Advertisement

Structure-Functional Analysis of Channelrhodopsins

  • Hideaki E. KatoEmail author
  • Ryuichiro Ishitani
  • Osamu Nureki

Abstract

Channelrhodopsin (ChR) was the first light-gated cation channel to be discovered from green algae. Since the inward flow of cations triggers neuron firing, neurons expressing ChRs can be optically controlled, even within freely moving mammals. Although ChR has been broadly applied to neuroscience research, little is known about its molecular mechanisms. In this chapter, we first describe the simple background of rhodopsin family proteins including ChR, and how optogenetics technology has been established since the discovery of ChR in 2002. We later introduce recent findings about the structure-functional relationship of ChR by especially focusing on a paper about the crystal structure of chimeric ChR (C1C2). After we explain the molecular architecture, the initial photoreactions, the ion-conducting pathway, and the putative channel gates of C1C2, we use three recent studies as examples to further explore the possibility of the structure-based engineering of ChR variants with properties that are more ideal for use as optogenetics tools.

Keywords

Membrane protein Light-gated ion channel Channelrhodopsin Optogenetics X-ray crystallography Structure-based engineering Electrophysiology 

References

  1. Adamantidis AR, Zhang F, Aravanis AM et al (2007) Neural substrates of awakening probed with optogenetic control of hypocretin neurons. Nature 450:420–424PubMedCrossRefGoogle Scholar
  2. Bamann C, Gueta R, Kleinlogel S et al (2010) Structural guidance of the photocycle of channelrhodopsin-2 by an interhelical hydrogen bond. Biochemistry (Mosc) 49:267–278CrossRefGoogle Scholar
  3. Berndt A, Yizhar O, Gunaydin LA et al (2009) Bi-stable neural state switches. Nat Neurosci 12:229–234PubMedCrossRefGoogle Scholar
  4. Berndt A, Schoenenberger P, Mattis J et al (2011) High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. Proc Natl Acad Sci U S A 108:7595–7600PubMedCentralPubMedCrossRefGoogle Scholar
  5. Berndt A, Lee SY, Ramakrishnan C et al (2014) Structure-guided transformation of channelrhodopsin into a light-activated chloride channel. Science 344:420–424PubMedCentralPubMedCrossRefGoogle Scholar
  6. Berthold P, Tsunoda SP, Ernst OP et al (2008) Channelrhodopsin-1 initiates phototaxis and photophobic responses in chlamydomonas by immediate light-induced depolarization. Plant Cell 20:1665–1677PubMedCentralPubMedCrossRefGoogle Scholar
  7. Bi A, Cui J, Ma YP et al (2006) Ectopic expression of a microbial-type rhodopsin restores visual responses in mice with photoreceptor degeneration. Neuron 50:23–33PubMedCentralPubMedCrossRefGoogle Scholar
  8. Bogomolni RA, Spudich JL (1982) Identification of a third rhodopsin-like pigment in phototactic Halobacterium halobium. Proc Natl Acad Sci U S A 79:6250–6254PubMedCentralPubMedCrossRefGoogle Scholar
  9. Boyden ES, Zhang F, Bamberg E et al (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8:1263–1268PubMedCrossRefGoogle Scholar
  10. Chaudhury D, Walsh JJ, Friedman AK et al (2012) Rapid regulation of depression-related behaviours by control of midbrain dopamine neurons. Nature 493:532–6Google Scholar
  11. Ciocchi S, Herry C, Grenier F et al (2010) Encoding of conditioned fear in central amygdala inhibitory circuits. Nature 468:277–282PubMedCrossRefGoogle Scholar
  12. Deininger W, Kroger P, Hegemann U et al (1995) Chlamyrhodopsin represents a new type of sensory photoreceptor. EMBO J 14:5849–5858PubMedCentralPubMedGoogle Scholar
  13. Deisseroth K (2011) Optogenetics. Nat Methods 8:26–29PubMedCrossRefGoogle Scholar
  14. Dixon RA, Kobilka BK, Strader DJ et al (1986) Cloning of the gene and cDNA for mammalian beta-adrenergic receptor and homology with rhodopsin. Nature 321:75–79PubMedCrossRefGoogle Scholar
  15. Doyle DA, Morais Cabral J, Pfuetzner RA et al (1998) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280:69–77PubMedCrossRefGoogle Scholar
  16. Dutzler R, Campbell EB, Cadene M et al (2002) X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity. Nature 415:287–294PubMedCrossRefGoogle Scholar
