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Chapter 39: Combining Phage Display and Unrelated Orthogonal Approaches to Determine Interaction Networks Mediated by Protein Recognition Modules—References

Aasland R., Abrams C., Ampe C., Ball L.J., Bedford M.T., Cesareni G., Gimona M., Hurley J.H., Jarchau T., Lehto V.P., Lemmon M.A., Linding R., Mayer B.J., Nagai M., Sudol M., Walter U., and Winder S.J. 2002. Normalization of nomenclature for peptide motifs as ligands of modular protein domains. FEBS Lett. 513: 141–144.

Allen M., Friedler A., Schon O., and Bycroft M. 2002. The structure of an FF domain from human HYPA/FBP11. J. Mol. Biol. 323: 411–416.

Bailey T.L. and Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology (ed. R. Altman et al.), pp. 28–36. AAAI Press, Menlo Park, California.

Ball L.J., Jarchau T., Oschkinat H., and Walter U. 2002. EVH1 domains: Structure, function and interactions. FEBS Lett. 513: 45–52.

Cesareni G., Gimona M., Sudol M., and Yaffe M., eds. 2004. Modular protein domains. Wiley-VCH, Weinheim, Germany.

Cesareni G., Panni S., Nardelli G., and Castagnoli L. 2002. Can we infer peptide recognition specificity mediated by SH3 domains? FEBS Lett. 513: 38–44.

Dente L., Vetriani C., Zucconi A., Pelicci G., Lanfrancone L., Pelicci P.G., and Cesareni G. 1997. Modified phage peptide libraries as a tool to study specificity of phosphorylation and recognition of tyrosine containing peptides. J. Mol. Biol. 269: 694–703.

Durocher D. and Jackson S.P. 2002. The FHA domain. FEBS Lett. 513: 58–66.

Elia A.E., Cantley L.C., and Yaffe M.B. 2003. Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates. Science 299: 1228–1231.

Felici F., Castagnoli L., Musacchio A., Jappelli R., and Cesareni G. 1991. Selection of antibody ligands from a large library of oligopeptides expressed on a multivalent exposition vector. J. Mol. Biol. 222: 301–310.

Frank R. 1992. Spot-synthesis: An easy technique for the positionally addressable, parallel chemical synthesis on a membrane support. Tetrahedron 48: 9217–9232.

Freund C., Kuhne R., Park S., Thiemke K., Reinherz E.L., and Wagner G. 2003. Structural investigations of a GYF domain covalently linked to a proline-rich peptide. J. Biomol. NMR 27: 143–149.

Fuh G. and Sidhu S.S. 2000. Efficient phage display of polypeptides fused to the carboxy-terminus of the M13 gene-3 minor coat protein. FEBS Lett. 480: 231–234.

Fuh G., Pisabarro M.T., Li Y., Quan C., Lasky L.A., and Sidhu S.S. 2000. Analysis of PDZ domain-ligand interactions using carboxyl-terminal phage display. J. Biol. Chem. 275: 21486–21491.

Garner E., Cannon P., Romero P., Obradovic Z., and Dunker A.K. 1998. Predicting disordered regions from amino acid sequence: Common themes despite differing structural characterization. Genome Inform. Ser. Workshop Genome Inform. 9: 201–213.

Ghaemmaghami S., Huh W.K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., and Weissman J.S. 2003. Global analysis of protein expression in yeast. Nature 425: 737–741.

Greenwood J., Willis A.E., and Perham R.N. 1991. Multiple display of foreign peptides on a filamentous bacteriophage. Peptides from Plasmodium falciparum circumsporozoite protein as antigens. J. Mol. Biol. 220: 821–827.

Huh W.K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., and O'Shea E.K. 2003. Global analysis of protein localization in budding yeast. Nature 425: 686–691.

Iannolo G., Minenkova O., Gonfloni S., Castagnoli L., and Cesareni G. 1997. Construction, exploitation and evolution of a new peptide library displayed at high density by fusion to the major coat protein of filamentous phage. Biol. Chem. 378: 517–521.

Jacobs S.A., Taverna S.D., Zhang Y., Briggs S.D., Li J., Eissenberg J.C., Allis C.D., and Khorasanizadeh S. 2001. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 20: 5232–5241.

Karaoz U., Murali T.M., Letovsky S., Zheng Y., Ding C., Cantor C.R., and Kasif S. 2004. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc. Natl. Acad. Sci. 101: 2888–2893.

Kornau H.C., Schenker L.T., Kennedy M.B., and Seeburg P.H. 1995. Domain interaction between NMDA receptor subunits and the postsynaptic density protein PSD-95. Science 269: 1737–1740.

Kumar A., Agarwal S., Heyman J.A., Matson S., Heidtman M., Piccirillo S., Umansky L., Drawid A., Jansen R., Liu Y., Cheung K.H., Miller P., Gerstein M., Roeder G.S., and Snyder M. 2002. Subcellular localization of the yeast proteome. Genes Dev. 16: 707–719.

Linding R., Russell R.B., Neduva V,. and Gibson T.J. 2003. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31: 3701–3708.

Macias M.J., Wiesner S., and Sudol M. 2002. WW and SH3 domains, two different scaffolds to recognize proline-rich ligands. FEBS Lett. 513: 30–37.

