Skip to main content
SpringerLink
Log in

Protein-Controlled Isomerization in Rhodopsins

  • Chapter
Chemical Science of π-Electron Systems

Abstract

Rhodopsins are photoactive proteins containing a retinal chromophore in animals and microbes. In animal and microbial rhodopsins, 11-cis and all-trans retinal, respectively, forms a Schiff base linkage with a Lys of the 7th helix, which is mostly protonated. Upon light absorption, ultrafast photoisomerization takes place from the 11-cis to the all-trans form in animal rhodopsins and from the all-trans to the 13-cis form in microbial rhodopsins. Retinal isomerization in the restricted protein environment causes light energy to be stored in the primary intermediate states, leading to each function in a late timescale. π-Electrons along the retinal chromophore play crucial roles in the functions of rhodopsins through their specific interactions with the protein moiety. First, a specific chromophore-protein interaction determines the energy gap of light absorption, i.e., the color of rhodopsins. Second, the isomerization reaction is fast and efficient in protein, even though the retinal-binding pocket is structurally restricted. Third, light energy is efficiently stored by the chromophore-protein interaction, to which steric effect and hydrogen-bonding alteration contribute. Finally, the relaxation from such a high-energy state leads to each function in much slower timescales. In this chapter, the ultrafast isomerization processes and their energy storages in animal and microbial rhodopsins are reviewed. The molecular mechanism of highly efficient photoisomerization will also be discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown LS, Kandori H (2014) Chem Rev 114:126–163

    Article  CAS  Google Scholar 

  2. Spudich JL, Yang C-S, Jung K-H, Spudich EN (2000) Annu Rev Cell Dev Biol 16:365–392

    Article  CAS  Google Scholar 

  3. Palczewski K (2006) Annu Rev Biochem 75:743

    Article  CAS  Google Scholar 

  4. Kandori H (2011) Protein-controlled ultrafast photoisomerization in rhodopsin and bacteriorhodopsin. In: Ramamurthy V, Inoue Y (eds) Supramolecular photochemistry. Wiley, Hoboken, pp 571–595

    Chapter  Google Scholar 

  5. Blatz PE, Mohler JH, Navangul HV (1972) Biochemistry 11:848

    Article  CAS  Google Scholar 

  6. Andersen LH, Nielsen IB, Kristensen MB, El Ghazaly MOA, Haacke S, Nielsen MB, Petersen MA (2005) J Am Chem Soc 127:12347–12350

    Article  CAS  Google Scholar 

  7. Furutani Y, Ido K, Sasaki M, Ogawa M, Kandori H (2007) Angew Chem Int Ed 46:8010–8012

    Article  CAS  Google Scholar 

  8. Wang W, Nossoni Z, Berbasova T, Watson CT, Yapici I, Lee KS, Vasileiou C, Geiger JH, Borhan B (2012) Science 338:1340

    Article  CAS  Google Scholar 

  9. Dartnall HJA (1967) Vis Res 8:339–358

    Article  Google Scholar 

  10. Tittor J, Oesterhelt D (1990) FEBS Lett 263:269–273

    Article  CAS  Google Scholar 

  11. Furutani Y, Terakita A, Shichida Y, Kandori H (2005) Biochemistry 44:7988–7997

    Article  CAS  Google Scholar 

  12. Koyama Y, Kubo K, Komori M, Yasuda H, Mukai Y (1991) Photochem Photobiol 54:433–443

    Article  CAS  Google Scholar 

  13. Yoshizawa T, Wald G (1963) Nature 197:1279–1286

    Article  CAS  Google Scholar 

  14. Busch GE, Applebury ML, Lamola AA, Rentzepis PM (1972) Proc Natl Acad Sci U S A 69:2802–2806

    Article  CAS  Google Scholar 

  15. Kandori H, Matuoka S, Shichida Y, Yoshizawa T, Ito M, Tsukida K, Balogh-Nair V, Nakanishi K (1989) Biochemistry 28:6460–6467

    Article  CAS  Google Scholar 

  16. Mizukami T, Kandori H, Shichida Y, Chen A-H, Derguini F, Caldwell CG, Bigge C, Nakanishi K, Yoshizawa T (1993) Proc Natl Acad Sci U S A 90:4072–4076