  17. Eisenhauer K, Kuhne J, Ritter E et al (2012) In channelrhodopsin-2 Glu-90 is crucial for ion selectivity and is deprotonated during the photocycle. J Biol Chem 287:6904–6911PubMedCentralPubMedCrossRefGoogle Scholar
  18. Gaiko O, Dempski RE (2013) Transmembrane domain three contributes to the ion conductance pathway of channelrhodopsin-2. Biophys J 104:1230–1237PubMedCentralPubMedCrossRefGoogle Scholar
  19. Gordeliy VI, Labahn J, Moukhametzianov R et al (2002) Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex. Nature 419:484–487PubMedCrossRefGoogle Scholar
  20. Govorunova EG, Sineshchekov OA, Li H et al (2013) Characterization of a highly efficient blue-shifted channelrhodopsin from the marine alga Platymonas subcordiformis. J Biol Chem 288:29911–29922PubMedCentralPubMedCrossRefGoogle Scholar
  21. Gunaydin LA, Yizhar O, Berndt A et al (2010) Ultrafast optogenetic control. Nat Neurosci 13:387–392PubMedCrossRefGoogle Scholar
  22. Hou X, Pedi L, Diver MM et al (2012) Crystal structure of the calcium release-activated calcium channel Orai. Science 338:1308–1313PubMedCentralPubMedCrossRefGoogle Scholar
  23. Ishizuka T, Kakuda M, Araki R et al (2006) Kinetic evaluation of photosensitivity in genetically engineered neurons expressing green algae light-gated channels. Neurosci Res 54:85–94PubMedCrossRefGoogle Scholar
  24. Ji ZG, Ishizuka T, Yawo H (2012) Channelrhodopsins-their potential in gene therapy for neurological disorders. Neurosci Res 196:29–47Google Scholar
  25. Kato HE, Zhang F, Yizhar O et al (2012) Crystal structure of the channelrhodopsin light-gated cation channel. Nature 482:369–374PubMedCentralPubMedCrossRefGoogle Scholar
  26. Kianianmomeni A, Stehfest K, Nematollahi G et al (2009) Channelrhodopsins of Volvox carteri are photochromic proteins that are specifically expressed in somatic cells under control of light, temperature, and the sex inducer. Plant Physiol 151:347–366PubMedCentralPubMedCrossRefGoogle Scholar
  27. Klapoetke NC, Murata Y, Kim SS et al (2014) Independent optical excitation of distinct neural populations. Nat Methods 11:338–346PubMedCentralPubMedCrossRefGoogle Scholar
  28. Kleinlogel S, Feldbauer K, Dempski RE et al (2011) Ultra light-sensitive and fast neuronal activation with the Ca(2)+ −permeable channelrhodopsin CatCh. Nat Neurosci 14:513–518PubMedCrossRefGoogle Scholar
  29. Krause N, Engelhard C, Heberle J et al (2013) Structural differences between the closed and open states of channelrhodopsin-2 as observed by EPR spectroscopy. FEBS Lett 587:3309–3313PubMedCrossRefGoogle Scholar
  30. Kravitz AV, Freeze BS, Parker PR et al (2010) Regulation of parkinsonian motor behaviours by optogenetic control of basal ganglia circuitry. Nature 466:622–626PubMedCentralPubMedCrossRefGoogle Scholar
  31. Li X, Gutierrez DV, Hanson MG et al (2005) Fast noninvasive activation and inhibition of neural and network activity by vertebrate rhodopsin and green algae channelrhodopsin. Proc Natl Acad Sci U S A 102:17816–17821PubMedCentralPubMedCrossRefGoogle Scholar
  32. Lin JY, Lin MZ, Steinbach P et al (2009) Characterization of engineered channelrhodopsin variants with improved properties and kinetics. Biophys J 96:1803–1814PubMedCentralPubMedCrossRefGoogle Scholar
  33. Lorenz-Fonfria VA, Resler T, Krause N et al (2013) Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating. Proc Natl Acad Sci U S A 110:E1273–E1281PubMedCentralPubMedCrossRefGoogle Scholar
  34. Matsuno-Yagi A, Mukohata Y (1977) Two possible roles of bacteriorhodopsin; a comparative study of strains of Halobacterium halobium differing in pigmentation. Biochem Biophys Res Commun 78:237–243PubMedCrossRefGoogle Scholar
  35. Muller M, Bamann C, Bamberg E et al (2011) Projection structure of channelrhodopsin-2 at 6 A resolution by electron crystallography. J Mol Biol 414:86–95PubMedCrossRefGoogle Scholar
  36. Nagel G, Ollig D, Fuhrmann M et al (2002) Channelrhodopsin-1: a light-gated proton channel in green algae. Science 296:2395–2398PubMedCrossRefGoogle Scholar
  37. Nagel G, Szellas T, Huhn W et al (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci U S A 100:13940–13945PubMedCentralPubMedCrossRefGoogle Scholar
