Femtosecond primary events in bacteriorhodopsin and its retinal modified analogs: Revision of commonly accepted interpretation of electronic spectra of transient intermediates in the bacteriorhodopsin photocycle

Journal of Chemical Physics

Volumn 120, Issue 23, 2004, Pages 11120-11132

  Abramczyk, Halina ^a  

^a LODZ UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOPHORES; ELECTRONIC STRUCTURE; MATHEMATICAL MODELS; NONLINEAR EQUATIONS; PERTURBATION TECHNIQUES; PHOTOCHEMICAL REACTIONS; POTENTIAL ENERGY; VIBRATION MEASUREMENT;

ELECTRONIC SPECTRA; ELECTRONIC TRANSITION; POTENTIAL ENERGY SURFACE (PES); VIBRATIONAL COUPLING;

MOLECULAR DYNAMICS;

BACTERIORHODOPSIN; RETINAL;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; KINETICS; LIGHT; PHOTOCHEMISTRY; RADIATION EXPOSURE; SPECTROSCOPY; TIME;

BACTERIORHODOPSINS; COMPUTER SIMULATION; KINETICS; LIGHT; MODELS, BIOLOGICAL; MODELS, CHEMICAL; MODELS, MOLECULAR; PHOTOBIOLOGY; PHOTOCHEMISTRY; RETINALDEHYDE; SPECTRUM ANALYSIS; TIME FACTORS;

EID: 3042598390     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1737731     Document Type: Article

References (53)