Manke I.A., Lowery D.M., Nguyen A., and Yaffe M.B. 2003. BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science 302: 636–639.

Maruyama I.N., Maruyama H.I., and Brenner S. 1994. Lambda foo: A lambda phage vector for the expression of foreign proteins. Proc. Natl. Acad. Sci. 91: 8273–8277.

Mongiovì A.M., Romano P.R., Panni S., Mendoza M., Wong W.T., Musacchio A., Cesareni G., and Di Fiore P.P. 1999. A novel peptide-SH3 interaction. EMBO J. 18: 5300–5309.

Otte L., Wiedemann U., Schlegel B., Pires J.R., Beyermann M., Schmieder P., Krause G., Volkmer-Engert R., Schneider-Mergener J., and Oschkinat H. 2003. WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains. Protein Sci. 12: 491–500.

Paoluzi S., Castagnoli L., Lauro I., Salcini A.E., Coda L., Fre' S., Confalonieri S., Pelicci P.G., Di Fiore P.P., and Cesareni G. 1998. Recognition specificity of individual EH domains of mammals and yeast. EMBO J. 17: 6541–6550.

Pawson T. 2004. Specificity in signal transduction: From phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 116: 191–203.

Puertollano R., Aguilar R.C., Gorshkova I., Crouch R.J., and Bonifacino J.S. 2001. Sorting of mannose 6-phosphate receptors mediated by the GGAs. Science 292: 1712–1716.

Rodriguez M., Yu X., Chen J., and Songyang Z. 2003. Phosphopeptide binding specificities of BRCA1 COOH-terminal (BRCT) domains. J. Biol. Chem. 278: 52914–52918.

Rosenberg A., Griffin K., Studier W.S., McCormick M., Berg J., Novy R., and Mierendorf R. 1996. T7 select phage display system: A powerful new protein display system based on bacteriophage T7. Innovations 6: 1–6.

Salcini A.E., Confalonieri S., Doria M., Santolini E., Tassi E., Minenkova O., Cesareni G., Pelicci P.G., and Di Fiore P.P. 1997. Binding specificity and in vivo targets of the EH domain, a novel protein-protein interaction module. Genes Dev. 11: 2239–2249.

Santini C., Brennan D., Mennuni C., Hoess R.H., Nicosia A., Cortese R., and Luzzago A. 1998. Efficient display of an HCV cDNA expression library as C-terminal fusion to the capsid protein D of bacteriophage lambda. J. Mol. Biol. 282: 125–135.

Scott J.K. and Smith G.P. 1990. Searching for peptide ligands with an epitope library. Science 249: 386–390.

Simpson J.C., Wellenreuther R., Poustka A., Pepperkok R., and Wiemann S. 2000. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep. 1: 287–292.

Smith G.P. and Petrenko V.A. 1997. Phage display. Chem. Rev. 97: 391–410.

Sternberg N. and Hoess R.H. 1995. Display of peptides and proteins on the surface of bacteriophage lambda. Proc. Natl. Acad. Sci. 92: 1609–1613.

Tommasi di Vignano A., Di Zenzo G., Sudol M., Cesareni G., and Dente L. 2000. Contribution of the different modules in the utrophin carboxy-terminal region to the formation and regulation of the DAP complex. FEBS Lett. 471: 229–234.

Tong A.H., Drees B., Nardelli G., Bader G.D., Brannetti B., Castagnoli L., Evangelista M., Ferracuti S., Nelson B., Paoluzi S., Quondam M., Zucconi A., Hogue C.W., Fields S., Boone C., and Cesareni G. 2002. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295: 321–324.

Vaccaro P. and Dente L. 2002. PDZ domains: Troubles in classification. FEBS Lett. 512: 345–349.

Vaccaro P., Brannetti B., Montecchi-Palazzi L., Philipp S., Citterich M.H., Cesareni G., and Dente L. 2001. Distinct binding specificity of the multiple PDZ domains of INADL, a human protein with homology to INAD from Drosophila melanogaster. J. Biol. Chem. 276: 42122–42130.

von Mering C., Huynen M., Jaeggi D., Schmidt S., Bork P., and Snel B. 2003. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 31: 258–261.

Yaffe M.B., Rittinger K., Volinia S., Caron P.R., Aitken A., Leffers H., Gamblin S.J., Smerdon S.J., and Cantley L.C. 1997. The structural basis for 14-3-3:phosphopeptide binding specificity. Cell 91: 961–971.

Yan K.S., Kuti M., and Zhou M.M. 2002. PTB or not PTB—That is the question. FEBS Lett. 513: 67–70.

Zeng L. and Zhou M.M. 2002. Bromodomain: An acetyl-lysine binding domain. FEBS Lett. 513: 124–128.

Zozulya S., Lioubin M., Hill R.J., Abram C., and Gishizky M.L. 1999. Mapping signal transduction pathways by phage display. Nat. Biotechnol. 17: 1193–1198.

Zucconi A., Dente L., Santonico E., Castagnoli L., and Cesareni G. 2001. Selection of ligands by panning of domain libraries displayed on phage lambda reveals new potential partners of synaptojanin 1. J. Mol. Biol. 307: 1329–1339.

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