Frontiers in Biology

, Volume 8, Issue 2, pp 216–227 | Cite as

Current technologies to identify protein kinase substrates in high throughput



Since the discovery of protein phosphorylation as an important modulator of many cellular processes, the involvement of protein kinases in diseases, such as cancer, diabetes, cardiovascular diseases, and central nervous system pathologies, has been extensively documented. Our understanding of many disease pathologies at the molecular level, therefore, requires the comprehensive identification of substrates targeted by protein kinases. In this review, we focus on recent techniques for kinase substrate identification in high throughput, in particular on genetic and proteomic approaches. Each method with its inherent advantages and limitations is discussed.


phosphorylation kinase substrate in vitro kinase assay high throughput screening mass spectrometry phosphoproteomics 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Amanchy R, Zhong J, Molina H, Chaerkady R, Iwahori A, Kalume D E, Grønborg M, Joore J, Cope L, Pandey A (2008). Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. J Proteome Res, 7(9): 3900–3910PubMedCrossRefGoogle Scholar
  2. Amano M, Tsumura Y, Taki K, Harada H, Mori K, Nishioka T, Kato K, Suzuki T, Nishioka Y, Iwamatsu A, Kaibuchi K (2010). A proteomic approach for comprehensively screening substrates of protein kinases such as Rho-kinase. PLoS ONE, 5(1): e8704PubMedCrossRefGoogle Scholar
  3. Belozerov V E, Lin Z Y, Gingras A C, McDermott J C, MichaelSiu KW (2012). High-resolution protein interaction map of the Drosophila melanogaster p38 mitogen-activated protein kinases reveals limited functional redundancy. Mol Cell Biol, 32(18): 3695–3706PubMedCrossRefGoogle Scholar
  4. Blethrow J, Zhang C, Shokat K M, Weiss E L (2004). Design and use of analog-sensitive protein kinases. Curr Protoc Mol Biol, Chapter 18, Unit 18 11.Google Scholar
  5. Blume-Jensen P, Hunter T (2001). Oncogenic kinase signalling. Nature, 411(6835): 355–365PubMedCrossRefGoogle Scholar
  6. Breitkreutz A, Choi H, Sharom J R, Boucher L, Neduva V, Larsen B, Lin Z Y, Breitkreutz B J, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin Z S, Pawson T, Gingras A C, Nesvizhskii A I, Tyers M (2010). A global protein kinase and phosphatase interaction network in yeast. Science, 328(5981): 1043–1046PubMedCrossRefGoogle Scholar
  7. Buss H, Dörrie A, Schmitz M L, Frank R, Livingstone M, Resch K, Kracht M (2004). Phosphorylation of serine 468 by GSK-3β negatively regulates basal p65 NF-κB activity. J Biol Chem, 279(48): 49571–49574PubMedCrossRefGoogle Scholar
  8. Cañas B, López-Ferrer D, Ramos-Fernández A, Camafeita E, Calvo E (2006). Mass spectrometry technologies for proteomics. Brief Funct Genomics Proteomics, 4(4): 295–320CrossRefGoogle Scholar
  9. Clark I E, Dodson M W, Jiang C, Cao J H, Huh J R, Seol J H, Yoo S J, Hay B A, Guo M (2006). Drosophila pink1 is required for mitochondrial function and interacts genetically with parkin. Nature, 441(7097): 1162–1166PubMedCrossRefGoogle Scholar
  10. Coba M P, Pocklington A J, Collins M O, Kopanitsa M V, Uren R T, Swamy S, Croning M D, Choudhary J S, Grant S G (2009). Neurotransmitters drive combinatorial multistate postsynaptic density networks. Sci Signal, 2(68): ra19PubMedCrossRefGoogle Scholar
  11. Cohen P (2001). The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture. Eur J Biochem, 268(19): 5001–5010CrossRefGoogle Scholar
  12. Cohen P (2002). Protein kinases—the major drug targets of the twenty-first century? Nat Rev Drug Discov, 1(4): 309–315PubMedCrossRefGoogle Scholar
