Role of water in transient cytochrome c2 docking

Journal of Physical Chemistry B

Volumn 108, Issue 52, 2004, Pages 20376-20387

  Autenrieth, Felix ^a   Tajkhorshid, Emad ^a   Schulten, Klaus ^a   Luthey Schulten, Zaida ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOLOGICAL MEMBRANES; COMPLEXATION; ELECTRON TRANSITIONS; MOLECULAR DYNAMICS; PIGMENTS; X RAYS;

CHARGE SEPARATION; ELECTRON TRANSFER; ELECTROSTATIC DOCKING; X-RAY STRUCTURE;

PROTEINS;

EID: 11444263102     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp047994q     Document Type: Article

References (45)

1. Axelrod, H. L.; Abresch, E. C.; Okamura, M. Y.; Yeh, A. P.; Rees, D. C.; Feher, G. J. Mol. Biol. 2002, 319, 501.
2. Autenrieth, F.; Tajkhorshid, E.; Baudry, J.; Luthey-Schulten, Z. J. Comput. Chem. 2004, 25, 1613.
3. Lange, C.; Hunte, C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2800.
4. Hu, X.; Ritz, T.; Damjanović, A.; Autenrieth, F.; Schulten, K. Q. Rev. Biophys. 2002, 35, 1.
5. Allen, J. P.; Feher, G.; Yeates, T. O.; Komiya, H.; Rees, D. C. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6162.
6. Adir, N.; Axelrod, H. L.; Beroza, P.; Isaacson, R. A.; Rongey, S. H.; Okamura, M. Y.; Feher, G. Biochemistry 1996, 35, 2535.
7. Tiede, D. M.; Vashishta, A. C.; Gunner, M. R. Biochemistry 1993, 32, 4515.
8. Lancaster, C. R. D.; Michel, H. Structure 1997, 5, 1339.
9. Tetreault, M.; Rongey, S. H.; Feher, G.; Okamura, M. Y. Biochemistry 2001, 40, 8452.
10. Tetreault, M.; Cusanovich, M.; Meyer, T.; Axelrod, H.; Okamura, M. Y. Biochemistry 2002, 41, 5807.
11. Dickerson, R. E. Nature 1980, 283, 210.
12. Berg, J.; Tymoczko, J.; Stryer, L. Biochemistry; W. H. Freeman and Company: San Francisco, CA, 2002.
13. Deisenhofer, J.; Epp, O.; Miki, K.; Huber, R.; Michel, H. Nature 1985, 318, 618.
14. Farchaus, J. W.; Wachtveitl, J.; Mathis, P.; Oesterhelt, D. Biochemistry 1993, 32, 10885.
15. Farchaus, J. W.; Wachtveitl, J.; Mathis, P.; Oesterhelt, D. Biochemistry 1993, 32, 10894.
16. Tezcan, F. A.; Crane, B. R.; Winkler, J. R.; Gray, H. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5002.
17. Gong, X. M.; Paddock, M. L.; Okamura, M. Y. Biochemistry 2003, 42, 14492.
18. Miyashita, O.; Okamura, M. Y.; Onuchic, J. N. J. Phys. Chem. B 2003, 107, 1230.
19. Holzapfel, W.; Finkele, U.; Kaiser, W.; Oesterhelt, D.; Scheer, H.; Stilz, H. U.; Zinth, W. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 5168.
20. Pelletier, H.; Kraut, J. Science 1992, 258, 1748.
21. Larson, J. W.; Wraight, C. A. Biochemistry 2000, 39, 14822.
22. Izrailev, S.; Stepaniants, S.; Isralewitz, B.; Kosztin, D.; Lu, H.; Molnar, F.; Wriggers, W.; Schulten, K. In Steered Molecular Dynamics; Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A. E., Reich, S., Skeel, R. D.; Eds.; Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering 4; Springer-Verlag: Berlin, 1998; pp 39-65.
23. Lu, H.; Isralewitz, B.; Krammer, A.; Vogel, V.; Schulten, K. Biophys. J. 1998, 75, 662.
24. Isralewitz, B.; Gao, M.; Schulten, K. Curr. Opin. Struct. Biol. 2001, 11, 224.
25. Miyashita, O.; Onuchic, J. N.; Okamura, M. Y. Biochemistry 2003, 42, 11651.
26. InsightII, Molecular Simulations Inc. Technical report, Burlington, MA, 2000.
27. Stowell, M. H. B.; McPhillips, T. M.; Rees, D. C.; Soltis, S. M.; Abresch, E.; Feher, G. Science 1997, 276, 812.
28. Ducruix, A.; Reiss-Husson, F. J. Mol. Biol. 1987, 20, 419.
29. Damjanović, A.; Kosztin, I.; Kleinekathöfer, U.; Schulten, K. Phys. Rev. E 2002, 65, 031919.
30. Humphrey, W. F.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33.
31. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
32. MacKerell, A. D.; Bashford, D.; Bellot, M.; Dunbrack, R. L., Jr.; Evansec, J. D.; Field, M. J.; Fisher, S.; Gao, J.; Guo, H.; Ha, S.; Joseph, D.; Kuchnir, L.; K, K. Kuczera; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, I. W. E.; Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe, M.: Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
33. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
34. Kalé, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283.
35. Grubmüller, H. Technical report, Theoretical Biophysics Group, Institute for Medical Optics, Ludwig-Maximilians University, Munich, 1996.
36. Zhang, L.; Hermans, J. Proteins Struct. Funct. Genet. 1996, 24, 433.
37. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.
38. Grubmüller, H.; Heller, H.; Windemuth, A.; Schulten, K. Mol. Simu. 1991, 6, 121.
39. Bayas, M. V.; Schulten, K.; Leckband, D. Biophys. J. 2003, 84, 2223.
40. Lo Conte, L.; Chothia, C.; Janin, J. J. Mol. Biol. 1999, 285, 2177.
41. Henchman, R. H.; McCammon, J. A. Protein Sci. 2002, 11, 2080.
42. Tajkhorshid, E.; Nollert, P.; Jensen, M. Ø.; Miercke, L. J. W.; O'Connell, J.; Stroud, R. M.; Schulten, K. Science 2002, 296, 525.
43. Jensen, M. Ø.; Tajkhorshid, E.; Schulten, K. Biophys. J. 2003, 85, 2884.
44. Wraight, C. Personal communication.
45. Onuchic, J.; Okamura, M. Personal communication.