Skip to main content
Log in

QM/MM Investigations on the Bioluminescent Decomposition of Coelenterazine Dioxetanone in Obelin

  • Published:
Chemical Research in Chinese Universities Aims and scope

Abstract

The bioluminescent mechanism of colenterazine dioxetanone(CZD) in the photoprotein of Obelia(obelin) was investigated by the combined quantum and molecular mechanics(QM/MM) method at TD-DFT level, which involved the real protein environment in decomposition of 1,2-dioxetanones. The anionic decomposition of CZD in (CZD+H2O) model can go through a charge transfer(CT) catalyzed asynchronous-concerted process, which can be elucidated by the gradual reversible CT initiated luminescence(GRCTIL) mechanism. The neutral CZD in (CZDH+H2O) decomposes through an uncatalyzed non-CT biradical process. The anionic decomposition catalyzed by CT, in which the S0/S1 surface “double crossing” hence has ability to provide high quantum yield of singlet chemiexcitation is thus more possible in bioluminescence of photoprotein.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Morin J. G., Coelenterate Bioluminescence, Coelenterate Biology, Academic Press, New York, 1974, 397

    Book  Google Scholar 

  2. Shimomura O., Johnson F. H., Saiga Y., J. Cellular Comparative Physi., 1962, 59(3), 223

    Article  CAS  Google Scholar 

  3. Shimomura O., The Coelenterazines, Bioluminescence: Chemical Principles and Methods, World Scientific, Singapore, 2006

    Book  Google Scholar 

  4. Campbell A. K., Biochem. J., 1974, 143(2), 411

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Widder E. A., Science, 2010, 328(5979), 704

    Article  CAS  PubMed  Google Scholar 

  6. Lourenço J. M., Esteves da Silva J. C. G., Pinto da Silva L., J. Lumin., 2018, 194, 139

    Article  CAS  Google Scholar 

  7. Shimomura O., Johnson F. H., Proc. Natl. Acad. Sci., 1978, 75(6), 2611

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Markova S. V., Vysotski E. S., Blinks J. R., Burakova L. P., Wang B. C., Lee J., Biochemistry, 2002, 41(7), 2227

    Article  CAS  PubMed  Google Scholar 

  9. Hermann A., Cox J. A., Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 1995, 111(3), 337

    Article  CAS  Google Scholar 

  10. Charbonneau H., Walsh K. A., McCann R. O., Prendergast F. G., Cormier M. J., Vanaman T. C., Biochemistry, 1985, 24(24), 6762

    Article  CAS  PubMed  Google Scholar 

  11. Fagan T. F., Ohmiya Y., Blinks J. R., Inouye S., Tsuji F. I., FEBS Lett., 1993, 333(3), 301

    Article  CAS  PubMed  Google Scholar 

  12. Lewit-Bentley A., Réty S., Current Opinion in Structural Biology, 2000, 10(6), 637

    Article  CAS  PubMed  Google Scholar 

  13. Rizzuto R., Simpson A. W. M., Brini M., Pozzan T., Nature, 1992, 358(6384), 325

    Article  CAS  PubMed  Google Scholar 

  14. Usami K., Isobe M., Tetrahedron Lett., 1995, 36(47), 8613

    Article  CAS  Google Scholar 

  15. van Oort B., Eremeeva E. V., Koehorst R. B. M., Laptenok S. P., van Amerongen H., van Berkel W. J. H., Malikova N. P., Markova S. V., Vysotski E. S., Visser A. J. W. G., Lee J., Biochemistry, 2009, 48(44), 10486

    Article  CAS  PubMed  Google Scholar 

  16. Naumov P., Wu C., Liu Y. J., Ohmiya Y., Photoch. Photobio. Sci., 2012, 11(7), 1151

    Article  CAS  Google Scholar 

  17. Matsumoto M., J. Photochem. Photobiol. C: Photochem. Rev., 2004, 5(1), 27

    Article  CAS  Google Scholar 

  18. Zhang Y., Chen L., Ju W., Xu Y., Chem. Res. Chinese Universities, 2014, 30(2), 194

    Article  CAS  Google Scholar 

  19. Yue L., Roca-Sanjuán D., Lindh R., Ferré N., Liu Y. J., J. Chem. Theory Comput., 2012, 8(11), 4359

    Article  CAS  PubMed  Google Scholar 

  20. Yue L., Liu Y. J., J. Chem. Theory Comput., 2013, 9(5), 2300

    Article  CAS  PubMed  Google Scholar 

  21. Yue L., Liu Y. J., Fang W. H., J. Am. Chem. Soc., 2012, 134(28), 11632

    Article  CAS  PubMed  Google Scholar 

  22. Yue L., Lan Z., Liu Y. J., J. Phys. Chem. Lett., 2015, 6(3), 540

    Article  CAS  PubMed  Google Scholar 

  23. Ding B. W., Liu Y. J., J. Am. Chem. Soc., 2017, 139(3), 1106

    Article  CAS  PubMed  Google Scholar 

  24. Min C. G., Leng Y., Yang X. K., Ren A. M., Cui X. Y., Xu M. L., Wang S. H., Chem. Res. Chinses Universities, 2013, 29(5), 982

    Article  CAS  Google Scholar 

  25. Min C., Leng Y., Yang X. K., Huang S., Ren A., Chem. J. Chinese Universities, 2014, 35(3), 564

    CAS  Google Scholar 

  26. Li Z. S., Zou L. Y., Ren A. M., Feng J. K., Chem. J. Chinese Universities, 2012, 33(12), 2757

    CAS  Google Scholar 

  27. Wang X., Han B., Gao Y., Wang L., Bai M., Chem. Res. Chinese Universities, 2016, 32(3), 325

    Article  CAS  Google Scholar 

  28. Vacher M., Fdez Galván I., Ding B. W., Schramm S., Berraud-Pache R., Naumov P., Ferré N., Liu Y. J., Navizet I., Roca-Sanjuán D., Baader W. J., Lindh R., Chem. Rev., 2018, 118(15), 6927