    Article  CAS  Google Scholar 

  17. De Vico L, Garavelli M, Bernardi F, Olivucci M (2005) J Am Chem Soc 127:2433–2442

    Article  Google Scholar 

  18. Schoenlein RW, Peteanu LA, Mathies RA, Shank CV (1991) Science 254:412–415

    Article  CAS  Google Scholar 

  19. Wang Q, Schoenlein RW, Peteanu LA, Mathies RA, Shank CV (1994) Science 266:422–424

    Article  CAS  Google Scholar 

  20. Eyring G, Mathies RA (1979) Proc Natl Acad Sci U S A 76:33–37

    Article  CAS  Google Scholar 

  21. Nakamichi H, Okada T (2006) Angew Chem Int Ed 45:1–5

    Article  Google Scholar 

  22. Kukura P, McCamant DW, Yoon S, Wandschneider DB, Mathies RA (2005) Science 310:1006–1009

    Article  CAS  Google Scholar 

  23. Frutos LM, Andruniow T, Santoro F, Ferre N, Olivucci M (2007) Proc Natl Acad Sci U S A 104:7764–7769

    Article  CAS  Google Scholar 

  24. Cooper A (1979) Nature 282:531–533

    Article  CAS  Google Scholar 

  25. Eyring G, Curry B, Broek A, Lugtenburg J, Mathies RA (1982) Biochemistry 21:384–393

    Article  CAS  Google Scholar 

  26. Palings I, van den Berg EMM, Lugtenburg J, Mathies RA (1989) Biochemistry 28:1498–1507

    Article  CAS  Google Scholar 

  27. Kochendoerfer GG, Verdegem PJE, van der Hoef I, Lugtenburg J, Mathies RA (1996) Biochemistry 35:16230–16240

    Article  CAS  Google Scholar 

  28. Sugihara M, Hufen J, Buss V (2006) Biochemistry 45:801–810

    Article  CAS  Google Scholar 

  29. Ganter UM, Schmid ED, Perez-Sala D, Rando RR, Siebert F (1989) Biochemistry 28:5954–5962

    Article  CAS  Google Scholar 

  30. Kandori H, Katsuta Y, Ito M, Sasabe H (1995) J Am Chem Soc 117:2669–2670

    Article  CAS  Google Scholar 

  31. Dobler J, Zinth W, Kaiser W (1988) Chem Phys Lett 144:215–220

    Article  CAS  Google Scholar 

  32. Delaney JK, Brack TL, Atkinson GH, Ottolenghi M, Steinberg G, Sheves M (1995) Proc Natl Acad Sci U S A 92:2101–2105

    Article  CAS  Google Scholar 

  33. Zhong Q, Ruhman S, Ottolenghi M, Sheves M, Friedman N (1996) J Am Chem Soc 118:12828–12829

    Article  CAS  Google Scholar 

  34. Atkinson GH, Ujj L, Zhou Y (2000) J Phys Chem A 104:4130–4139

    Article  CAS  Google Scholar 

  35. Herbst J, Heyne K, Diller R (2002) Science 297:822–825

    Article  CAS  Google Scholar 

  36. Kobayashi T, Saito T, Ohtani H (2001) Nature 414:531–534

    Article  CAS  Google Scholar 

  37. Doig SJ, Reid PJ, Mathies RA (1991) J Phys Chem 95:6372–6379

    Article  CAS  Google Scholar 

  38. Kandori H, Furutani Y, Nishimura S, Shichida Y, Chosrowjan H, Shibata Y, Mataga N (2001) Chem Phys Lett 334:271

    Article  CAS  Google Scholar 

  39. Kandori H, Yoshihara K, Tomioka H, Sasabe H (1992) J Phys Chem 96:6066–6071

    Article  CAS  Google Scholar 

  40. Song L, El-Sayed MA, Lanyi JK (1993) Science 261:891–894

    Article  CAS  Google Scholar 

  41. Schenkl S, van Mourik F, van der Zwan G, Haacke S, Chergui M (2005) Science 309:917–920

    Article  CAS  Google Scholar 

  42. Birge RR, Cooper TM (1983) Biophys J 42:61–69

    Article  CAS  Google Scholar 

  43. Edman K, Nollert P, Royant A, Belrhali H, Pebey-Peyroula E, Hajdu J, Neutze R, Landau EM (1999) Nature 401:822–826

    Article  CAS  Google Scholar 

  44. Schobert B, Cupp-Vickery J, Hornak V, Smith SO, Lanyi JK (2002) J Mol Biol 321:715–726

    Article  CAS  Google Scholar 

  45. Matsui Y, Sakai K, Murakami M, Shiro Y, Adachi S, Okumura H, Kouyama T (2002) J Mol Biol 324:469–481