  13. Cohen P, Knebel A (2006). KESTREL: a powerful method for identifying the physiological substrates of protein kinases. Biochem J, 393(Pt 1): 1–6PubMedGoogle Scholar
  14. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear E D, Sevier C S, Ding H, Koh J L, Toufighi K, Mostafavi S, Prinz J, St Onge R P, Vander Sluis B, Makhnevych T, Vizeacoumar F J, Alizadeh S, Bahr S, Brost R L, Chen Y, Cokol M, Deshpande R, Li Z, Lin Z Y, Liang W, Marback M, Paw J, San Luis B J, Shuteriqi E, Tong A H, van Dyk N, Wallace I M, Whitney J A, Weirauch M T, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth F P, Giaever G, Nislow C, Troyanskaya O G, Bussey H, Bader G D, Gingras A C, Morris Q D, Kim P M, Kaiser C A, Myers C L, Andrews B J, Boone C (2010). The genetic landscape of a cell. Science, 327(5964): 425–431PubMedCrossRefGoogle Scholar
  15. Daub H, Olsen J V, Bairlein M, Gnad F, Oppermann F S, Körner R, Greff Z, Kéri G, Stemmann O, Mann M (2008). Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell, 31(3): 438–448PubMedCrossRefGoogle Scholar
  16. Delom F, Chevet E (2006). Phosphoprotein analysis: from proteins to proteomes. Proteome Sci, 4(1): 15PubMedCrossRefGoogle Scholar
  17. Dente L, Vetriani C, Zucconi A, Pelicci G, Lanfrancone L, Pelicci P G, 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(5): 694–703PubMedCrossRefGoogle Scholar
  18. Dephoure N, Howson R W, Blethrow J D, Shokat K M, O’Shea E K (2005). Combining chemical genetics and proteomics to identify protein kinase substrates. Proc Natl Acad Sci USA, 102(50): 17940–17945PubMedCrossRefGoogle Scholar
  19. Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva A C, Shales M, Collins S R, van Wageningen S, Kemmeren P, Holstege F C, Weissman J S, Keogh M C, Koller D, Shokat K M, Krogan N J (2009). Functional organization of the S. cerevisiae phosphorylation network. Cell, 136(5): 952–963PubMedCrossRefGoogle Scholar
  20. Fujii K, Zhu G, Liu Y, Hallam J, Chen L, Herrero J, Shaw S (2004). Kinase peptide specificity: improved determination and relevance to protein phosphorylation. Proc Natl Acad Sci USA, 101(38): 13744–13749PubMedCrossRefGoogle Scholar
  21. Fukunaga R, Hunter T (1997). MNK1, a new MAP kinase-activated protein kinase, isolated by a novel expression screening method for identifying protein kinase substrates. EMBO J, 16(8): 1921–1933PubMedCrossRefGoogle Scholar
  22. Gavin A C, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen L J, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier M A, Hoffman V, Hoefert C, Klein K, Hudak M, Michon A M, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick J M, Kuster B, Bork P, Russell R B, Superti-Furga G (2006). Proteome survey reveals modularity of the yeast cell machinery. Nature, 440(7084): 631–636PubMedCrossRefGoogle Scholar
  23. Gavin A C, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick J M, Michon A M, Cruciat C M, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier M A, Copley R R, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415(6868): 141–147PubMedCrossRefGoogle Scholar
  24. Habelhah H, Shah K, Huang L, Burlingame A L, Shokat K M, Ronai Z (2001). Identification of new JNK substrate using ATP pocket mutant JNK and a corresponding ATP analogue. J Biol Chem, 276(21): 18090–18095PubMedCrossRefGoogle Scholar
  25. Huang S Y, Tsai ML, Chen G Y, Wu C J, Chen S H (2007). A systematic MS-based approach for identifying in vitro substrates of PKA and PKG in rat uteri. J Proteome Res, 6(7): 2674–2684PubMedCrossRefGoogle Scholar
  26. Huang Y, Houston N L, Tovar-Mendez A, Stevenson S E, Miernyk J A, Randall D D, Thelen J J (2010). A quantitative mass spectrometrybased approach for identifying protein kinase clients and quantifying kinase activity. Anal Biochem, 402(1): 69–76PubMedCrossRefGoogle Scholar
