Optogenetics pp 89-107 | Cite as

Color Tuning in Retinylidene Proteins

  • Kota Katayama
  • Sivakumar Sekharan
  • Yuki SudoEmail author


Retinylidene proteins (also called rhodopsins) are membrane-embedded photoreceptors that contain a vitamin A aldehyde linked to a lysine residue by a Schiff base as their light-sensing chromophore. The chromophore is surrounded by seven-transmembrane α-helices and absorbs light at different wavelengths due to differences in the electronic energy gap between its ground and excited states. The variation in the wavelength of maximal absorption (λmax: 360–620 nm) of rhodopsins arises due to interaction between the apoprotein (opsin) and the retinyl chromophore, the ‘opsin shift’. This chapter reviews the color tuning mechanisms in type-1 microbial and type-2 animal rhodopsins as revealed mainly by our experimental and theoretical studies.


Retinal Color tuning Rhodopsin π-conjugation Color variant Visible light Water molecule Vitamin-A 


  1. Altenbach C, Kusnetzow AK, Ernst OP et al (2008) High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation. Proc Natl Acad Sci U S A 105:7439–7444PubMedCentralPubMedCrossRefGoogle Scholar
  2. Andersen LH, Nielsen IB, Kristensen MB et al (2005) Absorption of Schiff-base retinal chromophore in Vacuo. J Am Chem Soc 127:12347–12350PubMedCrossRefGoogle Scholar
  3. Bailes HJ, Zhuang L-Y, Lucas RJ (2012) Reproducible and sustained regulation of Gαs signalling using a metazoan opsin as an optogenetic tool. PLoS One 7:e30774PubMedCentralPubMedCrossRefGoogle Scholar
  4. Balashov SP, Imasheva ES, Boichenko VA (2005) Xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna. Science 309:2061–2064PubMedCentralPubMedCrossRefGoogle Scholar
  5. Birge RR (1990) Photophysics and molecular electronic applications of the rhodopsins. Annu Rev Phys Chem 41:683–733PubMedCrossRefGoogle Scholar
  6. Boyden ES, Zhang F, Bamberg E et al (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8:1263–1268PubMedCrossRefGoogle Scholar
  7. Briggs WR, Spudich JL (2005) Handbook of photosensory receptors. Wiley-VCH, WeinheimCrossRefGoogle Scholar
  8. Cembran A, Luque RG, Altoè P et al (2005) Structure, spectroscopy, and spectral tuning of the gas-phase retinal chromophore: the beta-ionone “handle” and alkyl group effect. J Phys Chem A 109:6597–6605PubMedCrossRefGoogle Scholar
  9. Chow BY, Han X, Dobry AS et al (2010) High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature 463:98–102PubMedCentralPubMedCrossRefGoogle Scholar
  10. Cornell WD, Cieplak P, Bayly CI et al (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179–5197CrossRefGoogle Scholar
  11. Coto PB, Strambi A, Ferré N et al (2006) The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution. Proc Natl Acad Sci U S A 103:17154–17159PubMedCentralPubMedCrossRefGoogle Scholar
  12. Farrens DL, Altenbach C, Yang K et al (1996) Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 274:768–770PubMedCrossRefGoogle Scholar
  13. Fasick JI, Applebury ML, Oprian DD (2002) Spectral tuning in the mammalian short-wavelength sensitive cone pigments. Biochemistry 41:6860–6865PubMedCrossRefGoogle Scholar
  14. Garczarek F, Gerwert K (2006) Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439:109–112PubMedCrossRefGoogle Scholar
  15. Grote M, Engelhard M, Hegemann P (2014) Of ion pumps, sensors and channels – perspectives on microbial rhodopsins between science and history. Biochim Biophys Acta 1837:533–545PubMedCrossRefGoogle Scholar
  16. Hara T, Hara R, Takeuchi J (1967) Vision in octopus and squid: rhodopsin and retinochrome in the octopus retina. Nature 214:572–573PubMedCrossRefGoogle Scholar
