Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: Dielectric response, vibrational cooling and the J, K intermediates

Biophysical Journal

Volumn 70, Issue 1, 1996, Pages 453-460

  Xu, Dong ^a,c   Martin, Charles ^a   Schulten, Klaus ^a,b  

^a United States of America   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN;

ARTICLE; CHEMICAL REACTION; DIELECTRIC CONSTANT; EXTRACELLULAR MATRIX; MOLECULAR DYNAMICS; NONHUMAN; PHOTOSYNTHESIS; PROTEIN PROTEIN INTERACTION; SOLVATION; VIBRATION;

EID: 0030058834     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79588-7     Document Type: Article

References (38)

1. Birge, R. 1995. Protein-based computers. Sci. Am. 3:90-95.
2. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMm: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
3. Brünger, A. T. 1992. X-PLOR, Version 3.1, A System for X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
4. Delaney, J. K., T. L. Brack, G. H. Atkinson, M. Ottolenghi, G. Steinberg, and M. Sheves. 1995. Primary picosecond molecular events in the photoreaction of the BR5.12 artificial bacteriorhodopsin pigment. Proc. Natl. Acad. Sci. USA. 92:2101-2105.
5. 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.
6. Doig, S. J., P. J. Reid, and R. A. Mathies. 1991. Picosecond time-resolved resonance Raman spectroscopy of bacteriorhodopsin's J. K, and KL intermediates. J. Phys. Chem. 95:6372-6379.
7. Ebrey, T. 1993. Light energy transduction in bacteriorhodopsin. In Thermodynamics of Membranes, Receptors and Channels, M. Jacobson, editor. CRC Press, New York. 353-387.
8. 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspartic acids and structural implications of single site mutations. Eur. Biophys. J. 18:17-24.
9. Frederick, J. H., Y. Fujiwara, J. H. Penn, K. Yoshihara, and H. Petek. 1991. Model for stilbene photoisomerization: Experimental and theoretical studies of the excited-state dynamics of 1,2-diphenylcycloalkenes. J. Phys Chem. 95:2845-2858.
10. Gerwert, K., B. Hess, J. Soppa, and D. Oesterhelt. 1989. Role of Asp-96 in proton translocation by bacteriorhodopsin. Proc. Natl. Acad. Sci. USA. 86:4943-4947.
11. Govindjee, R., S. P. Balashov, and T. G. Ebrey. 1990. Quantum efficiency of the photochemical cycle of bacteriorhodopsin. Biophys. J. 58:597-608.
12. 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.
13. Humphrey, W., I. Logunov, K. Schulten, and M. Sheves. 1994. Molecular dynamics study of bacteriorhodopsin and artificial pigments. Biochemistry. 33.3668-3678.
14. Humphrey, W., D. Xu, K. Schulten, and M. Sheves. 1995. Molecular dynamics study of the early intermediates in the bacteriorhodopsin photocycle. Submitted. [Beckman Institute Technical Report TB-95-05].
15. Jimenez, R., G. R. Fleming, P. V. Kumar, and M. Maroncelli. 1994. Femtosecond solvation dynamics of water. Nature. 369:471-473.
16. Jorgensen, W. L., J. Chandrasekhar. J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
17. Lanyi, J. K. 1992 Proton-transfer and energy coupling in the bacteriorhodopsin photocycle. J. Bioenerg. Biomembr. 24:169-179.
18. Logunov, I., and K. Schulten. 1995. Quantum chemistry of in situ retinal: studies of the spectral properties and dark adaptation of bacteriorhodopsin. Proc. Ecole Phys. Houches., Paris. In press.
19. Lozier, R. H., R. A Bogomolni, and W. Stoeckenius. 1975. Bacteriorhodopsin: a light-driven proton pump in halobacterium halobium. Biophys. J. 15:955-962.