  27. Hunter T (2000). Signaling—2000 and beyond. Cell, 100(1): 113–127PubMedCrossRefGoogle Scholar
  28. Iliuk A B, Martin V A, Alicie B M, Geahlen R L, Tao W A (2010). Indepth analyses of kinase-dependent tyrosine phosphoproteomes based on metal ion-functionalized soluble nanopolymers. Mol Cell Proteomics, 9(10): 2162–2172PubMedCrossRefGoogle Scholar
  29. Jeong J S, Jiang L Z, Albino E, Marrero J, Rho H S, Hu J F, Hu S H, Vera C, Bayron-Poueymiroy D, Rivera-Pacheco Z A, Ramos L, Torres-Castro C, Qian J, Bonaventura J, Boeke J D, Yap W Y, Pino I, Eichinger D J, Zhu H, Blackshaw S (2012). Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics, 11(6): 016253PubMedGoogle Scholar
  30. Jiang W, Jimenez G, Wells N J, Hope T J, Wahl G M, Hunter T, Fukunaga R (1998). PRC1: a human mitotic spindle-associated CDK substrate protein required for cytokinesis. Mol Cell, 2(6): 877–885PubMedCrossRefGoogle Scholar
  31. Jin L L, Tong J F, Prakash A, Peterman S M, St-Germain J R, Taylor P, Trudel S, Moran M F (2010). Measurement of protein phosphorylation stoichiometry by selected reaction monitoring mass spectrometry. J Proteome Res, 9(5): 2752–2761PubMedCrossRefGoogle Scholar
  32. Johnson S A, Hunter T (2005). Kinomics: methods for deciphering the kinome. Nat Methods, 2(1): 17–25PubMedCrossRefGoogle Scholar
  33. Kettenbach A N, Schweppe D K, Faherty B K, Pechenick D, Pletnev A A, Gerber S A (2011). Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells. Sci Signal, 4(179): rs5PubMedCrossRefGoogle Scholar
  34. Khati M, Pillay T S (2004). Phosphotyrosine phosphoepitopes can be rapidly analyzed by coexpression of a tyrosine kinase in bacteria with a T7 bacteriophage display library. Anal Biochem, 325(1): 164–167PubMedCrossRefGoogle Scholar
  35. Kim M, Shin D S, Kim J, Lee Y S (2010). Substrate screening of protein kinases: detection methods and combinatorial peptide libraries. Biopolymers, 94(6): 753–762PubMedCrossRefGoogle Scholar
  36. Kim Y G, Shin D S, Kim EM, Park H Y, Lee C S, Kim J H, Lee B S, Lee Y S, Kim B G (2007). High-throughput identification of substrate specificity for protein kinase by using an improved one-bead-one-compound library approach. Angew Chem Int Ed Engl, 46(28): 5408–5411PubMedCrossRefGoogle Scholar
  37. Knebel A, Morrice N, Cohen P (2001). A novel method to identify protein kinase substrates: eEF2 kinase is phosphorylated and inhibited by SAPK4/p38delta. EMBO J, 20(16): 4360–4369PubMedCrossRefGoogle Scholar
  38. Kosako H, Nagano K (2011). Quantitative phosphoproteomics strategies for understanding protein kinase-mediated signal transduction pathways. Expert Rev Proteomics, 8(1): 81–94PubMedCrossRefGoogle Scholar
  39. Kreegipuu A, Blom N, Brunak S, Järv J (1998). Statistical analysis of protein kinase specificity determinants. FEBS Lett, 430(1–2): 45–50PubMedCrossRefGoogle Scholar
  40. Krogan N J, Cagney G, Yu H Y, Zhong G Q, Guo X H, Ignatchenko A, Li J, Pu S Y, Datta N, Tikuisis A P, Punna T, Peregrín-Alvarez J M, Shales M, Zhang X, Davey M, Robinson M D, Paccanaro A, Bray J E, Sheung A, Beattie B, Richards D P, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete M M, Vlasblom J, Wu S, Orsi C, Collins S R, Chandran S, Haw R, Rilstone J J, Gandi K, Thompson N J, Musso G, St Onge P, Ghanny S, Lam M H, Butland G, Altaf-Ul A M, Kanaya S, Shilatifard A, O’Shea E, Weissman J S, Ingles C J, Hughes T R, Parkinson J, Gerstein M, Wodak S J, Emili A, Greenblatt J F (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440(7084): 637–643PubMedCrossRefGoogle Scholar