  17. Hara-Nishimura I, Matsumoto T, Mori H et al (1993) Cloning and nucleotide sequence of cDNA for rhodopsin of the squid Todarodes pacificus. FEBS Lett 317:5–11PubMedCrossRefGoogle Scholar
  18. Hubbard R, St George RCC (1958) The rhodopsin system of the squid. J Gen Physiol 41:501–528PubMedCentralPubMedCrossRefGoogle Scholar
  19. Hubbell WL, Altenbach C, Hubbell CM et al (2003) Rhodopsin structure, dynamics, and activation: a perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking. Adv Protein Chem 63:243–290PubMedGoogle Scholar
  20. Inoue K, Tsukamoto T, Sudo Y (2014) Molecular and evolutionary aspects of microbial sensory rhodopsins. Biochim Biophys Acta 1837:562–577PubMedCrossRefGoogle Scholar
  21. Irieda H, Reissig L, Kawanabe A et al (2011) Structural characteristics around the β-ionone ring of the retinal chromophore in Salinibacter sensory rhodopsin I. Biochemistry 50:4912–4922PubMedCrossRefGoogle Scholar
  22. Irieda H, Morita T, Maki K et al (2012) Photo-induced regulation of the chromatic adaptive gene expression by Anabaena sensory rhodopsin. J Biol Chem 287:32485–32493PubMedCentralPubMedCrossRefGoogle Scholar
  23. Jongejan A, Bruysters M, Ballesteros JA et al (2005) Linking agonist binding to histamine H1 receptor activation. Nat Chem Biol 1:98–103PubMedCrossRefGoogle Scholar
  24. Katayama K, Furutani Y, Imai H et al (2012) Protein-bound water molecules in primate red- and green-sensitive visual pigments. Biochemistry 51:1126–1133PubMedCrossRefGoogle 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. Kitajima-Ihara T, Furutani Y, Suzuki D et al (2008) Salinibacter sensory rhodopsin: sensory rhodopsin I-like protein from a eubacterium. J Biol Chem 283:23533–23541PubMedCentralPubMedCrossRefGoogle Scholar
  27. Kito Y, Partridge JC, Seidou M et al (1992) The absorbance spectrum and photosensitivity of a new synthetic “visual pigment” based on 4-hydroxyretinal. Vision Res 32:3–10PubMedCrossRefGoogle Scholar
  28. Kolbe M, Besir H, Essen LO et al (2000) Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution. Science 288:1390–1396PubMedCrossRefGoogle Scholar
  29. Kouyama T, Kanada S, Takeguchi Y et al (2010) Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonis. J Mol Biol 396:564–579PubMedCrossRefGoogle Scholar
  30. Koyanagi M, Terakita A (2008) Gq-coupled rhodopsin subfamily composed of invertebrate visual pigment and melanopsin. Photochem Photobiol 84:1024–1030PubMedCrossRefGoogle Scholar
  31. Lanyi JK (2004) Bacteriorhodopsin. Annu Rev Physiol 66:665–688PubMedCrossRefGoogle Scholar
  32. Luecke H, Schobert B, Richter HT et al (1999) Structure of bacteriorhodopsin at 1.55 A resolution. J Mol Biol 291:899–911PubMedCrossRefGoogle Scholar
  33. Luecke H, Schobert B, Stagno J et al (2008) Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Proc Natl Acad Sci U S A 105:16561–16565PubMedCentralPubMedCrossRefGoogle Scholar
  34. Matsui S, Seidou M, Uchiyama I et al (1988) 4-Hydroxyretinal, a new visual pigment chromophore found in the bioluminescent squid, Watasenia scintillans. Biochim Biophys Acta 966:370–374PubMedCrossRefGoogle Scholar
  35. Merbs SL, Nathans J (1992) Absorption spectra of human cone pigments. Nature 356:433–435PubMedCrossRefGoogle Scholar
  36. Michinomae M, Masuda H, Seidou M et al (1994) Structural basis for wavelength discrimination in the banked retina of the firefly squid, Warasenia scintillans. J Exp Biol 193:1–12PubMedGoogle Scholar
  37. Mori A, Yagasaki J, Homma M et al (2013) Investigation of the chromophore binding cavity in the 11-cis acceptable microbial rhodopsin MR. Chem Phys 419:23–29CrossRefGoogle Scholar
  38. Mukohata Y, Ihara K, Tamura T et al (1999) Halobacterial rhodopsins. J Biochem 125:649–657PubMedCrossRefGoogle Scholar
