Photoproducts of bacteriorhodopsin mutants: A molecular dynamics study

Biophysical Journal

Volumn 72, Issue 3, 1997, Pages 1347-1356

  Humphrey, William ^a   Bamberg, Ernst ^b   Schulten, Klaus ^a  

^a University of Illinois at Urbana Champaign   (United States)

^b MAX PLANCK INSTITUTE OF BIOPHYSICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; BACTERIORHODOPSIN; MUTANT PROTEIN; PROTON PUMP; RETINAL;

ARTICLE; CIS TRANS ISOMERISM; HYDROGEN BOND; ILLUMINATION; MOLECULAR DYNAMICS; PHOTOCHEMISTRY; PHOTOREACTIVITY; SITE DIRECTED MUTAGENESIS;

EID: 0031041820     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78781-2     Document Type: Article

References (33)

1. a's of aspartate-85 and control of thermal isomerization and proton release in the arginine-82 to lysine mutant of bacteriorhodopsin. Biochemistry. 34:8820-8834.
2. Bamberg, E., J. Tittor, and D. Oesterhelt. 1992. Light-driven proton or chloride pumping by halorhodopsin. Proc. Natl. Acad. Sci. USA. 90: 473-486.
3. 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.
4. Brown, L. S., J. Sasaki, H. Kandori, A. Maeda, R. Needleman, and J. K. Lanyi. 1995. Glutamic acid 204 is the terminal proton release group at the extracellular surface of bacteriorhodopsin. J. Biol. Chem. 270: 27122-27126.
5. Brünger, A. T. 1988. X-PLOR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
6. Ebrey, T. 1993. Light energy transduction in bacteriorhodopsin. In Thermodynamics of Membranes, Receptors and Channels. M. Jacobson, editor. CRC Press, New York. 353-387.
7. Govindjee, R., S. P. Balashov, and T. G. Ebrey. 1990. Quantum efficiency of the photochemical cycle of bacteriorhodopsin. Biophys. J. 58: 597-608.
8. Govindjee, R., M. Kono, S. P. Balashov, E. Imasheva, M. Sheves, and T. G. Ebrey. 1995. Effects of substitution of tyrosine 57 with asparagine and phenylalanine on the properties of bacteriorhodopsin. Biochemistry. 34:4828-4838.
9. 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 cryomicroscopy. J. Mol. Biol. 213: 899-929.
10. Holz, M., L. A. Drachev, T. Mogi, H. Otto, A. D. Kaulen, M. P. Heyn, V. P. Skulachev, and H. G. Khorana. 1989. Replacement of aspartic acid-96 by asparagine in bacteriorhodopsin slows both the decay of the M intermediate and the associated proton movement. Proc. Natl. Acad. Sci. USA. 86:2167-2171.
11. Humphrey, W., I. Logunov, K. Schulten, and M. Sheves. 1994. Molecular dynamics study of bacteriorhodopsin and artificial pigments. Biochemistry. 33:3668-3678.
12. Humphrey, W., D. Xu, M. Sheves, and K. Schulten. 1995. Molecular dynamics study of the early intermediates in the bacteriorhodopsin photocycle. J. Phys. Chem. 99:14549-14560.
13. Korenstein, R., and B. Hess. 1977. Hydration effects on cis-trans isomerization of bacteriorhodopsin. FEBS Lett. 82:7-11.
14. Lanyi, J. K. 1992. Proton-transfer and energy coupling in the bacteriorhodopsin photocycle. J. Bioenerg. Biomembr. 24:169-179.
15. Lozier, R. H., R. A. Bogomolni, and W. Stoeckenius. 1975. Bacteriorhodopsin: a light-driven proton pump in Halobacterium halobium. Biophys. J. 15:955-962.
16. Maeda, A., J. Sasaki, Y. Yamazaki, R. Needleman, and J. K. Lanyi. 1994. Interaction of aspartate-85 with a water molecule and the protonated Schiff base in the L intermediate of bacteriorhodopsin - a Fourier-transform infrared spectroscopic study. Biochemistry. 33:1713-1717.
17. Mogi, T., L. Stern, T. Marti, B. Chao, and H. Khorana. 1988. Aspartic acid substitutions affect proton translocation by bacteriorhodopsin. Proc. Natl. Acad. Sci. USA. 85:4148-4152.
18. 85 both participate in a counterion and proton complex near the Schiff base. J. Biol. Chem. 266:11478-11484.
19. Nelson, M., W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. D. Skeel, and K. Schulten. 1996. NAMD - a parallel, object-oriented molecular dynamics program. J. Supercomput. Appl. 10:251-268.
20. Oesterhelt, D., and W. Stoeckenius. 1973. Functions of a new photoreceptor membrane. Proc. Natl. Acad. Sci. USA. 70:2853-2857.
21. Oesterhelt, D., J. Tittor, and E. Bamberg. 1992. A unifying concept for ion translocation in retinal proteins. J. Bioenerg. Biomembr. 24:181-191.
22. Otto, H., T. Marti, M. Holz, T. Mogi, L. J. Stern, F. Engel, H. G. Khorana, and M. P. Heyn. 1990. Substitution of amino acids Asp-85, Asp-212, and Arg-82 in bacteriorhodopsin affects the proton release phase of the pump and the pK of the Schiff base. Proc. Natl. Acad. Sci. USA. 87:1018-1022.
23. Papadopoulos, G., N. Dencher, G. Zaccai, and G. Büldt. 1990. Water molecules and exchangeable hydrogen ions at the active centre of bacteriorhodopsin localized by neutron diffraction. J. Mol. Biol. 214: 15-19.
24. Richter, H.-T, L. S. Brown, R. Needleman, and J. K. Lanyi. 1996. A linkage of the pKa's of Asp-85 and Glu-204 forms part of the reprotonation switch of bacteriorhodopsin. Biochemistry. 35:4054-4062.
25. 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.
26. Schulten, K., W. Humphrey, I. Logunov, M. Sheves, and D. Xu. 1995. Molecular dynamics studies of bacteriorhodopsin's photocycles. Isr. J. Chem. 35:447-464.
27. Subramaniam, S., T. Marti, and H. G. Khorana. 1990. Protonation state of Asp (Glu)-85 regulates the purple-to-blue transition in bacteriorhodopsin mutants Arg-82 → Ala and Asp-85 → Glu: the blue form is inactive in proton translocation. Proc. Natl. Acad. Sci. USA. 87:1013-1017.
28. Tittor, J., and D. Oesterhelt. 1990. The quantum yield of bacteriorhodopsin. FEBS Lett. 263:269-273.
29. Tittor, J., D. Oesterhelt, and E. Bamberg. 1995. Bacteriorhodopsin mutants D85N, D85T, and D85,96N as proton pumps. Biophys. Chem. 56: 153-157.
30. Tittor, J., U. Schweiger, D. Oesterhelt, and E. Bamberg. 1994. Inversion of proton translocation in bacteriorhodopsin mutants D85N, D85T, and D85,96N. Biophys. J. 67:1682-1690.
31. Xu, D., C. Martin, and K. Schulten. 1996. 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.
32. Xu, D., M. Sheves, and K. Schulten. 1995. Molecular dynamics study of the M412 intermediate of bacteriorhodopsin. Biophys. J. 69:2745-2760.
33. Zhou, F., A. Windemuth, and K. Schulten. 1993. Molecular dynamics study of the proton pump cycle of bacteriorhodopsin. Biochemistry. 32:2291-2306.