  38. Nagel G, Brauner M, Liewald JF et al (2005) Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Curr Biol 15:2279–2284Google Scholar
  39. Oesterhelt D, Stoeckenius W (1971) Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol 233:149–152PubMedCrossRefGoogle Scholar
  40. Payandeh J, Scheuer T, Zheng N et al (2011) The crystal structure of a voltage-gated sodium channel. Nature 475:353–358PubMedCentralPubMedCrossRefGoogle Scholar
  41. Pebay-Peyroula E, Rummel G, Rosenbusch JP et al (1997) X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 277:1676–1681PubMedCrossRefGoogle Scholar
  42. Ran T, Ozorowski G, Gao Y et al (2013) Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes. Acta Crystallogr D Biol Crystallogr 69:1965–1980PubMedCrossRefGoogle Scholar
  43. Rasmussen SG, Choi HJ, Rosenbaum DM et al (2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450:383–387PubMedCrossRefGoogle Scholar
  44. Richards R, Dempski RE (2012) Re-introduction of transmembrane serine residues reduce the minimum pore diameter of channelrhodopsin-2. PLoS One 7:e50018PubMedCentralPubMedCrossRefGoogle Scholar
  45. Sattig T, Rickert C, Bamberg E et al (2013) Light-induced movement of the transmembrane helix B in channelrhodopsin-2. Angewandte Chemie 52:9705–9708PubMedCrossRefGoogle Scholar
  46. Sineshchekov OA, Litvin FF, Keszthelyi L (1990) Two components of photoreceptor potential in phototaxis of the flagellated green alga Haematococcus pluvialis. Biophys J 57:33–39PubMedCentralPubMedCrossRefGoogle Scholar
  47. Sineshchekov OA, Jung KH, Spudich JL (2002) Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 99:8689–8694PubMedCentralPubMedCrossRefGoogle Scholar
  48. Spudich JL, Yang CS, Jung KH et al (2000) Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol 16:365–392PubMedCrossRefGoogle Scholar
  49. Stabell B, Stabell U (2009) Duplicity theory of vision. Cambridge University PressCrossRefGoogle Scholar
  50. Sudo Y, Ihara K, Kobayashi S et al (2011) A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties. J Biol Chem 286:5967–5976PubMedCentralPubMedCrossRefGoogle Scholar
  51. Suzuki T, Yamasaki K, Fujita S et al (2003) Archaeal-type rhodopsins in Chlamydomonas: model structure and intracellular localization. Biochem Biophys Res Commun 301:711–717PubMedCrossRefGoogle Scholar
  52. Takeshita K, Sakata S, Yamashita E et al (2014) X-ray crystal structure of voltage-gated proton channel. Nat Struct Mol Biol 21:352–357PubMedCrossRefGoogle Scholar
  53. Tanimoto S, Sugiyama Y, Takahashi T et al (2012) Involvement of glutamate 97 in ion influx through photo-activated channelrhodopsin-2. Neurosci Res 75:13–22Google Scholar
  54. Wang H, Sugiyama Y, Hikima T et al (2009) Molecular determinants differentiating photocurrent properties of two channelrhodopsins from chlamydomonas. J Biol Chem 284:5685–5696PubMedCrossRefGoogle Scholar
  55. Wang W, Nossoni Z, Berbasova T et al (2012) Tuning the electronic absorption of protein-embedded all-trans-retinal. Science 338:1340–1343Google Scholar
  56. Watanabe HC, Welke K, Sindhikara DJ et al (2013) Towards an understanding of channelrhodopsin function: simulations lead to novel insights of the channel mechanism. J Mol Biol 425:1795–1814PubMedCrossRefGoogle Scholar
  57. Wen L, Wang H, Tanimoto S et al (2010) Opto-current-clamp actuation of cortical neurons using a strategically designed channelrhodopsin. PLoS One 5:e12893PubMedCentralPubMedCrossRefGoogle Scholar
  58. Wietek J, Wiegert JS, Adeishvili N et al (2014) Conversion of channelrhodopsin into a light-gated chloride channel. Science 344:409–412PubMedCrossRefGoogle Scholar
  59. Yizhar O, Fenno LE, Prigge M et al (2011) Neocortical excitation/inhibition balance in information processing and social dysfunction. Nature 477:171–178PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Japan 2015

Authors and Affiliations

  • Hideaki E. Kato
    • 1
    Email author
  • Ryuichiro Ishitani
    • 2
  • Osamu Nureki
    • 2
  1. 1.Department of Molecular and Cellular PhysiologyStanford UniversityStanfordUSA
  2. 2.Department of Biophysics and BiochemistryGraduate School of Science, The University of Tokyo,TokyoJapan

Personalised recommendations