Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories

Journal of Chemical Physics

Volumn 122, Issue 3, 2005, Pages

  Pan, Patricia Wang ^a,b   Dickson, Russell J ^a,b   Gordon, Heather L ^a,b   Rothstein, Stuart M ^a,b   Tanaka, Shigenori ^b  

^a BROCK UNIVERSITY   (Canada)

^b KOBE UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL CLUSTERING; MOLECULAR DYNAMICS TRAJECTORIES; STRUCTURAL FLUCTUATIONS;

COMPUTER SIMULATION; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; SOLVENTS; TRAJECTORIES; VECTORS;

PROTEINS;

BACTERIAL PROTEIN; SOLVENT; SPO0F PROTEIN, BACILLUS SUBTILIS;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; MOLECULAR GENETICS; MOTION; PROTEIN TERTIARY STRUCTURE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOTION; PROTEIN STRUCTURE, TERTIARY; SOLVENTS;

EID: 34548098038     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1830434     Document Type: Article

References (37)

1. A. Kitao and N. Go, Curr. Opin. Struct. Biol. 9, 164 (1999).
2. M. L. Teodoro and L. E. Kavraki, Curr. Pharm. Design 9, 1635 (2003).
3. M. L. Teodoro, G. N. Phillips, Jr., and K. E. Kavraki, J. Comput. Biol. 10, 617 (2003).
4. A. Kitao, S. Hayward, and N. Go, Proteins: Struct., Funct., Genet. 33, 496 (1998).
5. A. Amadei, A. B. B. Linssen, B. L. de Groot, D. M. F. van Aalten, and H. J. C. Berendsen, J. Biomol. Struct. Dyn. 13, 615 (1996).
6. N. Elmaci and R. S. Berry, J. Chem. Phys. 110, 10606 (1999).
7. S. A. Larrass, L. M. Pegram, H. L. Gordon, and S. M. Rothstein, J. Chem. Phys. 119, 13149 (2003).
8. J. M. Troyer and F. E. Cohen, Proteins: Struct., Funct., Genet. 23, 97 (1995).
9. R. J. Rummel, Applied Factor Analysis (Northwestern University, Evanston, 1970).
10. H. H. Harman, Modern Factor Analysis, 3rd ed. (University of Chicago, Chicago, 1976).
11. D. Eisenberg and A. McLachlan, Nature (London) 319, 199 (1986).
12. V. A. Feher and J. Cavanagh, Nature (London) 400, 289 (1999).
13. M. Karplus and J. N. Kushick, Macromolecules 14, 325 (1981).
14. R. M. Levy, M. Karplus, J. Kushick, and D. Perahia, Macromolecules 17, 1370 (1984).
15. R. M. Levy, A. R. Srinivasan, W. K. Olson, and J. A. McCammon, Biopolymers 23, 1099 (1984).
16. A. Kitao, F. Hirata, and N. Go, Chem. Phys. 158, 447 (1991).
17. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins 17, 412 (1993).
18. A. E. Garcia and J. G. Harman, Protein Sci. 5, 62 (1996).
19. S. Hayward and N. Go, Annu. Rev. Phys. Chem. 46, 223 (1995).
20. G. Moraitakis, A. G. Purkiss, and J. M. Goodfellow, Rep. Prog. Phys. 66, 383 (2003).
21. L. L. Thurstone, Multiple-factor Analysis: A Development and Expansion of the Vectors of the Mind (University of Chicago, Chicago, 1965).
22. M. M. Tatsuoka, Multivariate Analysis; Techniques for Educational and Psychological Research (Macmillan, New York, 1988).
23. A. C. Rencher, Methods of Multivariate Analysis (Wiley, New York, 1995).
24. R. A. Johnson and D. W. Wichern, Applied Multivariate Statistical Analysis (Prentice Hall, Upper Saddle River, NJ, 2002).
25. M. Snajdr, J. R. Dwyer, and S. M. Rothstein, J. Chem. Phys. 111, 9971 (1999).
26. V. A. Feher, J. W. Zapf, J. A. Hoch et al., Biochemistry 36, 10015 (1997).
27. Y.-L. Tzeng and J. A. Hoch, J. Mol. Biol. 272, 200 (1997).
28. H. Frauenfelder, F. Parak, and R. D. Young, Annu. Rev. Biophys. Biophys. Chem. 17, 451 (1988).
29. W. D. Cornell, P. Cieplak, C. I. Bayly et al., J. Am. Chem. Soc. 117, 5179 (1995).
30. P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot, and A. Pohorille, in Computer Simulation of Biomolecular Systems, edited by W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson (Kluwer Academic, Netherlands, 1997), Vol. 3, pp. 83-96.
31. J. W. Ponder, TINKER: Software Tools for Molecular Design, Version 4.2 (Washington University School of Medicine, St. Louis, 2004).
32. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Di Nola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
33. S. Toyoda, H. Miyagawa, K. Kitamura, T. Amisaki, E. Hashimoto, H. Ikeda, A. Kusumi, and N. Miyakawa, J. Comput. Chem. 20, 185 (1999).
34. T. Amisaki, S. Toyoda, H. Miyagawa, and K. Kitamura, J. Comput. Chem., Japan 1, 73 (2002).
35. T. Ichiye and M. Karplus, Proteins 11, 205 (1991).
36. P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991).
37. R. A. Laskowski, M. W. MacArthur, D. S. Moss, and J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1993).