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Rational Design and Applications of Semisynthetic Modular Biosensors: SNIFITs and LUCIDs

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Synthetic Protein Switches

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

Abstract

Biosensors are used in many fields to measure the concentration of analytes, both in a cellular context and in human samples for medical care. Here, we outline the design of two types of modular biosensors: SNAP-tag-based indicators with a Fluorescent Intramolecular Tether (SNIFITs) and LUCiferase-based Indicators of Drugs (LUCIDs). These semisynthetic biosensors quantitatively measure analyte concentrations in vitro and on cell surfaces by an intramolecular competitive mechanism. We provide an overview of how to design and apply SNIFITs and LUCIDs.

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References

  1. Vigneshvar S, Sudhakumari CC, Senthilkumaran B, Prakash H (2016) Recent advances in biosensor technology for potential applications—an overview. Front Bioeng Biotechnol 4:11. doi:10.3389/fbioe.2016.00011

    Article  CAS  Google Scholar 

  2. Zhang D, Liu Q (2016) Biosensors and bioelectronics on smartphone for portable biochemical detection. Biosens Bioelectron 75:273–284. doi:10.1016/j.bios.2015.08.037

    Article  CAS  Google Scholar 

  3. Hochreiter B, Garcia AP, Schmid JA (2015) Fluorescent proteins as genetically encoded FRET biosensors in life sciences. Sensors (Basel, Switzerland) 15(10):26281–26314. doi:10.3390/s151026281

    Article  CAS  Google Scholar 

  4. Tainaka K, Sakaguchi R, Hayashi H, Nakano S, Liew FF, Morii T (2010) Design strategies of fluorescent biosensors based on biological macromolecular receptors. Sensors (Basel) 10(2):1355–1376. doi:10.3390/s100201355

    Article  CAS  Google Scholar 

  5. Thestrup T, Litzlbauer J, Bartholomaus I, Mues M, Russo L, Dana H, Kovalchuk Y, Liang Y, Kalamakis G, Laukat Y, Becker S, Witte G, Geiger A, Allen T, Rome LC, Chen T-W, Kim DS, Garaschuk O, Griesinger C, Griesbeck O (2014) Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes. Nat Methods 11(2):175–182. doi:10.1038/nmeth.2773

    Article  CAS  Google Scholar 

  6. Hamers D, Voorst Vader L, Borst JW, Goedhart J (2013) Development of FRET biosensors for mammalian and plant systems. Protoplasma 251(2):333–347. doi:10.1007/s00709-013-0590-z

    Article  Google Scholar 

  7. Xiong TC, Ronzier E, Sanchez F, Corratge-Faillie C, Mazars C, Thibaud JB (2014) Imaging long distance propagating calcium signals in intact plant leaves with the BRET-based GFP-aequorin reporter. Front Plant Sci 5:43. doi:10.3389/fpls.2014.00043

    Article  Google Scholar 

  8. Vallée-Bélisle A, Plaxco KW (2010) Structure-switching biosensors: inspired by nature. Curr Opin Struct Biol 20(4):518–526. doi:10.1016/j.sbi.2010.05.001

    Article  Google Scholar 

  9. Keppler A, Gendreizig S, Gronemeyer T, Pick H, Vogel H, Johnsson K (2003) A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat Biotechnol 21(1):86–89. doi:10.1038/nbt765

    Article  CAS  Google Scholar 

  10. Keppler A, Kindermann M, Gendreizig S, Pick H, Vogel H, Johnsson K (2004) Labeling of fusion proteins of O6-alkylguanine-DNA alkyltransferase with small molecules in vivo and in vitro. Methods 32(4):437–444. doi:10.1016/j.ymeth.2003.10.007

    Article  CAS  Google Scholar 

  11. Gautier A, Juillerat A, Heinis C, Corrêa IR Jr, Kindermann M, Beaufils F, Johnsson K (2008) An engineered protein tag for multiprotein labeling in living cells. Chem Biol 15(2):128–136. doi:10.1016/j.chembiol.2008.01.007

    Article  CAS  Google Scholar 

  12. Los GV, Encell LP, McDougall MG, Hartzell DD, Karassina N, Zimprich C, Wood MG, Learish R, Ohana RF, Urh M, Simpson D, Mendez J, Zimmerman K, Otto P, Vidugiris G, Zhu J, Darzins A, Klaubert DH, Bulleit RF, Wood KV (2008) HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem Biol 3(6):373–382. doi:10.1021/cb800025k

    Article  CAS  Google Scholar 

  13. Hinner MJ, Johnsson K (2010) How to obtain labeled proteins and what to do with them. Curr Opin in Biotechnol 21(6):766–776. doi:10.1016/j.copbio.2010.09.011

    Article  CAS  Google Scholar 

  14. Chen X, Wu Y-W (2016) Selective chemical labeling of proteins. Org Biomol Chem. doi:10.1039/C6OB00126B

    Google Scholar 

  15. Xue L, Karpenko IA, Hiblot J, Johnsson K (2015) Imaging and manipulating proteins in live cells through covalent labeling. Nat Chem Biol 11(12):917–923. doi:10.1038/nchembio.1959