20. Mathies, R. A., C. H. Brito Cruz, W. T. Pollard, and C. V. Shank 1988. Direct observation of the femtosecond excited-state cis-trans isomerization in bacteriorhodopsin. Science. 240:777-779.
21. Mathies. R. A., S. W. Lin, J. B. Ames, and W. T. Pollard. 1991. From femtoseconds to biology: mechanism of bacteriorhodopsin's light-driven proton pump. Ann. Rev. Biochem. Bioeng. 20:491-518.
22. B transfer in the photosynthetic reaction center. J. Phys. Chem. 95:2059-2067.
23. Oesterhelt, D., J. Tittor, and E. Bamberg. 1992. A unifying concept for ion translocation in retinal proteins. J. Bioenerg. Biomembr. 24:181-191.
24. Pollard, W. T., C. H. Brito Cruz, C. V. Shank, and R. A. Mathies 1989. Direct observation of the excited-state cis-trans photoisomerization of bacteriorhodopsin: multilevel line shape theory for femtosecond dynamic hole burning and its application. J. Chem. Phys. 90:199-208.
25. Rosenthal, S. J., R. Jimenez, G. R. Fleming, P. V. Kumar, and M. Maroncelli. 1994. Solvation dynamics of methanol: experimental and molecular dynamics simulations studies. J. Mol. Liq. 60:25-56
26. Schneider, G., R. Diller, and M. Stockburger. 1989. Photochemical quantum yield of bacteriorhodopsin from resonance Raman scattering as a probe for photolysis. Chem. Phys. 131:17-29.
27. Schulten, K., W. Humphrey, J. Logunov, M. Sheves, and D. Xu. 1995. Molecular dynamics studies of bacteriorhodopsin's photocycles Isr. J. Chem. In press.
28. Schulten, K., and M. Tesch. 1991. Coupling of protein motion to electron transfer: molecular dynamics and stochastic quantum mechanics study of photosynthetic reaction centers. Chem. Phys. 158:421-446.
29. Sension, R. J., S. T. Repinec, A. Z. Szarka, and R. M. Hochstrasser 1993. Femtosecond laser studies of the cis-stilbene photoisomerization reaction. J. Chem. Phys. 98:6291-6315.
30. Sension, R. J., A. Z. Szarka, and R. M. Hochstrasser. 1992. Vibrational energy redistribution and relaxation in the photoisomerization of cis-stilbene. J. Chem. Phys. 97:5239-5242.
31. Tesch, M. and K. Schulten. 1990. A simulated cooling process for proteins. Chem. Phys. Lett. 169:97-102.
32. Tittor, J. and D. Oesterhelt. 1990. The quantum yield of bacteriorhodopsin. FEBS Lett. 263:269-273.
33. Todd, D. C., and G. R. Fleming. 1993. Cis-stilbene isomerization: temperature dependence and the role of mechanical friction. J. Chem. Phys. 98:269-276.
34. Vachev, V. D., J. H. Frederick, B. A. Grishanin, V. N. Zadkov, and N. I. Koroteev. 1993. Stilbene isomerization dynamics on multidimensional potential energy surface. molecular dynamics simulation. Chem. Phys. Lett. 215:306-314.
35. Waldeck. D. H. 1991. Photoisomerization dynamics of sulbene. Chem. Rev. 91:415-436.
36. Xu, D., and K Schulten. 1992. Multi-mode coupling of protein motion to electron transfer in the photosynthetic reaction center: spin-boson theory based on a classical molecular dynamics simulation. In The Photosynthetic Bacterial Reaction Center: II Structure, Spectroscopy and Dynamics NATO ASI Series A: Life Sciences. J. Breton, and A. Vermeglio, editors. Plenum Press, New York. 301-312.
37. Xu, D., and K. Schulten. 1994. Coupling of protein motion to electron transfer in a photosynthetic reaction center: investigating the low temperature behaviour in the framework of the spin-boson model. Chem. Phys. 182:91-117.
38. Zhou, F., A. Windemuth, and K. Schulten. 1993. Molecular dynamics study of the proton pump cycle of bacteriorhodopsin. Biochemistry. 32:2291-2306.