Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
권호 표지
DOI QR코드

DOI QR Code

Concerted Asynchronous Proton Transfer in H-Bonding Relay Model: An Implication of Green Fluorescent Protein

  • Kang, Baotao (Department of Chemistry, Sungkyunkwan University) ;
  • Karthikeyan, S. (Department of Chemistry, Sungkyunkwan University) ;
  • Jang, Du-Jeon (Department of Chemistry, Seoul National University) ;
  • Kim, Heeyoung (Supercomputing Center, Korea Institute of Science and Technology Information) ;
  • Lee, Jin Yong (Department of Chemistry, Sungkyunkwan University)
  • Received : 2013.03.24
  • Accepted : 2013.04.01
  • Published : 2013.07.20
Download PDF
⟨ Previous Next ⟩

Abstract

Theoretical investigations have been performed for the ground state ($S_0$) and the first excited state ($S_1$) of the hydrogen bonded green fluorescent protein (GFP) model. The potential energy surface (PESs) of $S_0$ was obtained by B3LYP method and that of $S_1$ was obtained by CIS method. Based on the relative stabilities of species and the energy barriers for the proton transfer, it was found that proton transfer could take place both under the ground state and the first excited state. As determined by the proton motions along the reaction coordinate, both the ground state proton transfer (GSPT) and the excited state proton transfer (ESPT) are considered as a concerted and asynchronous process.

