Low-frequency vibrations and their role in ultrafast photoisomerization reaction dynamics of photoactive yellow protein

Journal of Physical Chemistry B

Volumn 108, Issue 8, 2004, Pages 2686-2698

  Chosrowjan, Haik ^a   Taniguchi, Seiji ^a   Mataga, Noboru ^a   Unno, Masashi ^b   Yamauchi, Seigo ^b   Hamada, Norio ^c   Kumauchi, Masato ^c   Tokunaga, Fumio ^c  

^a INSTITUTE FOR LASER TECHNOLOGY   (Japan)

^b TOHOKU UNIVERSITY   (Japan)

^c OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CALCULATIONS; CHROMOPHORES; ISOMERIZATION; MOLECULAR VIBRATIONS; PHOTOCHEMICAL REACTIONS; PROBABILITY DENSITY FUNCTION; RAMAN SPECTROSCOPY; REACTION KINETICS; TIME DOMAIN ANALYSIS;

LOW FREQUENCY VIBRATIONS; PHOTOACTIVE YELLOW PROTEIN; ULTRAFAST PHOTOISOMERIZATION REACTION DYNAMICS;

PROTEINS;

EID: 1442318737     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp031126w     Document Type: Article

References (63)

1. Meyer, T. E. Biochim. Biophys. Acta 1985, 806, 175.
2. Hoff, W. D.; Dux, P.; Devreese, B.; Roodzant-Nugteren, I. M.; Crielaard, W.; Boelens, R.; Kaptain, R.; Van Beeumen, J.; Hellingwerf, K. J. Biochemistry 1994, 33, 13959.
3. Baca, M.; Borgstahl, G. E. O.; Boissinot, M.; Burke, P. M.; Williams, D. R.; Slater, K. A.; Getzoff, E. D. Biochemistry 1994, 33, 14369.
4. Imamoto, Y.; Ito, T.; Kataoka, M.; Tokunaga, F. FEBS Lett. 1995, 374, 157.
5. Kort, R.; Hoff, W. D.; Van West. M.; Kroon, A. R.; Hoffer, S. M.; Vlieg, K. H.; Crielaard, W.; Van Beeumen, J.; Hellingwerf, K. J. EMBO J. 1996, 15, 3209.
6. Mihara, K.; Histomi, O.; Imamoto, Y.; Kataoka, M.; Tokunaga, F. J. Biochem. 1997, 121, 876.
7. Hoff, W. D.; van Stokkum, I. H. M.; van Ramesdonk, H. J.; van Brederode, M. E.; Browver, A. M.; Fitch, J. C.; Meyer, T. E.; van Grondelle, R.; Hellingwerf, K. J. Biophys. J. 1994, 67, 1691.
8. Imamoto, Y.; Kataoka, M.; Tokunaga, F. Biochemistry 1996, 35, 14047.
9. Ujj, L.; Devanathan, S.; Meyer, T. E.; Cusanovich, M. A.; Tollin, G.; Atkinson, G. H. Biophys. J. 1998, 75, 406.
10. Takeshita K.; Imamoto, Y.; Kataoka, M.; Tokunaga, F.; Terajima, M. Biochemistry 2002, 41, 3037.
11. Chosrowjan, H.; Mataga, N.; Nakashima, N.; Imamoto, Y.; Tokunagam F. Chem. Phys. Lett. 1997, 270, 267.
12. Baltuska, A.; van Stokkum, I. H. M.; Kroon, A.; Monshouwer, R.; Hellingwerf, K. J.; van Grondelle, R. Chem. Phys. Lett. 1997, 270, 263.
13. Changenet, P.; Zhang, H.; van der Meer, M. J.; Hellingwerf, K. J.; Glasbeek, M. Chem. Phys. Lett. 1998, 282, 276.
14. Chosrowjan, H.; Mataga, N.; Shibata, Y.; Imamoto, Y.; Tokunaga, F. J. Phys. Chem. B 1998, 102, 7695.
15. Mataga, N.; Chosrowjan, H.; Shibata, Y.; Imamoto, Y.; Tokunaga, F. J. Phys. Chem. B 2000, 104, 5191.
