PDZ domains recognise short sequence motifs at the extreme C-termini of proteins. A model based on microarray data has been recently published for predicting the binding preferences of PDZ domains to five residue long C-terminal sequences. Here we investigated the potential of this predictor for discovering novel protein interactions that involve PDZ domains. When tested on real negative data assembled from published literature, the predictor displayed a high false positive rate (FPR). We predicted and experimentally validated interactions between four PDZ domains derived from the human proteins MAGI1 and SCRIB and 19 peptides derived from human and viral C-termini of proteins. Measured binding intensities did not correlate with prediction scores, and the high FPR of the predictor was confirmed. Results indicate that limitations of the predictor may arise from an incomplete model definition and improper training of the model. Taking into account these limitations, we identified several novel putative interactions between PDZ domains of MAGI1 and SCRIB and the C-termini of the proteins FZD4, ARHGAP6, NET1, TANC1, GLUT7, MARCH3, MAS, ABC1, DLL1, TMEM215 and CYSLTR2. These proteins are localised to the membrane or suggested to act close to it and are often involved in G protein signalling. Furthermore, we showed that, while extension of minimal interacting domains or peptides toward tandem constructs or longer peptides never suppressed their ability to interact, the measured affinities and inferred specificity patterns often changed significantly. This suggests that if protein fragments interact, the full length proteins are also likely to interact, albeit possibly with altered affinities and specificities. Therefore, predictors dealing with protein fragments are promising tools for discovering protein interaction networks but their application to predict binding preferences within networks may be limited.
References
[1]
Diella F, Haslam N, Chica C, Budd A, Michael S, et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13: 6580–6603.
[2]
Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211–D222.
[3]
Letunic I, Doerks T, Bork P (2009) SMART 6: recent updates and new developments. Nucleic Acids Res 37: D229–D232.
[4]
Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, et al. (2010) ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res 38: D167–D180.
[5]
Edwards RJ, Davey NE, Shields DC (2007) SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2: e967.
[6]
Velthuis AJWT, Sakalis PA, Fowler DA, Bagowski CP (2011) Genome-wide analysis of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network. PLoS One 6: e16047.
[7]
Songyang Z, Fanning AS, Fu C, Xu J, Marfatia SM, et al. (1997) Recognition of unique carboxylterminal motifs by distinct PDZ domains. Science 275: 73–77.
[8]
Stricker NL, Christopherson KS, Yi BA, Schatz PJ, Raab RW, et al. (1997) PDZ domain of neuronal nitric oxide synthase recognizes novel C-terminal peptide sequences. Nat Biotechnol 15: 336–342.
[9]
Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H (2005) PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics 21: 827–828.
[10]
Encinar JA, Fernandez-Ballester G, Sánchez IE, Hurtado-Gomez E, Stricher F, et al. (2009) ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs. Bioinformatics 25: 2418–2424.
[11]
Roh MH, Margolis B (2003) Composition and function of PDZ protein complexes during cell polarization. Am J Physiol Renal Physiol 285: F377–F387.
[12]
Ide N, Hata Y, Nishioka H, Hirao K, Yao I, et al. (1999) Localization of membrane-associated guanylate kinase (MAGI)-1/BAI-associated protein (BAP) 1 at tight junctions of epithelial cells. Oncogene 18: 7810–7815.
[13]
Wegmann F, Ebnet K, Pasquier LD, Vestweber D, Butz S (2004) Endothelial adhesion molecule ESAM binds directly to the multidomain adaptor MAGI-1 and recruits it to cell contacts. Exp Cell Res 300: 121–133.
[14]
Yoshihara K, Ikenouchi J, Izumi Y, Akashi M, Tsukita S, et al. (2011) Phosphorylation state regulates the localization of Scribble at adherens junctions and its association with E-cadherincatenin complexes. Exp Cell Res 317: 413–422.
[15]
Ivanov AI, Young C, Beste KD, Capaldo CT, Humbert PO, et al. (2010) Tumor suppressor scribble regulates assembly of tight junctions in the intestinal epithelium. Am J Pathol 176: 134–145.
