Free-energy simulations of the retinal Cis → Trans isomerization in bacteriorhodopsin

Biochemistry

Volumn 37, Issue 9, 1998, Pages 2843-2853

  Hermone, Ann ^a   Kuczera, Krzysztof ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN;

ARTICLE; CIS TRANS ISOMERISM; COMPUTER MODEL; ENERGY METABOLISM; ISOMERISM; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STABILITY; SIMULATION;

BACTERIORHODOPSINS; ISOMERISM; MODELS, MOLECULAR; MOLECULAR STRUCTURE; RETINALDEHYDE; THERMODYNAMICS;

EID: 0032478274     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9717789     Document Type: Article

References (42)

1. Fodor, S., Ames, J. B., Gebhard, R., van der Berg, E. M., Stoekenius, W., Lugtenburg, J., and Mathies, R. A. (1988) Chromophore structure in bacteriorhodopin's n intermediate: Implications for the proton-pumping mechanism. Biochemistry 27, 7097-7101.
2. Lanyi, J. (1992) Proton transfer and energy coupling in the bacteriorhodopsin photocycle, J. Bioenerg. Biomembr. 24, 169-261.
3. Váro, G., and Lanyi, J. K. (1990) Protonation and deprotonation of the m, n, and o intermediates during the bacteriorhodopsin photocycle, Biochemistry 29, 6858-6965.
4. Mathies, R. A., Lin, S. W., Ames, J. B., and Pollard, W. T. (1991) From femtoseconds to biology: mechanism of bacteriorhodopin's light-driven proton pump, Annu. Rev. Biophys. Biophys. Chem. 20, 491-518.
5. Humphrey, W., Logunov, I., Schulten, K., and Sheves, M. (1994) Molecular dynamics study of bacteriorhodopsin and artificial pigments, Biochemistry 33, 3668-3678.
6. Mathies, R. A., Cruz, C. H. B., Pollard, W. T., and Shank, C. V. (1988) Direct observation of the femtosecond excited state cis-trans isomerization in bacteriorhodopsin, Science 240, 777-779.
7. Váro, G., and Lanyi, J. K. (1991) Thermodynamics and energy coupling in the bacteriorhopsin photocycle, Biochemistry 30, 5016-5022.
8. Brown, L. S., Sasake, J., Kandori, H., Maeda, A., Needleman, R., and Lanyi, J. (1995) Glutamic acid 204 is the terminal proton release group at the extracellular surface of bacteriorhodopsin, J. Biol. Chem. 270, 27122-27126.
9. Zhou, F., Windemuth, A., and Schulten, K. (1993) Molecular dynamics study of the proton pump cycle of bacteriorhodopsin, Biochemistry 32, 2291-2306.
10. 548) of bacteriorhodopsin and its photocycle, Biophys. J. 68, 1270-1282.
11. Chou, K. C., Carlacci, L., Maggiora, G. M., Parodi, L. A., Schulz, M. W. (1992) An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin, Protein Sci. 1, 810-827.
12. Scharnagl, C., Hettenkofer, J., and Fischer, S. F. (1995) Electrostatic and conformational effects on the proton translocation steps in bacteriorhodopsin: analysis of multiple m structures, J. Phys. Chem. 99, 7787-7800.
13. Nina, M., Roux, B., and Smith, J. C. (1995) Functional interactions in bacteriorhodopsin: A theoretical analysis of retinal hydrogen bonding with water, Biophys. J. 68, 25-39.
14. Voet, D., Voet, J. G. (1990) Biochemistry, John Wiley and Sons, New York.
15. Albery, W. J., and Knowles, J. R. (1976) Evolution of enzymes and development of catalytic efficiency, Biochemistry 15, 7181-7190.
16. Song, Q., Harms, G. S., Wan, C., and Johnson, C. K. (1994) Reorientations in the bacteriorhodopsin photocycle, Biochemistry 33, 14026-14033.
17. Braiman, M., Bousche, O., and Rothschild, K. (1991) Protein dynamics in the bacteriorhodopsin photocycle: Submillisecond fourier transform infrared spectra of the L, M, and N photointermediates, Proc. Natl. Acad. Sci. U.S.A. 88, 2388-2392.
18. Brooks, B. R., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M. (1983) CHARMM: A program for macromolecular energy, minimization and dynamics calculations, J. Comput. Chem. 4, 187-217.
