Mechanochemical Coupling in Myosin: A Theoretical Analysis with Molecular Dynamics and Combined QM/MM Reaction Path Calculations

Journal of Physical Chemistry B

Volumn 108, Issue 10, 2004, Pages 3342-3357

  Li, Guohui ^a   Cui, Qiang ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; CATALYSIS; COMPUTER SIMULATION; CRYSTALLOGRAPHY; ELECTRON MICROSCOPY; HYDROLYSIS; MOLECULAR DYNAMICS; PERTURBATION TECHNIQUES; PHOSPHATES; QUANTUM THEORY;

MYOSIN; REACTION PATH CALCULATION;

ADENOSINETRIPHOSPHATE;

EID: 1842584700     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0371783     Document Type: Article

References (98)

1. Alberts, B.; Bray, D.; Lewis, J.; Raff, M.; Roberts, K.; Watson, J. D. Molecular biology of the Cell, 3rd. ed.; Garland Publishing: New York and London, 1994.
2. Keike, M. C.; Titus, M. A. In Molecular Motors; Schliwa, M., Ed.; Wiley-VCH: Munchen, Germany. 2003.
3. Hirokawa, N.; Takemura, R. In Molecular motors: Schliwa, M., Ed.; Wiley-VCH: Munchen, Germany, 2003.
4. Lee, A. G.; East, J. M. Biochem. J. 2001, 356, 665-683.
5. Gao, Y.; Yang, W.; Marcus, R. A.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 11339-11344.
6. Strajbl, M.; Shurki, A.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 2093, 100, 14834-14839.
7. Vale, R. D.; Milligan, R. A. Science 2000, 288, 88-95.
8. Bustamante, C.; Keller, D.; Oster, G. Acc. Chem. Res. 2001, 34, 412-420.
9. Karplus, M.; McCammon, J. A. Nature, Struct. Biol. 2002, 9, 646-652.
10. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700-733.
11. Gao, J. In Reviews in Computational Chemistry; Lipkowitza, K. B., Boyd, D. B., Eds.; VCH: New York. 1996; Vol. 7, p 119.
12. Gao, J.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467-505.
13. Åqvist, J.; Warshel, A. Chem. Rev. 1993, 93, 2523.
14. Warshel, A. Annu. Rev. Biophys. Biomol. 2003, 32, 425-443.
15. Li, G.; Cui, Q. Biophys. J. 2004, 86, 743.
16. Li, G.; Cui, Q. Biophys. J. 2002, 83, 2457-2474.
17. Cui, Q.; Li, G.; Ma, J.; Karplus, M. J. Mol. Biol. 2003, submitted for publication.
18. Bagshaw, C. R. In Molecular Motors; Banting, G., Higgins, S. J., Eds.; Portland Press: London, 2000; Vol. 35, pp 19-31.
19. Holmes, K. C.; Geeves, M. A. Annu. Rev. Biochem. 1999, 68, 687-728.
20. Sablin, E. P.; Fletterick, R. J. Curr. Opin. Struct. Biol. 2001, 11, 716-724.
21. Lymn, R. W.; Taylor, E. W. Biochemistry 1971, 10, 4617-4624.
22. Trentham, D. R.; Eccleston, J. F.; Bagshaw, C. R. Q. Rev. Biophys. 1976, 9, 217-281.
23. Rayment, I. J. Biol. Chem. 1996, 271, 15850-15853.
24. Rayment, I.; Holden, H. W.; Whitaker, M.; Yohn, C. B.; Lorenz, M.; Holmes, K. C.; Milligan, R. A. Science 1993, 261, 58-61.
25. Houdusse, A.; Sweeney, H. L. Curr. Opin. Struct. Biol. 2001, 11, 182-194.
26. Houdusse, A.; Szent-Gyorgyi, A. G.; Cohen, C. Proc. Natl. Acad. Sci. U.S.A. 2000, 97.
27. Reubold, T. F.; Eschenburg, S.; Becker, A.; Kull, F. J.; Manstein, D. J. Nature, Stuct. Biol. 2003, 10, 826-830.
28. Gourinath, S.; Himmel, D. M.; Brown, J. H.; Reshetnikova, L.; Szent-Gyorgyi, A. G.; Cohen, C. Structure 2003, 11, 1621-1627.