[16]
Humbert PO, Dow LE, Russell SM (2006) The Scribble and Par complexes in polarity and migration: friends or foes? Trends Cell Biol 16: 622–630.
[17]
Kotelevets L, van Hengel J, Bruyneel E, Mareel M, van Roy F, et al. (2005) Implication of the MAGI-1b/PTEN signalosome in stabilization of adherens junctions and suppression of invasiveness. FASEB J 19: 115–117.
[18]
Zhan L, Rosenberg A, Bergami KC, Yu M, Xuan Z, et al. (2008) Deregulation of scribble promotes mammary tumorigenesis and reveals a role for cell polarity in carcinoma. Cell 135: 865–878.
[19]
Javier RT (2008) Cell polarity proteins: common targets for tumorigenic human viruses. Oncogene 27: 7031–7046.
[20]
Liu H, Golebiewski L, Dow EC, Krug RM, Javier RT, et al. (2010) The ESEV PDZ-binding motif of the avian inuenza A virus NS1 protein protects infected cells from apoptosis by directly targeting Scribble. J Virol 84: 11164–11174.
[21]
Glaunsinger BA, Lee SS, Thomas M, Banks L, Javier R (2000) Interactions of the PDZ-protein MAGI-1 with adenovirus E4-ORF1 and high-risk papillomavirus E6 oncoproteins. Oncogene 19: 5270–5280.
[22]
Nakagawa S, Huibregtse JM (2000) Human scribble (Vartul) is targeted for ubiquitin-mediated degradation by the high-risk papillomavirus E6 proteins and the E6AP ubiquitin-protein ligase. Mol Cell Biol 20: 8244–8253.
[23]
Simonson SJS, Difilippantonio MJ, Lambert PF (2005) Two distinct activities contribute to human papillomavirus 16 E6's oncogenic potential. Cancer Res 65: 8266–8273.
[24]
Brannetti B, Zanzoni A, Montecchi-Palazzi L, Cesareni G, Helmer-Citterich M (2001) iSPOT: A web tool for the analysis and recognition of protein domain specificity. Comp Funct Genomics 2: 314–318.
[25]
Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, et al. (2008) A specificity map for the PDZ domain family. PLoS Biol 6: e239.
[26]
Stiffler MA, Chen JR, Grantcharova VP, Lei Y, Fuchs D, et al. (2007) PDZ domain binding selectivity is optimized across the mouse proteome. Science 317: 364–369.
[27]
Chen JR, Chang BH, Allen JE, Stiffler MA, MacBeath G (2008) Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotechnol 26: 1041–1045.
[28]
Schultz J, Hoffmüller U, Krause G, Ashurst J, Macias MJ, et al. (1998) Specific interactions between the syntrophin PDZ domain and voltage-gated sodium channels. Nat Struct Biol 5: 19–24.
[29]
Smialowski P, Pagel P, Wong P, Brauner B, Dunger I, et al. (2010) The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res 38: D540–D544.
[30]
Hui S, Bader GD (2010) Proteome scanning to predict PDZ domain interactions using support vector machines. BMC Bioinformatics 11: 507.
[31]
Shao X, Tan CSH, Voss C, Li SSC, Deng N, et al. (2011) A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. Bioinformatics 27: 383–390.
[32]
Gerek ZN, Keskin O, Ozkan SB (2009) Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior. Proteins 77: 796–811.
[33]
Kalyoncu S, Keskin O, Gursoy A (2010) Interaction prediction and classification of PDZ domains. BMC Bioinformatics 11: 357.
[34]
Smith CA, Kortemme T (2010) Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. J Mol Biol 402: 460–474.
[35]
Gerek ZN, Ozkan SB (2010) A exible docking scheme to explore the binding selectivity of PDZ domains. Protein Sci 19: 914–928.
[36]
Imamura F, Maeda S, Doi T, Fujiyoshi Y (2002) Ligand binding of the second PDZ domain regulates clustering of PSD-95 with the Kv1.4 potassium channel. J Biol Chem 277: 3640–3646.
