Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations

Journal of Chemical Physics

Volumn 126, Issue 16, 2007, Pages

  Van Der Vaart, Arjan ^a,b   Karplus, Martin ^a,c  

^a HARVARD UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c UNIVERSITÉ LOUIS PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SYSTEMS; FREE ENERGY PROFILES; MINIMUM FREE ENERGY PATHWAYS;

CHEMICAL MODIFICATION; COMPUTER SIMULATION; FREE ENERGY; MOLECULAR DYNAMICS; MONTE CARLO METHODS; OPTIMIZATION;

CONFORMATIONS;

ALANINE; DIPEPTIDE;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; MONTE CARLO METHOD; PROTEIN CONFORMATION; THEORETICAL MODEL; THERMODYNAMICS;

ALANINE; COMPUTER SIMULATION; DIPEPTIDES; MODELS, THEORETICAL; MONTE CARLO METHOD; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 34247860779     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2719697     Document Type: Article

References (71)

1. A. van der Vaart, Theor. Chem. Acc. 116, 183 (2006).
2. M. Perutz, A. Wilkinson, M. Paoli, and G. Dodson, Annu. Rev. Biophys. Biomol. Struct. 27, 1 (1998).
3. S. Benkovic and S. Hammes-Schiffer, Science 301, 1196 (2003).
4. M. Huse and J. Kuriyan, Cell 109, 275 (2002).
5. D. Doyle, Trends Neurosci. 27, 298 (2004).
6. K. Swartz, Nat. Rev. Neurosci. 5, 905 (2004).
7. G. Woolley and T. Lougheed, Curr. Opin. Chem. Biol. 7, 710 (2003).
8. R. Mallik and S. Gross, Curr. Biol. 14, R971 (2004).
9. M. Schliwa and G. Woehlke, Nature (London) 422, 759 (2003).
10. M. Karplus and Y. Gao, Curr. Opin. Struct. Biol. 14, 250 (2004).
11. O. Millet, R. Hudson, and L. Kay, Proc. Natl. Acad. Sci. U.S.A. 100, 12700 (2003).
12. C. Vonrhein, G. Schlauderer, and G. Schulz, Structure (London) 3, 483 (1995).
13. T. Heyduk, Curr. Opin. Biotechnol. 13, 292 (2002).
14. M. Gerstein, A. Lesk, and C. Chothia, Biochemistry 33, 6739 (1994).
15. M. Gerstein and W. Krebs, Nucleic Acids Res. 26, 4280 (1998).
16. S. Hayward and H. Berendsen, Proteins 30, 144 (1998).
17. J. Ma, P. B. Sigler, Z. Xu, and M. Karplus, J. Mol. Biol. 302, 303 (2000).
18. N. Ranson, G. Farr, A. Roseman, B. Gowen, W. Fenton, A. Horwich, and H. Saibil, Cell 107, 869 (2001).
19. W. Krebs and M. Gerstein, Nucleic Acids Res. 28, 1665 (2000).
20. Computational Biochemistry and Biophysics, edited by, O. Becker, J. A. D. MacKerell, B. Roux, and, M. Watanabe, (Dekker, New York, 2001).
21. C. Brooks, M. Karplus, and B. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics, Advances in Chemical Physics Vol. 71 (Wiley, New York, 1988).
22. S. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992).
23. H. Jónsson, G. Mills, and K. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by, B. Berne, G. Ciccotti, and, D. Coker, (World Scientific, Singapore, 1998).
24. R. Elber and M. Karplus, Chem. Phys. Lett. 139, 375 (1987).
25. M. E.-C. El-Kattani, K. Zakrzewska, J. Durup, and R. Lavery, Proteins 16, 393 (1993).
26. R. Elber, A. Cárdenas, A. Ghosh, and H. Stern, Adv. Chem. Phys. 126, 93 (2003).
27. S. Huo and J. Straub, J. Chem. Phys. 107, 5000 (1997).
28. D. Passerone, M. Ceccarelli, and M. Parrinello, J. Chem. Phys. 118, 2025 (2003).
29. D. Tobias and C. Brooks, J. Chem. Phys. 89, 5115 (1988).
30. S. Harvey and H. Gabb, Biopolymers 33, 1167 (1993).
31. J. Schlitter, M. Engels, P. Krüger, E. Jacoby, and A. Wollmer, Mol. Simul. 10, 291 (1993).
32. H. Grubmüller, B. Heymann, and P. Tavan, Science 271, 997 (1996).