  39. Murakami M, Kouyama T (2008) Crystal structure of squid rhodopsin. Nature 453:363–367PubMedCrossRefGoogle Scholar
  40. Nakanishi K (1991) 11-cis-retinal, a molecule uniquely suited for vision. Pure Appl Chem 63:161–170CrossRefGoogle Scholar
  41. Nathans J, Hogness DS (1983) Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin. Cell 34:807–814PubMedCrossRefGoogle Scholar
  42. Nathans J, Thomas D, Hogness DS (1986) Molecular genetics of human color vision: the genes encoding blue, green, and red pigments. Science 232:193–202PubMedCrossRefGoogle Scholar
  43. Neese FA (2003) A spectroscopy oriented configuration interaction procedure. J Chem Phys 119:9428–9443CrossRefGoogle Scholar
  44. Nielsen IB, Lammich L, Andersen LH (2006) S1 and S2 excited states of gas-phase Schiff-base retinal chromophores. Phys Rev Lett 96:018304PubMedCrossRefGoogle Scholar
  45. Okada T, Fujiyoshi Y, Silow M et al (2002) Functional role of internal water molecules in rhodopsin revealed by x-ray crystallography. Proc Natl Acad Sci U S A 99:5982–5987PubMedCentralPubMedCrossRefGoogle Scholar
  46. Okada T, Sugihara M, Bondar AN et al (2004) The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol 342:571–583PubMedCrossRefGoogle Scholar
  47. Oprian DD, Asenjo AB, Lee N et al (1991) Design, chemical synthesis, and expression of genes for the three human color vision pigments. Biochemistry 30:11367–11372PubMedCrossRefGoogle Scholar
  48. Ota T, Furutani Y, Terakita A et al (2006) Structural changes in the Schiff base region of squid rhodopsin upon photoisomerization studied by low-temperature FTIR spectroscopy. Biochemistry 45:2845–2851PubMedCrossRefGoogle Scholar
  49. Pal R, Sekharan S, Batista VS (2013) Spectral tuning in Halorhodopsin: the chloride pump photoreceptor. J Am Chem Soc 135:9624–9627PubMedCrossRefGoogle Scholar
  50. Palczewski K, Kumasaka T, Hori T et al (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739–745PubMedCrossRefGoogle Scholar
  51. Pardo L, Deupi X, Dölker N et al (2007) The role of internal water molecules in the structure and function of the rhodopsin family of G protein-coupled receptors. Chem Bio Chem 8:19–24PubMedCrossRefGoogle Scholar
  52. Pastrana E (2011) Perfecting ChR2. Nat Methods 8:447PubMedCrossRefGoogle Scholar
  53. Provencio I, Jiang G, De Grip WJ et al (1998) Melanopsin: an opsin in melanophores, brain, and eye. Proc Natl Acad Sci U S A 95:340–345PubMedCentralPubMedCrossRefGoogle Scholar
  54. Provencio I, Rodriguez IR, Jiang G et al (2000) A novel human opsin in the inner retina. J Neurosci 20:600–605PubMedGoogle Scholar
  55. Reissig L, Iwata T, Kikukawa T et al (2012) Influence of halide binding on the hydrogen bonding network in the active site of Salinibacter sensory rhodopsin I. Biochemistry 51:8802–8813PubMedCrossRefGoogle Scholar
  56. Royant A, Nollert P, Edman K et al (2001) X-ray structure of sensory rhodopsin II at 2.1-Å resolution. Proc Natl Acad Sci U S A 98:10131–10136PubMedCentralPubMedCrossRefGoogle Scholar
  57. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  58. Seidou M, Sugahara M, Uchiyama H et al (1990) On the three visual pigments in the retina of the firefly squid, Warasenia scintillans. J Comp Physiol A 166:769–773CrossRefGoogle Scholar
  59. Sekharan S (2009) Water-mediated spectral shifts in rhodopsin and bathorhodopsin. Photochem Phobiol 85:517–520CrossRefGoogle Scholar
  60. Sekharan S, Buss V (2008) Glutamic acid 181 is uncharged in dark-adapted visual rhodopsin. J Am Chem Soc 130:17220–17221PubMedCrossRefGoogle Scholar
  61. Sekharan S, Morokuma K (2011a) QM/MM study of the structure, energy storage, and origin of the bathochromic shift in vertebrate and invertebrate bathorhodopsins. J Am Chem Soc 133:4734–4737PubMedCentralPubMedCrossRefGoogle Scholar
