Molecular Dynamics Simulation of the Excited-State Dynamics of Bacteriorhodopsi

Photochemistry and Photobiology

Volumn 66, Issue 6, 1997, Pages 735-740

  Yamato, Takahisa ^a   Kakitani, Toshiaki ^b  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^b NAGOYA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001293178     PISSN: 00318655     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1751-1097.1997.tb03217.x     Document Type: Article

References (28)

1. Oesterhelt, D. and W. Stoechenius (1973) Functions of a new photoreceptor membrane. Proc. Natl. Acad. Sci. USA 70, 2853-2857.
2. Grigorieff, N., T. A. Ceska, K. H. Downing, J. M. Baldwin and R. Henderson (1996) Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259, 393-421.
3. Dobler, J., W. Zinth, W. Kaiser and D. Oesterhelt (1988) Excited-state reaction dynamics of bacteriorhodopsin studied by femtosecond spectroscopy. Chem. Phys. Lett. 144, 215-220.
4. Mathies, R. A., C. H. Brito, W. T. Pollard and C. V. Shank (1988) Direct observation of the femtosecond excited-state cis-trans isomerization in bacteriorhodopsin. Science 240, 777-779.
5. Myers, A. B., R. A. Harris and R. A. Mathies (1983) Resonance Raman excitation profiles of bacteriorhodopsin. J. Chem. Phys. 79, 603-613.
6. Du, M. and G. R. Fleming (1993) Femtosecond time-resolved fluorescence spectroscopy of bacteriorhodopsin: direct observation of excited state dynamics in the primary step of the proton pump cycle. Biophys. Chem. 48, 101-111.
7. Akiyama, R., T. Kakitani, Y. Imamoto, Y. Shichida and Y. Hatano (1995) Temperature dependence of femtosecond excited state dynamics of bacteriorhodopsin analyzed by the Fourier transform of optical absorption spectra. J. Phys. Chem. 99, 7147-7153.
8. Akiyama, R., A. Yoshimori, T. Kakitani, Y. Imamoto, Y. Shichida and Y. Hatano (1996) Analysis of the temperature dependence of femtosecond excited state dynamics of bacteriorhodopsin by spin-boson model. Chem. Phys. Lett. 256, 165-171.
9. Akiyama, R., A. Yoshimori, T. Kakitani, Y. Imamoto, Y. Shichida and Y. Hatano (1997) Analysis of the excited-state dynamics of 13-trans-locked-bacteriorhodopsin. J. Phys. Chem. 101, 412-417.
10. Warshel, A. (1976) Bicycle-pedal model for the first step in the vision process. Nature 260, 679-683.
11. Birge, R. R. and T. M. Cooper (1983) Energy storage in the primary step of photocycle of bacteriorhodopsin. Biophys. J. 42, 61-69.
12. Birge, R. R., L. A. Findsen and B. M. Pierce (1987) Molecular dynamics of the primary photochemical event in bacteriorhodopsin. Theoretical evidence for an excited singlet state assignment for the J intermediate. J. Am. Chem. Soc. 109, 5041-5043.
13. Zhou, F., A. Windemuth and K. Schulten (1993) Molecular dynamics study of the proton pump cycle of bacteriorhodopsin. Biochemistry 32, 2291-2306.
14. Humphrey, W., I. Logunov, K. Schulten and M. Sheves (1994) Molecular dynamics study of bacteriorhodopsin and artificial pigments. Biochemistry 33, 3668-3678.
15. Logunov, I., W. Humphrey, K. Schulten and M. Sheves (1995) Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: dielectric response, vibrational cooling and the J, K intermediates. Biophys. J. 70, 453-460.
16. Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rogders, O. Kennard, T. Shimanouchi and M. Tasumi (1977) The protein data bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
17. Cornell, W. D., P. Cieplank, C. I. Bayly, I. R. Gould, K. M. Mertz, Jr., D. M. Fergunson, D. C. Spellmeyer, T. Fox, J. W. Cladwell and P. A. Kollman (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179-5197.
18. Shrake, A. and J. A. Ruply (1973) Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79, 351-371.
19. Yamato, T. (1996) Strain tensor field in proteins. J. Mol. Graphics 14, 105-107.
20. Du, P. and E. R. Davidson (1990) Ab initio study on the excitation energies of the protonated Schiff base of 11-cis retinal. J. Phys. Chem. 94, 7013-7020.
21. Stewart, J. J. P. (1989) Optimization of parameters for semiempirical methods II. Applications. J. Comput. Chem. 10, 221-264.
22. Song, L., M. A. El-Sayed and J. K. Lanyi (1993) Protein catalysis of the retinal subpicosecond photoisomerization in the primary process of bacteriorhodopsin photosynthesis. Science 261, 891-894.
23. Morikami, K., T. Nakai, A. Kidera, M. Saito and H. Nakamura (1993) PRESTO (Protein Engineering SimulaTOr): a vectorized molecular mechanics program for biopolymers. Comput. Chem. 16, 243-248.
24. Yamato, T., N. Niimura and N. Gō (1997) Molecular dynamics study of femtosecond events in photoactive yellow protein after photoexcitation of the chromophore. Proteins, (in press).
25. Verlet, L. (1967) Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159, 98-103.
26. van Gunsteren, W. F. and M. Karplus (1982) Effects of constraints on the dynamics of macromolecules. Macromolecules 15, 1528-1544.
27. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola and J. R. Haak (1984) Molecular dynamics with coupling to an external heat bath. J. Chem. Phys. 81, 3684-3690.
28. Henderson, R., J. M. Baldwin, T. A. Ceska, F. Zemlin, E. Beckmann and K. H. Downing (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213, 899-929.