Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes

Journal of Physical Chemistry B

Volumn 110, Issue 13, 2006, Pages 6458-6469

  Riccardi, Demian ^a   Schaefer, Patricia ^a   Yang, Yang ^a   Yu, Haibo ^a   Ghosh, Nilanjan ^a   Prat Resina, Xavier ^a   König, Peter ^b   Li, Guohui ^c   Xu, Dingguo ^d   Guo, Hua ^d   Elstner, Marcus ^b,e   Cui, Qiang ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF PADERBORN   (Germany)

^c HARVARD MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF NEW MEXICO   (United States)

^e GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; BOUNDARY CONDITIONS; CHEMICAL REACTIONS; ELECTROSTATICS; FREE ENERGY; PERTURBATION TECHNIQUES; PROTONS;

BIOMOLECULAR ION PUMPS; BOUNDARY POTENTIAL METHODS; COMPLEX BIOLOGICAL PROCESSES; QUANTUM MECHANICAL/MOLECULAR MECHANICAL (QM/MM) METHODS;

QUANTUM THEORY;

EID: 33646356998     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp056361o     Document Type: Article

References (96)

1. Alberts, B.; Bray, D.; Lewis, J.; Raff, M.; Roberts, K.; Watson, J. D. Molecular biology of the cell; Garland Publishing: New York, 1994.
2. Burley, S. K.; Almo, S. C.; Bonanno, J. B.; Capel, M.; Chance, M. R.; Gaasterland, T.; Lin, D.; Sali, A.; Studier, F. W.; Swaminathan, S. Nature Genet. 1999, 23, 151-157.
3. Sali, A.; Glaeser, R.; Earnest, T.; Baumeister, W. Nature 2003, 422, 216-225.
4. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11(6), 700-733.
5. Gao, J. In Reviews in Computational Chemistry VII; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1995.
6. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solution; Wiley: New York, 1991.
7. Friesner, R. A.; Guallar, V. Annu. Rev. Phys. Chem. 2005, 56, 389-427.
8. Shurki, A.; Warshel, A. Adv. Protein Chem. 2003, 66, 249.
9. Gao, J.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467.
10. Liu, H.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Hermans, J.; Yang, W. Proteins 2001, 44, 484.
11. Shaik, S.; Kumar, D.; de Visser, S. P.; Altun, A.; Thiel, W. Chem. Rev. 2005, 105, 2279-2328.
12. Xu, D. G.; Wei, Y. S.; Wu, J. B.; Dunaway-Mariano, D.; Guo, H.; Cui, Q.; Gao, J. L. J. Am. Chem. Soc. 2004, 126, 13649-13658.
13. Wu, N.; Mo, Y. R.; Gao, J. L.; Pai, E. F. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2017-2022.
14. Li, G.; Cui, Q. J. Am. Chem. Soc. 2003, 125, 15028-15038.
15. Zhang, X.; Harrison, D.; Cui, Q. J. Am. Chem. Soc. 2002, 124, 14871-14878.
16. Klahn, M.; Schlitter, J.; Gerwert, K. Biophys. J. 2005, 88, 3829-3844.
17. Cui, Q. Theor. Chem. Acc. in press.
18. Cui, Q.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Karplus, M. J. Phys. Chem. B 2001, 105(2), 569-585.
19. Zhang, Y. K.; Liu, H. Y.; Yang, W. T. J. Chem. Phys. 2000, 112, 3483-3492.
20. Elstner, M.; Porezag, D.; Jungnickel, G.; Elstner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Phys. Rev. B 1998, 58(11), 7260-7268.
21. Elstner, M.; Frauenheim, T.; Suhai, S. THEOCHEM 2003, 652, 29.
22. Kruger, T.; Elstner, M.; Schiffels, P.; Frauenheim, T. J. Chem. Phys. 2005, 122, 114110.
