Calculation of proton transfers in bacteriorhodopsin bR and M intermediates

Biochemistry

Volumn 42, Issue 33, 2003, Pages 9875-9888

  Song, Yifan ^a   Mao, Junjun ^a   Gunner, M R ^a  

^a CITY COLLEGE OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR MECHANICS;

CRYSTAL STRUCTURE; ELECTROSTATICS; IONIZATION; ISOMERIZATION; PH EFFECTS;

PROTONS;

BACTERIORHODOPSIN; SCHIFF BASE;

ARTICLE; BINDING KINETICS; CRYSTAL STRUCTURE; ELECTROCHEMISTRY; EQUILIBRIUM CONSTANT; IONIZATION; ISOMERISM; MOLECULAR MECHANICS; PH; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STABILITY; PROTON TRANSPORT; STRUCTURE ANALYSIS; TRANSPORT KINETICS;

ASPARTIC ACID; BACTERIORHODOPSINS; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTONS; SCHIFF BASES; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; WATER;

BACTERIA (MICROORGANISMS);

EID: 0041471589     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi034482d     Document Type: Article

References (74)

1. Lanyi, J. K. (1993) Biochim. Biophys. Acta 1183, 241-261.
2. Lanyi, J. K. (1997) J. Biol. Chem. 272, 31209-31212.
3. Haupts, U., Tittor, J., and Oesterhelt, D. (1999) Annu. Rev. Biophys. Biomol. Struct. 28, 367-399.
4. Balashov, S. P. (2000) Biochim. Biophys. Acta 1460, 75-94.
5. Luecke, H. (2000) Biochim. Biophys. Acta 1460, 133-156.
6. Oesterhelt, D. (1998) Curr. Opin. Struct. Biol. 8, 489-500.
7. Spudich, J. L., Yang, C.-S., Jung, K.-H., and Spudich, E. N. (2000) Annu. Rev. Cell Dev. Biol. 16, 365-393.
8. Rammelsberg, R., Huhn, G., Lubben, M., and Gerwert, K. (1998) Biochemistry 37, 5001-5009.
9. Spassov, V. Z., Luecke, H., Gerwert, K., and Bashford, D. (2001) J. Mol. Biol. 312, 203-219.
10. Rummel, G., Hardmeyer, A., Widmer, C., Chiu, M. L., Nollert, P., Locher, K. P., Pedruzzi, I. I., Landau, E. M., and Rosenbusch, J. P. (1998) J. Struct. Biol. 121, 82-91.
11. Luecke, H., Schobert, B., Richter, H. T., Caartailler, J.-P., and Lanyi, J. K. (1999) J. Mol. Biol. 291, 899-911.
12. Luecke, H., Schobert, B., Richter, H. T., Cartailler, J. P., and Lanyi, J. K. (1999) Science 286, 255-261.
13. Lanyi, J., and Schobert, B. (2002) J. Mol. Biol. 321, 727-737.
14. Schobert, B., Cupp-Vickery, J., Hornak, V., Smith, S., and Lanyi, J. (2002) J. Mol. Biol. 321, 715-726.
15. Edman, K., Nollert, P., Royant, A., Belrhali, H., Pebay-Peyroula, E., Hajdu, J., Neutze, R., and Landau, E. M. (1999) Nature 401, 822-826.
16. Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648.
17. Facciotti, M. T., Rouhani, S., Burkard, F. T., Betancourt, F. M., Downing, K. H., Rose, R. B., McDermott, G., and Glaeser, R. M. (2001) Biophys. J. 81, 3442-3455.
18. Luecke, H., Schobert, B., Cartailler, J. P., Richter, H. T., Rosengarth, A., Needleman, R., and Lanyi, J. K. (2000) J. Mol. Biol. 300, 1237-1255.
19. Rouhani, S., Cartailler, J. P., Facciotti, M. T., Walian, P., Needleman, R., Lanyi, J. K., Glaeser, R. M., and Luecke, H. (2001) J. Mol. Biol. 313, 615-628.
20. Sampogna, R. V., and Honig, B. (1994) Biophys. J. 66, 1341-1352.
21. Bashford, D., and Gerwert, K. (1992) J. Mol. Biol. 224, 473-486.
22. Engels, M., Gerwert, K., and Bashford, D. (1995) Biophys. Chem. 56, 95-104.
23. Sandberg, L., and Edholm, O. (1997) Biophys. Chem. 65, 189-204.
24. Baudry, J., Tajkhorshid, E., Molnar, F., Phillips, J., and Schulten, K. (2001) J. Phys. Chem. B 105, 905-918.
25. Tajkhorshid, E., Baudry, J., Schulten, K., and Suhai, S. (2000) Biophys. J. 78, 683-693.
26. Crouzy, S., Baudry, J., Smith, J. C., and Roux, B. (1999) J. Comput. Chem. 20, 1644-1658.
27. Nonella, M. (2000) J. Phys. Chem. B 104, 11379-11388.
28. Warshel, A., and Chu, Z. T. (2001) J. Phys. Chem. B 105, 9857-9871.
29. Baudry, J., Crouzy, S., Roux, B., and Smith, J. C. (1999) Biophys. J. 76, 1909-1917.
30. Humphrey, W., Lu, H., Logunov, I., Werner, H. J., and Schulten, K. (1998) Biophys. J. 75, 1689-1699.
31. Zhang, G. P., Zong, X. F., and George, T. F. (1999) J. Chem. Phys. 110, 9765-9768.
32. Scharnagl, C., and Fischer, S. F. (1996) Chem. Phys. 212, 231-246.
