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Combinatorial Assembly of Lumitoxins

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Part of the Methods in Molecular Biology book series (MIMB,volume 1684)

Abstract

Ion channels are among the most important proteins in neuroscience and serve as drug targets for many brain disorders. During development, learning, disease progression, and other processes, the activity levels of specific ion channels are tuned in a cell-type specific manner. However, it is difficult to assess how cell-specific changes in ion channel activity alter emergent brain functions. We have developed a protein architecture for fully genetically encoded light-activated modulation of endogenous ion channel activity. Fusing a genetically encoded photoswitch and an ion channel-modulating peptide toxin in a computationally designed fashion, this reagent, which we call Lumitoxins, can mediate light-modulation of specific endogenous ion channel activities in targeted cells. The modular lumitoxin architecture may be useful in a diversity of neuroscience tools. Here, we delineate how to construct lumitoxin genes from synthesized components, and provide a general outline for how to test their function in mammalian cell culture.

Key words

  • Peptide toxin
  • LOV2
  • Optogenetic
  • Ion channel
  • Electrophysiology
  • Protein engineering

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References

  1. Boyden ES, Zhang F, Bamberg E et al (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8:1263–1268

    CAS  CrossRef  PubMed  Google Scholar 

  2. Boyden ES (2011) A history of optogenetics: the development of tools for controlling brain circuits with light. F1000 Biol Rep 3:11

    CrossRef  PubMed  PubMed Central  Google Scholar 

  3. Kleinlogel S, Feldbauer K, Dempski RE et al (2011) Ultra light-sensitive and fast neuronal activation with the Ca2+−permeable channelrhodopsin CatCh. Nat Neurosci 14:513–518

    CAS  CrossRef  PubMed  Google Scholar 

  4. Wietek J, Wiegert JS, Adeishvili N et al (2014) Conversion of channelrhodopsin into a light-gated chloride channel. Science 344:409–412

    CAS  CrossRef  PubMed  Google Scholar 

  5. Volgraf M, Gorostiza P, Numano R et al (2006) Allosteric control of an ionotropic glutamate receptor with an optical switch. Nat Chem Biol 2:47–52

    CAS  CrossRef  PubMed  Google Scholar 

  6. Szobota S, Gorostiza P, Del Bene F et al (2007) Remote control of neuronal activity with a light-gated glutamate receptor. Neuron 54:535–545

    CAS  CrossRef  PubMed  Google Scholar 

  7. Zemelman BV, Nesnas N, Lee GA et al (2003) Photochemical gating of heterologous ion channels: remote control over genetically designated populations of neurons. Proc Natl Acad Sci U S A 100:1352–1357

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  8. Lima SQ, Miesenbock G (2005) Remote control of behavior through genetically targeted photostimulation of neurons. Cell 121:141–152

    CAS  CrossRef  PubMed  Google Scholar 

  9. Sandoz G, Levitz J, Kramer RH et al (2012) Optical control of endogenous proteins with a photoswitchable conditional subunit reveals a role for TREK1 in GABA(B) signaling. Neuron 74:1005–1014

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  10. Ibañez-Tallon I, Wen H, Miwa JM et al (2004) Tethering naturally occurring peptide toxins for cell-autonomous modulation of ion channels and receptors in vivo. Neuron 43:305–311

    CrossRef  PubMed  Google Scholar 

  11. Auer S, Stürzebecher AS, Jüttner R et al (2010) Silencing neurotransmission with membrane-tethered toxins. Nat Methods 7:229–236

    CAS  CrossRef  PubMed  Google Scholar 

  12. Choi C, Nitabach MN (2013) Membrane-tethered ligands: tools for cell-autonomous pharmacological manipulation of biological circuits. Physiology (Bethesda) 28:164–171

    CAS  CrossRef  Google Scholar 

  13. Schmidt D, Tillberg PW, Chen F et al (2014) A fully genetically encoded protein architecture for optical control of peptide ligand concentration. Nat Commun 5:3019

    PubMed  PubMed Central  Google Scholar 

  14. Koh DCI, Armugam A, Jeyaseelan K (2006) Snake venom components and their applications in biomedicine. Cell Mol Life Sci 63:3030–3041

    CAS  CrossRef  PubMed  Google Scholar 

  15. Nirthanan S, Gwee MCE (2004) Three-finger alpha-neurotoxins and the nicotinic acetylcholine receptor, forty years on. J Pharmacol Sci 94:1–17

    CAS  CrossRef  PubMed  Google Scholar 

  16. Terlau H, Olivera BM (2004) Conus venoms: a rich source of novel ion channel-targeted peptides. Physiol Rev 84:41–68

    CAS  CrossRef  PubMed  Google Scholar 

  17. Corzo G, Escoubas P (2003) Pharmacologically active spider peptide toxins. Cell Mol Life Sci 60:2409–2426

    CAS  CrossRef  PubMed  Google Scholar 

  18. Blumenthal KM, Seibert AL (2003) Voltage-gated sodium channel toxins: poisons, probes, and future promise. Cell Biochem Biophys 38:215–238

