Predicting CK2 beta-dependent substrates using linear patterns

Guerra, 2008, Protein kinase CK2 in human diseases, Curr. Med. Chem., 15, 1870, 10.2174/092986708785132933 Salvi, 2009, Extraordinary pleiotropy of protein kinase CK2 revealed by weblogo phosphoproteome analysis, Biochim. Biophys. Acta, 1793, 847, 10.1016/j.bbamcr.2009.01.013 Meggio, 2003, One-thousand-and-one substrates of protein kinase CK2?, FASEB J., 17, 349, 10.1096/fj.02-0473rev Pinna, 2002, Protein kinase CK2: a challenge to canons, J. Cell Sci., 115, 3873, 10.1242/jcs.00074 Olsen, 2012, Protein kinase CK2 localizes to sites of DNA double-strand break regulating the cellular response to DNA damage, BMC Mol. Biol., 13, 7, 10.1186/1471-2199-13-7 Di Maira, 2007, Pharmacological inhibition of protein kinase CK2 reverts the multidrug resistance phenotype of a CEM cell line characterized by high CK2 level, Oncogene, 26, 6915, 10.1038/sj.onc.1210495 St-Denis, 2009, Protein kinase CK2 in health and disease: From birth to death: the role of protein kinase CK2 in the regulation of cell proliferation and survival, Cell. Mol. Life Sci., 66, 1817, 10.1007/s00018-009-9150-2 Perea, 2008, CIGB-300, a novel proapoptotic peptide that impairs the CK2 phosphorylation and exhibits anticancer properties both in vitro and in vivo, Mol. Cell. Biochem., 316, 163, 10.1007/s11010-008-9814-5 Litchfield, 2003, Protein kinase CK2: structure, regulation and role in cellular decisions of life and death, Biochem. J., 369, 1, 10.1042/bj20021469 Niefind, 2001, Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme, EMBO J., 20, 5320, 10.1093/emboj/20.19.5320 Filhol, 2003, Live-cell fluorescence imaging reveals the dynamics of protein kinase CK2 individual subunits, Mol. Cell. Biol., 23, 975, 10.1128/MCB.23.3.975-987.2003 Bibby, 2005, The multiple personalities of the regulatory subunit of protein kinase CK2: CK2 dependent and CK2 independent roles reveal a secret identity for CK2beta, Int. J. Biol. Sci., 1, 67, 10.7150/ijbs.1.67 Zanin, 2015, Chimeric peptides as modulators of CK2-dependent signaling: mechanism of action and off-target effects, Biochim. Biophys. Acta, 10.1016/j.bbapap.2015.04.026 Meggio, 1994, Casein kinase 2 down-regulation and activation by polybasic peptides are mediated by acidic residues in the 55-64 region of the beta-subunit A study with calmodulin as phosphorylatable substrate, Biochemistry, 33, 4336, 10.1021/bi00180a030 Arrigoni, 2004, Phosphorylation of calmodulin fragments by protein kinase CK2 Mechanistic aspects and structural consequences, Biochemistry, 43, 12788, 10.1021/bi049365c Marin, 2000, Unique features of HIV-1 Rev protein phosphorylation by protein kinase CK2 (’casein kinase-2’), FEBS Lett., 481, 63, 10.1016/S0014-5793(00)01971-2 Meggio, 2001, HIV-1 Rev transactivator: a beta-subunit directed substrate and effector of protein kinase CK2, Mol. Cell. Biochem., 227, 145, 10.1023/A:1013177326481 Poletto, 2008, The regulatory beta subunit of protein kinase CK2 contributes to the recognition of the substrate consensus sequence A study with an eIF2 beta-derived peptide, Biochemistry, 47, 8317, 10.1021/bi800216d Ford, 2000, Cell cycle-regulated phosphorylation of the human SIX1 homeodomain protein, J. Biol. Chem., 275, 22245, 10.1074/jbc.M002446200 Huillard, 2010, Disruption of CK2beta in embryonic neural stem cells compromises proliferation and oligodendrogenesis in the mouse telencephalon, Mol. Cell. Biol., 30, 2737, 10.1128/MCB.01566-09 Meng, 2010, CK2 phosphorylation of Pdx-1 regulates its transcription factor activity, Cell. Mol. Life Sci., 67, 2481, 10.1007/s00018-010-0348-0 Hochscherf, 2014, Development of a high-throughput screening-compatible assay to identify