1. T.G. Ebrey, in Thermodynamics of Membranes, Receptors and Channels (CRC, New York, 1993), p. 353.
2. J.K. Lanyi, Biochim. Biophys. Acta 241, 241 (1993).
3. J.K. Lanyi, J. Phys. Chem. B 104, 11441 (2000).
4. R.A. Mathies, C.H. Brito Cruz, W.T. Pollard, and CH.V. Shank, Science 240, 777 (1988).
5. J.W. Petrich, J. Brenton, J.L. Martin, and A. Antonetti, Chem. Phys. Lett. 137, 369 (1987).
6. J. Dobler, W. Znith, W. Kaiser, and D. Oesterhelt, Chem. Phys. Lett. 144, 215 (1988).
7. J. Herbst, K. Heyne, and R. Diller, Science 297, 822 (2002).
8. G.H. Atkinson, L. Ujj, and Y. Zhou, J. Phys. Chem. A 104, 4130 (2000).
9. L. Song and M.A. El-Sayed, J. Am. Chem. Soc. 120, 8889 (1998).
10. M. Garavelli, P. Celani, F. Bernardi, M.A. Robb, and M. Olivuci, J. Am. Chem. Soc. 119, 6891 (1997).
11. M. Du and G.R. Fleming, Biophys. Chem. 48, 101 (1993).
12. K.C. Hasson, F. Gai, and P.A. Anfinrud, Proc. Natl. Acad. Sci. U.S.A. 93, 15124 (1996).
13. F. Gai, K.C. Hasson, J. Cooper McDonald, and P.A. Anfinrund, Science 79, 1886 (1998).
14. T. Ye, N. Friedman, Y. Gat, G.H. Atkinson, M. Sheves, M. Ottolenghi, and S. Ruhman, J. Phys. Chem. B 103, 5122 (1999).
15. S. Mukamel, Principles of Nonlinear Optical Spectroscopy (Oxford University Press, New York, 1995), p. 328.
16. W.T. Pollard, S.L. Dexheimer, Q. Wang, L.A. Petanu, Ch.V. Shank, and R.A. Mathies, J. Phys. Chem. 96, 6147 (1992).
17. T. Ye, E. Gershgoren, N. Friedman, M. Ottolenghi, M. Sheves, and S. Ruhman, Chem. Phys. Lett. 314, 429 (1989).
18. J.C. Palanayi and A.H. Zewail, Acc. Chem. Res. 28, 119 (1995).
19. T. Kobayashi, T. Salto, and H. Ohtani, Nature (London) 414, 531 (2001).
20. R. Akiyama, A. Yoshimori, T. Kakitani, Y. Imamoto, Y. Schichida, and J. Hatano, J. Phys. Chem. A 101, 417 (1997).
21. G.H. Atkinson, Y. Zhou, L. Ujj, A. Aharoni, M. Sheves, and M. Ottolenghi, J. Phys. Chem. A 106, 3325 (2002).
22. L. Ujj, Y. Zhou, M. Sheves, M. Ottolenghi, S. Ruhman, and G.H. Atkinson, J. Am. Chem. Soc. 122, 96 (2000).
23. M. Garavelli, F. Negri, and M. Olivucci, J. Phys. Chem. Soc. 121, 1023 (1999).
24. G. Eyring, B. Curry, A. Brock, J. Lugtenburg, and R. Mathies, Biochemistry 21, 384 (1982).
25. S.W. Lin, M. Groesbeek, I. van der Hoef, P. Werdegem, J. Lugtenburg, and R.A. Mathies, J. Phys. Chem. B 102, 2787 (1998).
26. L. Zhu, J. Kim, and R.A. Mathies, J. Raman Spectrosc, 30, 777 (1999).
27. A. Warshel and N. Barboy, J. Am. Chem. Soc. 104, 1469 (1982).
28. A. Warshel, Nature (London) 260, 679 (1976).
29. R.G. Luque, M. Garavelli, F. Bernardi, M. Merchan, M.A. Robb, and M.O. Livucci, Proc. Natl. Acad. Sci. U.S.A. 97, 9379 (2000).
30. A. Warshel and W.W. Parson, Q. Rev. Biophys. 34, 563 (2001).
31. S. Ruhman, B. Hou, N. Friedman, M. Ottolenghi, and M. Sheves, J. Am. Chem. Soc. 124, 8854 (2002).
32. S. Mukamel, Principles of Nonlinear Optical Spectroscopy (Oxford University Press, New York, 1995), pp. 203, 209.
33. M. Kolodziejski, G. Waliszewska, and H. Abramczyk, Chem. Phys. 213, 341 (1996).
34. H. Abramczyk, Chem. Phys. 144, 319 (1990).
35. W.H. Louisell, Quantum Statistical Properties of Radiation (Wiley, New York, 1973), p. 151.
36. H. Abramczyk, Chem. Phys. 144, 305 (1990).
37. S. Koide, Z. Naturforsch. A 15A, 123 (1962).
38. S. Mukamel, Principles of Nonlinear Optical Spectroscopy (Oxford University Press, New York, 1995), p. 336.
39. A.B. Myers, R.A. Harris, and R.A. Mathies, J. Chem. Phys. 79, 603 (1983).
40. S.O. Smith, M.S. Braiman, A.B. Myers, J.A. Pardoen, J.M.L. Courtin, Ch. Winkel, J. Lugtenbury, and R.A. Mathies, J. Am. Chem. Soc. 109, 3108 (1987).
41. L. Ujj, B.L. Volodin, A. Popp, J.K. Delaney, and G.H. Atkinson, Chem. Phys. 182, 291 (1994).
42. Q. Wang, R.W. Schoenlein, L.A. Peteanu, R. Mathies, and Ch.V. Shank, Science 266, 422 (1994).
43. J.E. Kim and R.A. Mathies, J. Phys. Chem. 106, 8508 (2002).
44. H. Abramczyk and J. Kroh, J. Phys. Chem. 95, 615 (1991).
45. T. Rosenfeld, B. Honig, and M. Ottolenghi, Pure Appl. Chem. 49, 341 (1977).
46. A. Warshel and Z.T. Chu, J. Phys. Chem. B 105, 9857 (2001).
47. R.R. Birge, Biochim. Biophys. Acta 327, 1016 (1990).
48. R. Weiss and A. Warshel, J. Am. Chem. Soc. 101, 6131 (1979).
49. W.W. Humprey, H. Lu, I. Logunov, H.J. Werner, and K. Schulten, Biophys. J. 75, 1689 (1998).
50. M. Ben-Nun, F. Molnar, H. Lu, J.C. Philips, T.J. Martinez, and K. Schulten, Faraday Discuss. 110, 447 (1998).
51. S.L. Dexheimer, Q. Wang, L.A Petanu, W.T. Pollard, Ch.V. Shank, and R.A. Mathies, Chem. Phys. Lett. 188, 61 (1992).
52. J. Tittor and D. Oesterhelt, FEBS Lett. 263, 269 (1990).
53. A.C. Terentis, H. Abramczyk, L. Ujj, and G.H. Atkinson (unpublished).