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Engineering Small Molecule Responsive Split Protein Kinases

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1596))

Abstract

The over 500 human protein kinases are estimated to phosphorylate at least one-third of the proteome. This posttranslational modification is of paramount importance to intracellular signaling and its deregulation is linked to numerous diseases. Deciphering the specific cellular role of a protein kinase of interest remains challenging given their structural similarity and potentially overlapping activity. In order to exert control over the activity of user-defined kinases and allow for understanding and engineering of complex signal transduction pathways, we have designed ligand inducible split protein kinases. In this approach, protein kinases are dissected into two fragments that cannot spontaneously assemble and are thus inactive. The two kinase fragments are attached to chemical inducers of dimerization (CIDs) that allow for ligand induced heterodimerization and concomitant activation of kinase activity.

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References

  1. Deribe YL, Pawson T, Dikic I (2010) Post-translational modifications in signal integration. Nat Struct Mol Biol 17:666–672

    Article  CAS  Google Scholar 

  2. Hunter T (1995) Protein kinases and phosphatases: review the yin and yang of protein phosphorylation and signaling. Cell 80:225–236

    Article  CAS  Google Scholar 

  3. Sharma K, D’Souza RCJ, Tyanova S et al (2014) Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep 8:1583–1594

    Article  CAS  Google Scholar 

  4. Hornbeck PV, Kornhauser JM, Tkachev S et al (2011) 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–D270

    Article  Google Scholar 

  5. Manning G (2002) The protein kinase complement of the human genome. Science 298:1912–1934

    Article  CAS  Google Scholar 

  6. Cohen P (2002) Protein kinases: the major drug targets of the twenty-first century? Nat Rev Drug Discov 1:309–315

    Article  CAS  Google Scholar 

  7. Hotamisligil GS (2006) Inflammation and metabolic disorders. Nature 444:860–867

    Article  CAS  Google Scholar 

  8. Kyriakis JM, Avruch J (2012) Mammalian MAPK signal transduction pathways activated by stress and inflammation: a 10-year update. Physiol Rev 92:689–737

    Article  CAS  Google Scholar 

  9. Mueller BK, Mack H, Teusch N (2005) Rho kinase, a promising drug target for neurological disorders. Nat Rev Drug Discov 4:387–398

    Article  CAS  Google Scholar 

  10. Knight ZA, Lin H, Shokat KM (2010) Targeting the cancer kinome through polypharmacology. Nat Rev Cancer 10:130–137

    Article  CAS  Google Scholar 

  11. Zhang J, Yang PL, Gray NS (2009) Targeting cancer with small molecule kinase inhibitors. Nat Rev Cancer 9:28–39

    Article  Google Scholar 

  12. Lamba V, Ghosh I (2012) New directions in targeting protein kinases: focusing upon true allosteric and bivalent inhibitors. Curr Pharm Des 18:2936–2945

    Article  CAS  Google Scholar 

  13. Krebs EG, Fischer EH (1956) The phosphorylase b to a converting enzyme of rabbit skeletal muscle. Biochim Biophys Acta 20:150–157

    Article  CAS  Google Scholar 

  14. Hunter T, Sefton BM (1980) Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc Natl Acad Sci 77:1311–1315

    Article  CAS  Google Scholar 

  15. Hubbard SR, Till JH (2000) Protein tyrosine kinase structure and function. Annu Rev Biochem 69:373–398

    Article  CAS  Google Scholar 

  16. Endicott JA, Noble MEM, Johnson LN (2012) The structural basis for control of eukaryotic protein kinases. Annu Rev Biochem 81:587–613

    Article  CAS  Google Scholar 

  17. Taylor SS, Kornev AP (2011) Protein kinases: evolution of dynamic regulatory proteins. Trends Biochem Sci 36:65–77

    Article  CAS  Google Scholar 

  18. Bishop AC, Kung C-Y, Shah K et al (1999) Generation of monospecific nanomolar tyrosine kinase inhibitors via a chemical genetic approach. J Am Chem Soc 121:627–631

    Article  CAS  Google Scholar 

  19. Liu Y, Shah K, Yang F et al (1998) Engineering Src family protein kinases with unnatural nucleotide specificity. Chem Biol 5:91–101

    Article  CAS  Google Scholar 

  20. Bishop AC, Ubersax JA, Petsch DT et al (2000) A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature 407:395–401

    Article  CAS  Google Scholar 

  21. Karginov AV, Ding F, Kota P et al (2010) Engineered allosteric activation of kinases in living cells. Nat Biotechnol 28:743–747

    Article  CAS  Google Scholar 

  22. Karginov AV, Zou Y, Shirvanyants D et al (2011) Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc 133:420–423

    Article  CAS  Google Scholar 

  23. Gautier A, Nguyen DP, Lusic H et al (2010) Genetically encoded photocontrol of protein localization in mammalian cells. J Am Chem Soc 132:4086–4088

    Article  CAS  Google Scholar 

  24. Shekhawat SS, Ghosh I (2011) Split-protein systems: beyond binary protein–protein interactions. Curr Opin Chem Biol 15:789–797

    Article  CAS  Google Scholar 

  25. Camacho-Soto K, Castillo-Montoya J, Tye B, Ghosh I (2014) Ligand-gated split-kinases. J Am Chem Soc 136:3995–4002

    Article  CAS  Google Scholar 

  26. Camacho-Soto K, Castillo-Montoya J, Tye B et al (2014) Small molecule gated split-tyrosine phosphatases and orthogonal split-tyrosine kinases. J Am Chem Soc 136:17078–17086

    Article  CAS  Google Scholar 

  27. Fegan A, White B, Carlson JCT, Wagner CR (2010) Chemically controlled protein assembly: techniques and applications. Chem Rev 110:3315–3336. doi:10.1021/cr8002888

    Article  CAS  Google Scholar 

  28. Liang FS, Ho WQ, Crabtree GR (2011) Engineering the ABA plant stress pathway for regulation of induced proximity. Sci Signal 4:rs2

    Article  Google Scholar 

  29. Miyazono K-I, Miyakawa T, Sawano Y et al (2009) Structural basis of abscisic acid signalling. Nature 462:609–614

    Article  CAS  Google Scholar 

  30. Miyamoto T, DeRose R, Suarez A et al (2012) Rapid and orthogonal logic gating with a gibberellin-induced dimerization system. Nat Chem Biol 8:465–470

    Article  CAS  Google Scholar 

  31. Murase K, Hirano Y, Sun T-P, Hakoshima T (2008) Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature 456:459–463

    Article  CAS  Google Scholar 

  32. Roberts BE, Paterson BM (1973) Efficient translation of tobacco mosaic virus RNA and rabbit globin 9S RNA in a cell-free system from commercial wheat germ. Proc Natl Acad Sci 70:2330–2334

    Article  CAS  Google Scholar 

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Acknowledgment

We thank members of the Ghosh lab, Dr. Reena Zutshi, and Luceome Biotechnologies for helpful comments and reagents. Indraneel Ghosh is the CSO at Luceome Biotechnologies, Tucson, AZ. We thank the NIH (1R01GM115595-01) and NSF (CHE-1506091) for supporting this research.

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Correspondence to Indraneel Ghosh .

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Castillo-Montoya, J., Ghosh, I. (2017). Engineering Small Molecule Responsive Split Protein Kinases. In: Stein, V. (eds) Synthetic Protein Switches. Methods in Molecular Biology, vol 1596. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6940-1_19

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  • DOI: https://doi.org/10.1007/978-1-4939-6940-1_19

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6938-8

  • Online ISBN: 978-1-4939-6940-1

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