  41. Lam K S, Wu J Z, Lou Q (1995). Identification and characterization of a novel synthetic peptide substrate specific for Src-family protein tyrosine kinases. Int J Pept Protein Res, 45(6): 587–592PubMedCrossRefGoogle Scholar
  42. Lander E S, Linton L M, Birren B, Nusbaum C, Zody M C, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov J P, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin J C, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston R H, Wilson R K, Hillier L W, McPherson J D, Marra MA, Mardis E R, Fulton L A, Chinwalla A T, Pepin K H, Gish W R, Chissoe S L, Wendl M C, Delehaunty K D, Miner T L, Delehaunty A, Kramer J B, Cook L L, Fulton R S, Johnson D L, Minx P J, Clifton S W, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng J F, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs R A, Muzny D M, Scherer S E, Bouck J B, Sodergren E J, Worley K C, Rives C M, Gorrell J H, Metzker M L, Naylor S L, Kucherlapati R S, Nelson D L, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith D R, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee H M, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis R W, Federspiel N A, Abola A P, Proctor M J, Myers R M, Schmutz J, Dickson M, Grimwood J, Cox D R, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans G A, Athanasiou M, Schultz R, Roe B A, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie W R, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey J A, Bateman A, Batzoglou S, Birney E, Bork P, Brown D G, Burge C B, Cerutti L, Chen H C, Church D, Clamp M, Copley R R, Doerks T, Eddy S R, Eichler E E, Furey T S, Galagan J, Gilbert J G, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson L S, Jones T A, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin E V, Korf I, Kulp D, Lancet D, Lowe T M, McLysaght A, Mikkelsen T, Moran J V, Mulder N, Pollara V J, Ponting C P, Schuler G, Schultz J, Slater G, Smit A F, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf Y I, Wolfe K H, Yang S P, Yeh R F, Collins F, Guyer M S, Peterson J, Felsenfeld A, Wetterstrand K A, Patrinos A, Morgan M J, de Jong P, Catanese J J, Osoegawa K, Shizuya H, Choi S, Chen Y J, and the International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature, 409(6822): 860–921PubMedCrossRefGoogle Scholar
  43. Leberer E, Thomas D Y, Whiteway M(1997). Pheromone signalling and polarized morphogenesis in yeast. Curr Opin Genet Dev, 7(1): 59–66PubMedCrossRefGoogle Scholar
  44. Lesaicherre M L, Uttamchandani M, Chen G Y J, Yao S Q (2002). Antibody-based fluorescence detection of kinase activity on a peptide array. Bioorg Med Chem Lett, 12(16): 2085–2088PubMedCrossRefGoogle Scholar
  45. Linding R, Jensen L J, Ostheimer G J, van Vugt M A, Jørgensen C, Miron I M, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park J G, Samson L D, Woodgett J R, Russell R B, Bork P, Yaffe M B, Pawson T (2007). Systematic discovery of in vivo phosphorylation networks. Cell, 129(7): 1415–1426PubMedCrossRefGoogle Scholar
  46. Lou Q, Leftwich M E, Lam K S (1996). Identification of GIYWHHY as a novel peptide substrate for human p60c-src protein tyrosine kinase. Bioorg Med Chem, 4(5): 677–682PubMedCrossRefGoogle Scholar
  47. Mah A S, Elia A E, Devgan G, Ptacek J, Schutkowski M, Snyder M, Yaffe M B, Deshaies R J (2005). Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening. BMC Biochem, 6(1): 22PubMedCrossRefGoogle Scholar
  48. Manning B D, Cantley L C (2002). Hitting the target: emerging technologies in the search for kinase substrates. Sci STKE, 2002(162): pe49PubMedCrossRefGoogle Scholar
