Quantum chemical and free energy simulation analysis of retinal conformational energetics

Journal of Chemical Information and Computer Sciences

Volumn 37, Issue 6, 1997, Pages 1018-1024

  Baudry, Jérôme ^a   Crouzy, Serge ^b   Roux, Benoît ^c   Smith, Jeremy C ^a  

^a CEA SACLAY   (France)

^b CEA GRENOBLE   (France)

^c UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0343155178     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci9702398     Document Type: Article

References (23)

1. Oesterhelt, D. Stoeckenius, W. Rhodopsin-like protein from the purple membrane of Halobacterium halohium. Nature (London), New Biol. 1971, 233, 149-152.
2. Henderson, R.; Baldwin, J. M.; Ceska, T. A.; Zemlin, F.; Beckmann, E.; Downing, K. H. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 1990, 213, 899-929.
3. Grigorieff, T. A.; Ceska, K. H.; Downing, K. H.; Baldwin, J. M.; Henderson, R. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 1996, 259, 393-421.
4. Humphrey, W.; Logunov, I.; Schulten, K.; Sheves, M. Molecular dynamics study of bacteriorhodopsin and artificial pigments. Biochemistry 1994, 33, 3668-3678.
5. Humphrey, W.; Xu, D.; Sheves, M.; Schulten, K. Molecular dynamics study of the early intermediates in the hacteriorhodopsin photocycle. J. Phys. Chem. 1995, 99, 14549-14560.
6. Zhou, F.; Windemuth, A.; Schulten, K. Molecular dynamics study of the proton pump cycle of bacteriorhodopsin. Biochemistry 1993, 32(9), 2291-2306.
7. Ferrand, M.; Zaccai, G.; Nina, M.; Smith, J. C.; Etchebest, C.; Roux, B. Structure and dynamics of bacteriorhodopsin: comparison of experiment and simulations. FEBS Lett. 1993, 327(3), 256-260.
8. Nina, M.; Smith, J. C.; Roux, B. Ab initio quantum chemical analysis of retinal Schiff base hydration in bacteriorhodopsin. J. Mol. Struct. (THEOCHEM) 1993, 286, 231-245.
9. Nina, M.; Roux, B.; Smith, J. C. Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water. Biophys. J. 1995, 68, 25-39.
10. Roux, B.; Nina, M.; Pomes. R.; Smith, J. C. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys. J. 1996, 71, 670-681.
11. Harbison, G. S.; Smith, S. O.; Pardoen, J. A.; Winkel, C.; Lugtenburg, J.; Herzfeld, J.; Mathies, R.; Griffin, R. G. Dark-adapted bacteriorhodopsin contains 13-cis, 15-syn and all-trans, 15-anti retinal Schiff bases. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 1706-1709.
12. Song, L.; Yang, D.; El-Sayed, M. A.; Lanyi, J. K. Retinal isomer composition in some bacteriorhodopsin mutants under light and dark adaptation conditions. J. Phys. Chem. 1995, 99, 10052-10055.
13. Shulte, A.; Bradley II, L.; Williams, C. Equilibrium composition of retinal isomers in Dark-Adapted bacteriorhodopsin and effect of high pressure probed by near-infrared Raman spectroscopy. Appl. Spectrosc. 1995, 49, 80-83.
14. Shulte, A.; Bradley II, L. High-pressure near-infrared Raman spectroscopy of bacteriorhodopsin light to dark adaptation. Biophys. J. 1995, 69, 1554-1562.
15. 548) of bacteriorhodopsin and its photocycle. Biophys. J. 1995, 68, 1270-1282.
16. Logunov, I.; Schulten, K. Quantum Chemistry: Molecular dynamics study of the dark-adaptation process in bacteriorhodopsin. J. Am. Chem. Soc. 1996, 118, 9727-9735.
17. Humphrey, W. Personal communication.
18. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The Weighted Histogram Analysis Method for free-energy calculations on biomolecules. I) The method. J. Comput. Chem. 1992, 13, 1011-1021.
19. Roux, B. The calculation of the potential of mean force using computer simulations. Comput. Phys. Commun. 1995, 91, 275-282.
20. Frish, M. J.; Head-Gordon, M.; Trucks, G. W.; Foresman, J. B.; Schlegel, H. B.; Raghavachari, K.; Robb, M.; Binkley, J. S.; Gonzales, C.; Defrees, D. J.; Fox, D. J.; Whitesick, R. A.; Seeger, R.; Melius, C. F.; Baker, J.; Martin, R. L.; Khan, L. R.; Stewart, J. J. P.; Topiol, S.; Pople, J. A. GAUSSIAN 90; Carnegie-Mellon University: Pittsburgh, PA.
21. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.: Swaminathan, S.; Karplus, M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 1983, 4, 187-217.
22. Warshel, A. Bicycle-pedal model for the first step in the vision process. Nature 1976, 260, 679-683.
23. Seltzer, S. MNDO barrier heights for catalyzed bicycle-pedal, hulatwist, and ordinary cis-trans isomerizations of protonated Schiff base. J. Am. Chem. Soc. 1987, 109, 1627-1631.