References

Aloy P, Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev

Mol Cell Biol 7:188-197 Amara JF, Clackson T, Rivera VM, Guo T, Keenan T, Natesan S, Pollock R, Yang W, Courage NL, Holt DA, Gilman M (1997) A versatile synthetic dimerizer for the regulation of proteinprotein interactions. Proc Natl Acad Sci USA 94:10618-10623 Andreeva A, Howorth D, Brenner SE, Hubbard TJP, Chothia C, Murzin AG (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 32: D226-D229

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM, Consortium I (2000) InterPro - an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16:1145-1150 Archakov AI, Govorun VM, Dubanov AV, Ivanov YD, Veselovsky AV, Lewi P, Janssen P (2003)

Protein-protein interactions as a target for drugs in proteomics. Proteomics 3:380-391 Arkin MR, Wells JA (2004) Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 3:301-317 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. Gene Ontol Consort Nat Genet 25:25-29 Attwood TK (2002) The PRINTS database: a resource for identification of protein families. Brief Bioinform 3:252-263

Austin DJ, Crabtree GR, Schreiber SL (1994) Proximity versus allostery: the role of regulated protein dimerization in biology. Chem Biol 1:131-136 Belshaw PJ, Ho SN, Crabtree GR, Schreiber SL (1996) Controlling protein association and subcellular localization with a synthetic ligand that induces heterodimerization of proteins. Proc Natl Acad Sci USA 93:4604-4607 Bennett MJ, Schlunegger MP, Eisenberg D (1995) 3D domain swapping: a mechanism for oligomer assembly. Protein Sci 4:2455-2468 Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE

(2000) The protein data bank. Nucleic Acids Res 28:235-242 Bhattacharyya RP, Remenyi A, Yeh BJ, Lim WA (2006) Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 75:655-680

Bornberg-Bauer E, Beaussart F, Kummerfeld SK, Teichmann SA, Weiner J (2005) The evolution of domain arrangements in proteins and interaction networks. Cell Mol Life Sci 62:435-445 Brooijmans N, Sharp KA, Kuntz ID (2002) Stability of macromolecular complexes. Proteins 48:645-653

Buchan DWA, Rison SCG, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA (2003) Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res 31:469-473

Castagnoli L, Costantini A, Dall'Armi C, Gonfloni S, Montecchi-Palazzi L, Panni S, Paoluzi S, Santonico E, Cesareni G (2004) Selectivity and promiscuity in the interaction network mediated by protein recognition modules. FEBS Lett 567:74-79 Cestra G, Castagnoli L, Dente L, Minenkova O, Petrelli A, Migone N, Hoffmüller U, Schneider-Mergener J, Cesareni G (1999) 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 274:32001-32007 Chothia C, Gough J, Vogel C, Teichmann SA (2003) Evolution of the protein repertoire. Science 300:1701-3

Clemons PA (1999) Design and discovery of protein dimerizers. Curr Opin Chem Biol 3:112-115

Deng M, Mehta S, Sun F, Chen T (2002) Inferring domain-domain interactions from proteinprotein interactions. Genome Res 12:1540-8 Dente L, Vetriani C, Zucconi A, Pelicci G, Lanfrancone L, Pelicci PG, 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 Dueber JE, Yeh BJ, Bhattacharyya RP, Lim WA (2004) Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr Opin Struct Biol 14:690-699 Elofsson A, Sonnhammer EL (1999) A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics 15:480-500 Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247-D251 Frank R (2002) The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports-

principles and applications. J Immunol Methods 267:13-26 Freund C, Kühne R, Park S, Thiemke K, Reinherz EL, Wagner G (2003) Structural investigations of a GYF domain covalently linked to a proline-rich peptide. J Biomol NMR 27:143-149 Gough J, Karplus K, Hughey R, Chothia C (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 313:903-919

Gruenheid S, DeVinney R, Bladt F, Goosney D, Gelkop S, Gish GD, Pawson T, Finlay BB (2001) Enteropathogenic E. coli Tir binds Nck to initiate actin pedestal formation in host cells. Nat Cell Biol 3:856-859

Haft DH, Selengut JD, White O (2003) The TIGRFAMs database of protein families. Nucleic Acids Res 31:371-373

Holland TA, Veretnik S, Shindyalov IN, Bourne PE (2006) Partitioning protein structures into domains: why is it so difficult? J Mol Biol 361:562-590 Hulo N, Bairoch A, Bulliard V, Cerutti L, Castro ED, Langendijk-Genevaux PS, Pagni M, Sigrist

CJA (2006) The PROSITE database. Nucleic Acids Res 34:D227-D230 Jiang S, Li P, Peach ML, Bindu L, Worthy KW, Fisher RJ, Burke TR, Nicklaus M, Roller PP (2006) Structure-based design of potent Grb2-SH2 domain antagonists not relying on phosphotyrosine mimics. Biochem Biophys Res Commun 349:497-503 Jones S, Marin A, Thornton JM (2000) Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Eng 13:77-82 Jothi R, Cherukuri PF, Tasneem A, Przytycka TM (2006) Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating proteinprotein interactions. J Mol Biol 362:861-875

Kopytek SJ, Standaert RF, Dyer JC, Hu JC (2000) Chemically induced dimerization of dihydro-

folate reductase by a homobifunctional dimer of methotrexate. Chem Biol 7:313-321 Lacount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, Schoenfeld LW, Ota I, Sahasrabudhe S, Kurschner C, Fields S, Hughes RE (2005) A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438:103-107 Landgraf C, Panni S, Montecchi-Palazzi L, Castagnoli L, Schneider-Mergener J, Volkmer-Engert R,