  49. Manning B D, Tee A R, Logsdon M N, Blenis J, Cantley L C (2002a). Identification of the tuberous sclerosis complex-2 tumor suppressor gene product tuberin as a target of the phosphoinositide 3-kinase/akt pathway. Mol Cell, 10(1): 151–162PubMedCrossRefGoogle Scholar
  50. Manning G, Whyte D B, Martinez R, Hunter T, Sudarsanam S (2002b). The protein kinase complement of the human genome. Science, 298(5600): 1912–1934PubMedCrossRefGoogle Scholar
  51. Morandell S, Grosstessner-Hain K, Roitinger E, Hudecz O, Lindhorst T, Teis D, Wrulich O A, Mazanek M, Taus T, Ueberall F, Mechtler K, Huber L A (2010). QIKS—Quantitative identification of kinase substrates. Proteomics, 10(10): 2015–2025PubMedCrossRefGoogle Scholar
  52. Neville D C, Rozanas C R, Price E M, Gruis D B, Verkman A S, Townsend R R (1997). Evidence for phosphorylation of serine 753 in CFTR using a novel metal-ion affinity resin and matrix-assisted laser desorption mass spectrometry. Protein Sci, 6(11): 2436–2445PubMedCrossRefGoogle Scholar
  53. Obenauer J C, Cantley L C, Yaffe M B (2003). Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res, 31(13): 3635–3641PubMedCrossRefGoogle Scholar
  54. Paradis S, Ruvkun G (1998). Caenorhabditis elegans Akt/PKB transduces insulin receptor-like signals from AGE-1 PI3 kinase to the DAF-16 transcription factor. Genes Dev, 12(16): 2488–2498PubMedCrossRefGoogle Scholar
  55. Pawson T (2004). Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell, 116(2): 191–203PubMedCrossRefGoogle Scholar
  56. Pillay T S (2004). A fisherman’s tale: Phage display as a discovery tool. Discov Med, 4(23): 315–318PubMedGoogle Scholar
  57. Pinkse M W, Uitto P M, Hilhorst M J, Ooms B, Heck A J (2004). Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem, 76(14): 3935–3943PubMedCrossRefGoogle Scholar
  58. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney R R, Schmidt M C, Rachidi N, Lee S J, Mah A S, Meng L, Stark M J, Stern D F, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki P F, Snyder M (2005). Global analysis of protein phosphorylation in yeast. Nature, 438(7068): 679–684PubMedCrossRefGoogle Scholar
  59. Rubin GM, Yandell MD, Wortman J R, Gabor Miklos G L, Nelson C R, Hariharan I K, Fortini M E, Li P W, Apweiler R, Fleischmann W, Cherry J M, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski M S, Brody T, Brokstein P, Celniker S E, Chervitz S A, Coates D, Cravchik A, Gabrielian A, Galle R F, Gelbart W M, George R A, Goldstein L S, Gong F, Guan P, Harris N L, Hay B A, Hoskins R A, Li J, Li Z, Hynes R O, Jones S J, Kuehl P M, Lemaitre B, Littleton J T, Morrison D K, Mungall C, O’Farrell P H, Pickeral O K, Shue C, Vosshall L B, Zhang J, Zhao Q, Zheng X H, Lewis S (2000). Comparative genomics of the eukaryotes. Science, 287(5461): 2204–2215PubMedCrossRefGoogle Scholar
  60. Schmitz R, Baumann G, Gram H (1996). Catalytic specificity of phosphotyrosine kinases Blk, Lyn, c-Src and Syk as assessed by phage display. J Mol Biol, 260(5): 664–677PubMedCrossRefGoogle Scholar
  61. Sha D, Chin L S, Li L (2010). Phosphorylation of parkin by Parkinson disease-linked kinase PINK1 activates parkin E3 ligase function and NF-κB signaling. Hum Mol Genet, 19(2): 352–363PubMedCrossRefGoogle Scholar
  62. Shah K, Liu Y, Deirmengian C, Shokat K M (1997). Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc Natl Acad Sci USA, 94(8): 3565–3570PubMedCrossRefGoogle Scholar
  63. Shin D S, Kim Y G, Kim EM, Kim M, Park H Y, Kim J H, Lee B S, Kim B G, Lee Y S (2008). Solid-phase peptide library synthesis on HiCore resin for screening substrate specificity of Brk protein tyrosine kinase. J Comb Chem, 10(1): 20–23PubMedCrossRefGoogle Scholar
