ADP-specific sensors enable universal assay of protein kinase activity

Chemistry and Biology

Volumn 11, Issue 4, 2004, Pages 499-508

  Srinivasan, Jayaram ^a   Cload, Sharon T ^a   Hamaguchi, Nobuko ^a   Kurz, Jeffrey ^a   Keene, Sara ^a   Kurz, Markus ^a   Boomer, Ryan M ^a   Blanchard, Jill ^a   Epstein, David ^a   Wilson, Charles ^a   Diener, John L ^a  

^a Archemix Corporation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; LIGAND; PROTEIN KINASE; RIBOZYME;

ARTICLE; CHEMISTRY; ENZYME SPECIFICITY; FLUORESCENCE; GENETIC PROCEDURES; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SIGNAL TRANSDUCTION; TIME;

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; BASE SEQUENCE; BIOSENSING TECHNIQUES; FLUORESCENCE; LIGANDS; MOLECULAR SEQUENCE DATA; PROTEIN KINASES; RNA, CATALYTIC; SIGNAL TRANSDUCTION; SUBSTRATE SPECIFICITY; TIME FACTORS;

EID: 1942477473     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2004.03.014     Document Type: Article

References (77)

1. Saito H. Histidine phosphorylation and two-component signaling in eukaryotic cells. Chem. Rev. 101:2001;2497-2509.
2. Manning G., Whyte D.B., Martinez R., Hunter T., Sudarsanam S. The protein kinase complement of the human genome. Science. 298:2002;1912-1934.
3. Moelling K., Strack B., Radziwill G. Signal transduction as target of gene therapy. Recent Results Cancer Res. 142:1996;63-71.
4. Fabbro D., Garcia-Echeverria C. Targeting protein kinases in cancer therapy. Curr. Opin. Drug Discov. Dev. 5:2002;701-712.
5. Orchard S. Kinases as targets. prospects for chronic therapy Curr. Opin. Drug Discov. Dev. 5:2002;713-717.
6. Chen G., Goeddel D.V. TNF-R1 signaling. a beautiful pathway Science. 296:2002;1634-1635.
7. Alton G., Schwamborn K., Satoh Y., Westwick J.K. Therapeutic modulation of inflammatory gene transcription by kinase inhibitors. Expert Opin. Biol. Ther. 2:2002;621-632.
8. Chen W., Wahl S.M. TGF-beta. receptors, signaling pathways and autoimmunity Curr. Dir. Autoimmun. 5:2002;62-91.
9. Shawver L.K., Slamon D., Ullrich A. Smart drugs. tyrosine kinase inhibitors in cancer therapy Cancer Cell. 1:2002;117-123.
10. Buchdunger E., O'Reilly T., Wood J. Pharmacology of imatinib (STI571). Eur. J. Cancer. 38(Suppl 5):2002;S28-S36.
11. McGary E.C., Weber K., Mills L., Doucet M., Lewis V., Lev D.C., Fidler I.J., Bar-Eli M. Inhibition of platelet-derived growth factor-mediated proliferation of osteosarcoma cells by the novel tyrosine kinase inhibitor STI571. Clin. Cancer Res. 8:2002;3584-3591.
12. Ranson M., Hammond L.A., Ferry D., Kris M., Tullo A., Murray P.I., Miller V., Averbuch S., Ochs J., Morris C.et al. ZD1839, a selective oral epidermal growth factor receptor-tyrosine kinase inhibitor, is well tolerated and active in patients with solid, malignant tumors. results of a phase I trial J. Clin. Oncol. 20:2002;2240-2250.
13. Ciardiello F., Bianco R., Damiano V., Fontanini G., Caputo R., Pomatico G., De Placido S., Bianco A.R., Mendelsohn J., Tortora G. Antiangiogenic and antitumor activity of anti-epidermal growth factor receptor C225 monoclonal antibody in combination with vascular endothelial growth factor antisense oligonucleotide in human GEO colon cancer cells. Clin. Cancer Res. 6:2000;3739-3747.
14. Schlessinger J. A solid base for assaying protein kinase activity. Nat. Biotechnol. 20:2002;232-233.
15. Zaman G.J., Garritsen A., de Boer T., van Boeckel C.A. Fluorescence assays for high-throughput screening of protein kinases. Comb. Chem. High Throughput Screen. 6:2003;313-320.