33. E. Paci and M. Karplus, J. Mol. Biol. 288, 441 (1999).
34. B. Isralewitz, J. Baudry, J. Gullingsrud, D. Kosztin, and K. Schulten, J. Mol. Graphics 19, 13 (2001).
35. J. Apostolakis, P. Ferrara, and A. Caflisch, J. Chem. Phys. 110, 2099 (1999).
36. A. van der Vaart and M. Karplus, J. Chem. Phys. 122, 114903 (2005).
37. S. Park, F. Khalili-Araghi, E. Tajkhorshid, and K. Schulten, J. Chem. Phys. 119, 3559 (2003).
38. G. Hummer and A. Szabo, Acc. Chem. Res. 38, 504 (2005).
39. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996).
40. I. Bahar, A. Atilgan, and B. Erman, Folding Des. 2, 173 (1997).
41. F. Tama, M. Valle, J. Frank, and C. Brooks, Proc. Natl. Acad. Sci. U.S.A. 100, 9319 (2003).
42. O. Miyashita, J. Onichic, and P. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 100, 12570 (2003).
43. P. Maragakis and M. Karplus, J. Mol. Biol. 352, 807 (2005).
44. P. Bolhuis, D. Chandler, C. Dellago, and P. Geissler, Annu. Rev. Phys. Chem. 53, 291 (2002).
45. H. Grubmüller, Phys. Rev. E 52, 2893 (1995).
46. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
47. D. Hamelberg, J. Mongan, and J. McCammon, J. Chem. Phys. 120, 11919 (2004).
48. M. Hagan, A. Dinner, D. Chandler, and A. Chakraborty, Proc. Natl. Acad. Sci. U.S.A. 100, 13922 (2003).
49. R. Radhakrishnan and T. Schlick, Proc. Natl. Acad. Sci. U.S.A. 101, 5970 (2004).
50. B. Schulze, H. Grubmüller, and J. Evanseck, J. Am. Chem. Soc. 122, 8700 (2000).
51. R. Elber and M. Karplus, J. Am. Chem. Soc. 112, 9161 (1990).
52. D. Branduardi, F. Gervasio, A. Cavalli, M. Recanatini, and M. Parrinello, J. Am. Chem. Soc. 127, 9147 (2005).
53. D. Hamelberg and J. McCammon, J. Am. Chem. Soc. 127, 13778 (2005).
54. A. Ma and A. Dinner, J. Phys. Chem. B 109, 6769 (2005).
55. S. Krivov and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 101, 14766 (2004).
56. A. Anderson and J. Hermans, Proteins 3, 262 (1988).
57. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997).
58. M. Allen and D. Tildesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987).
59. Y. Kong, Y. Shen, T. Warth, and J. Ma, Proc. Natl. Acad. Sci. U.S.A. 99, 5999 (2002).
60. J. Diaz, B. Wroblowski, J. Schlitter, and Y. Engelborghs, Proteins 28, 434 (1997).
61. W. Press, S. Teukolsky, W. Vetterling, and B. Flannery, Numerical Recipes in C, 2nd ed. (Cambridge University Press, New York, 1992), pp. 650-655.
62. W. Ren, E. Vanden-Eijnden, P. Maragakis, and W. E, J. Chem. Phys. 123, 134109 (2005).
63. R. Hooft, B. van Eijck, and J. Kroon, J. Chem. Phys. 97, 6690 (1992).
64. A. Ferrenberg and R. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
65. D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd ed. (Academic, New York, 2002).
66. B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaninathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
67. J. Ryckaert, G. Ciccotti, and H. Berendsen, J. Comput. Phys. 23, 327 (1977).
68. M. Schaefer and M. Karplus, J. Phys. Chem. 100, 1578 (1996).
69. E. Neria, S. Fischer, and M. Karplus, J. Chem. Phys. 105, 1902 (1996).
70. See EPAPS Document No. E-JCPSA6-126-508715 for simulation results on a four-dimensional system (the alanine tripeptide). This document can be reached via a direct link in the online article's HTML reference section or via the EPAPS homepage (http://www.aip.org/pubservs/epaps.html).
71. E. Dijkstra, Numer. Math. 1, 269 (1959).