title: Biochemical and computational analysis of LNX1 interacting proteins.
abstract: PDZ (Post-synaptic density, 95 kDa, Discs large, Zona Occludens-1) domains are protein interaction domains that bind to the carboxy-terminal amino acids of binding partners, heterodimerize with other PDZ domains, and also bind phosphoinositides. PDZ domain containing proteins are frequently involved in the assembly of multi-protein complexes and clustering of transmembrane proteins. LNX1 (Ligand of Numb, protein X 1) is a RING (Really Interesting New Gene) domain-containing E3 ubiquitin ligase that also includes four PDZ domains suggesting it functions as a scaffold for a multi-protein complex. Here we use a human protein array to identify direct LNX1 PDZ domain binding partners. Screening of 8,000 human proteins with isolated PDZ domains identified 53 potential LNX1 binding partners. We combined this set with LNX1 interacting proteins identified by other methods to assemble a list of 220 LNX1 interacting proteins. Bioinformatic analysis of this protein list was used to select interactions of interest for future studies. Using this approach we identify and confirm six novel LNX1 binding partners: KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2 and PBK, and suggest that LNX1 functions as a signalling scaffold.
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, Canada.
authors.forename: Cheryl D
authors.initials: CD
authors.lastname: Wolting
authors.forename: Emily K
authors.initials: EK
authors.lastname: Griffiths
authors.forename: Renu
authors.initials: R
authors.lastname: Sarao
authors.forename: Brittany C
authors.initials: BC
authors.lastname: Prevost
authors.forename: Leanne E
authors.initials: LE
authors.lastname: Wybenga-Groot
authors.forename: C Jane
authors.initials: CJ
authors.lastname: McGlade
mesh_terms: D019295:Computational Biology; D004353:Drug Evaluation, Preclinical; D006801:Humans; D054731:PDZ Domains; D011485:Protein Binding; D025941:Protein Interaction Mapping; D015398:Signal Transduction; D044767:Ubiquitin-Protein Ligases / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology
chemical_list: C484733:LNX1 protein, human; D044767:Ubiquitin-Protein Ligases
references.citation: Exp Cell Res. 2006 Apr 1;312(6):817-30
references.pmid: 16410001
references.citation: Nat Biotechnol. 2002 Oct;20(10):991-7
references.pmid: 12355115
references.citation: Front Biosci (Landmark Ed). 2009 Jan 01;14:2386-99
references.pmid: 19273207
references.citation: BMC Bioinformatics. 2007 Nov 22;8:460
references.pmid: 18034891
references.citation: J Cell Sci. 2009 Apr 1;122(Pt 7):985-94
references.pmid: 19295125
references.citation: J Biol Chem. 2004 May 14;279(20):20807-15
references.pmid: 14990566
references.citation: Genomics. 1993 Feb;15(2):463-4
references.pmid: 8449523
references.citation: Pflugers Arch. 2007 Aug;454(5):821-47
references.pmid: 17487503
references.citation: Biochem Genet. 2001 Apr;39(3-4):117-26
references.pmid: 11521506
references.citation: J Cell Biol. 2001 Nov 26;155(5):809-20
references.pmid: 11724822
references.citation: J Cell Biol. 2004 Jan 19;164(2):301-11
references.pmid: 14734538
references.citation: Immunol Rev. 2009 Mar;228(1):273-87
references.pmid: 19290934
references.citation: Int Rev Cell Mol Biol. 2008;267:253-98
references.pmid: 18544501
references.citation: Eur J Biochem. 2000 Jun;267(11):3116-22
references.pmid: 10824095
references.citation: Annu Rev Immunol. 1995;13:369-98
references.pmid: 7612228
references.citation: Trends Biochem Sci. 2008 Aug;33(8):394-403
references.pmid: 18639460
references.citation: PLoS Biol. 2008 Sep 30;6(9):e239
references.pmid: 18828675
