harrison S.C. Peptide-surface association: the case of PDZ and PTB domains. Cell. 86:1996;341-343.
14. Harris B.Z., Lim W.A. Mechanism and role of PDZ domains in signaling complex assembly. J. Cell. Sci. 114:2001;3219-3231.
15. Hung A.Y., Sheng M. PDZ domains: structural modules for protein complex assembly. J. Biol. Chem. 277:2002;5699-5702.
16. Songyang Z., Fanning A.S., Fu C., Xu J., Marfatia S.M., Chishti A.H., Crompton A., Chan A.C., Anderson J.M., Cantley L.C. Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science. 275:1997;73-77.
17. Stricker N.L., Christopherson K.S., Yi B.A., Schatz P.J., Raab R.W., Dawes G., Bassett D.E. Jr., Bredt D.S., Li M. PDZ domain of neuronal nitric oxide synthase recognizes novel C-terminal peptide sequences. Nature Biotechnol. 15:1997;336-342.
18. Fuh G., Pisabarro M.T., Li Y., Quan C., Lasky L.A., Sidhu S.S. Analysis of PDZ domain-ligand interactions using carboxyl-terminal phage display. J. Biol. Chem. 275:2000;21486-21491.
19. Laura R.P., Witt A.S., Held H.A., Gerstner R., Deshayes K., Koehler M.F., Kosik K.S., Sidhu S.S., Lasky L.A. The Erbin PDZ domain binds with high affinity and specificity to the carboxyl termini of delta-catenin and ARVCF. J. Biol. Chem. 277:2002;12906-12914 This paper demonstrates that phage-derived peptide sequences can be used to identify natural binding partners for PDZ domains. The work also emphasizes the need for several independent methods to definitively validate a biologically relevant protein-protein interaction. Using database mining with phage-derived consensus sequences, followed by affinity measurements with synthetic peptides and cell biology experiments, the p120-related catenins were shown to be high-affinity ligands for the Erbin PDZ domain.
20. Vaccaro P., Brannetti B., Montecchi-Palazzi L., Philipp S., Citterich M.H., Cesareni G., Dente L. Distinct binding specificity of the multiple PDZ domains of INADL, a human protein with homology to INAD from Drosophila melanogaster. J. Biol. Chem. 276:2001;42122-42130.
21. Skelton NJ, Koehler MFT, Zobel K, Wong WL, Yeh S, Pisabarro MT, Yin JP, Lasky LA, Sidhu SS: Origins of PDZ domain ligand specificity: structure determination and mutagenesis of the Erbin PDZ domain. J Biol Chem 2002, in press.
22. Aarts M., Liu Y., Liu L., Besshoh S., Arundine M., Gurd J.W., Wang Y.-T., Salter M.W., Tymianski M. Treatment of ischemic brain damage by perturbing NMDA receptor-PSD-95 protein interactions. Science. 298:2002;846-850 This report demonstrates that PDZ domains may be valid therapeutic targets, and furthermore, that peptide ligands may be useful for target validation in vivo. Peptides were used to disrupt the interaction between PSD-95 PDZ2 and the NMDA receptor in the brains of live rats. This dissociated the NMDA receptor from downstream neurotoxic signaling but, importantly, did not block NMDA receptor functions that mediate essential neuronal excitation. As a result, treated animals were protected from focal ischaemic brain damage during stroke, without suffering from the deleterious effects associated with blocking the NMDA receptor.
23. Macias M.J., Wiesner S., Sudol M. WW and SH3 domains, two different scaffolds to recognize proline-rich ligands. FEBS Lett. 513:2002;30-37.
24. Mayer B.J. SH3 domains: complexity in moderation. J. Cell. Sci. 14:2001;1253-1263.
25. Federov A.A., Fedorov E., Gertler F., Almo S.C. Structure of EVH1, a novel prolin-rich ligand-binding module involved in cytoskeletal dynamics and neural function. Nat. Struct. Biol. 6:1999;661-665.
26. Rickles R.J., Botfield M.C., Zhou X.-M., Henry P.A., Brugge J.S., Zoller M.J. Phage display selection of ligand residues important for Src homology 3 domain binding specificity. Proc. Natl. Acad. Sci. USA. 92:1995;10909-10913.
27. Sparks A.B., Rider J.E., Hoffman N.G., Fowlkes D.M., Quilliam L.A., Kay B.K. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCγ, Crk, and Grb2. Proc. Natl. Acad. Sci. USA. 93:1996;1540-1544.
28. Mongiovi A.M., Romano P.R., Panni S., Mendoza M., Wong W.T., Musacchio A., Cesareni G., Di Fiore P.P. A novel peptide-SH3 interaction. EMBO J. 18:1999;5300-5309.
29. Cestra G., Castagnoli L., Dente L., Minenkova O., Petrelli A., Migone N., Hoffmuller U., Cesareni G. The SH3 domains of endophilin and amphiphysin bind to the proline-rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity. J. Biol. Chem. 274:1999;32001-32007.
30. Fazi B., Cope M.J.T.V., Douangamath A., Ferracuti S., Schirwitz K., Zucconi A., Drubin D.G., Wilmanns M., Cesareni G., Castagnoli L. Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis. J. Biol. Chem. 277:2002;5290-5298.
31. Sparks A.B., Quilliam L.A., Thorn J.M., Der C.J., Kay B.K. Identification and characterization of Src SH3 ligands from phage-displayed random peptide libraries. J. Biol. Chem. 269:1994;23853-23856.
32. Rickles R.J., Botfield M.C., Weng Z., Taylor J.A., Green O.M., Brugge J.S., Zoller M.J. Identification of Src, Fyn, Lyn, PI3K and Abl SH3 domain ligands using phage display libraries. EMBO J. 13:1994;5598-5604.
33. Linn H., Ermekova K.S., Rentschler S., Sparks A.B., Kay B.K., Sudol M. Using molecular repertoires to identify high-affinity peptide ligands of the WW domain of human and mouse YAP. Biol. Chem. 78:1997;531-537.
34. Kasanov J., Pirozzi G., Uveges A.J., Kay B.K. Characterizing class I WW domains defines key specificity determinants and generates mutant domains with novel specificities. Chem. Biol. 8:2001;231-241.
35. Tong A.H.Y., Drees B., Nardelli G., Bader G.D., Brannetti B., Castagnoli L., Evangelista M., Ferracuti S., Nelson B., Paoluzi S.et al. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science. 295:2002;321-324 This work describes the integration of phage display data with yeast-two-hybrid data to produce high quality interaction predictions on a large scale. With the aid of computational methods, orthogonal datasets of genome-wide, putative interaction networks for 20 yeast SH3 domains were filtered against each other to produce a much smaller overlap network containing few false positives. The successful integration of data from different methods is certain to play an increasingly important role in functional genomics and proteomics.
36. Legrain P. Protein domain networking. Nat. Biotechnol. 20:2002;128-129.
37. Hiipakka M., Poikonen K., Saksela K. SH3 domains with high affinity and engineered ligand specificities targeted to HIV-1 Nef. J. Mol. Biol. 293:1999;1097-1106.
38. Panni S., Dente L., Cesareni G. In vitro evolution of recognition specificity mediated by SH3 domains reveals target recognition rules. J. Biol. Chem. 277:2002;21666-21674 The authors produced an SH3 domain library designed to resemble the binding surfaces of natural SH3 domains. Such repertoires should be useful in generating not only binding domains for peptides of interest but, perhaps more importantly, they may help to identify natural SH3 domains that bind particular natural proline-rich ligands. In combination with data from peptide-phage libraries, these data may reveal general recognition rules for SH3 domain-ligand interactions.