16. Imamoto, Y.; Kataoka, M.; Tokunaga, F.; Asahi, T.; Masuhara, H. Biochemistry 2001, 40, 6047.
17. Devanathan, S.; Pacheco, A.; Ujj, L.; Cusanovich, M.; Tollin, G.; Lins, S.; Woodbury, N. Biophys. J. 1999, 77, 1017.
18. Mataga, N.; Chosrowjan, H.; Shibata, Y.; Imamoto, Y.; Kataoka, M.; Tokunaga, F. Chem. Phys. Lett. 2002, 352, 220.
19. Chosrowjan, H.; Mataga, N.; Taniguchi, S.; Shibata, Y.; Hamada, N.; Tokunaga, F. Imamoto, Y.; Kataoka, M. J. Photosci. 2002, 9, 122.
20. Mataga, N.; Chosrowjan, H.; Taniguchi, S.; Hamada, N.; Tokunaga, F.; Imamoto, Y.; Kataoka, M. Phys. Chem. Chem. Phys. 2003, 5, 2454.
21. Gensch, T.; Gradinaru, C. C.; van Stokkum, I. H. M.; Hendricks, J.; Hellingwerf, K. J.; van Grondelle, R. Chem. Phys. Lett. 2002, 356, 347.
22. Nakamura, R.; Kanematsu, Y.; Kumauchi, M.; Hamada, N.; Tokunaga, F. J. Lumin. 2003, 102-103C, 21.
23. Yoshizawa, T.; Wald, G. Nature 1963, 197, 1279.
24. Birge, R. R. Annu. Rev. Phys. Chem. 1990, 41, 683.
25. Du, M.; Flemming, G. R. Biophys. Chem. 1993, 48, 101.
26. Kochendoerfer, G. G.; Mathies, R. A. Isr. J. Chem. 1995, 35, 211.
27. Chosrowjan, H.; Mataga, N.; Shibata, Y.; Tachibanaki, S.; Kandori, H.; Shichida, Y.; Osaka, T.; Kouyama, T. J. Am. Chem. Soc. 1998, 120, 9706.
28. Kandori, H.; Furutani, Y.; Nishimura, S.; Shichida, Y.; Chosrowjan, H.; Shibata, Y.; Mataga, N. Chem. Phys. Lett. 2001, 334, 271.
29. Changenet-Barret, P.; Plaza, P.; Martin, M. M. Chem. Phys. Lett. 2001, 336, 439.
30. Changenet-Barret, P.; Espagne, A.; Katsonis, N.; Charier, S.; Baudin, J.-B.; Jullien, L.; Plaza, P.; Martin, M. M. Chem. Phys. Lett. 2000, 365, 285.
31. Genick, U. K.; Soltis, S. M.; Kuhn, P.; Canestrelli, I. L.; Getzoff, E. D. Nature 1998, 392, 206.
32. Perman, B.; Srajer, V. ; Ren, Z.; Teng, T.-Y.; Praderwand, C.; Ursby, T.; Bourgeois, D.; Schotte, F.; Wulff, M.; Kort, R. Hellingwerf, K. J.; Moffat, K. Science 1998, 279, 1946.
33. Imamoto, Y.; Mihara, K.; Hisatomi, O.; Kataokam M.; Tokunaga, F.; Bojkova, N.; Yoshihara, K. J. Biol. Chem. 1997, 272, 12905.
34. Unno, M.; Kumauchi, M.; Sasaki, J.; Tokunaga, F.; Yamauchi, S. Biochemistry 2002, 41, 5668.
35. Yamada, A.; Yamamoto, S.; Yamato, T.; Kakitani, T. THEOCHEM 2001, 536, 195.
36. (a) Hellingwerf, K. J.; Hedriks, J.; Gensch, T. J. Phys. Chem. A 2003, 107, 1082.
37. (b) Cusanovich, M.; Meyer, T. E. Biochemistry 2003, 42, 4759.
38. (a) Saltiel, J.; Megarity, E. D. J. Am. Chem. Soc. 1972, 94, 2742.
39. (b) Hochtrasser R. M. Pure Appl. Chem. 1980, 52, 2683.
40. (c) Fleming, G. R. Chemical Applications of Ultrafast Spectroscopy; Oxford University Press: New York, 1986; p 179
41. Note: This, however, may not be true when multiple excited states are involved.
42. Kobayashi, T.; Saito, T.; Ohtani, H. Nature 2001, 414, 531.