33. Nagel, J., Edholm, O., Berger, O., and Jahnig, F. (1997) Biochemistry 36, 2875-2883.
34. Sampogna, R. V., and Honig, B. (1996) Biophys. J. 71, 1165-1171.
35. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242.
36. Guex, N., and Peitsch, M. C. (1997) Electrophoresis 18, 2714-2723.
37. Alexov, E. G., and Gunner, M. R. (1997) Biophys. J. 72, 2075-2093.
38. Alexov, E., and Gunner, M. (1999) Biochemistry 38, 8253-8270.
39. Georgescu, R. E., Alexov, E. G., and Gunner, M. R. (2002) Biophys. J. 83, 1731-1748.
40. Dunbrack, R. L., and Karplus, M. (1994) Nat. Struct. Biol. 1, 334-340.
41. Dunbrack, R. L., and Cohen, F. E. (1997) Protein Sci. 6, 1661-1681.
42. Gilson, M. K., and Honig, B. (1988) Proteins 3, 32-52.
43. Simonson, T. (2001) Curr. Opin. Struct. Biol. 11, 243-252.
44. Nicholls, A., and Honig, B. (1991) J. Comput. Chem. 12, 435-445.
45. Sitkoff, D., Sharp, K. A., and Honig, B. (1994) J. Phys. Chem. 98, 1978-1988.
46. Baasov, T., and Sheves, M. (1986) Biochemistry 25, 5249-5258.
47. Sridharan, S., Nicholls, A., and Honig, B. (1992) Biophys. J. 61, A174.
48. Gunner, M. R., and Alexov, E. (2000) Biochim. Biophys. Acta 1458, 63-87.
49. Fahmy, K., Weidlich, O, Engelhard, M., Tittor, J., Oesterhelt, D., and Siebert, F. (1992) Photochem. Photobiol. 56, 1073-1083.
50. Lewis, A., Spoonhower, J., Bogomolni, R. A., Lozier, R. H., and Stoeckenius, W. (1974) Proc. Natl. Acad. Sci. U.S.A. 71, 4462-4466.
51. Zimanyi, L., Varo, G., Chang, M., Ni, B., Needleman, R., and Lanyi, J. K. (1992) Biochemistry 31, 8535-8543.
52. Gunner, M. R., Saleh, M., Cross, E., ud-Doula, A., and Wise, M. (2000) Biophys. J. 78, 1126-1144.
53. Metz, G., Siebert, F., and Engelhard, M. (1992) FEBS Lett. 303, 237-241.
54. Fahmy, K., Weidlich, O., Engelhard, M., Sigrist, H., and Siebert, F. (1993) Biochemistry 32, 5862-5869.
55. Subramniam, S., Marti, T., and Khorana, H. G. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 1013-1017.
56. Balashov, S. P., Govindjee, R., Imasheva, E. S., Misra, S., Ebrey, T. G., Feng, Y., Crouch, R. K., and Menick, D. R. (1995) Biochemistry 34, 8820-8834.
57. Balashov, S. P., Imasheva, E. S., Govindjee, R., and Ebrey, T. G. (1996) Biophys. J. 70, 473-481.
58. Brown, L. S., Bonet, L., Needleman, R., and Lanyi, J. K. (1993) Biophys. J. 65, 124-130.
59. Subramaniam, S., Marti, T., and Khorana, H. G. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 1013-1017.
60. Druckmann, S., Ottolenghi, M., Pande, A., Pande, J., and Callender, R. H. (1982) Biochemistry 21, 4953-4959.
61. Balashov, S. P., Govindjee, R., and Ebrey, T. G. (1991) Biophys. J. 60, 475-490.
62. Kono, M., Misra, S., and Ebrey, T. G. (1993) FEBS Lett. 331, 31-34.
63. Brown, L. S., and Lanyi, J. K. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 1731-1734.
64. Needleman, R., Chang, M., Ni, B., Varo, G., Fornes, J., White, S. H., and Lanyi, J. K. (1991) J. Biol. Chem. 266, 11478-11484.
65. Richter, H. T., Brown, L. S., Needleman, R., and Lanyi, J. K. (1996) Biochemistry 35, 4054-4062.
66. Luecke, H., Schobert, B., Richter, H. T., Cartailler, J. P., and Lanyi, J. K. (1999) Science 286, 255-261.
67. Brown, L. S., Dioumaev, A. K., Needleman, R., and Lanyi, J. K. (1998) Biochemistry 37, 3982-3993.
68. Engles, M., Gerwert, K., and Bashford, D. (1995) Biophys. Chem. 56, 95-104.
69. Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E., and Downing, K. H. (1990) J. Mol. Biol. 213, 899-929.
70. Bashford, D., and Karplus, M. (1990) Biochemistry 29, 10219-10225.
71. Hayashi, S., Tajkhorshid, E., and Schulten, K. (2002) Biophys. J. 83, 1281-1297.
72. Balashov, S. P., Imasheva, E. S., Ebrey, T. G., Chen, N., Menick, D. R., and Crouch, R. K. (1997) Biochemistry 36, 8671-8676.
73. Dioumaev, A. K., Richter, H. T., Brown, L. S., Tanio, M., Tuzi, S., Saito, H., Kimura, Y., Needleman, R., and Lanyi, J. K. (1998) Biochemistry 37, 2496-2506.
74. Essen, L., Siegert, R., Lehmann, W. D., and Oesterhelt, D. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 11673-11678.