[37]
Wang L, Piserchio A, Mierke DF (2005) Structural characterization of the intermolecular interactions of synapse-associated protein-97 with the NR2B subunit of N-methyl-D-aspartate receptors. J Biol Chem 280: 26992–26996.
[38]
Birrane G, Chung J, Ladias JAA (2003) Novel mode of ligand recognition by the Erbin PDZ domain. J Biol Chem 278: 1399–1402.
[39]
Kachel N, Erdmann KS, Kremer W, Wolff P, Gronwald W, et al. (2003) Structure determination and ligand interactions of the PDZ2b domain of PTP-Bas (hPTP1E): splicing-induced modulation of ligand specificity. J Mol Biol 334: 143–155.
[40]
Fournane S, Charbonnier S, Chapelle A, Kieffer B, Orfanoudakis G, et al. (2010) Surface plasmon resonance analysis of the binding of high-risk mucosal HPV E6 oncoproteins to the PDZ1 domain of the tight junction protein MAGI-1. J Mol Recognit.
[41]
Charbonnier S, Nominé Y, Ramírez J, Luck K, Chapelle A, et al. (2011) The structural and dynamic response of MAGI-1 PDZ1 with noncanonical domain boundaries to the binding of human papillomavirus E6. J Mol Biol 406: 745–763.
[42]
Wang CK, Pan L, Chen J, Zhang M (2010) Extensions of PDZ domains as important structural and functional elements. Protein Cell 1: 737–751.
[43]
Feng W, Zhang M (2009) Organization and dynamics of PDZ-domain-related supramodules in the postsynaptic density. Nat Rev Neurosci 10: 87–99.
[44]
Harris BZ, Lau FW, Fujii N, Guy RK, Lim WA (2003) Role of electrostatic interactions in PDZ domain ligand recognition. Biochemistry 42: 2797–2805.
[45]
Doyle DA, Lee A, Lewis J, Kim E, Sheng M, et al. (1996) Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell 85: 1067–1076.
[46]
Dev KK, Nakanishi S, Henley JM (2004) The PDZ domain of PICK1 differentially accepts protein kinase C-alpha and GluR2 as interacting ligands. J Biol Chem 279: 41393–41397.
[47]
Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, et al. (2009) Ensembl 2009. Nucleic Acids Res 37: D690–D697.
[48]
Consortium U (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38: D142–D148.
[49]
Zhang Y, Yeh S, Appleton BA, Held HA, Kausalya PJ, et al. (2006) Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families. J Biol Chem 281: 22299–22311.
[50]
Thomas M, Glaunsinger B, Pim D, Javier R, Banks L (2001) HPV E6 and MAGUK protein interactions: determination of the molecular basis for specific protein recognition and degradation. Oncogene 20: 5431–5439.
[51]
Schillinger C, Boisguerin P, Krause G (2009) Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions. Bioinformatics 25: 1632–1639.
[52]
Stein A, Aloy P (2008) Contextual specificity in peptide-mediated protein interactions. PLoS One 3: e2524.
[53]
Wiedemann U, Boisguerin P, Leben R, Leitner D, Krause G, et al. (2004) Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J Mol Biol 343: 703–718.
[54]
Dobrosotskaya IY (2001) Identification of mNET1 as a candidate ligand for the first PDZ domain of MAGI-1. Biochem Biophys Res Commun 283: 969–975.
[55]
Mino A, Ohtsuka T, Inoue E, Takai Y (2000) Membrane-associated guanylate kinase with inverted orientation (MAGI)-1/brain angiogenesis inhibitor 1-associated protein (BAP1) as a scaffolding molecule for Rap small G protein GDP/GTP exchange protein at tight junctions. Genes Cells 5: 1009–1016.
[56]
Yao R, Natsume Y, Noda T (2004) MAGI-3 is involved in the regulation of the JNK signaling pathway as a scaffold protein for frizzled and Ltap. Oncogene 23: 6023–6030.
[57]
Zhang H, Wang D, Sun H, Hall RA, Yun CC (2007) MAGI-3 regulates LPA-induced activation of Erk and RhoA. Cell Signal 19: 261–268.