    Article  CAS  PubMed  Google Scholar 

  29. McCapra F., Chang Y. C., Chem. Commun., 1967, (19), 1011

    Google Scholar 

  30. Usami K., Isobe M., Tetrahedron, 1996, 52(37), 12061

    Article  CAS  Google Scholar 

  31. Min C. G., Ferreira P. J. O., Pinto da Silva L., J. Photochem. Photobiol. B: Biol., 2017, 174(2017), 18

    Article  CAS  Google Scholar 

  32. Min C. G., Pinto da Silva L., Esteves da Silva J. C. G., Yang X. K., Huang S. J., Ren A. M., Zhu Y. Q., Chem. Phys. Chem., 2017, 18(1), 117

    Article  CAS  PubMed  Google Scholar 

  33. Liu Z. J., Vysotski E. S., Deng L., Lee J., Rose J., Wang B. C., Biochem. Biophys. Res. Commun., 2003, 311(2), 433

    Article  CAS  PubMed  Google Scholar 

  34. Liu Z. J., Stepanyuk G. A., Vysotski E. S., Lee J., Markova S. V., Malikova N. P., Wang B. C., Proc. Natl. Acad. Sci., 2006, 103(8), 2570

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Case D. A., Darden T. A., Cheatham T. E. III, Simmerling C. L., Wang J., Duke R. E., R. Luo R. C. W., Zhang W., Merz K. M., Roberts B., Hayik S., Roitberg A., Seabra G., Swails J., Goetz A. W., Kolossváry I., Wong K. F., Paesani F., Vanicek J., Wolf R. M., Liu J., Wu X., Brozell S. R., Steinbrecher T., Gohlke H., Cai Q., Ye X., Wang J., Hsieh M. J., Cui G., Roe D. R., Mathews D. H., Seetin M. G., Salomon-Ferrer R. C., Sagui V. B., Luchko T., Gusarov S., Kovalenko A., Kollman P. A., AMBER 12, University of California, 2012

    Google Scholar 

  36. Šali A., Blundell T. L., J. Mol. Biol., 1993, 234(3), 779

    Article  PubMed  Google Scholar 

  37. Vreven T., Morokuma K., Farkas Ö., Schlegel H. B., Frisch M. J., J. Comput. Chem., 2003, 24(6), 760

    Article  CAS  PubMed  Google Scholar 

  38. Melaccio F., Olivucci M., Lindh R., Ferré N., Int. J. Quantum Chem., 2011, 111(13), 3339

    Article  CAS  Google Scholar 

  39. Gonzalez C., Schlegel H. B., J. Phys. Chem., 1990, 94(14), 5523

    Article  CAS  Google Scholar 

  40. Yanai T., Tew D. P., Handy N. C., Chem. Phys. Lett., 2004, 393(1—3), 51

    Article  CAS  Google Scholar 

  41. Peach M. J. G., Helgaker T., Salek P., Keal T. W., Lutnæs O. B., Tozer D. J., Handy N. C., Phys. Chem. Chem. Phys., 2006, 8(5), 558

    Article  CAS  PubMed  Google Scholar 

  42. Hariharan P. C., Pople J. A., Theoret. Chim. Acta, 1973, 28(3), 213

    Article  CAS  Google Scholar 

  43. Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Scalmani G., Barone V., Mennucci B., Petersson G. A., Nakatsuji H., Caricato M., X. Li H. P. H., Izmaylov A. F., Bloino J., Zheng G., Sonnenberg J. L., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Vreven T., Montgomery J. A. Jr., Peralta J. E., Ogliaro F., Bearpark M., Heyd J. J., Brothers E., Kudin K. N., Staroverov V. N., Kobayashi R., Normand J., Raghavachari K., Rendell A., Burant J. C., Iyengar S. S., Tomasi J., Cossi M., Rega N., Millam J. M., Klene M., Knox J. E., Cross J. B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R. E., Yazyev O., Austin A. J., Cammi R., Pomelli C., Ochterski J. W., Martin R. L., Morokuma K., Zakrzewski V. G., Voth G. A., Salvador P., Dannenberg J. J., Dapprich S., Daniels A. D., Farkas O., Foresman J. B., Ortiz J. V., Cioslowski J., Fox D. J., Gaussian 09, Revision A. 02, Gaussian Inc., Wallingford CT, 2009

    Google Scholar 

  44. Senn H. M., Thiel W., Angew. Chem. Int. Ed., 2009, 48(7), 1198

    Article  CAS  Google Scholar 

  45. Rokob T. A., Rulíšek L., J. Comput. Chem., 2012, 33(12), 1197

    CAS  PubMed  Google Scholar 

  46. Singh U. C., Kollman P. A., J. Comput. Chem., 1984, 5(2), 129

    Article  CAS  Google Scholar 

  47. Nakamura H., Truhlar D. G., J. Chem. Phys., 2003, 118(15), 6816

    Article  CAS  Google Scholar 

  48. Adam W., Baader W. J., J. Am. Chem. Soc., 1985, 107(2), 410

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ling Yue.

Additional information

Supported by the National Natural Science Foundation of China(No.21503156) and the China Postdoctoral Science Found ation(No.2015M572544).

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yue, L. QM/MM Investigations on the Bioluminescent Decomposition of Coelenterazine Dioxetanone in Obelin. Chem. Res. Chin. Univ. 34, 758–766 (2018). https://doi.org/10.1007/s40242-018-8237-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40242-018-8237-4

Keywords

Navigation