    Article  CAS  Google Scholar 

  16. Giepmans BNG, Adams SR, Ellisman MH, Tsien RY (2006) The fluorescent toolbox for assessing protein location and function. Science 312(5771):217–224. doi:10.1126/science.1124618

    Article  CAS  Google Scholar 

  17. Yan Q, Bruchez MP (2015) Advances in chemical labeling of proteins in living cells. Cell Tissue Res 360(1):179–194. doi:10.1007/s00441-015-2145-4

    Article  CAS  Google Scholar 

  18. Thorne N, Inglese J, Auld DS (2010) Illuminating insights into firefly luciferase and other bioluminescent reporters used in chemical biology. Chem Biol 17(6):646–657. doi:10.1016/j.chembiol.2010.05.012

    Article  CAS  Google Scholar 

  19. Hall MP, Unch J, Binkowski BF, Valley MP, Butler BL, Wood MG, Otto P, Zimmerman K, Vidugiris G, Machleidt T, Robers MB, Benink HA, Eggers CT, Slater MR, Meisenheimer PL, Klaubert DH, Fan F, Encell LP, Wood KV (2012) Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate. ACS Chem Biol 7(11):1848–1857. doi:10.1021/cb3002478

    Article  CAS  Google Scholar 

  20. Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D (2013) Computational design of ligand-binding proteins with high affinity and selectivity. Nature 501(7466):212–216. doi:10.1038/nature12443

    Article  CAS  Google Scholar 

  21. Krishnamurthy VM, Semetey V, Bracher PJ, Shen N, Whitesides GM (2007) Dependence of effective molarity on linker length for an intramolecular protein−ligand system. J Am Chem Soc 129(5):1312–1320. doi:10.1021/ja066780e

    Article  CAS  Google Scholar 

  22. Brun MA, Tan K-T, Nakata E, Hinner MJ, Johnsson K (2009) Semisynthetic fluorescent sensor proteins based on self-labeling protein tags. J Am Chem Soc 131(16):5873–5884. doi:10.1021/ja900149e

    Article  CAS  Google Scholar 

  23. Evers TH, van Dongen EMWM, Faesen AC, Meijer EW, Merkx M (2006) Quantitative understanding of the energy transfer between fluorescent proteins connected via flexible peptide linkers. Biochemistry 45(44):13183–13192. doi:10.1021/bi061288t

    Article  CAS  Google Scholar 

  24. Schuler B, Lipman EA, Steinbach PJ, Kumke M, Eaton WA (2005) Polyproline and the “spectroscopic ruler” revisited with single-molecule fluorescence. Proc Natl Acad Sci USA 102(8):2754–2759. doi:10.1073/pnas.0408164102

    Article  CAS  Google Scholar 

  25. Brun MA, Griss R, Reymond L, Tan K-T, Piguet J, Peters RJRW, Vogel H, Johnsson K (2011) Semisynthesis of fluorescent metabolite sensors on cell surfaces. J Am Chem Soc 133(40):16235–16242. doi:10.1021/ja206915m

    Article  CAS  Google Scholar 

  26. Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6(5):343–345. http://www.nature.com/nmeth/journal/v6/n5/suppinfo/nmeth.1318_S1.html

  27. Brun MA, Tan K-T, Griss R, Kielkowska A, Reymond L, Johnsson K (2012) A semisynthetic fluorescent sensor protein for glutamate. J Am Chem Soc 134(18):7676–7678. doi:10.1021/ja3002277

    Article  CAS  Google Scholar 

  28. Masharina A, Reymond L, Maurel D, Umezawa K, Johnsson K (2012) A fluorescent sensor for GABA and synthetic GABAB receptor ligands. J Am Chem Soc 134(46):19026–19034. doi:10.1021/ja306320s

    Article  CAS  Google Scholar 

  29. Schena A, Johnsson K (2014) Sensing acetylcholine and anticholinesterase compounds. Angew Chem Int Ed 53(5):1302–1305. doi:10.1002/anie.201307754

    Article  CAS  Google Scholar 

  30. Griss R, Schena A, Reymond L, Patiny L, Werner D, Tinberg CE, Baker D, Johnsson K (2014) Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nat Chem Biol 10(7):598–603. doi:10.1038/nchembio.1554

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. National Centre of Competence in Research (NCCR) Chemical Biology, Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, École Polytechnique Fédéralede Lausanne (EPFL), 1015, Lausanne, Switzerland

    Helen Farrants, Julien Hiblot, Rudolf Griss & Kai Johnsson

  2. Max-Planck Institute for Medical Research, Department of Chemical Biology, 69120, Heidelberg, Germany

    Kai Johnsson

Authors
  1. Helen Farrants
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  2. Julien Hiblot
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  3. Rudolf Griss
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  4. Kai Johnsson
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Corresponding author

Correspondence to Kai Johnsson .

Editor information

Editors and Affiliations

  1. Fachbereich Biologie, Technische Universität Darmstadt, Darmstadt, Germany

    Viktor Stein

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Farrants, H., Hiblot, J., Griss, R., Johnsson, K. (2017). Rational Design and Applications of Semisynthetic Modular Biosensors: SNIFITs and LUCIDs. 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_7

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  • DOI: https://doi.org/10.1007/978-1-4939-6940-1_7

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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

  • eBook Packages: Springer Protocols

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