    CAS  CrossRef  PubMed  Google Scholar 

  19. Hasson U, Chen J, Honey CJ (2015) Hierarchical process memory: memory as an integral component of information processing. Trends Cogn Sci 19:304–313

    CrossRef  PubMed  PubMed Central  Google Scholar 

  20. Kiebel SJ, Daunizeau J, Friston KJ (2008) A hierarchy of time-scales and the brain. PLoS Comput Biol 4:e1000209

    CrossRef  PubMed  PubMed Central  Google Scholar 

  21. Kato S, Kaplan HS, Schrödel T et al (2015) Global brain dynamics embed the motor command sequence of Caenorhabditis elegans. Cell 163:656–669

    CAS  CrossRef  PubMed  Google Scholar 

  22. Thorlabs–Mounted LEDs. https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=2692&tabname=Multi-LED%20Source

  23. Engler C, Gruetzner R, Kandzia R et al (2009) Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS One 4:e5553

    CrossRef  PubMed  PubMed Central  Google Scholar 

  24. conoserver.org, http://conoserver.org

  25. arachnoserver.org, http://www.arachnoserver.org

  26. protchem.hunnu.edu.cn/toxin/. http://protchem.hunnu.edu.cn/toxin/

  27. www.peptides.be, http://www.peptides.be

  28. uniprot.org/program/Toxins, http://www.uniprot.org/program/Toxins

  29. Gasparini S, Danse JM, Lecoq A et al (1998) Delineation of the functional site of alpha-dendrotoxin. The functional topographies of dendrotoxins are different but share a conserved core with those of other Kv1 potassium channel-blocking toxins. J Biol Chem 273:25393–25403

    CAS  CrossRef  PubMed  Google Scholar 

  30. Gui J, Liu B, Cao G et al (2014) A tarantula-venom peptide antagonizes the TRPA1 nociceptor ion channel by binding to the S1–S4 gating domain. Curr Biol 24:473–483

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  31. Doupnik CA, Parra KC, Guida WC (2015) A computational design approach for virtual screening of peptide interactions across K(+) channel families. Comput Struct Biotechnol J 13:85–94

    CAS  CrossRef  PubMed  Google Scholar 

  32. Harper SM, Neil LC, Gardner KH (2003) Structural basis of a phototropin light switch. Science 301:1541–1544

    CAS  CrossRef  PubMed  Google Scholar 

  33. Yao X, Rosen MK, Gardner KH (2008) Estimation of the available free energy in a LOV2-J alpha photoswitch. Nat Chem Biol 4:491–497

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  34. Ma B, Tsai C-J, Haliloğlu T et al (2011) Dynamic allostery: linkers are not merely flexible. Structure (London 1993) 19:907–917

    CAS  CrossRef  Google Scholar 

  35. Papaleo E, Saladino G, Lambrughi M et al (2016) The role of protein loops and linkers in conformational dynamics and allostery. Chem Rev 116:6391–6423

    CAS  CrossRef  PubMed  Google Scholar 

  36. Anantharaman V, Balaji S, Aravind L (2006) The signaling helix: a common functional theme in diverse signaling proteins. Biol Direct 1:25

    CrossRef  PubMed  PubMed Central  Google Scholar 

  37. Kennis JTM, Crosson S, Gauden M et al (2003) Primary reactions of the LOV2 domain of phototropin, a plant blue-light photoreceptor. Biochemistry 42:3385–3392

    CAS  CrossRef  PubMed  Google Scholar 

  38. EMBOSS Backtranseq. http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/

  39. Kim JH, Lee S-R, Li L-H et al (2011) High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PLoS One 6:e18556

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  40. Bidirectional promoter vectors. http://www.clontech.com/US/Products/Fluorescent_Proteins_and_Reporters/Coexpression/Bidirectional_Promoter

  41. Kaech S, Banker G (2006) Culturing hippocampal neurons. Nat Protoc 1:2406–2415

    CAS  CrossRef  PubMed  Google Scholar 

  42. Jiang M, Chen G (2006) High Ca2+-phosphate transfection efficiency in low-density neuronal cultures. Nat Protoc 1:695–700

    CAS  CrossRef  PubMed  Google Scholar 

  43. Wang S, Cho YK (2016) An optimized calcium-phosphate transfection method for characterizing genetically encoded tools in primary neurons. Meth Mol Biol (Clifton, NJ) 1408:243–249

    CAS  CrossRef  Google Scholar 

  44. The axon guide. https://www.moleculardevices.com/axon-guide

  45. Thomas P, Smart TG (2005) HEK293 cell line: a vehicle for the expression of recombinant proteins. J Pharmacol Toxicol Methods 51:187–200

    CAS  CrossRef  PubMed  Google Scholar 

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Correspondence to Daniel Schmidt .

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Nedrud, D., Schmidt, D. (2018). Combinatorial Assembly of Lumitoxins. In: Shyng, SL., Valiyaveetil, F., Whorton, M. (eds) Potassium Channels. Methods in Molecular Biology, vol 1684. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7362-0_15

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  • DOI: https://doi.org/10.1007/978-1-4939-7362-0_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7361-3

  • Online ISBN: 978-1-4939-7362-0

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