19. Ciccotti, G., Ryckaert, J. P., Berendsen, H. J. C. (1977) Numerical integration of the cartesian equations of motion with constraints: molecular dynamics of n-alkanes, J. Comput. Phys. 23, 327-341.
20. Grigorieff, N., Ceska, T. A., Downing, K. H., Baldwin, J. M., and Henderson, R. (1996) Electron-crystallographic refinement of the structure of bacteriorhodopsin, J. Mol. Biol. 259, 393-421.
21. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79, 926-935.
22. Brooks, C. L., III, and Karplus, M. (1989) Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme, J. Mol. Biol. 208, 159-181.
23. 13C Asp resonances. Biochemistry 31, 455-462.
24. Tobias, D. J., and Brooks, C., III. (1990) Thermodynamics of solvophobic effects: A molecular-dynamics study of n-butane in carbon tetrachloride and water, J. Chem. Phys. 92, 2582-2592.
25. Kataoka, M., Kamikubo, H., Tokunaga, F., Brown, L. S., Yamazaki, Y., Maeda, A., Sheves, M., Needleman, R., and Lanyi, J. K. (1994) Energy coupling in an ion pump the reprotonation switch of bacteriorhodopsin. J. Mol. Biol. 243, 621-638.
26. Kuczera, K. One and multidimensional conformational free-energy simulations, J. Comput. Chem. 17, 1726-1749.
27. Mezei, M., and Beveridge, D. L. (1986) Free energy simulations, Ann. N.Y. Acad. Sci. 482, 1-23.
28. Smith, D. E., and Haymet, A. D. J. (1993) Free energy, entropy and internal energy of hydrophobic interactions: computer simulations. J. Chem. Phys. 98, 6445-6454.
29. Bevington, P. R. (1992) Data Reduction and Error Analysis for the Physical Sciences, 2nd ed., McGraw-Hill, New York.
30. Kramers, H. A. (1940) Brownian motion in a field of force and the diffusion model of chemical reactions, Physica 7, 284-304.
31. Northrup, S. H., Pear, M. R., Lee, C.-Y., McCammon, J. A., and Karplus, M. (1982) Dynamical theory of activated processes in globular proteins, Proc. Natl. Acad. Sci. U.S.A. 79, 4035-4039.
32. Zimanyi, L., Váro, G., Chang, M., Ni, B., Needleman, R., and Lanyi, J. Pathways of proton release in the bacteriorhodopsin photocycle, Biochemistry 31, 8535-8543.
33. Rothschild, K. (1992) FTIR difference spectroscopy of bacteriorhodopsin: Toward a molecular model, J. Bionenerg. Biomembr. 24, 147-167.
34. Otto, H., Marti, T., Holz, M., Mogi, T., Stern, L. Engel, F., Khorona, G., and Heyn, M. (1988) 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. U.S.A. 87, 1018-1022.
35. Mogi, T., Stern, L. J., Marti, T., Chao, B. H., and Khorana, H. G. (1988) Aspartic acid substitutions affect proton translocation in bacteriorhodopsin, Proc. Natl. Acad. Sci. U.S.A. 85, 4148-4152.
36. Kuczera, K., and Wiorkiewicz-Kuczera, J. MOLVIB - a program for analysis of molecular vibrational spectra. Program available from authors upon request.
37. Panchenko, Y., Pulay, P., and Torok, F. J. (1976) The calculation of the vibrational frequencies of the cis and trans forms of glyoxal, acrolein, and 1,3 butadiene, J. Mol. Struct. 34, 283-289.
38. Traetteberg, M. (1968) The molecular structure of 1,3,5 transhexatriene, Acta Chem. Scand. 22, 628.
39. Hamilton, T. P., and Pulay, P. (1988) Ab initio force constants and the reassignment of the vibrational spectra all-trans-and all-cis-1,3,5,7-octatetraene, J. Phys. Chem. 93, 2341-2347.
40. Foresman, J., and Frisch, A. (1993) Exploring Chemistry with Electronic Structure Methods: A Guide to using Gaussian, Gaussian, Inc., Pittsburgh, PA.
41. Frisch, C. M. J., Trucks, G. W., Head-Gordon, M., Gill, P. M. W., Wong, M. W., Foresman, J. B., Johnson, B. G., Schlegel, H. B., Robb, M. A., Replogle, E. S., Gomperts, R., Andres, J. L., Raghavachari, K., Binkley, J. S., Gonzalez, C., Martin, R. L., Fox, D. J., Defrees, D. J., Baker, J., Stewart, J. J. P., and Pople, J. A., (1992) GAUSSIAN 92, Revision C, Gaussian, Inc., Pittsburgh, PA.
42. Cox, S. R., and Williams, D. E. (1981) J. Comput. Chem. 2, 204.