[58]
Audebert S, Navarro C, Nourry C, Chasserot-Golaz S, Lécine P, et al. (2004) Mammalian Scribble forms a tight complex with the betaPIX exchange factor. Curr Biol 14: 987–995.
[59]
Nola S, Sebbagh M, Marchetto S, Osmani N, Nourry C, et al. (2008) Scrib regulates PAK activity during the cell migration process. Hum Mol Genet 17: 3552–3565.
[60]
Momboisse F, Lonchamp E, Calco V, Ceridono M, Vitale N, et al. (2009) betaPIX-activated Rac1 stimulates the activation of phospholipase D, which is associated with exocytosis in neuroendocrine cells. J Cell Sci 122: 798–806.
[61]
Lahuna O, Quellari M, Achard C, Nola S, Méduri G, et al. (2005) Thyrotropin receptor trafficking relies on the hScrib-betaPIX-GIT1-ARF6 pathway. EMBO J 24: 1364–1374.
[62]
Tsukamoto K, Hirano K, Tsujii K, Ikegami C, Zhongyan Z, et al. (2001) ATP-binding cassette transporter-1 induces rearrangement of actin cytoskeletons possibly through Cdc42/N-WASP. Biochem Biophys Res Commun 287: 757–765.
[63]
Okuhira K, Fitzgerald ML, Tamehiro N, Ohoka N, Suzuki K, et al. (2010) Binding of PDZ-RhoGEF to ATP-binding cassette transporter A1 (ABCA1) induces cholesterol effux through RhoA activation and prevention of transporter degradation. J Biol Chem 285: 16369–16377.
[64]
Stetak A, H？rndli F, Maricq AV, van den Heuvel S, Hajnal A (2009) Neuron-specific regulation of associative learning and memory by MAGI-1 in C. elegans. PLoS One 4: e6019.
[65]
Sun Y, Aiga M, Yoshida E, Humbert PO, Bamji SX (2009) Scribble interacts with beta-catenin to localize synaptic vesicles to synapses. Mol Biol Cell 20: 3390–3400.
[66]
Moreau MM, Piguel N, Papouin T, Koehl M, Durand CM, et al. (2010) The planar polarity protein Scribble1 is essential for neuronal plasticity and brain function. J Neurosci 30: 9738–9752.
[67]
Nonaka H, Takei K, Umikawa M, Oshiro M, Kuninaka K, et al. (2008) MINK is a Rap2 effector for phosphorylation of the postsynaptic scaffold protein TANC1. Biochem Biophys Res Commun 377: 573–578.
[68]
Jaleco AC, Neves H, Hooijberg E, Gameiro P, Clode N, et al. (2001) Differential effects of Notch ligands Delta-1 and Jagged-1 in human lymphoid differentiation. J Exp Med 194: 991–1002.
[69]
Woszczek G, Chen LY, Nagineni S, Alsaaty S, Harry A, et al. (2007) IFN-gamma induces cysteinyl leukotriene receptor 2 expression and enhances the responsiveness of human endothelial cells to cysteinyl leukotrienes. J Immunol 178: 5262–5270.
[70]
Fukuda H, Nakamura N, Hirose S (2006) MARCH-III is a novel component of endosomes with properties similar to those of MARCH-II. J Biochem 139: 137–145.
[71]
Canals M, Jenkins L, Kellett E, Milligan G (2006) Up-regulation of the angiotensin II type 1 receptor by the MAS proto-oncogene is due to constitutive activation of Gq/G11 by MAS. J Biol Chem 281: 16757–16767.
[72]
Li Q, Manolescu A, Ritzel M, Yao S, Slugoski M, et al. (2004) Cloning and functional characterization of the human GLUT7 isoform SLC2A7 from the small intestine. Am J Physiol Gastrointest Liver Physiol 287: G236–G242.
[73]
Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422–1423.
[74]
Luck K, Travé G (2011) Phage display can select over-hydrophobic sequences that may impair prediction of natural domain-peptide interactions. Bioinformatics 27: 899–902.
[75]
Katoh K, Toh H (2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics 23: 372–374.
[76]
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189–1191.
[77]
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The protein data bank. Nucleic Acids Res 28: 235–242.