inhibitors of the CK2α/CK2β interaction, Anal. Biochem., 468C, 4 Maizel, 2002, Engrailed homeoprotein secretion is a regulated process, Development, 129, 3545, 10.1242/dev.129.15.3545 Palmeri, 2014, Exploiting holistic approaches to model specificity in protein phosphorylation, Front. Genet., 5, 315, 10.3389/fgene.2014.00315 Newman, 2014, Toward a systems-level view of dynamic phosphorylation networks, Front. Genet., 5, 263, 10.3389/fgene.2014.00263 M.Torii, G.Li, Z.Li, R.Oughtred, F.Diella, I.Celen, C.N.Arighi, H.Huang, K.Vijay-Shanker, C.H.Wu, RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information, Database (Oxford)., 2014 (2014). Chen, 2004, Content-rich biological network constructed by mining PubMed abstracts, BMC Bioinformatics, 5, 147, 10.1186/1471-2105-5-147 Hornbeck, 2012, PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse, Nucleic Acids Res., 40, D261, 10.1093/nar/gkr1122 Bian, 2013, Global screening of CK2 kinase substrates by an integrated phosphoproteomics workflow, Sci. Rep., 3, 3460, 10.1038/srep03460 de Castro, 2006, ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Res., 34, W362, 10.1093/nar/gkl124 Berman, 2002, The Protein Data Bank, Acta Crystallogr. D. Biol. Crystallogr., 58, 899, 10.1107/S0907444902003451 Pettersen, 2004, UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 Wu, 2003, The Protein Information Resource, Nucleic Acids Res., 31, 345, 10.1093/nar/gkg040 Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, 7, 539 Huang, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211 Tabas-Madrid, 2012, GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics, Nucleic Acids Res., 40, W478, 10.1093/nar/gks402 Wang, 2014, NetVenn: an integrated network analysis web platform for gene lists, Nucleic Acids Res., 42, W161, 10.1093/nar/gku331 M.Magrane, U.Consortium, UniProt Knowledgebase: a hub of integrated protein data, Database (Oxford)., 2011 (2011) bar009. Doms, 2005, GoPubMed: exploring PubMed with the Gene Ontology, Nucleic Acids Res., 33, W783, 10.1093/nar/gki470 Xia, 2014, NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration, Nucleic Acids Res., 42, W167, 10.1093/nar/gku443 Berkey, 2006, A specific catalytic subunit isoform of protein kinase CK2 is required for phosphorylation of the repressor Nrg1 in Saccharomyces cerevisiae, Curr. Genet., 50, 1, 10.1007/s00294-006-0070-5 Bureik, 2005, Phosphorylation of bovine adrenodoxin by protein kinase CK2 affects the interaction with its redox partner cytochrome P450scc (CYP11A1), Biochemistry, 44, 3821, 10.1021/bi047697b Venerando, 2013, Detection of phospho-sites generated by protein kinase CK2 in CFTR: mechanistic aspects of Thr1471 phosphorylation, PLoS One, 8, e74232, 10.1371/journal.pone.0074232 Matthews, 2011, Stoichiometry versus hydrophobicity in protein folding, J. Biomol. Struct. Dyn., 28, 669 Diella, 2004, PhosphoELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins, BMC Bioinformatics, 5, 79, 10.1186/1471-2105-5-79 Bidwai, 1993, Phosphorylation of calmodulin by the catalytic subunit of casein kinase II is inhibited by the regulatory subunit, Arch. Biochem. Biophys., 300, 265, 10.1006/abbi.1993.1037 Meggio, 1992, The effect of polylysine on casein-kinase-2 activity is influenced by both the structure of the protein/peptide substrates and the subunit composition of the enzyme, Eur. J. Biochem., 205, 939, 10.1111/j.1432-1033.1992.tb16860.x Nelson, 2002, The EF-hand domain: a globally cooperative structural unit, Protein Sci., 11, 198, 10.1110/ps.33302 Sivachandran, 2010, Epstein-Barr virus nuclear antigen 1 Hijacks the host kinase CK2 to disrupt PML nuclear bodies, J. Virol., 84, 11113, 10.1128/JVI.01183-10 Wadd, 1999, The