  62. Sekharan S, Morokuma K (2011b) Why 11-cis-retinal? Why not 7-cis, 9-cis or 13-cis-retinal in the eye? J Am Chem Soc 133:19052–19055PubMedCentralPubMedCrossRefGoogle Scholar
  63. Sekharan S, Weingart O, Buss V (2006) Ground and excited states of retinal Schiff base chromophores by multiconfigurational perturbation theory. Biophys J 91:L07–L09PubMedCentralPubMedCrossRefGoogle Scholar
  64. Sekharan S, Sugihara M, Buss V (2007a) Origin of spectral tuning in rhodopsin-it is not the binding pocket. Angew Chem Int Ed Engl 46:269–271PubMedCrossRefGoogle Scholar
  65. Sekharan S, Sugihara M, Weingart O et al (2007b) Protein assistance in the photoisomerization of rhodopsin and 9-cis-rhodopsin—insights from experiment and theory. J Am Chem Soc 129:1052–1054PubMedCrossRefGoogle Scholar
  66. Sekharan S, Altun A, Morokuma K (2010a) Photochemistry of visual pigment in a Gq proton-coupled receptor (GPCR)-insights from structural and spectral tuning studies on squid rhodopsin. Chem Eur J 16:1744–1749PubMedCentralPubMedCrossRefGoogle Scholar
  67. Sekharan S, Altun A, Morokuma K (2010b) QM/MM study of dehydro and dihydro β-ionone retinal analogues in squid and bovine rhodopsins: implications for vision in salamander rhodopsin. J Am Chem Soc 132:15856–15859PubMedCentralPubMedCrossRefGoogle Scholar
  68. Sekharan S, Yokoyama S, Morokuma K (2011) Quantum mechanical/molecular mechanical structure, enantioselectivity, and spectroscopy of hydroxyretinals and insights into the evolution of color vision in small white butterflies. J Phys Chem B 115:15380–15388PubMedCentralPubMedCrossRefGoogle Scholar
  69. Sekharan S, Wei JN, Batista VS et al (2012a) The active site of melanopsin: the biological clock photoreceptor. J Am Chem Soc 134:19536–19539PubMedCrossRefGoogle Scholar
  70. Sekharan S, Katayama K, Kandori H et al (2012b) Color vision: “OH-site” rule for seeing red and green. J Am Chem Soc 134:10706–10712PubMedCentralPubMedCrossRefGoogle Scholar
  71. Sekharan S, Mooney VL, Rivalta I et al (2013) Spectral tuning of ultraviolet cone pigments: an interhelical lock mechanism. J Am Chem Soc 135:19064–19067PubMedCrossRefGoogle Scholar
  72. Sheikh SP, Zvyaga T, Lichtarge O et al (1996) Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F. Nature 383:347–350PubMedCrossRefGoogle Scholar
  73. Shichida Y, Imai H (1998) Visual pigment: G-protein-coupled receptor for light signals. Cell Mol Life Sci 54:1299–1315PubMedCrossRefGoogle Scholar
  74. Shimamura T, Hiraki K, Takahashi N et al (2008) Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region. J Biol Chem 283:17753–17756PubMedCentralPubMedCrossRefGoogle Scholar
  75. Shimono K, Ikeura Y, Sudo Y et al (2001) Environment around the chromophore in pharaonis phoborhodopsin: mutation analysis of the retinal binding site. Biochim Biophys Acta 1515:92–100PubMedCrossRefGoogle Scholar
  76. Shimono K, Hayashi T, Ikeura Y et al (2003) Importance of the broad regional interaction for spectral tuning in Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II). J Biol Chem 278:23882–23889PubMedCrossRefGoogle Scholar
  77. Sineshchekov OA, Govorunova EG, Wang J et al (2012) Enhancement of the long-wavelength sensitivity of optogenetic microbial rhodopsins by 3,4-dehydroretinal. Biochemistry 51:4499–4506PubMedCentralPubMedCrossRefGoogle Scholar
  78. Spudich JL, Bogomolni RA (1984) Mechanism of colour discrimination by a bacterial sensory rhodopsin. Nature 312:509–513PubMedCrossRefGoogle Scholar
  79. 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
  80. Sudo Y, Spudich JL (2006) Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor. Proc Natl Acad Sci U S A 103:16129–16134PubMedCentralPubMedCrossRefGoogle Scholar
