Force field-dependant structural divergence revealed during long time simulations of calbindin d9k

Journal of Computational Chemistry

Volumn 31, Issue 9, 2010, Pages 1864-1872

  Project, Elad ^a   Nachliel, Esther ^a   Gutman, M ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Experimental structure; Force field; Molecular dynamics; Protein folding; Secondary structure; Structural divergence

Indexed keywords

EXPERIMENTAL STRUCTURE; FORCE FIELD; FORCE FIELDS; SECONDARY STRUCTURES; STRUCTURAL DIVERGENCE;

PROTEIN FOLDING; RESONANCE;

MOLECULAR DYNAMICS;

CALBINDIN; CALCIUM;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; METABOLISM; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

CALCIUM; CALCIUM-BINDING PROTEIN, VITAMIN D-DEPENDENT; COMPUTER SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY;

EID: 77953208542     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21473     Document Type: Article

References (50)

1. Yoda, T.; Sugita, Y.; Okamoto, Y. Chem Phys 2004, 307, 269.
2. Price, D. J.; Brooks, C. L. J Comput Chem 2002, 23, 1045.
3. Best, R. B.; Buchete, N. V.; Hummer, G. Biophys J 2008, 95, L7.
4. Villa, A.; Fan, H.; Wassenaar, T.; Mark, A. E. J Phys Chem B 2007, 111, 6015.
5. Freddolino, P. L.; Liu, F.; Gruebele, M.; Schulten, K. Biophys J 2008, 94, L75.
6. Freddolino, P. L.; Park, S.; Roux, B.; Schulten, K. Biophys J 2009, 96, 3772.
7. Mackerell, A. D.; Feig, M.; Brooks, C. L. J Comput Chem. 2004, 25, 1400.
8. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; 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.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stole, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
9. 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 GROMOS 96 manual and user guide; Hochschulverlag AG der ETH: Zürich. 1996, 1.
10. Oostenbrink, C.; Villa, A.; Mark, A. E.; Van. Gunsteren, W. F. J Comput Chem 2004, 25, 1656.
11. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
12. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J. M.; Kollman, P. J Comput Chem 2003, 24, 1999.
13. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. J Am Chem Soc 1996, 118, 11225.
14. Wang, J. M.; Cieplak, P.; Kollman, P. A. J Comput Chem 2000, 21, 1049.
15. Sorb, E. J.; Pande, V. S. Biophys J 2005, 88, 2472.
16. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins Struct Funct Bioinformatics 2006, 65, 712.
17. Garcia, A. E.; Sanbonmatsu, K. Y. Proc Natl Acad Sci USA 2002, 99, 2782.
18. Nymeyer, H.; Garcia, A. E. Proc Natl Acad Sci USA 2003, 100, 13934.
19. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Nature 1969, 224, 175.
20. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
21. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comp Phys Comm 1995, 91, 43.
22. Lindahl, E.; Hess, B.; Van der Spoel, E. J Mol Model, 2001, 7, 306.
23. Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J Comput Chem 2005, 26, 1701.
24. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J Chem Theory Comput 2008, 4, 435.
25. Project, E.; Nachliel, E.; Gutman, M. J Comput Chem 2008, 29, 1163.
26. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235.
27. Szebenyi, D. M. E.; Moffat, K. J Biol Chem 1986, 261, 8761,
28. Kordel, J.; Pearlman, D. A.; Chazin, W. J. J Biomol NMR 1997, 10, 231.
29. Berendsen, H. J. C.; Postma, J. P. M.; DiNola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
30. Essman, U.; Perela, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pederse, L. G. J Chem Phys 1995, 103, 8577.
31. Hess, B; Bekker, H; Berendsen, H. J. C; Fraaije J. G. E. M. J Comput Chem 1997, 18, 1463.
32. Miyamoto, S.; Kollman, P. A. J Comput Chem 1992, 13, 952.
33. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
34. Lipari, G.; Szabo, A. J Am. Chem Soc 1982, 104, 4546.
35. Clore, G. M.; Szabo, A.; Bax, A.; Kay, L. E.; Driscoll, P. C.; Gronenborn, A. M. J Am Chem Soc 1990, 112, 4989.
36. Akke, M.; Skelton, N. J.; Kordel, J.; Palmer, A. G.; Chazin, W. J. Biochemistry 1993, 32, 9832.
37. Kordel, J.; Skelton, N. J.; Akke, M.; Palmer, A. G.; Chazin, W. J. Biochemistry 1992, 31, 4856.
38. Willis, B. T. M.; Pryor, A.W. Thermal Vibrations in Crystallography; Cambridge University Press Cambridge: Cambridge, 1975.
39. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graph. 1996, 14, 33.
40. Maiti, R.; Van Domselaar, G. H.; Zhang, H.; Wishart, D. S. Nucleic Acids Res 2004, 32, W590.
41. Akke, M.; Drakenberg, T.; Chazin, W. J. Biochemistry 1992, 31, 1011.
42. Nelson, M. R.; Thulin, E.; Fagan, P. A.; Forsen, S.; Chazin, W. J. Protein Sci 2002, 11, 198.
43. Best, R. B.; Hummert, G. J Phys Chem B 2009, 113, 9004.
44. Svensson, L. A.; Thulin, E.; Forsen, S. J Mol Biol 1992, 223, 601.
45. Marchand, S.; Roux, B. Proteins Struct Funct Genet 1998, 33, 265.
46. Koller, A. N.; Schwalbe, H.; Gohlke, H. Biophys J 2008, 95, L4.
47. Chazin, W. J.; Kordel, J.; Drakenberg, T.; Thulin, E.; Brodin, P.; Grundstrom, T.; Forsen, S. Proc Natl Acad Sci USA 1989, 86, 2195.
48. Kordel, J.; Forsen, S.; Drakenberg, T.; Chazin, W. J. Biochemistry 1990, 29, 4400.
49. Akke, M.; Forsen, S.; Chazin, W. J. Magn Reson Chem 1993, 31, S128.
50. Case, D. A. Ace Chem Res 2002, 35, 325.