Cesareni G (2004) Protein interaction networks by proteome peptide scanning. PLoS Biol 2:E14 Lee H, Deng M, Sun F, Chen T (2006) An integrated approach to the prediction of domaindomain interactions. BMC Bioinform 7:269 Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 34:D257-D260 Liu J, Rost B (2004) CHOP proteins into structural domain-like fragments. Proteins 55:678-688 Longnecker R, Miller CL (1996) Regulation of Epstein-Barr virus latency by latent membrane protein 2. Trends Microbiol 4:38-42 MacCorkle RA, Freeman KW, Spencer DM (1998) Synthetic activation of caspases: artificial death switches. Proc Natl Acad Sci USA 95:3655-3660 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJA, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C (2007) New developments in the InterPro database. Nucleic Acids Res 35:D224-D228 Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 3:e405 Ng S-K, Zhang Z, Tan S-H (2003) Integrative approach for computationally inferring protein domain interactions. Bioinformatics 19:923-9 Nye TMW, Berzuini C, Gilks WR, Babu MM, Teichmann SA (2005) Statistical analysis of domains in interacting protein pairs. Bioinformatics 21:993-1001 Paoluzi S, Castagnoli L, Lauro I, Salcini AE, Coda L, Confalonieri SFaS, Pelicci PG, Fiore PPD, Cesareni G (1998) Recognition specificity of individual EH domains of mammals and yeast. EMBO J 17:6541-6550

Park J, Lappe M, Teichmann SA (2001) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol 307:929-938 Pawson T (2007) Dynamic control of signaling by modular adaptor proteins. Curr Opin Cell Biol 19:112-116

Pawson T, Gish GD, Nash P (2001) SH2 domains, interaction modules and cellular wiring. Trends Cell Biol 11:504-511

Pawson T, Raina M, Nash P (2002) Interaction domains: from simple binding events to complex cellular behavior. FEBS Lett 513:2-10 Pearl FMG, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA (2003) The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res 31:452-455 Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen M-Y, Kelly L, Melo F, Sali A (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34:D291-D295

Pommier Y, Cherfils J (2005) Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery. Trends Pharmacol Sci 26:138-145 Rain JC, Selig L, Reuse HD, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schächter V, Chemama Y, Labigne A, Legrain P (2001) The protein-protein interaction map of Helicobacter pylori. Nature 409:211-215

Rickles RJ, Botfield MC, Weng Z, Taylor JA, Green OM, Brugge JS, Zoller MJ (1994) Identification of Src,Fyn,Lyn,PI3K and Abl SH3 domain ligands using phage display libraries. EMBO J 13:5598-5604

Riley R, Lee C, Sabatti C, Eisenberg D (2005) Inferring protein domain interactions from databases of interacting proteins. Genome Biol 6:R89 Romano AMMPR, Panni S, Mendoza M, Wong WT, Musacchio A, Cesareni G, Fiore PPD (1999)

A novel peptide-SH3 interaction. EMBO J 18:5300-5309 Santonico E, Castagnoli L, Cesareni G (2005) Methods to reveal domain networks. Drug Discov Today 10:1111-1117

Schmidt EE, Davies CJ (2007) The origins of polypeptide domains. Bioessays 29:262-270 Scott JK, Smith GP (1990) Searching for peptide ligands with an epitope library. Science 249:386-390

Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, Peyruc D, Kahn D (2002) ProDom: automated clustering of homologous domains. Brief Bioinform 3:246-251 Shoemaker BA, Panchenko AR, Bryant SH (2006) Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Sci 15:352-361 Singh SK, Maithal K, Balaram H, Balaram P (2001) Synthetic peptides as inactivators of multimeric enzymes: inhibition of Plasmodium falciparum triosephosphate isomerase by interface peptides. FEBS Lett 501:19-23 Sonnhammer EL, Eddy SR, Durbin R (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405-420 Sparks AB, Quilliam LA, Thorn JM, Der CJ, Kay BK (1994) Identification and characterization of Src SH3 ligands from phage-displayed random peptide libraries. J Biol Chem 269:23853-23856

Sprinzak E, Margalit H (2001) Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 311:681-692 Sudol M (1998) From Src homology domains to other signaling modules: proposal of the 'protein recognition code'. Oncogene 17:1469-1474 Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13:2129-2141 Turkson J, Kim JS, Zhang S, Yuan J, Huang M, Glenn M, Haura E, Sebti S, Hamilton AD, Jove R (2004) Novel peptidomimetic inhibitors of signal transducer and activator of transcription 3 dimerization and biological activity. Mol Cancer Ther 3:261-269 Vaccaro P, Brannetti B, Montecchi-Palazzi L, Philipp S, Citterich MH, Cesareni G, 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

Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN (2004) Toward consistent assignment of structural domains in proteins. J Mol Biol 339:647-678 Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34:D187-D191 Wu CH, Nikolskaya A, Huang H, Yeh L-SL, Natale DA, Vinayaka CR, Hu Z-Z, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, Cardenas JL, Chung S, Castro-Alvear J, Dinkov G, Barker WC (2004) PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res 32:D112-D114 Yaffe MB (2006) "Bits"and pieces. Sci STKE 2006:pe28

Yaffe MB, Cantley LC (2000) Mapping specificity determinants for protein-protein association using protein fusions and random peptide libraries. Methods Enzymol 328:157-170 Zutshi R, Brickner M, Chmielewski J (1998) Inhibiting the assembly of protein-protein interfaces. Curr Opin Chem Biol 2:62-66

0 0

Post a comment