Brute-force molecular dynamics simulations of villin headpiece: Comparison with NMR parameters

Journal of Physical Chemistry B

Volumn 107, Issue 40, 2003, Pages 11178-11187

  Van Der Spoel, David ^a   Lindahl, Erik ^b  

^a UPPSALA UNIVERSITY   (Sweden)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; COMPUTER SIMULATION; HYDROGEN; HYDROGEN BONDS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PH; WATER;

GLUTAMATE RESIDUES; MOLECULAR DYNAMICS SIMULATIONS; PROTONATION STATES; VILLIN HEADPIECE;

MOLECULAR BIOLOGY;

EID: 0242292035     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp034108n     Document Type: Article

References (92)

1. Berendsen, H. J. C. Science 1996, 271, 954-955.
2. Duan, Y.; Kollman, P. A. Science 1998, 282, 740-744.
3. Daura, X.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. J. Mol. Biol. 1998, 280, 925-932.
4. Marrink, S. J.; Tieleman, D. P.; Mark, A. E. J. Phys. Chem. B 2000, 104, 12165-12173.
5. Lindahl, E. Edholm, O. Biophys. J. 2000, 79, 426-433.
6. Marrink, S. J.; Lindahl, E.; Edholm, O.; Mark, A. E. J. Am. Chem. Soc. 2001, 123, 8638-8639.
7. Tieleman, D.; Berendsen, H. Biophys. J. 1998, 74, 2786-2801.
8. Izrailev, S.; Crofts, A. R.; Berry, E. A.; Schulten, K. Biophys. J. 1999, 77, 1753-1768.
9. de Groot, B. L.; Grubmüller, H. Science 2001, 294, 2353-2357.
10. Tajkhorshid, E.; Nollert, P.; Jensen, M. O.; Miercke, J. L. W.; O'Connell, J.; Stroud, R. M.; Schulten, K. Science 2002, 296, 525-530.
11. Shirts, M. R.; Pande, V. S. Phys. Rev. Lett. 2001, 86, 4983-4986.
12. See http://folding.stanford.edu for more information.
13. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56.
14. Lindahl, E.; Hess, B. A.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317.
15. Bekker, H.; Berendsen, H. J. C.; Dijkstra, E. J.; Achterop, S.; van Drunen, R.; van der Spoel, D.; Sijbers, A.; Keegstra, H.; Reitsma, B.; Renardus, M. K. R. In Physics Computing 92; de Groot, R. A., Nadrchal, J., Eds.; World Scientific: Singapore, 1993; pp 257-261.
16. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 953-962.
17. Barth, E.; Kuczera, K.; Leimkuhler, B.; Skeel, R. D. J. Comput. Chem. 1995, 16, 1192-1209.
18. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Faaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472.
19. Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. J. Comput. Chem. 1999, 20, 786-798.
20. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
21. Essman, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8592.
22. The GROMACS program is available free of charge under the GNU general public license from http://www.gromacs.org.
23. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
24. Hermans, J.; Berendsen, H. J. C.; van Gunsteren, W. F.; Postma, J. P. M. Biopolymers 1984, 23, 1513-1518.
25. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comput. Chem. 1986, 7, 230-252.
26. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657-1666.
27. Hagler, A.; Huler, E.; Lifson, S. J. Am. Chem. Soc. 1974, 96, 5319-5327.
28. Lifson, S.; Hagler, A.; Dauber, P. J. Am. Chem. Soc. 1974, 101, 5111-5121.
29. Drenth, J. Principles of Protein X-ray Crystallography; Springer: New York, 1994.
30. Doreleijers, J. F.; Rullmann, J. A. C.; Kaptein, R. J. Mol. Biol. 1998, 281, 149-164.
31. Tolman, J. R. Curr. Opin. Struct. Biol. 2001, 11, 532-539.
32. Sass, H. J.; Musco, G.; Stahl, S. J.; Wingfield, P. T.; Grzesiek, S. J. Biomol. NMR 2001, 21, 275-280.
33. Spronk, C. A. E. M.; Linge, J. P.; Hilbers, C. W.; Vuister, G. W. J. Biomol. NMR 2002, 22, 281-289.
34. McKnight, C. J.; Matsudaira, P. T.; Kim, P. S. Nature Struct. Biol. 1997, 4, 180-184.
35. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Hochschuleverlag AG an der ETH Zürich: Zürich, Switzerland, 1996.
36. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2001, 105, 6474-6487.
37. Jorgensen, W. L. Encyclopedia of Computational Chemistry; Wiley: New York, 1998; Vol. 3, Chapter OPLS, Force Fields, pp 1986-1989.
38. Åqvist, J. FEBS Lett. 1999, 457, 414-418.
39. 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.
40. MacKerell, A. D.; Wiorkiewicz-Kuczera, J.; Karplus, M. J. Am. Chem. Soc. 1995, 117, 11946-11975.
41. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
42. van Gunsteren, W. F.; Berendsen, H. J. C. Gromos-S7 Manual; Biomos BV: Groningen, The Netherlands, 1987.
43. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing Company: Dordrecht, The Netherlands, 1981; pp 331-342.
44. van der Spoel, D.; van Maaren, P. J.; Berendsen, H. J. C. J. Chem. Phys. 1998, 108, 10220-10230.
45. Mark, P.; Nilsson, L. J. Phys. Chem. A 2001, 105, 9954-9960.
46. van der Spoel, D.; van Buuren, A. R.; Tieleman, D. P.; Berendsen, H. J. C. J. Biomol. NMR 1996, 8, 229-238.
47. Mark, P.; Nilsson, L. J. Phys. Chem. B 2001, 105, 8028-8035.
48. Elofsson, A.; Nilsson, L. J. Mol. Biol. 1993, 233, 766-780.
49. McKnight, C. J.; Doering, D. S.; Matsudaira, P. T.; Kim, P. S. J. Mol. Biol. 1996, 260, 126-134.
50. See http://people.bu.edu/cjmck/index.htm.
51. Schulz, G. E.; Schirmer, R. H. Principles of Protein Structure; Springer-Verlag: New York, 1978.
52. Berendsen, H. J. C.; Postma, J. P. M.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
53. Berendsen, H. J. C.; Mavri, J. Int. J. Quantum Chem. 1996, 57, 975- 984.
54. Torda, A. E.; Scheek, R. M.; van Gunsteren, W. F. Chem. Phys. Lett. 1989, 157, 289-294.
55. Karplus, M. J. Chem. Phys. 1959, 30, 11-15.
56. Vuister, G. W.; Bax, A. J. Am. Chem. Soc. 1993, 115, 7772-7777.
57. Pardi, A.; Billeter, M.; Wüthrich, K. J. Mol. Biol. 1984, 180, 741-751.
58. Smith, L. J.; Sutcliffe, M. J.; Redfield, C.; Dobson, C. M. Biochemistry 1991, 30, 986-996.
59. Ludvigsen, S.; Andersen, K. V.; Poulsen, F. M. J. Mol. Biol. 1991, 217, 731-736.
60. Ösapay, K.; Case, D. A. J. Am. Chem. Soc. 1991, 113, 9436-9444.
61. Case, D. A. J. Biomol. NMR 1995, 6, 341-346.
62. Dejaegere, A. P.; Bryce, R. A.; Case, D. A. In Modeling NMR Chemical Shifts, Facelli, J. A., de Dios, A. C., Eds.; American Chemical Society: Washington, DC, 1999; pp 194-206.
63. Merutka, G.; Dyson, H. J.; Wright, P. E. J. Biomol. NMR 1995, 5, 14-24.
64. Eisenhaber, F.; Lijnzaad, P.; Argos, P.; Sander, C.; Scharf, M. J. Comput. Chem. 1995, 16, 273-284.
65. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577-2637.
66. Baldwin, R. L. Curr. Opin. Struct. Biol. 1993, 3, 84-91.
67. Frank, B. S.; Vardar, D.; Buckley, D. A.; McKnight, C. J. Protein Sci. 2002, 11, 680-687.
68. van der Spoel, D.; Vogel, H. J.; Berendsen, H. J. C. Proteins: Struct. Funct. Genet. 1996, 24, 450-466.
69. Gellman, S. H.; Woolfson, D. N. Nature Struct. Biol. 2002, 9, 408-410.
70. Neidigh, J. W.; Fesinmeyer, R. M.; Andersen, N. H. Nature Struct. Biol. 2002, 9, 425-430.
71. Feldman, H. J.; Hogue, C. W. V. Proteins: Struct. Funct. Genet. 2002, 46, 8-23.
72. Levinthal, C. J. Chim. Phys. 1968, 65, 44-45.
73. van Gunsteren, W. F.; Karplus, M. Nature 1981, 293, 677-678.
74. Walser, R.; Hünenberger, P. H.; van Gunsteren, W. F. Proteins 2002, 48, 327-340.
75. Colombo, G.; Roccatano, D.; Mark, A. E. Proteins: Struct. Funct. Genet. 2002, 46, 380-392.
76. van der Spoel, D. Biochem. Cell Biol. 1998, 76, 164-170.
77. Wishart, D. S.; Sykes, B. D. Methods Enzymol. 1994, 239, 363-391.
78. Case, D. A.; Dyson, H. J.; Wright, P. E. Methods Enzymol. 1994, 239, 392-415.
79. Ösapay, K.; Theriault, Y.; Wright, P. E.; Case, D. A. J. Mol. Biol. 1994, 244, 183-197.
80. Wishart, D. S.; Nip, A. M. Biochem. Cell Biol. 1998, 76, 153-163.
81. Williamson, M. P.; Asakura, T. J. Magn. Reson. Ser. B 1993, 101, 63-71.
82. Duan, Y.; Wang, L.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 9897-9902.
83. Lee, M. R.; Baker, D.; Kollman, P. A. J. Am. Chem. Soc. 2001, 123, 1040-1046.
84. Berendsen, H. J. C. Science 1998, 282, 642-643.
85. Zagrovic, B.; Snow, C. D.; Shirts, M. R.; Pande, V. S. J. Mol. Biol. 2002, 323, 927-937.
86. Zagrovic, B.; Snow, C. D.; Khaliq, S.; Shirts, M. R.; Pande, V. S. J. Mol. Biol. 2002, 323, 153-164.
87. Sullivan, D. C.; Kuntz, I. D. Proteins: Struct. Funct. Genet. 2001, 42, 495-511.
88. Sullivan, D. C.; Kuntz, I. D. J. Phys. Chem. B 2002, 106, 325-3262.
89. de Groot, B. L.; Amadei, A.; Scheek, R. M.; van Nuland, N. A. J.; Berendsen, H. J. C. Proteins: Struct. Funct. Genet. 1996, 26, 314-322.
90. Amadei, A.; de Groot, B. L.; Ceruso, M. A.; Paci, M.; Di Nola, A.; Berendsen, H. J. C. Proteins: Struct. Funct. Genet. 1999, 35, 283-292.
91. Feenstra, K. A.; Peter, C.; Scheek, R. M.; van Gunsteren, W. F.; Mark, A. J. Biomol. NMR 2002, 23, 181-194.
92. Smith, L. J.; Dobson, C. M.; van Gunsteren, W. F. Proteins: Struct. Funct. Genet. 1999, 36, 77-86.