Protein conformational gate controlling binding site preference and migration for ubiquinone-B in the photosynthetic reaction center of Rhodobacter sphaeroides

Journal of Physical Chemistry B

Volumn 106, Issue 11, 2002, Pages 3001-3006

  Walden, Susan E ^a   Wheeler, Ralph A ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOTOSYNTHETIC REACTIONS;

BACTERIOLOGY; COMPUTER SIMULATION; CONFORMATIONS; DATA REDUCTION; ELECTRON TRANSITIONS; ELECTRONS; HYDROGEN BONDS; MOLECULAR DYNAMICS; PHOTOSYNTHESIS; X RAY ANALYSIS;

PROTEINS;

EID: 0037149804     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0136664     Document Type: Article

References (53)

1. Fyfe, P.K.; Jones, M.R. Biochim. Biophys. Acta 2000, 1459, 413-421.
2. Lancaster, C.R.D.; Ermler, U.; Michel, H. The structures of photosynthetic reaction centers from purple bacteria as revealed by x-ray crystallography. In Adv. Photosynth. 2: Anoxygenic Photosynthetic Bacteria; Blankenship, R.E., Madigan, M.T., Bauer, C.E., Eds.; Kluwer Academic: Dordrecht, The Netherlands, 1995; Vol. 2; pp 503-526.
3. Okamura, M.Y.; Feher, G. Proton-coupled electron-transfer reactions of QB in reaction centers from photosynthetic bacteria. In Adv. Photosynth. 2: Anoxygenic Photosynthetic Bacteria; Blankenship, R.E., Madigan, M.T., Bauer, C.E., Eds.; Kluwer Academic: Dordrecht, The Netherlands, 1995; Vol. 2; pp 577-594.
4. Okamura, M.Y.; Paddock, M.L.; Graige, M.S.; Feher, G. Biochim. Biophys. Acta 2000, 1458, 148-163.
5. Parson, W.W.; Warshei, A. Theoretical analyses of electron-transfer reactions. In Adv. Photosynth. 2: Anoxygenic Photosynthetic Bacteria; Blankenship, R.E., Madigan, M.T., Bauer, C.E., Eds.; Kluwer Academic: Dordrecht, The Netherlands, 1995; Vol. 2; pp 559-575.
6. Feher, G.; Alien, J.P.; Okamura, M.Y.; Rees, D.C. Nature 1989, 339, 111-116.
7. Chang, C.H.; el-Kabbani, O.; Tiede, D.; Norris, J.; Schiller, M. Biochemistry 1991, 30, 5352-5360.
8. el-Kabbani, O.; Chang, C.H.; Tiede, D.; Norris, J.; Schiffer, M. Biochemistry 1991, 30, 5361-5369.
9. Allen, J.P.; Feher, G.; Yeates, T.O.; Komiya, H.; Rees, D.C. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 5730-5734.
10. Allen, J.P.; Feher, G.; Yeates, T.O.; Komiya, H.; Rees, D.C. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6162-6166.
11. Yeates, T.O.; Komiya, H.; Chirino, A.; Rees, D.C.; Allen, J.P.; Feher, G. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7993-7997.
12. Allen, J.P.; Feher, G.; Yeates, T.O.; Komiya, H.; Rees, D.C. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 8487-8491.
13. Chirino, A.J.; Lous, E.J.; Huber, M.; Alien, J.P.; Schenck, C.C.; Paddock, M.L.; Feher, G.; Rees, D.C. Biochemistry 1994, 33, 4584-4593.
14. Arnoux, B.; Gaucher, J.-F.; Ducruix, A.; Reiss-Husson, F. Acta Crystallogr., Sect. D: Biol. Crystallogr. 1995, D51, 368-379.
15. Arnoux, B.; Reiss-Husson, F. Eur. Biophys. J. 1996, 24, 233-242.
16. Ermler, U.; Fritzsch, G.; Buchanan, S.K.; Michel, H. Structure 1994, 2, 925-936.
17. Ermler, U.; Michel, H.; Schiffer, M. J. Bioener. Biomemb. 1994, 26, 5-15.
18. Stowell, M.H.B.; McPhillips, T.M.; Rees, D.C.; Soltis, S.M.; Abresch, E.; Feher, G. Science 1997, 276, 812-816.
19. Kuglstatter, A.; Ermler, U.; Michel, H.; Baciou, L.; Fritzsch, G. Biochemistry 2001, 40, 4253-4260.
20. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. Nucleic Acids Res. 2000, 28, 235-242.
21. The PDB identification codes for the different protein structures will be used throughout the paper as a simple reference to an individual structure.
