Skip to main content

Analysis of molecular oxygen exit pathways in cyanobacterial photosystem II: Molecular dynamics studies

Abstract

In thylakoids of cyanobacteria and other photosynthetic organisms, the light-induced production of molecular oxygen is catalyzed by the giant lipid-pigment-protein complex called photosystem II (PSII). The oxygen-evolving complex is buried deep in the lumenal part of PSII, and dioxygen molecules need to pass through the protein environment in order to leave the active site of the enzyme free. Previous studies aimed at finding oxygen channels in PSII were based on either an analysis of the cavities within is static structure or experiments on the insertion of noble gas molecules into PSII crystals under elevated pressure. In these studies, some possible exit pathways for the molecules were found and the static positions of molecular oxygen were determined. In the present work, the oxygen movement in the transport system of PSII is simulated by molecular dynamics.

This is a preview of subscription content, access via your institution.

References

  1. G. Renger and T. Renger, Photosynth. Res. 98, 53 (2008).

    Article  Google Scholar 

  2. A. Guskov, A. Gabdulkhakov, M. Broser, et al., Chem. Phys. Chem. 11, 1160 (2010).

    Google Scholar 

  3. A. G. Gabdulkhakov and M. V. Dontsova, Usp. Biol. Khim. 53, 323 (2013).

    Google Scholar 

  4. B. Kok, B. Forbush, and M. McGloin, Photochem. Photobiol. 11, 457 (1970).

    Article  Google Scholar 

  5. J. Kern and G. Renger, Photosynth. Res. 94, 183 (2007).

    Article  Google Scholar 

  6. Y. Umena, K. Kawakami, J.-R. Shen, et al., Nature 473, 55 (2011).

    Article  ADS  Google Scholar 

  7. M. Broser, A. Gabdulkhakov, J. Kern, et al., J. Biol. Chem. 285, 26255 (2010).

    Article  Google Scholar 

  8. A. Guskov, J. Kern, A. Gabdulkhakov, et al., Nat. Struct. Mol. Biol. 16, 334 (2009).

    Article  Google Scholar 

  9. P. Pospísil, Biochim. Biophys. Acta 1787, 1151 (2009).

    Article  Google Scholar 

  10. V. Klimov, G. Ananyev, O. Zastryzhnaya, et al., Photosynth. Res. 38, 409 (1993).

    Article  Google Scholar 

  11. D. A. Force, D. W. Randall, G. A. Lorigan, et al., J. Am. Chem. Soc. 120, 13321 (1998).

    Article  Google Scholar 

  12. J. M. Anderson and W. S. Chow, Philos. Trans. R. Soc. London B: Biol. Sci. 357, 1421 (2002).

    Article  Google Scholar 

  13. C. A. Wraight, Biochim. Biophys. Acta, Bioenerg. 1757, 886 (2006).

    Article  Google Scholar 

  14. A. Zouni, H. T. Witt, J. Kern, et al., Nature 409, 739 (2001).

    Article  ADS  Google Scholar 

  15. A. W. Rutherford and P. Faller, Trends Biochem. Sci. 26, 341 (2001).

    Article  Google Scholar 

  16. A. K. Williamson, Photosynth. Res. 98, 365 (2008).

    Article  Google Scholar 

  17. K. N. Ferreira, T. M. Iverson, K. Maghlaoui, et al., Science 303, 1831 (2004).

    Article  ADS  Google Scholar 

  18. M. Petrek, M. Otyepka, P. Banás, et al., BMC Bioinformatics 7, 316 (2006).

    Article  Google Scholar 

  19. J. W. Murray and J. Barber, J. Struct. Biol. 159, 228 (2007).

    Article  Google Scholar 

  20. F. M. Ho and S. Styring, Biochim. Biophys. Acta, Bioenerg. 1777, 140 (2008).

    Article  Google Scholar 

  21. A. Gabdulkhakov, A. Guskov, M. Broser, et al., Structure 17, 1223 (2009).

    Article  Google Scholar 

  22. J. Cohen, K. Kim, P. King, et al., Structure 13, 1321 (2005).

    Article  Google Scholar 

  23. S. Vassiliev, P. Comte, A. Mahboob, et al., Biochemistry 49, 1873 (2010).

    Article  Google Scholar 

  24. S. Vassiliev, T. Zaraiskaya, and D. Bruce, Biochim. Biophys. Acta, Bioenerg. 1817, 1671 (2012).

    Article  Google Scholar 

  25. K. Ogata, T. Yuki, M. Hatakeyama, et al., J. Am. Chem. Soc. 135, 15670 (2013).

    Article  Google Scholar 

  26. A. G. Gabdulkhakov, V. G. Klyashtornyi, and M. V. Dontsova, Crystallogr. Rep. 60 (1), 83 (2015).

    Article  ADS  Google Scholar 

  27. T. Zaraiskaya, S. Vassiliev, and D. Bruce, J. Comput. Sci. 5, 549 (2014).

    Article  Google Scholar 

  28. B. Hess, C. Kutzner, D. van der Spoel, et al., J. Chem. Theory Comput. 4, 435 (2008).

    Article  Google Scholar 

  29. A. D. MacKerell, D. Bashford, M. Bellott, et al., J. Phys. Chem. B 102, 3586 (1998).

    Article  Google Scholar 

  30. A. D. Mackerell, M. Feig, and C. L. Brooks, J. Comput. Chem. 25, 1400 (2004).

    Article  Google Scholar 

  31. B. Hess, H. Bekker, H. J. C. Berendsen, et al., J. Comput. Chem. 18, 1463 (1997).

    Article  Google Scholar 

  32. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).

    Article  ADS  Google Scholar 

  33. U. Essmann, L. Perera, M. L. Berkowitz, et al., J. Chem. Phys. 103, 8577 (1995).

    Article  ADS  Google Scholar 

  34. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, et al., J. Chem. Phys. 81, 3684 (1984).

    Article  ADS  Google Scholar 

  35. R. A. Laskowski, D. S. Moss, and J. M. Thornton, J. Mol. Biol. 231, 1049 (1993).

    Article  Google Scholar 

  36. V. G. Klyashtornyi, T. Yu. Fufina, L. G. Vasil’eva, et al., Crystallogr. Rep. 59 (4), 536 (2014).

    Article  ADS  Google Scholar 

  37. A. V. Lyashenko, I. Bento, V. N. Zaitsev, et al., J. Biol. Inorg. Chem. 11, 963 (2006).

    Article  Google Scholar 

  38. L. I. Trubitsina, S. V. Tishchenko, A. G. Gabdulkhakov, et al., Biochimie 112, 151 (2015).

    Article  Google Scholar 

  39. M. Suga, F. Akita, K. Hirata, et al., Nature 517, 99 (2015).

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to A. G. Gabdulkhakov.

Additional information

Original Russian Text © A.G. Gabdulkhakov, V.G. Kljashtorny, M.V. Dontsova, 2015, published in Kristallografiya, 2015, Vol. 60, No. 6, pp. 926–931.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Gabdulkhakov, A.G., Kljashtorny, V.G. & Dontsova, M.V. Analysis of molecular oxygen exit pathways in cyanobacterial photosystem II: Molecular dynamics studies. Crystallogr. Rep. 60, 884–888 (2015). https://doi.org/10.1134/S1063774515060085

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1063774515060085

Keywords

  • Crystallography Report
  • Oxygen Molecule
  • Molecular Dynamic Trajectory
  • Manganese Cluster
  • Krypton Atom