29. Coureux, P.; Wells, A. L.; Menetrey, J.; Yengo, C. M.; Morris, C. A.; Sweeney, H. L.; Houdusse, A. Nature (London) 2003, 425, 419-423.
30. Whittaker, M.; Wilsonkubalek, E. M.; Smith, J. E.; Faust, L.; Milligan, R. A.; Sweeney, H. L. Nature (London) 1995, 378, 748-751.
31. Holmes, K. C.; Angert, I.; Kull, F. J.; Jahn, W.; Schroder, R. R. Nature 2003, 425, 423-427.
32. Kambara, T.; Rhodes, T. E.; Ikebe, R.; Tamada, M.; White, H. D.; Ikebe, M. J. Biol. Chem. 1999, 274, 16400-16406.
33. Li, X.; Rhodes, T. E.; Ikebe, R.; Kambara, T.; White, H. D.; Ikebe, M. J. Biol. Chem. 1998, 273, 27404-27411.
34. Sasaki, N.; Shimada, T.; Sutoh, K. J. Biol. Chem. 1998, 273, 20334-20340.
35. Shimada, T.; Sasaki, N.; Ohkura, R.; Sutoh, K. Biochemistry 1997, 36, 14037-14043.
36. Ishijima, A.; Kojima, H.; Funatsu, T.; Tokunaga, M.; Higuchi, H.; Tanaka, H.; Yanagida, T. Cell 1998, 92, 161-171.
37. Ishii, Y.; Kitamura, K.; Tanaka, H.; Yanagida, T. Methods Enzymol. 2003, 361, 228-245.
38. Murphy, C. T.; Rock, R. S.; Spudich, J. A. Nature, Cell Biol. 2001, 3, 311-315.
39. Steffen, W.; Smith, D.; Sleep, J. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6434-6439.
40. Bauer, C. B.; Holden, H. W.; Thoden, J. B.; Smith, R.; Rayment, I. J. Biol. Chem. 2000, 275, 38494-38499.
41. Bohm, A.; Gaudet, R.; Sigler, P. B. Curr. Opin. Biotechnol. 1997, 8, 480-487.
42. Gulick, A. M.; Bauer, C. B.; Thoden, J. B.; Rayment, I. Biochemistry 1997, 36, 11619-11628.
43. Fisher, A. J.; Smith, C. A.; Thoden, J. B.; Smith, R.; Sutoh, K.; Holden, H. W.; Rayment, I. Biochemistry 1995, 34, 8960-8972.
44. Smith, C. A.; Rayment, I. Biochemistry 1996, 35, 5404-5417.
45. Dominguez, R.; Freyzon, Y.; Trybus, K. M.; Cohen, C. Cell 1998, 94, 559-571.
46. Hu, C. H.; Brinck, T. J. Phys. Chem. A 1999, 103, 5379-5386.
47. Wang, Y.; Topol, I. A.; Collins, J. R.; Burt, S. K. J. Am. Chem. Soc. 2003, 125, 13265-13273.
48. Minehardt, T. J.; Marzari, N.; Cooke, R.; Pate, E.; Kollman, P. A.; Car, R. Biophys. J. 2002, 82, 660-675.
49. Onishi, H.; Kojima, H.; Katoh, K.; Fujiwara, K.; Martinez, H. M.; Morales, M. F. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 6653-6658.
50. Onishi, H.; Ohki, T.; Mochizuki, N.; Morales, M. F. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15339-15344.
51. Brooks, C. L., III; Brünger, A.; Karplus, M. Biopolymer 1985, 24, 843.
52. Brooks, C. L., III; Karplus, M. J. Chem. Phys. 1983, 79, 6312-6325.
53. Brooks, C. L., III; Karplus, M. J. Mol. Biol. 1989, 208, 159-181.
54. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. J. Comput. Phys. 1977, 23, 327-341.
55. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
56. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stole, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Kraplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
57. Bashford, D.; Karplus, M. Biochem. 1990, 29, 10219-10225.
58. Simonson, T.; Archontis, G.; Karplus, M. J. Phys. Chem. B 1997, 101, 8349-8362.
59. Cui, Q.; Karplus, M. J. Am. Chem. Soc. 2001, 122, 2284-2290.
60. Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. J. Phys. Chem. A 2000, 104, 1720-1735.
61. Szabo, A.; Ostlund, N. S. Modern quantum chemistry-Introduction to advanced electronic structure theory; Dover Publications: New York, 1989.
62. Binkley, J. S.; Pople, J. A.; Hehre, W. J. J. Am. Chem. Soc. 1980, 102, 939.
63. Gordon, M. S.; Binkley, J. S.; Pople, J. A.; Peitro, W. J.; Hehre, W. J. J. Am. Chem. Soc. 1982, 104, 2797.
64. Becke, A. D. J. Chem. Phys. 1993, 95, 5648-5652.
65. Becke, A. D. Phys. Rev. A 1998, 38, 3098-3100.
66. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.
67. Hariharan, P. C.; Pople, J. A. Theor. Chim. Acta 1973, 25, 213-222.
68. Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. J. Chem. Phys. 1980, 72, 650-654.
69. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure, & Thermodynamics; John Wiley & Sons: 1988; Vol. LXXI.
70. Fischer, S.; Karplus, M. Chem. Phys. Lett. 1992, 194, 252-261.
71. Cui, Q.; Karplus, M. J. Am. Chem. Soc. 2002, 124, 3093-3124.
72. Cui, Q.; Karplus, M. J. Phys. Chem. B 2002, 106, 1768.
73. Strajbl, M.; Hong, G.; Warshel, A. J. Phys. Chem. B 2002, 106, 13333-13343.
74. Olsson, M. H. M.; Hong, G.; Warshel, A. J. Am. Chem. Soc. 2003, 125, 5025-5039.
75. Cui, Q.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Karplus, M. J. Phys. Chem. B 2001, 105, 569-585.
76. Li, G.; Cui, Q. J. Phys. Chem. B 2003, 107, 8643-8653.
77. Li, G.; Cui, Q. J. Am. Chem. Soc. 2003, 125, 15028-15038.
78. Okimoto, N.; Yamanaka, K.; Ueno, J.; Hata, M.; Hoshino, T.; Tsuda, M. Biophys. J. 2001, 57, 2786-2794.
79. Lahiri, S. D.; Zhang, G.; Dunaway-Mariano, D.; Allen, K. N. Science 2003, 299.
80. Bash, P. A.; Field, M. J.; Davenport, R. C.; Petsko, G. A.; Ringe, D.; Karplus, M. Biochemistry 1991, 30, 5826-5832.
81. Schweins, T.; Warshel, A. Biochemistry 1996, 35, 14232-14243.
82. Dittrich, M.; Hayashi, S.; Schulten, K. Biophys. J. 2003, 55, 2253-2266.
83. Yang, W.; Gao, Y.; Cui, Q.; Ma, J.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 874-879.
84. Bagshaw, C. R.; Trentham, D. R.; Wolcott, R. G.; Boyer, P. D. Proc. Natl. Acad. Sci. U.S.A. 1975, 72, 2592-2596.
85. Webb, M. R.; Trentham, D. R. J. Biol. Chem. 1981, 256, 10910-10916.
86. Dale, M. P.; Hackney, D. D. Biochem. 1987, 26, 8365-8372.
87. Rees, D. C.; Howard, J. B. J. Mol. Biol. 1999, 293, 343-350.
88. Wang, Q.; Wong, C. F.; Rabitz, H. Biophys. J. 1998, 75, 60-69.
89. Sagnella, D. E.; Straub, J. E. J. Phys. Chem. B 2001, 105, 7057-7063.
90. Boyer, P. D. Biochim. Biophys. Acta 1993, 1140, 215-250.
91. Florian, J.; Warshel, A. J. Phys. Chem. B 1998, 702, 719-734.
92. Glennon, T. M.; Villa, J.; Warshel, A. Biochemistry 2000, 39, 9641-9651.
93. Aqvist, J.; Kolmodin, K.; Florian, J.; Warshel, A. Chem. Biol. 1999, 6, R71-R80.
94. Cui, Q.; Elstner, M.; Karplus, M. J. Phys. Chem. B 2002, 106, 2721-2740.
95. Karplus, M. J. Phys. Chem. 2000, 104, 11-27.
96. Lu, H. P.; Xun, L.; Xie, X. Science 1998, 252, 1877.
97. Xie, X.; Lu, H. P. J. Biol. Chem. 1999, 274, 15967.
98. Xie, X. J. Chem. Phys. 2002, 117, 11024-11032.