Spectral signatures of the pentagonal water cluster in bacteriorhodopsin

ChemPhysChem

Volumn 9, Issue 18, 2008, Pages 2703-2707

  Baer, Marcel ^a   Mathias, Gerald ^a   Kuo, I Feng W ^b   Tobias, Douglas J ^c   Mundy, Christopher J ^d   Marx, Dominik ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Bacteriorhodopsin; Hydrogen bonds; Molecular dynamics; Protonation; Vibrational spectroscopy

Indexed keywords

MOLECULAR DYNAMICS; PROTONATION; VIBRATIONAL SPECTROSCOPY;

BACTERIORHODOPSIN; SPECTRAL SIGNATURE; WATER CLUSTER;

HYDROGEN BONDS;

EID: 58049187077     PISSN: 14394235     EISSN: 14397641     Source Type: Journal    
DOI: 10.1002/cphc.200800473     Document Type: Article

References (40)

1. a) T. E. DeCoursey, Physiol. Rev. 2003, 83, 475-579;
2. b) T. E. DeCoursey, Physiol. Rev. 2003, 83, 1067-1067;
3. c) T. E. DeCoursey, Physiol. Rev. 2004, 84, 1479-1479.
4. S. Cukierman, Biochim. Biophys. Acta 2006, 1757, 876-885.
5. U. Haupts, J. Tittor, D. Oesterhelt, Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 367-399.
6. J. K. Lanyi, Biochim. Biophys. Acta Bioenerg. 2006, 1757, 1012-1018.
7. F. Siebert, Methods Enzymol. 1995, 246, 501-526.
8. H. Kandori, Biochim. Biophys. Acta Bioenerg. 2000, 1460, 177-191.
9. R. Rammelsberg, G. Huhn, M. Lübben, K. Gerwert, Biochemistry 1998, 37, 5001-5009.
10. F. Garczarek, L. Brown, J. Lanyl, K. Gerwert, Proc. Natl. Acad. Sci. USA 2005, 102, 3633-3638.
11. F. Garczarek, K. Gerwert, Nature 2006, 439, 109-112.
12. R. Rousseau, V. Kleinschmidt, U. Schmitt, D. Marx, Phys. Chem. Chem. Phys. 2004, 6, 1848-1859.
13. R. Rousseau, V. Kleinschmidt, U. Schmitt, D. Marx, Angew. Chem. 2004, 116, 4908-4911;
14. Angew. Chem. Int. Ed. 2004, 43, 4804-4807.
15. G. Mathias, D. Marx, Proc. Natl. Acad. Sci. USA 2007, 104, 6980-6985.
16. H. Luecke, B. Schobert, H. Richter, J. Cartailler, J. Lanyi, J. Mol. Biol. 1999, 291, 899-911.
17. A. Maeda, J. Sasaki, Y. Yamazaki, R. Needleman, J. Lanyi, Biochemistry 1994, 33, 1713-1717.
18. H. Kandori, Y. Yamazaki, J. Sasaki, R. Needleman, J. Lanyi, A. Maeda, J. Am. Chem. Soc. 1995, 117, 2118-2119.
19. N. Shibata, H. Kandori, Biochemistry 2005, 44, 7406-7413.
20. H. Kandori, N. Kinoshita, Y. Shichida, A. Maeda, J. Phys. Chem. B 1998, 102, 7899-7905.
21. T. Tanimoto, Y. Furutani, H. Kandori, Biochemistry 2003, 42, 2300-2306.
22. H. Kandori, N. Kinoshita, Y. Yamazaki, A. Maeda, Y. Shichida, R. Needleman, J. Lanyi, M. Bizounok, J. Herzfeld, J. Raap, J. Lugtenburg, Proc. Natl. Acad. Sci. USA 2000, 97, 4643-4648.
23. S. Hayashi, I. Ohmine, J. Phys. Chem. B 2000, 104, 10678-10691.
24. S. Hayashi, E. Tajkhorshid, H. Kandori, K. Schulten, J. Am. Chem. Soc. 2004, 126, 10516-10517.
25. J. Neugebauer, B. A. Hess, J. Chem. Phys. 2003, 118, 7215-7225.
26. C. Kandt, J. Schlitter, K. Gerwert, Biophys. J. 2004, 86, 705-717.
27. A. Chaumont, M. Baer, G. Mathias, D. Marx, ChemPhysChem 2008, 9, 2571-2578.
28. H. Kandori, Y. Shichida, J. Am. Chem. Soc. 2000, 122, 11745-11746.
29. T. Tanimoto, M. Shibata, M. Belenky, J. Herzfeld, H. Kandori, Biochemistry 2004, 43, 9439-9447.
30. E. Lindahl, B. Hess, D. van der Spoel, J. Mol. Model. 2001, 7, 306-317.
31. G. Lippert, J. Hutter, M. Parrinello, Mol. Phys. 1997, 92, 477-487.
32. J. VandeVondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing, J. Hutter, Comput. Phys. Commun. 2005, 167, 103-128.
33. S. Goedecker, M. Teter, J. Hutter, Phys. Rev. B 1996, 54, 1703-1710.
34. C. Hartwigsen, S. Goedecker, J. Hutter, Phys. Rev. B 1998, 58, 3641-3662.
35. A. Becke, Phys. Rev. A 1988, 38, 3098-3100.
36. C. Lee, W. Yang, R. Parr, Phys. Rev. B 1988, 37, 785-789.
37. G. Martyna, M. Klein, M. Tuckerman, J. Chem. Phys. 1992, 97, 2635-2643.
38. T. Laino, F. Mohamed, A. Laio, M. Parrinello, J. Chem. Theory Comput. 2005, 1, 1176-1184.
39. F. Maseras, K. Morokuma, J. Comput. Chem. 1995, 16, 1170-1179.
40. R. Ramírez, T. López-Ciudad, P. P. Kumar, D. Marx, J. Chem. Phys. 2004, 121, 3973-3981.