  81. Sudo Y, Yuasa Y, Shibata J et al (2011a) Spectral tuning in sensory rhodopsin I from Salinibacter ruber. J Biol Chem 286:11328–11336PubMedCentralPubMedCrossRefGoogle Scholar
  82. Sudo Y, Ihara K, Kobayashi S et al (2011b) A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties. J Biol Chem 286:5967–5976PubMedCentralPubMedCrossRefGoogle Scholar
  83. Sudo Y, Okazaki A, Ono H et al (2013) A blue-shifted light-driven proton pump for neural silencing. J Biol Chem 288:20624–20632PubMedCentralPubMedCrossRefGoogle Scholar
  84. Suzuki T, Makino-Tasaka M, Miyata S et al (1985) Competition between retinal and 3-dehydroretinal for opsin in the regeneration of visual pigment. Vision Res 25:149–154PubMedCrossRefGoogle Scholar
  85. Suzuki D, Furutani Y, Inoue K et al (2009) Effects of chloride ion binding on the photochemical properties of salinibacter sensory rhodopsin I. J Mol Biol 392:48–62PubMedCrossRefGoogle Scholar
  86. Terakita A, Tsukamoto H, Koyanagi M et al (2008) Expression and comparative characterization of Gq-coupled invertebrate visual pigments and melanopsin. J Neurochem 105:883–890PubMedCrossRefGoogle Scholar
  87. Váró G, Brown LS, Sasaki J et al (1995) Light-driven chloride ion transport by halorhodopsin from Natronobacterium pharaonis. 1. The photochemical cycle. Biochemistry 34:14490–14499PubMedCrossRefGoogle Scholar
  88. Vogeley L, Sineshchekov OA, Trivedi VD et al (2004) Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 Å. Science 306:1390–1393PubMedCrossRefGoogle Scholar
  89. Vogt K (1983) Is the fly visual pigment a rhodopsin? Z Naturforsch Sect C Biosci 38:329–333Google Scholar
  90. Wald G (1935) Carotenoids and the visual cycle. J Gen Physiol 19:351–371PubMedCentralPubMedCrossRefGoogle Scholar
  91. Wald G (1936) Pigments of the retina. J Gen Physiol 20:45–56PubMedCentralPubMedCrossRefGoogle Scholar
  92. Wald G (1937a) Visual purple system in fresh-water fishes. Nature 139:1017–1018CrossRefGoogle Scholar
  93. Wald G (1937b) Photo-labile pigments of the chicken retina. Nature 140:545–546CrossRefGoogle Scholar
  94. Wald G (1939) The porphyropsin visual system. J Gen Physiol 22:775–794PubMedCentralPubMedCrossRefGoogle Scholar
  95. Williams SC, Deisseroth K (2013) Optogenetics. Proc Natl Acad Sci U S A 110:16287PubMedCentralPubMedCrossRefGoogle Scholar
  96. Xu W, Campillo M, Pardo L et al (2005) The seventh transmembrane domains of the δ and κ opioid receptors have different accessibility patterns and interhelical intrercations. Biochemistry 44:16014–16025PubMedCentralPubMedCrossRefGoogle Scholar
  97. Yan EC, Kazmi MA, Ganim Z et al (2003) Retinal couterion switch in the photoactivation of the G protein-coupled receptor rhodopsin. Proc Natl Acad Sci U S A 100:9262–9267PubMedCentralPubMedCrossRefGoogle Scholar
  98. Yokoyama S (2008) Evolution of dim-light and color vision pigments. Annu Rev Genomics Hum Genet 9:259–282PubMedCrossRefGoogle Scholar
  99. Yokoyama S, Radlwimmer F (1998) The “five-sites” rule and the evolution of red and green color vision in mammals. Mol Biol Evol 15:560–567PubMedCrossRefGoogle Scholar
  100. Yoshitsugu M, Shibata M, Ikeda D et al (2008) Color change of proteorhodopsin by a single amino acid replacement at a distant cytoplasmic loop. Angew Chem Int Ed Engl 47:3923–3926PubMedCrossRefGoogle Scholar

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© Springer Japan 2015

Authors and Affiliations

  1. 1.Department of Frontier MaterialsNagoya Institute of TechnologyNagoyaJapan
  2. 2.Department of ChemistryYale UniversityNew HavenUSA
  3. 3.Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry and Pharmaceutical SciencesOkayama UniversityOkayamaJapan

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