    Article  CAS  Google Scholar 

  46. Kandori H, Belenky M, Herzfeld J (2002) Biochemistry 41:6026–6031

    Article  CAS  Google Scholar 

  47. Kandori H, Shichida Y (2000) J Am Chem Soc 122:11745

    Article  CAS  Google Scholar 

  48. Shibata M, Tanimoto T, Kandori H (2003) J Am Chem Soc 125:13312

    Article  CAS  Google Scholar 

  49. Hayashi S, Tajkhorshid E, Kandori H, Schulten K (2004) J Am Chem Soc 126:10516–10517

    Article  CAS  Google Scholar 

  50. Shibata M, Ihara K, Kandori H (2006) Biochemistry 45:10633–10640

    Article  CAS  Google Scholar 

  51. Shibata M, Yoshitsugu M, Mizuide N, Ihara K, Kandori H (2007) Biochemistry 46:7525–7535

    Article  CAS  Google Scholar 

  52. Sasaki J, Brown LS, Chon Y-S, Kandori H, Maeda A, Needleman R, Lanyi JK (1995) Science 269:73–75

    Article  CAS  Google Scholar 

  53. Muroda K, Nakashima K, Shibata M, Demura M, Kandori H (2012) Biochemistry 51:4677–4684

    Article  CAS  Google Scholar 

  54. Kandori H, Furutani Y, Shimono K, Shichida Y, Kamo N (2001) Biochemistry 40:15693–15698

    Article  CAS  Google Scholar 

  55. Furutani Y, Sudo Y, Kamo N, Kandori H (2003) Biochemistry 42:4837–4842

    Article  CAS  Google Scholar 

  56. Sharma AK, Spudich JL, Doolittle WF (2006) Trends Microbiol 14:463–469

    Article  CAS  Google Scholar 

  57. Sudo Y, Furutani Y, Wada A, Ito M, Kamo N, Kandori H (2005) J Am Chem Soc 127:16036–16037

    Article  CAS  Google Scholar 

  58. Ito M, Sudo Y, Furutani Y, Okitsu T, Wada A, Homma M, Spudich JL, Kandori H (2008) Biochemistry 47:6208–6215

    Article  CAS  Google Scholar 

  59. Sudo Y, Spudich JL (2006) Proc Natl Acad Sci U S A 103:16129–16134

    Article  CAS  Google Scholar 

  60. Furutani Y, Shibata M, Kandori H (2005) Photochem Photobiol Sci 4:661–666

    Article  CAS  Google Scholar 

  61. Kandori H (2010) Hydrogen bonds of protein-bound water molecules in rhodopsins. In: Han K-L, Zhao G-J (eds) Hydrogen bonding and transfer in the excited state. Wiley, Chichester, pp 377–391

    Chapter  Google Scholar 

Download references

Acknowledgments

I thank the members of my laboratory and many collaborators. I also thank the project members of “Emergence of Highly Elaborated π-Space and its Function” for a fruitful discussion.

Author information

Authors and Affiliations

  1. Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan

    Hideki Kandori

Authors
  1. Hideki Kandori
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hideki Kandori .

Editor information

Editors and Affiliations

  1. Foundation for Advancement of International Science, Tsukuba, Japan

    Takeshi Akasaka

  2. Kyoto University, Kyoto, Japan

    Atsuhiro Osuka

  3. Department of Chemistry and Nano Science,, Ewha Womans University, Seoul, Korea (Republic of)

    Shunichi Fukuzumi

  4. Nagoya Institute of Technology, Nagoya, Japan

    Hideki Kandori

  5. Osaka University, Suita, Japan

    Yoshio Aso

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Japan

About this chapter

Cite this chapter

Kandori, H. (2015). Protein-Controlled Isomerization in Rhodopsins. In: Akasaka, T., Osuka, A., Fukuzumi, S., Kandori, H., Aso, Y. (eds) Chemical Science of π-Electron Systems. Springer, Tokyo. https://doi.org/10.1007/978-4-431-55357-1_41

Download citation

Publish with us

Policies and ethics

Search

Navigation