16. Mallari R., Swearingen E., Liu W., Ow A., Young S.W., Huang S.G. A generic high-throughput screening assay for kinases. protein kinase a as an example J. Biomol. Screen. 8:2003;198-204.
17. Ross H., Armstrong C.G., Cohen P. A non-radioactive method for the assay of many serine/threonine-specific protein kinases. Biochem. J. 366:2002;977-981.
18. Parker G.J., Law T.L., Lenoch F.J., Bolger R.E. Development of high throughput screening assays using fluorescence polarization. nuclear receptor-ligand-binding and kinase/phosphatase assays J. Biomol. Screen. 5:2000;77-88.
19. Seethala R., Menzel R. A fluorescence polarization competition immunoassay for tyrosine kinases. Anal. Biochem. 255:1998;257-262.
20. Sills M.A., Weiss D., Pham Q., Schweitzer R., Wu X., Wu J.J. Comparison of assay technologies for a tyrosine kinase assay generates different results in high throughput screening. J. Biomol. Screen. 7:2002;191-214.
21. Bader B., Butt E., Palmetshofer A., Walter U., Jarchau T., Drueckes P. A cGMP-dependent protein kinase assay for high throughput screening based on time-resolved fluorescence resonance energy transfer. J. Biomol. Screen. 6:2001;255-264.
22. Park Y.W., Cummings R.T., Wu L., Zheng S., Cameron P.M., Woods A., Zaller D.M., Marcy A.I., Hermes J.D. Homogeneous proximity tyrosine kinase assays. scintillation proximity assay versus homogeneous time-resolved fluorescence Anal. Biochem. 269:1999;94-104.
23. Braunwalder A.F., Yarwood D.R., Sills M.A., Lipson K.E. Measurement of the protein tyrosine kinase activity of c-src using time-resolved fluorometry of europium chelates. Anal. Biochem. 238:1996;159-164.
24. Rodems S.M.et al. A FRET-based assay platform for ultra-high density drug screening of protein kinases and phosphatases. Assay Drug Dev. Technol. 1:2002;9-19.
25. Beveridge M., Park Y.W., Hermes J., Marenghi A., Brophy G., Santos A. Detection of p56(lck) kinase activity using scintillation proximity assay in 384-well format and imaging proximity assay in 384- and 1536-well format. J. Biomol. Screen. 5:2000;205-212.
26. McDonald O.B., Chen W.J., Ellis B., Hoffman C., Overton L., Rink M., Smith A., Marshall C.J., Wood E.R. A scintillation proximity assay for the Raf/MEK/ERK kinase cascade. high-throughput screening and identification of selective enzyme inhibitors Anal. Biochem. 268:1999;318-329.
27. Jenkins W.T. The pyruvate kinase-coupled assay for ATPases. a critical analysis Anal. Biochem. 194:1991;136-139.
28. Bacher J.M., Ellington A.D. Nucleic acid selection as a tool for drug discovery. Drug Discov. Today. 3:1998;265-273.
29. Ellington A.D., Conrad R. Aptamers as potential nucleic acid pharmaceuticals. Biotechnol. Annu. Rev. 1:1995;185-214.
30. Osborne S.E., Matsumura I., Ellington A.D. Aptamers as therapeutic and diagnostic reagents. problems and prospects Curr. Opin. Chem. Biol. 1:1997;5-9.
31. Carmi N., Shultz L.A., Breaker R.R. In vitro selection of self-cleaving DNAs. Chem. Biol. 3:1996;1039-1046.
32. Breaker R.R. In vitro selection of catalytic polynucleotides. Chem. Rev. 97:1997;371-390.
33. Koizumi M., Breaker R.R. Molecular recognition of cAMP by an RNA aptamer. Biochemistry. 39:2000;8983-8992.
34. Koizumi M., Soukup G.A., Kerr J.N., Breaker R.R. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat. Struct. Biol. 6:1999;1062-1071.
35. Soukup G.A., Breaker R.R. Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA. 96:1999;3584-3589.
36. Hesselberth J., Robertson M.P., Jhaveri S., Ellington A.D. In vitro selection of nucleic acids for diagnostic applications. J. Biotechnol. 74:2000;15-25.