multifunctional herpes simplex virus IE63 protein interacts with heterogeneous ribonucleoprotein K and with casein kinase 2, J. Biol. Chem., 274, 28991, 10.1074/jbc.274.41.28991 Nüesch, 2006, NS1 interaction with CKII alpha: novel protein complex mediating parvovirus-induced cytotoxicity, J. Virol., 80, 4729, 10.1128/JVI.80.10.4729-4739.2006 Gao, 2009, Interaction of human cytomegalovirus pUL84 with casein kinase 2 is required for oriLyt-dependent DNA replication, J. Virol., 83, 2393, 10.1128/JVI.02339-08 Sun, 2011, Phosphorylation of RIG-I by casein kinase II inhibits its antiviral response, J. Virol., 85, 1036, 10.1128/JVI.01734-10 P.Henklein, U.Schubert, O.Kunert, S.Klabunde, V.Wray, K.D.Klöppel, M.Kiess, T.Portsmann, D.Schomburg, Synthesis and characterization of the hydrophilic C-terminal domain of the human immunodeficiency virus type 1-encoded virus protein U (Vpu), Pept. Res., 6 79–87. Schubert, 1994, The human immunodeficiency virus type 1 encoded Vpu protein is phosphorylated by casein kinase-2 (CK-2) at positions Ser52 and Ser56 within a predicted alpha-helix-turn-alpha-helix-motif, J. Mol. Biol., 236, 16, 10.1006/jmbi.1994.1114 Marshak, 1991, Synthetic peptide substrates for casein kinase II, Methods Enzymol., 200, 134, 10.1016/0076-6879(91)00135-J Grässer, 1992, Phosphorylation of the Epstein-Barr virus nuclear antigen 2, Biochem. Biophys. Res. Commun., 186, 1694, 10.1016/S0006-291X(05)81604-3 El-Guindy, 2006, Identification of constitutive phosphorylation sites on the Epstein-Barr virus ZEBRA protein, J. Biol. Chem., 281, 3085, 10.1074/jbc.M506076200 Kolman, 1993, Serine-173 of the Epstein-Barr virus ZEBRA protein is required for DNA binding and is a target for casein kinase II phosphorylation, Proc. Natl. Acad. Sci. U. S. A., 90, 10115, 10.1073/pnas.90.21.10115 El-Guindy, 2004, Phosphorylation of Epstein-Barr virus ZEBRA protein at its casein kinase 2 sites mediates its ability to repress activation of a viral lytic cycle late gene by Rta, J. Virol., 78, 7634, 10.1128/JVI.78.14.7634-7644.2004 Yeh, 1996, Casein kinase II and protein kinase C modulate hepatitis delta virus RNA replication but not empty viral particle assembly, J. Virol., 70, 6190, 10.1128/JVI.70.9.6190-6198.1996 Vincent, 1995, The human immunodeficiency virus type 1 Vpu protein: a potential regulator of proteolysis and protein transport in the mammalian secretory pathway, Virology, 213, 639, 10.1006/viro.1995.0035 Schubert, 1992, Human-immunodeficiency-virus-type-1-encoded Vpu protein is phosphorylated by casein kinase II, Eur. J. Biochem., 204, 875, 10.1111/j.1432-1033.1992.tb16707.x O’Brien, 1999, Casein Kinase 2 Binds to and Phosphorylates BRCA1, Biochem. Biophys. Res. Commun., 260, 658, 10.1006/bbrc.1999.0892 Homma, 2002, Association and regulation of casein kinase 2 activity by adenomatous polyposis coli protein, Proc. Natl. Acad. Sci. U. S. A., 99, 5959, 10.1073/pnas.092143199 McKendrick, 1999, Protein kinase CK2-dependent regulation of p53 function: evidence that the phosphorylation status of the serine 386 (CK2) site of p53 is constitutive and stable, Mol. Cell. Biochem., 191, 187, 10.1023/A:1006854109926 Becherel, 2010, CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response, Nucleic Acids Res., 38, 1489, 10.1093/nar/gkp1149 Slaton, 2004, Induction of apoptosis by antisense CK2 in human prostate cancer xenograft model, Mol. Cancer Res., 2, 712, 10.1158/1541-7786.712.2.12 Futreal, 2004, A census of human cancer genes, Nat. Rev. Cancer, 4, 177, 10.1038/nrc1299 Kappes, 2004, Phosphorylation by protein kinase CK2 changes the DNA binding properties of the human chromatin protein DEK, Mol. Cell. Biol., 24, 6011, 10.1128/MCB.24.13.6011-6020.2004