23. Li, G.; Zhang, X.; Cui, Q. J. Phys. Chem. B 2003, 107, 8643-8653.
24. Li, G.; Cui, Q. J. Phys. Chem. B 2003, 107, 14521-14528.
25. Riccardi, D.; Schaefer, P.; Cui, Q. J. Phys. Chem. B 2005, 109, 17715-17733.
26. Straatsma, T. P.; McCammon, J. A. Annu. Rev. Phys. Chem. 1992, 43, 407-435.
27. Kollman, P. Chem. Rev. 1993, 93, 2395-2417.
28. Siomonson, T. Computational biochemistry and biophysics; Marcel Dekker: New York, 2001.
29. Hu, H.; Yang, W. T. J. Chem. Phys. 2005, 123, 041102.
30. Rychaert, J. P.; Ciccotti, G.; Berendsen, H. J. J. Comput. Phys. 1977, 23, 327-341.
31. Boresch, S.; Karplus, M. J. Phys. Chem. A 1999, 103, 103-118.
32. Yang, W.; Bitetti-Putzer, R.; Karplus, M. J. Chem. Phys. 2004, 120, 9450-9453.
33. Schaefer, P.; Riccardi, D.; Cui, Q. J. Chem. Phys. 2005, 123, 014905.
34. Riccardi, D.; Li, G.; Cui, Q. J. Phys. Chem. B 2004, 108, 6467-6478.
35. Konig, P. H.; Hoffmann, M.; Frauenheim, T.; Cui, Q. J. Phys. Chem. B in press.
36. Amara, P.; Field, M. J. Theor. Chem. Acc. 2003, 109, 43-52.
37. Das, D.; Eurenius, K. P.; Billings, E. M.; Sherwood, P.; Chattfield, D. C.; Hodošček, M.; Brooks, B. R. J. Chem. Phys. 2002, 117, 10534-10547.
38. Antes, I.; Thiel, W. J. Phys. Chem. A 1999, 103, 9290.
39. Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. J. Phys. Chem. A 2000, 104, 1720-1735.
40. Gao, J.; Amara, P.; Alhambra, C.; Field, M. J. J. Phys. Chem. A 1998, 102, 4714-4721.
41. Zhang, Y.; Lee, T.; Yang, W. J. Chem. Phys. 1999, 110, 46-54.
42. Davis, M. E.; Mccammon, J. A. Chem. Rev. 1990, 90, 509-521.
43. Hünenberger, P. H.; Mccammon, J. A. J. Chem. Phys. 1999, 110, 1856-1872.
44. Sagui, C.; Darden, T. A. Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 155-179.
45. Gao, J.; Alhambra, C. J. Chem. Phys. 1997, 107, 1212-1217.
46. Nam, K.; Gao, J.; York, D. M. J. Chem. Theor. Comput. 2005, 1, 2-13.
47. Gregersen, B. A.; York, D. M. J. Phys. Chem. B 2005, 109, 536-556.
48. Warshel, A.; Russell, S. T. Q. Rev. Biophys. 1984, 17, 283.
49. Im, W.; Bernéche, S.; Roux, B. J. Chem. Phys. 2001, 114(7), 2924-2937.
50. Warshel, A.; King, G. Chem. Phys. Lett. 1985, 121, 124-129.
51. Darden, T.; Pearlman, D.; Pedersen, L. G. J. Chem. Phys. 1998, 109, 10921-10935.
52. Rossi, I.; Truhlar, D. G. Chem. Phys. Lett. 1995, 233, 231-236.
53. Elstner, M.; Cui, Q.; Munih, P.; Kaxiras, E.; Frauenheim, T.; Karplus, M. J. Comput. Chem. 2003, 24, 565.
54. Thiel, W. Adv. Chem. Phys. 1996, 93, 703-757.
55. Lennartz, C.; Schaefer, A.; Terstegen, F.; Thiel, W. J. Phys. Chem. B 2002, 106, 1758.
56. Range, K.; Riccardi, D.; Elstner, M.; Cui, Q.; York, D. PhysChem-ChemPhys 2005, 7, 3070-3079.
57. Elstner, M. Theor. Chem. Acc. in press.
58. Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Phys. Rev. B 1998, 58, 7260.
59. Yang, A.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins: Struct., Funct., Genet. 1993, 15, 252-265.
60. Konecny, R.; Li, J.; Fisher, C. L.; Dillet, V.; Bashford, D.; Noodleman, D. A. Inorg. Chem. 1999, 38, 940.