22. Deisenhofer, J.; Epp, O.; Miki, K.; Huber, R.; Michel, H. J. Mol. Biol. 1984, 180, 385-398.
23. Deisenhofer, J.; Epp, O.; Mild, K.; Huber, R.; Michel, H. Nature 1985, 318, 618-624.
24. Deisenhofer, J.; Michel, H. EMBO J. 1989, 8, 2149-2170.
25. Deisenhofer, J.; Epp, O.; Sinning, I.; Michel, H. J. Mol. Biol. 1995, 246, 429-457.
26. Lancaster, C.R.D.; Michel, H. Structure 1997, 5, 1339-1359.
27. Miksovska, J.; Kalman, L.; Schiffer, M.; Maroti, P.; Sebban, P.; Hanson, D.K. Biochemistry 1997, 36, 12216-12226.
28. Nabedryk, E.; Breton, J.; Hienerwadel, R.; Fogel, C.; Maentele, W.; Paddock, M.L.; Okamura, M.Y. Biochemistry 1995, 34, 14722-14732.
29. Takahashi, E.; Wraight, C.A. Biochemistry 1992, 31, 855-866.
30. Miksovska, J.; Schiller, M.; Hanson, D.K.; Sebban, P. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14348-14353.
31. Hienerwadel, R.; Grzybek, S.; Fogel, C.; Kreutz, W.; Okamura, M.Y.; Paddock, M.L.; Breton, J.; Nabedryk, E.; Maentele, W. Biochemistry 1995, 34, 2832-2843.
32. Miksovska, J.; Maroti, P.; Tandori, J.; Schiffer, M.; Hanson, D.K.; Sebban, P. Biochemistry 1996, 35, 15411-15417.
33. Rabenstein, B.; Ullmann, G.M.; Knapp, E.-W. Biochemistry 2000, 39, 10487-10496.
34. Alexov, E.G.; Gunner, M.R. Biochemistry 1999, 38, 8253-8270.
35. Grafton, A.K.; Wheeler, R.A. J. Phys. Chem. B 1999, 103, 5380-5387.
36. Zachariae, U.; Lancaster, C.R.D. Biochim. Biophys. Acta 2001, 1505, 280-290.
37. Graige, M.S.; Feher, G.; Okamura, M.Y. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 11679-11684.
38. Hoffman, B.M.; Ramer, M.A. J. Am. Chem. Soc. 1987, 109, 6237-6243.
39. Hoffman, B.M.; Ratner, M.A. J. Am. Chem. Soc. 1988, 110, 8267.
40. Case, D.A.; Pearlman, D.A.; Caldwell, J.W.; Cheatham, T.E., III.; Ross, W.S.; Simmerling, C.L.; Darden, T.A.; Merz, K.M.; Stanton, R.V.; Cheng, A.L.; Vincent, J.J.; Crowley, M.; Ferguson, D.M.; Radmer, R.J.; Seibel, G.L.; Singh, U.C.; Weiner, P.K.; Kollman, P.A. AMBER 5; University of California: San Francisco, CA, 1997.
41. Pearlman, D.A.; Caldwell, J.W.; Ross, W.S.; Cheatham, T.E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Case, D.A.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1-41.
42. Berendsen, H.J.C.; Postma, J.P.M.; Van Gunsteren, W.F.; DiNola, A.; Haak, J.R. J. Chem. Phys. 1984, 81, 3684-3690.
43. Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.; Merz, K.M., Jr.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
44. Jorgensen, W.L.; Chandreskhar, J.; Madura, J.D.; Impey, R.W.; Klein, M.L. J. Chem. Phys. 1982, 79, 926-935.
45. Wheeler, R.A. J. Am. Chem. Soc. 1994, 116, 11048-11051.
46. Raymond, K.S.; Grafton, A.K.; Wheeler, R.A. J. phys. Chem. B 1997, 101, 623-631.
47. Wise, K.E.; Grafton, A.K.; Wheeler, R.A. J. Phys. Chem. A 1997, 101, 1160-1165.
48. Boesch, S.E.; Wheeler, R.A. J. Phys. Chem. A 1997, 101, 5799-5804.
49. Walden, S.E.; Boesch, S.E.; Wheeler, R.A. 2002, to be published.
50. Paddock, M.L.; Rongey, S.H.; Feher, G.; Okamura, M.Y. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 6602-6606.
51. WebLab ViewerPro, 4.0 ed.; Molecular Simulations, Inc.: San Diego, CA, 2000.
52. Simmerling, C.; Elber, R.; Zhang, J. MOIL-View - A Program for Visualization of Structure and Dynamics of Biomolecules and STOA Program for Computing Stochastic Paths. In Modeling of Biomolecular Structure and Mechanisms; Pullman, A., et al., Eds.; Kluwer: Norwell, MA, 1995; pp 241-265.
53. Ferrin, T.E.; Huang, C.C.; Jarvis, L.E.; Langridge, R. J. Mol. Graphics 1988, 6, 13-27.