37. Marshall K.A., Ellington A.D. In vitro selection of RNA aptamers. Methods Enzymol. 318:2000;193-214.
38. Robertson M.P., Ellington A.D. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat. Biotechnol. 17:1999;62-66.
39. Kurz M., Breaker R.R. In vitro selection of nucleic acid enzymes. Curr. Top. Microbiol. Immunol. 243:1999;137-158.
40. Sassanfar M., Szostak J.W. An RNA motif that binds ATP. Nature. 364:1993;550-553.
41. Fitzwater T., Polisky B. A SELEX primer. Methods Enzymol. 267:1996;275-301.
42. Gold L. The SELEX process. a surprising source of therapeutic and diagnostic compounds Harvey Lect. 91:1995;47-57.
43. Tuerk C., MacDougal-Waugh S. In vitro evolution of functional nucleic acids. high-affinity RNA ligands of HIV-1 proteins Gene. 137:1993;33-39.
44. Prowse C.N., Deal M.S., Lew J. The complete pathway for catalytic activation of the mitogen-activated protein kinase, ERK2. J. Biol. Chem. 276:2001;40817-40823.
45. Prowse C.N., Lew J. Mechanism of activation of ERK2 by dual phosphorylation. J. Biol. Chem. 276:2001;99-103.
46. Robbins D.J., Zhen E., Owaki H., Vanderbilt C.A., Ebert D., Geppert T.D., Cobb M.H. Regulation and properties of extracellular signal-regulated protein kinases 1 and 2 in vitro. J. Biol. Chem. 268:1993;5097-5106.
47. English J.M., Cobb M.H. Pharmacological inhibitors of MAPK pathways. Trends Pharmacol. Sci. 23:2002;40-45.
48. Tang J., Breaker R.R. Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. Nucleic Acids Res. 26:1998;4214-4221.
49. Forster A.C., Symons R.H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell. 49:1987;211-220.
50. Prowse C.N., Hagopian J.C., Cobb M.H., Ahn N.G., Lew J. Catalytic reaction pathway for the mitogen-activated protein kinase ERK2. Biochemistry. 39:2000;14002.
51. Lipinski C.A., Lombardo F., Dominy B.W., Feeney P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 46:1997;3-26.
52. Zhang J.H., Chung T.D., Oldenburg K.R. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen. 4:1999;67-73.
53. Waas W.F., Lo H.H., Dalby K.N. The kinetic mechanism of the dual phosphorylation of the ATF2 transcription factor by p38 mitogen-activated protein (MAP) kinase alpha. Implications for signal/response profiles of MAP kinase pathways. J. Biol. Chem. 276:2001;5676-5684.
54. Horiuchi K.Y., Scherle P.A., Trzaskos J.M., Copeland R.A. Competitive inhibition of MAP kinase activation by a peptide representing the alpha C helix of ERK. Biochemistry. 37:1998;8879-8885.
55. Schindler J.F., Godbey A., Hood W.F., Bolten S.L., Broadus R.M., Kasten T.P., Cassely A.J., Hirsch J.L., Merwood M.A., Nagy M.A.et al. Examination of the kinetic mechanism of mitogen-activated protein kinase activated protein kinase-2. Biochim. Biophys. Acta. 1598:2002;88-97.
56. Trauger J.W., Lin F.F., Turner M.S., Stephens J., LoGrasso P.V. Kinetic mechanism for human Rho-Kinase II (ROCK-II). Biochemistry. 41:2002;8948-8953.
57. Turner M.S., Fen-Fen-Lin, Trauger J.W., Stephens J., LoGrasso P. Characterization and purification of truncated human Rho-kinase II expressed in Sf-21 cells. Arch. Biochem. Biophys. 405:2002;3-20.
58. Clare P.M., Poorman R.A., Kelley L.C., Watenpaugh K.D., Bannow C.A., Leach K.L. The cyclin-dependent kinases cdk2 and cdk5 act by a random, anticooperative kinetic mechanism. J. Biol. Chem. 276:2001;48292-48299.
59. Cole P.A., Burn P., Takacs B., Walsh C.T. Evaluation of the catalytic mechanism of recombinant human Csk (C-terminal Src kinase) using nucleotide analogs and viscosity effects. J. Biol. Chem. 269:1994;30880-30887.