  64. Song C, Ye M, Liu Z, Cheng H, Jiang X, Han G, Songyang Z, Tan Y, Wang H, Ren J, Xue Y, Zou H (2012). Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Mol Cell Proteomics, 11(10): 1070–1083PubMedCrossRefGoogle Scholar
  65. Songyang Z, Carraway K L 3rd, Eck M J, Harrison S C, Feldman R A, Mohammadi M, Schlessinger J, Hubbard S R, Smith D P, Eng C, Lorenzo MJ, Ponder B A J, Mayer B J, Cantley L C (1995). Catalytic specificity of protein-tyrosine kinases is critical for selective signalling. Nature, 373(6514): 536–539PubMedCrossRefGoogle Scholar
  66. Songyang Z, Lu K P, Kwon Y T, Tsai L H, Filhol O, Cochet C, Brickey D A, Soderling T R, Bartleson C, Graves D J, DeMaggio A J, Hoekstra M F, Blenis J, Hunter T, Cantley L C (1996). A structural basis for substrate specificities of protein Ser/Thr kinases: primary sequence preference of casein kinases I and II, NIMA, phosphorylase kinase, calmodulin-dependent kinase II, CDK5, and Erk1. Mol Cell Biol, 16(11): 6486–6493PubMedGoogle Scholar
  67. Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver S G, Cyert M, Hughes T R, Boone C, Andrews B (2006). Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell, 21(3): 319–330PubMedCrossRefGoogle Scholar
  68. Staudinger J, Zhou J, Burgess R, Elledge S J, Olson E N (1995). PICK1: a perinuclear binding protein and substrate for protein kinase C isolated by the yeast two-hybrid system. J Cell Biol, 128(3): 263–271PubMedCrossRefGoogle Scholar
  69. Tien A C, Lin M H, Su L J, Hong Y R, Cheng T S, Lee Y C, Lin W J, Still I H, Huang C Y (2004). Identification of the substrates and interaction proteins of aurora kinases from a protein-protein interaction model. Mol Cell Proteomics, 3(1): 93–104PubMedGoogle Scholar
  70. Troiani S, Uggeri M, Moll J, Isacchi A, Kalisz H M, Rusconi L, Valsasina B (2005). Searching for biomarkers of Aurora-A kinase activity: identification of in vitro substrates through a modified KESTREL approach. J Proteome Res, 4(4): 1296–1303PubMedCrossRefGoogle Scholar
  71. Vadlamudi R K, Li F, Adam L, Nguyen D, Ohta Y, Stossel T P, Kumar R (2002). Filamin is essential in actin cytoskeletal assembly mediated by p21-activated kinase 1. Nat Cell Biol, 4(9): 681–690PubMedCrossRefGoogle Scholar
  72. Witze E S, Old W M, Resing K A, Ahn N G (2007). Mapping protein post-translational modifications with mass spectrometry. Nat Methods, 4(10): 798–806PubMedCrossRefGoogle Scholar
  73. Wu R H, Haas W, Dephoure N, Huttlin E L, Zhai B, Sowa ME, Gygi S P (2011). A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat Methods, 8(8): 677–683PubMedCrossRefGoogle Scholar
  74. Xue L, Wang W H, Iliuk A, Hu L, Galan J A, Yu S, Hans M, Geahlen R L, Tao W A (2012). Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates. Proc Natl Acad Sci USA, 109(15): 5615–5620PubMedCrossRefGoogle Scholar
  75. Yaffe MB, Leparc G G, Lai J, Obata T, Volinia S, Cantley L C (2001). A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nat Biotechnol, 19(4): 348–353PubMedCrossRefGoogle Scholar
  76. Yang X, Hubbard E J, Carlson M (1992). A protein kinase substrate identified by the two-hybrid system. Science, 257(5070): 680–682PubMedCrossRefGoogle Scholar
  77. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean R A, Gerstein M, Snyder M (2001). Global analysis of protein activities using proteome chips. Science, 293(5537): 2101–2105PubMedCrossRefGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of BiochemistryPurdue UniversityWest LafayetteUSA
  2. 2.Department of Medicinal Chemistry & Molecular PharmacologyPurdue UniversityWest LafayetteUSA
  3. 3.Department of ChemistryPurdue UniversityWest LafayetteUSA
  4. 4.Purdue University Center for Cancer ResearchPurdue UniversityWest LafayetteUSA

Personalised recommendations