Keywords

References

  1. Arnaut, L. G.; Formosinho, S. J. J. Photochem. Photobiol. A: Chem. 1993, 75, 1-20. https://doi.org/10.1016/1010-6030(93)80157-5
  2. Formosinho, S. J.; Arnaut, L. G. J. Photochem. Photobiol. A: Chem. 1993, 75, 21-48. https://doi.org/10.1016/1010-6030(93)80158-6
  3. Schowen, K. B.; Limbach, H. H.; Denisov, G. S.; Schowen, R. L. Bba-Bioenergetics 2000, 1458, 43-62. https://doi.org/10.1016/S0005-2728(00)00059-1
  4. Zimmer, M. Chem. Rev. 2002, 102, 759-781. https://doi.org/10.1021/cr010142r
  5. Martynov, V. I.; Pakhomov, A. A. Chem. Biol. 2008, 15, 755-764. https://doi.org/10.1016/j.chembiol.2008.07.009
  6. Zimmer, M. Chem. Soc. Rev. 2009, 38, 2823-2832. https://doi.org/10.1039/b904023d
  7. Morise, H.; Shimomura, O.; Johnson, F. H.; Winant, J. Biochemistry-Us 1974, 13, 2656-2662. https://doi.org/10.1021/bi00709a028
  8. Ward, W. W.; Bokman, S. H. Biochemistry-Us 1982, 21, 4535-4540. https://doi.org/10.1021/bi00262a003
  9. Heim, R.; Prasher, D. C.; Tsien, R. Y. Proc. Natl. Acad. Sci. USA 1994, 91, 12501-12504. https://doi.org/10.1073/pnas.91.26.12501
  10. Weber, W.; Helms, V.; McCammon, J. A.; Langhoff, P. W. Proc. Natl. Acad. Sci. USA 1999, 96, 6177-6182. https://doi.org/10.1073/pnas.96.11.6177
  11. Chattoraj, M.; King, B. A.; Bublitz, G. U.; Boxer, S. G. Proc. Natl. Acad. Sci. USA 1996, 93, 8362-8367. https://doi.org/10.1073/pnas.93.16.8362
  12. Brejc, K.; Sixma, T. K.; Kitts, P. A.; Kain, S. R.; Tsien, R. Y.; Ormo, M.; Remington, S. J. Proc. Natl. Acad. Sci. USA 1997, 94, 2306-2311. https://doi.org/10.1073/pnas.94.6.2306
  13. Warren, A.; Zimmer, M. J. Mol. Graph. Model 2001, 19, 297-303. https://doi.org/10.1016/S1093-3263(00)00057-7
  14. Lill, M. A.; Helms, V. Proc. Natl. Acad. Sci. USA 2002, 99, 2778-2781. https://doi.org/10.1073/pnas.052520799
  15. Vendrell, O.; Gelabert, R.; Moreno, M.; Lluch, J. M. J. Am. Chem. Soc. 2006, 128, 3564-3574. https://doi.org/10.1021/ja0549998
  16. Wang, S.; Smith, S. C. Phys. Chem. Chem. Phys. 2007, 9, 452-458. https://doi.org/10.1039/b612760f
  17. Dewar, M. J. S. J. Am. Chem. Soc. 1984, 106, 209-219. https://doi.org/10.1021/ja00313a042
  18. Li, X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Morokuma, K. J. Phys. Chem. B 2010, 114, 1114-1126. https://doi.org/10.1021/jp909947c
  19. Ai, H.; Bu, Y.; Li, P.; Yan, S. H. J. Chem. Phys. 2005, 123, 134307. https://doi.org/10.1063/1.2042449
  20. Qin, Y.; Wheeler, R. A. J. Chem. Phys. 1995, 102, 1689-1698. https://doi.org/10.1063/1.468901
  21. Kang, B.; Ko, K. C.; Park, S. Y.; Jang, D. J.; Lee, J. Y. Phys. Chem. Chem. Phys. 2011, 13, 6332-6339. https://doi.org/10.1039/c0cp02347g
  22. 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.; Li, X.; Hratchian, H. P.; 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.; Keith, T.; 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.; Cio lowski, J.; Fox, D. J. Gaussian 09, Revision B.01, Gaussian, Inc., Wallingford CT, 2010.
  23. Cubitt, A. B.; Heim, R.; Adams, S. R.; Boyd, A. E.; Gross, L. A.; Tsien, R. Y. Trends Biochem. Sci. 1995, 20, 448-455. https://doi.org/10.1016/S0968-0004(00)89099-4
  24. Kummer, A. D.; Wiehler, J.; Rehaber, H.; Kompa, C.; Steipe, B.; Michel-Beyerle, M. E. J. Phys. Chem. B 2000, 104, 4791-4798. https://doi.org/10.1021/jp9942522
  25. Lossau, H.; Kummer, A.; Heinecke, R.; PollingerDammer, F.; Kompa, C.; Bieser, G.; Jonsson, T.; Silva, C. M.; Yang, M. M.; Youvan, D. C.; MichelBeyerle, M. E. Chem. Phys. 1996, 213, 1-16. https://doi.org/10.1016/S0301-0104(96)00340-0
  26. Winkler, K.; Lindner, J. R.; Subramaniam, V.; Jovin, T. M.; Vohringer, P. Phys. Chem. Chem. Phys. 2002, 4, 1072-1081. https://doi.org/10.1039/b108843b
  27. McAnaney, T. B.; Park, E. S.; Hanson, G. T.; Remington, S. J.; Boxer, S. G. Biochemistry-Us 2002, 41, 15489-15494. https://doi.org/10.1021/bi026610o
  28. Lesser, M. P.; Bou-Abdallah, F.; Chasteen, N. D. Bba-Gen Subjects 2006, 1760, 1690-1695. https://doi.org/10.1016/j.bbagen.2006.08.014
  29. Wang, S. F.; Smith, S. C. J. Phys. Chem. B 2006, 110, 5084-5093. https://doi.org/10.1021/jp056966k
  30. Ong, W. J. H.; Alvarez, S.; Leroux, I. E.; Shahid, R. S.; Samma, A. A.; Peshkepija, P.; Morgan, A. L.; Mulcahy, S.; Zimmer, M. Mol. Biosyst. 2011, 7, 984-992. https://doi.org/10.1039/c1mb05012e
  31. Polyakov, I. V.; Grigorenko, B. L.; Epifanovsky, E. M.; Krylov, A. I.; Nemukhin, A. V. J. Chem. Theory Comput. 2010, 6, 2377-2387. https://doi.org/10.1021/ct100227k
  32. Stoner-Ma, D.; Jaye, A. A.; Ronayne, K. L.; Nappa, J.; Meech, S. R.; Tonge, P. J. J. Am. Chem. Soc. 2008, 130, 1227-1235. https://doi.org/10.1021/ja0754507
  33. Schafer, L. V.; Groenhof, G.; Boggio-Pasqua, M.; Robb, M. A.; Grubmuller, H. Plos. Comput. Biol. 2008, 4.
  34. Leiderman, P.; Huppert, D.; Agmon, N. Biophys. J. 2006, 90, 1009-1018. https://doi.org/10.1529/biophysj.105.069393
  35. Shinobu, A.; Palm, G. J.; Schierbeek, A. J.; Agmon, N. J. Am. Chem. Soc. 2010, 132, 11093-11102. https://doi.org/10.1021/ja1010652
  36. Brakemann, T.; Stiel, A. C.; Weber, G.; Andresen, M.; Testa, I.; Grotjohann, T.; Leutenegger, M.; Plessmann, U.; Urlaub, H.; Eggeling, C.; Wahl, M. C.; Hell, S. W.; Jakobs, S. Nat. Biotechnol. 2011, 29, 942-U132. https://doi.org/10.1038/nbt.1952

Cited by

  1. Electric field effect on the ground state proton transfer in the H-bonded HBDI complex: an implication of the green fluorescent protein vol.4, pp.51, 2013, https://doi.org/10.1039/c4ra00974f