60. Cole P.A., Grace M.R., Phillips R.S., Burn P., Walsh C.T. The role of the catalytic base in the protein tyrosine kinase Csk. J. Biol. Chem. 270:1995;22105-22108.
61. Grace M.R., Walsh C.T., Cole P.A. Divalent ion effects and insights into the catalytic mechanism of protein tyrosine kinase Csk. Biochemistry. 36:1997;1874-1881.
62. Shaffer J., Adams J.A. An ATP-linked structural change in protein kinase A precedes phosphoryl transfer under physiological magnesium concentrations. Biochemistry. 38:1999;5572-5581.
63. Sondhi D., Cole P.A. Domain interactions in protein tyrosine kinase Csk. Biochemistry. 38:1999;11147-11155.
64. Vang T., Tasken K., Skalhegg B.S., Hansson V., Levy F.O. Kinetic properties of the C-terminal Src kinase, p50csk. Biochim. Biophys. Acta. 1384:1998;285-293.
65. Ablooglu A.J., Kohanski R.A. Activation of the insulin receptor's kinase domain changes the rate-determining step of substrate phosphorylation. Biochemistry. 40:2001;504-513.
66. Ablooglu A.J., Frankel M., Rusinova E., Ross J.B., Kohanski R.A. Multiple activation loop conformations and their regulatory properties in the insulin receptor's kinase domain. J. Biol. Chem. 276:2001;46933-46940.
67. Barker S.C., Kassel D.B., Weigl D., Huang X., Luther M.A., Knight W.B. Characterization of pp60c-src tyrosine kinase activities using a continuous assay. autoactivation of the enzyme is an intermolecular autophosphorylation process Biochemistry. 34:1995;14843-14851.
68. Boerner R.J., Kassel D.B., Edison A.M., Knight W.B. Examination of the dephosphorylation reactions catalyzed by pp60c-src tyrosine kinase explores the roles of autophosphorylation and SH2 ligand binding. Biochemistry. 34:1995;14852-14860.
69. Boerner R.J., Consler T.G., Gampe R.T. Jr., Weigl D., Willard D.H., Davis D.G., Edison A.M., Loganzo F. Jr., Kassel D.B., Xu R.X.et al. Catalytic activity of the SH2 domain of human pp60c-src; evidence from NMR, mass spectrometry, site-directed mutagenesis and kinetic studies for an inherent phosphatase activity. Biochemistry. 34:1995;15351-15358.
70. Boerner R.J., Barker S.C., Knight W.B. Kinetic mechanisms of the forward and reverse pp60c-src tyrosine kinase reactions. Biochemistry. 34:1995;16419-16423.
71. Edison A.M., Barker S.C., Kassel D.B., Luther M.A., Knight W.B. Exploration of the sequence specificity of pp60c-src tyrosine kinase. Minimal peptide sequence required for maximal activity. J. Biol. Chem. 270:1995;27112-27115.
72. Wong T.W., Goldberg A.R. Kinetics and mechanism of angiotensin phosphorylation by the transforming gene product of Rous sarcoma virus. J. Biol. Chem. 259:1984;3127-3131.
73. Milligan J.F., Groebe D.R., Witherell G.W., Uhlenbeck O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15:1987;8783-8798.
74. Yan M., Templeton D.J. Identification of 2 serine residues of MEK-1 that are differentially phosphorylated during activation by raf and MEK kinase. J. Biol. Chem. 269:1994;19067-19073.
75. Zheng C.F., Guan K.L. Properties of MEKs, the kinases that phosphorylate and activate the extracellular signal-regulated kinases. J. Biol. Chem. 268:1993;23933-23939.
76. Breaker R.R. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13:2002;31-39.
77. Huynh Q.K., Kishore N., Mathialagan S., Donnelly A.M., Tripp C.S. Kinetic mechanisms of IkappaB-related kinases (IKK) inducible IKK and TBK-1 differ from IKK-1/IKK-2 heterodimer. J. Biol. Chem. 277:2002;12550-12558.