43. Unno, M.; Kumauchi, M.; Sasaki, J.; Tokunaga, F.; Yamauchi, S. J. Phys. Chem. B 2003, 107, 2837.
44. Unno, M.; Kumauchi, M.; Sasaki, J.; Tokunaga, F.; Yamauchi, S. J. Am. Chem. Soc. 2000, 122, 4233.
45. Kim, M.; Mathies, R. A.; Hoff, W. D.; Hellingwerf, K. J. Biochemistry 1995, 33, 12669.
46. Brudler, R.; Meyer, T. E.; Genick, U. K.; Devanathan, S.; Woo, T. T.; Miller, D. P.; Gerwert, K.; Cusanovich, M. A.; Tollin, G.; Getzoff, E. Biochemistry 2000, 39, 13478.
47. Zhou, Y.; Ujj, L.; Meyer, T. E.; Cusanovich, M. A.; Atkinson, G. H. J. Phys. Chem. A 2001, 105, 5719.
48. William, S. W.; William, D. E., Jr. J. Am. Chem. Soc. 1961, 83, 1733.
49. L, it is in the cis configuration.
50. Koch, W.; Holthausen, M. C. A. Chemist's Guide to Density Functional Theory; Wiley-VCH: Weinheim, 2000.
51. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98; Gaussian, Inc.: Pittsburgh, PA, 1998.
52. Rubtsov, I. V.; Yoshihara, K. J. Phys. Chem. A 1999, 103, 10202.
53. We note that it would be deceptive to Fourier transform numerically extracted oscillatory components alone because important details such as peak intensities in the transformed spectra depend sensitively on the method used to subtract off the underlying nonexponential excited-state population decay. Hence, we present in Figures 2 and 5 the DFTS of whole fluorescence transients.
54. Mataga, N.; Chosrowjan, H.; Taniguchi, S.; Shibata, Y.; Yoshida, N.; Osuka, A.; Kikuzawa, T.; Okada, T. J. Phys. Chem. A 2002, 106, 12191.
55. Mataga, N.; Chosrowjan, H.; Taniguchi, S.; Tanaka, F.; Kido, N.; Kitamura, M. J. Phys. Chem. B 2002, 106, 8917.
56. van Aalten, D. M. F.; Crielaard, W.; Hellingwerf, K. J.; Joshua-Tor, L. Acta Crystallogr. D 2002, 58, 585.
57. Cordfunke, R.; Korth, R.; Pierik, A.; Gobets, B.; Koomen, G. J.; Verhoeven, J. W.; Hellingwerf, K. J. Proc. Natl. Acad. Sci. 1998, 95, 7396.
58. Jarzeba, W.; Walker, G. C.; Johnson, A. E.; Barbara, P. F. Chem. Phys. 1991, 152, 57.
59. - of the chromophore, although the H-bond energy is smaller in E46Q mutant compared with that of native PYP.
60. Mizutani, Y.; Kitagawa, T. Science 1997, 278, 443.
61. 39 for the similar modes for both native chromophore model (HCET) as well as locked chromophore analogue model (HCCET) and the later modes are marked with a dash.
62. Kroon, A. R.; Hoff, W. D.; Fennema, H.; Koomen, G. J.; Verhoeven, J. W.; Crielaard, W.; Hellingwerf, K. J. J. Biol. Chem. 1996, 271, 31949.
63. We note that a principal difference between low-frequency in-plane and out-of-plane modes might not be very clear in the real PYP system; i.e., in the low-frequency region, almost all modes might contain both in-plane and out-of-plane characteristics.