61. Schutz, C. N.; Warshel, A. Proteins: Struct., Funct., Genet. 2001, 44, 400-417.
62. Anderson, D. E.; Becktel, W. J.; Dahlquist, F. W. Biochemistry 1990, 29, 2403-2408.
63. Yang, W.; Bitetti-Putzer, R.; Karplus, M. J. Chem. Phys. 2004, 120, 2618-2628.
64. Dao-pin, S.; Söderlind, E.; Baase, W. A.; Wozniak, J. A.; Sauer, U.; Matthews, B. W. J. Mol. Biol. 1991, 221, 873-887.
65. Fersht, A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding; W. H. Freeman and Company: New York, 1999.
66. Nicholls, D. G.; Ferguson, S. J. Bioenergetics 3; Academic Press: New York, 2002.
67. Brzezinski, P. Trends Biochem. Sci. 2004, 29, 380.
68. Liang, Z.; Klinman, J. Curr. Opin. Struct. Biol. 2004, 14, 648-655.
69. Grotthus, C. Ann. Chim. 1806, 58, 54.
70. Sham, Y. Y.; Muegge, I.; Warshel, A. Proteins: Struct., Funct., Genet. 1999, 36, 484-500.
71. Eriksson, A. E.; Jones, T. A.; Liljas, A. Proteins: Struct., Funct., Genet. 1988, 4, 274.
72. Christianson, D. W.; Fierke, C. A. Acc. Chem. Res. 1996, 29, 331.
73. Tu, C.; Silverman, D. N.; Forsman, C.; Jonsson, B.-H.; Lindskog, S. Biochem. 1989, 28, 7913.
74. Schutz, C. N.; Warshel, A. J. Phys. Chem. B 2004, 108, 2066-2075.
75. Toba, S.; Colombo, G.; Merz, K. M. J. J. Am. Chem. Soc. 1999, 121, 2290-2302.
76. Lu, D.; Voth, G. A. Proteins: Struct., Funct., and Genet. 1998, 33, 119-134.
77. Brooks, C. L.; Karplus, M. J. Mol. Biol. 1989, 208, 159-181.
78. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667-683.
79. Håkansson, K.; Carlsson, M.; Svensson, L. A.; Liljas, A. J. Mol. Biol. 1992, 227, 1192.
80. Koenig, P.; Ghosh, N.; Huffman, M.; Elstner, M.; Tajkhorshid, E.; Frauenheim, T.; Cui, Q. J. Phys. Chem. B, in press.
81. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1339-1350.
82. Eigen, M.; Maeyer, L. Z. Elektrochem. 1955, 59, 986-993.
83. Strajbl, M.; Hong, G.; Warshel, A. J. Phys. Chem. B 2002, 106, 13333-13343.
84. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu. Rev. Phys. Chem. 2002, 53, 291-318.
85. Silverman, D. N. Methods Enzymol. 1995, 249, 479-503.
86. Borgis, D.; Hynes, J. T. Chem. Phys. 1993, 170, 315-346.
87. Silverman, D. N. Biochim. Biophys. Acta 2000, 1458, 88-103.
88. Åqvist, J.; Warshel, A. J. Mol. Biol. 1992, 224, 7-14.
89. Duda, D.; Tu, C.; Qian, M.; Laipis, P. J.; Agbandje-McKenna, M.; Silverman, D. N.; McKenna, R. Biochem. 2001, 40, 1741-1748.
90. Geissler, P. L.; Dellago, C.; Chandler, D.; Hutter, J.; Parrinello, M. Science 2001, 291, 2121-2124.
91. Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. J. Chem. Phys. 2001, 114, 5149-5155.
92. Bondar, A. N.; Fischer, S.; Smith, J. C.; Elstner, M.; Suhai, S. J. Am. Chem. Soc. 2004, 126, 14668-14677.
93. Ben-Nun, M.; Martinez, T. J. Adv. Chem. Phys. 2002, 121, 439.
94. Roux, B.; Allen, T. W.; Berneche, S.; Im, W. Q. Rev. Biophys. 2004, 37, 15-103.
95. Landau, D. P.; Binder, K. Monte Carlo Simulations in Statistical Physics; Cambridge University Press: Cambridge, 2000.
96. Murray, J. D. Mathematical Biology; Springer: Berlin, 2003.