references.citation: J Biol Chem. 1998 Apr 10;273(15):9179-87
references.pmid: 9535908
references.citation: Mol Cell Biol. 2003 Jun;23(12):4267-82
references.pmid: 12773569
references.citation: J Biol Chem. 2003 Feb 28;278(9):7439-44
references.pmid: 12468544
references.citation: Bioinformatics. 2005 Mar;21(6):827-8
references.pmid: 15513994
references.citation: Biochim Biophys Acta. 2006 Aug;1761(8):947-56
references.pmid: 16884951
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
references.pmid: 16381927
references.citation: Mol Biol Cell. 2000 Dec;11(12):4217-25
references.pmid: 11102519
references.citation: Curr Drug Targets. 2008 Aug;9(8):614-25
references.pmid: 18691009
references.citation: Oncogene. 2006 Aug 24;25(37):5071-84
references.pmid: 16832352
references.citation: Exp Cell Res. 2005 Sep 10;309(1):110-20
references.pmid: 15979067
references.citation: Genes Cells. 2003 Sep;8(9):759-68
references.pmid: 12940823
references.citation: J Mol Biol. 2000 Oct 27;303(3):359-70
references.pmid: 11031113
references.citation: Mol Cell Proteomics. 2006 Aug;5(8):1368-81
references.pmid: 16635984
references.citation: J Virol. 2004 Oct;78(19):10310-9
references.pmid: 15367597
references.citation: J Cell Biol. 2002 Aug 5;158(3):577-90
references.pmid: 12163476
references.citation: Bioinformatics. 2002;18 Suppl 2:S64
references.pmid: 12385984
references.citation: J Cell Sci. 2004 Sep 1;117(Pt 19):4401-9
references.pmid: 15304526
references.citation: Int J Biochem Cell Biol. 2005 Nov;37(11):2273-83
references.pmid: 16002321
references.citation: FEBS Lett. 2001 May 11;496(2-3):101-4
references.pmid: 11356191
references.citation: Cell. 1996 Jun 28;85(7):1067-76
references.pmid: 8674113
references.citation: Mol Cell Neurosci. 2005 Oct;30(2):238-48
references.pmid: 16122940
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: Genes Cells. 2004 Sep;9(9):811-9
references.pmid: 15330858
references.citation: Science. 2007 Jul 20;317(5836):364-9
references.pmid: 17641200
references.citation: Biochem Biophys Res Commun. 2007 Mar 16;354(3):686-92
references.pmid: 17257582
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
references.pmid: 20383002
references.citation: Nat Rev Neurosci. 2009 Feb;10(2):87-99
references.pmid: 19153575
references.citation: Mol Cell. 2007 Dec 14;28(5):886-98
references.pmid: 18082612
references.citation: Mol Cell Neurosci. 2001 Nov;18(5):525-40
references.pmid: 11922143
references.citation: FEBS Lett. 2007 Oct 30;581(26):5131-6
references.pmid: 17936276
references.citation: Nat Rev Cancer. 2006 Jun;6(6):459-71
references.pmid: 16723992
references.citation: Biochemistry. 2007 Nov 27;46(47):13629-37
references.pmid: 17979300
references.citation: Mol Cell. 2002 Jun;9(6):1215-25
references.pmid: 12086619
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D557-60
references.pmid: 17135199
references.citation: EMBO J. 2002 Jan 15;21(1-2):93-102
references.pmid: 11782429
references.citation: BMC Bioinformatics. 2006 Jul 12;7:338
references.pmid: 16836750
references.citation: Nature. 2005 Oct 20;437(7062):1173-8
references.pmid: 16189514
references.citation: EMBO J. 2007 Oct 31;26(21):4576-87
references.pmid: 17914463
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D590-4
references.pmid: 17158159
references.citation: Physiol Rev. 2008 Oct;88(4):1341-78
references.pmid: 18923184
references.citation: J Biol Chem. 1999 Nov 12;274(46):33097-104
references.pmid: 10551880
references.citation: Genomics. 1993 Dec;18(3):568-74
references.pmid: 7905852
references.citation: Mini Rev Med Chem. 2009 Apr;9(4):498-509
references.pmid: 19356127
references.citation: Mol Biol Rep. 2010 Jun;37(5):2431-7
references.pmid: 19701800