Investigation of the proton release channel of bacteriorhodopsin in different intermediates of the photo cycle. A molecular dynamics study

Biochemistry

Volumn 36, Issue 10, 1997, Pages 2875-2883

  Nagel, Jochen ^a   Edholm, Olle ^b   Berger, Oliver ^a   Jähnig, Fritz ^a  

^a MAX PLANCK INST FÜR BIOLOGIE   (Germany)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN; RETINAL; SCHIFF BASE;

ARTICLE; CHROMATOPHORE; ISOMERISM; MOLECULAR DYNAMICS; PHOTODYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION;

EID: 0030968284     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi962427h     Document Type: Article

References (40)

1. Balashov, S. P., Govindjee, R., Kono, M., Imasheva, E., Lukashev, E., Ebrey, T. G., Crouch, R. K., Menick, D. R., & Feng, Y. (1993) Biochemistry 32, 10331-10343.
2. Bashford, D., & Gerwert, K. (1992) J. Mol. Biol. 224, 473-486.
3. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNiola A., & Haak, J. R. (1984) J. Chem. Phys. 81, 3684-3690.
4. Birge, R. R. (1990) Biochim. Biophys. Acta 1016, 293-327.
5. Braiman, M. S., & Mathies, R. (1980) Biochemistry 19, 5421-5428.
6. Brown, L. S., Váró, G., Needleman, R., & Lanyi, J. K. (1995a) Biophys. J. 69, 2103-2111.
7. Brown, L. S., Sasaki, J., Kandori, H., Maeda, A., Needleman, R., & Lanyi, J. K. (1995b) J. Biol. Chem. 270 (N45), 27122-27126.
8. Edholm, O., & Ghosh, I. (1993) Mol. Simul. 10, 241-253.
9. Edholm, O., Berger, O., & Jähnig, F. (1995) J. Mol. Biol. 250, 94-111.
10. Engels, M., Gerwert, K., & Bashford, D. (1995) Biophys. Chem. 56, 95-104.
11. Esquerra, R. M., Che, D., Shapiro, D. B., Lewis, J. W., Bogomolni, R. A., Fukushima, J., & Kliger, D. (1996) Biophys. J. 70, 962-970.
12. Fahmy, K., Siebert, F., Grossjean, M. F., & Tavan, P. (1989) J. Mol. Struct. 214, 257-288.
13. Fahmy, K., Weidlich, O., Engelhard, M., Sigrist, H., & Siebert, F. (1993) Biochemistry 32, 5862-5869.
14. Fodor, S. P. A., Ames, J. B., Gebhard, R., van den Berg, A. M. M., Stoeckenius, W., Lugtenburg, J., & Mathies, R. A. (1988) Biochemistry 27, 7097-7101.
15. Grigorieff, N., Ceska, T. A., Downing, K. H., Baldwin, J. M., & Henderson, R. (1996) J. Mol. Biol. 259, 393-421.
16. de Groot, H. J. M., Smith , S. O., Courtin, J., van den Berg, E., Winkel, C., Lugtenburg, J., Griffin, R. G., & Herzfeld, J. (1990) Biochemistry 29, 6873-6883.
17. Hauss, T., Büldt, G., Heyn, M. P., & Dencher, N. A. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 11854-11858.
18. Hessling, B., Souvignier, G., & Gerwert, K. (1993) Biophys. J. 65, 1929-1941.
19. Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E., & Downing, K. H. (1990) J. Mol. Biol. 213, 899-929.
20. Hildebrandt, P., & Stockburger, M. (1984) Biochemistry 23, 5539-5548.
21. Humphrey, W., Logunov, I., Schulten, K., & Sheves, M. (1994) Biochemistry 33, 3668-3678.
22. Keszthelyi, L., & Ormos, P. (1980) FEBS Lett. 109, 189-193.
23. Kraulis, P. (1991) J. Appl. Crystallogr. 24, 946-950.
24. Mathies, R. A., Lin, S. W., Ames, J. B., & Pollard, W. T. (1991) Annu. Rev. Biophys. Chem. 20, 491-518.
25. Nonella, M., Windemuth, A., & Schulten, K. (1991) Photochem. Photobiol. 54, 937-948.
26. Oesterhelt, D., Tittor, J., & Bamberg, E. (1992) J. Bioenerg. Biomembr. 24, 181-191.
27. Papadopoulos, G., Dencher, N., Zaccai, G., & Büldt, G. (1990) J. Mol. Biol. 214, 15-19.
28. Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977) J. Comput. Phys. 23, 327-341.
29. Scharnagl, C., Hettenkofer, J., & Fischer, S. F. (1994) Int. J. Quantum Chem., Quantum Biol. Symp. 21, 33-56.
30. Scharnagl, C., Hettenkofer, J., & Fischer, S. F. (1995) J. Phys. Chem. 99, 7787-7800.
31. Scherrer, P., Mathew, M. K., Sperling, W., & Stoeckenius, W. (1989) Biochemistry 28, 829-834.
32. Schulten, K., Schulten, Z., & Tavan, P. (1984) Info and Energy Transd. in Biol. Membr. pp 113-131. Alan R. Liss, Inc., New York.
33. Smith, S. O., Myers, A. B., Pardoen, J. A., Winkel, C., Mulder, P. P. J., Lugtenburg, J., & Mathies, R. A. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 2055-2059.
34. Smith, S. O., Hornung, I., van der Steen, R., Pardoen, J. A., Braiman, M. S., Lugtenburg, J., & Mathies, R. A. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 967-971.
35. Song, L., Yang, D., El-Sayed, M. A., & Lanyi, J. K. (1995) J. Phys. Chem. 99, 10052-10055.
36. Subramaniam, S., Gerstein, M., Oesterhelt, D., & Henderson, R. (1993) EMBO J. 12, 1-8.
37. Ulrich, A. S., Wallat, I., Heyn, M. P., & Watts, A. (1994) Biochemistry 33, 5370-5375.
38. Ulrich, A. S., Wallat, I., Heyn, M. P., & Watts, A. (1995) Nat. Struct. Biol. 2, 190-192.
39. Xu, D., Sheves, M., & Schulten, K. (1995) Biophys. J. 69, 2745-2760.
40. Zhou, F., Windemuth, A., & Schulten, K. (1993) Biochemistry 32, 2291-2306.