Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects

Journal of Chemical Physics

Volumn 123, Issue 14, 2005, Pages

  Alakent, Burak ^a,b   Camurdan, Mehmet C ^a   Doruker, Pemra ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

^b YEDITEPE UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY LANDSCAPES; FRICTION COEFFICIENTS; HIERARCHICAL STRUCTURES; MODEL PARAMETERS;

COMPUTER SIMULATION; DATA REDUCTION; FRICTION; MOLECULAR DYNAMICS; NATURAL FREQUENCIES; PRINCIPAL COMPONENT ANALYSIS; TIME SERIES ANALYSIS;

PROTEINS;

AMYLASE; PEPTIDE; SOLVENT; TENDAMISTATE;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; DRUG ANTAGONISM; PROTEIN TERTIARY STRUCTURE; THEORETICAL MODEL;

ALPHA-AMYLASE; COMPUTER SIMULATION; MODELS, THEORETICAL; PEPTIDES; PROTEIN STRUCTURE, TERTIARY; SOLVENTS;

EID: 26944473403     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2042408     Document Type: Article

References (34)

1. M. Sundaralingam and Y. C. Sekharudu, Science 244, 1333 (1989).
2. J. Wu and D. G. Gorentein, J. Am. Chem. Soc. 115, 6843 (1993).
3. L. D. Barron, L. Hecht, and G. Wilson, Biochemistry 36, 13143 (1997).
4. F. Xu and T. A. Cross, Proc. Natl. Acad. Sci. U.S.A. 96, 9057 (1999).
5. A. Kitao, F. Hirata, and N. Go, Chem. Phys. 158, 447 (1991).
6. S. Hayward, A. Kitao, and N. Go, J. Mol. Biol. 234, 1207 (1993).
7. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins 17, 412 (1999).
8. D. M. F. van Aalten, A. Amadei, A. B. M. Linssen, V. G. H. Eijsink, G. Vriend, and H. J. C. Berendsen, Proteins 22, 45 (1995).
9. G. Lamm and A. Szabo, J. Chem. Phys. 85, 7334 (1986).
10. S. Swaminathan, T. Ichiye, W. van Gunsteren, and M. Karplus, Biochemistry 21, 5230 (1982).
11. W. Nadler, A. T. Brünger, K. Schulten, and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 84, 7933 (1987).
12. Y. Levy, J. Jortner, and O. M. Becker, Proc. Natl. Acad. Sci. U.S.A. 98, 2188 (2001).
13. B. Alakent, P. Doruker, and M. C. Camurdan, J. Chem. Phys. 120, 1072 (2004).
14. B. Alakent, P. Doruker, and M. C. Camurdan, J. Chem. Phys. 121, 4759 (2004).
15. B. Alakent, M. C. Camurdan, and P. Doruker, J. Chem. Phys. 123, 144910 (2005) (preceding paper).
16. Accelrys Inc. San Diego, CA, USA (INSIGHT II 98.0, DISCOVER III Module version 97.0/4.0.0).
17. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, Nucleic Acids Res. 28, 235 (2000).
18. J. W. Pflugrath, G. Wiegand, R. Huber, and L. Vertesy, J. Mol. Biol. 189, 383 (1986).
19. H. J. C. Berendsen, J. P. M. Postma, W. F. Van Gunsteren, and J. Hermans, in Intermolecular Forces, edited by, B. Pullman, (Reidel, Holland, 1981), pp. 331-342.
20. J. R. Maple, U. Dinur, and A. T. Hagler, Proc. Natl. Acad. Sci. U.S.A. 85, 5350 (1998).
21. H. J. C. Berendsen, J. P. M. Postma, W. M. van Gunsterena, A. Di Nola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
22. J. E. Jackson, J. Quality Technol. 12, 201 (1980).
23. G. E. P. Box and G. M. Jenkins, Time Series Analysis: Forecasting and Control, 1st ed. (Holden-Day, San Francisco, 1970), Vol. 1, Ch., pp. 9-108.
24. M. Billeter, T. Schaumann, W. Braun, and K. Wütrich, Biopolymers 29, 695 (1990).
25. M. Levitt and R. Sharon, Proc. Natl. Acad. Sci. U.S.A. 85, 7557 (1988).
26. S. Umeyama, IEEE Trans. Pattern Anal. Mach. Intell. 13, 376 (1991).
27. A. Amadei, B. L. de Groot, M.-A. Ceruso, M. Paci, A. Di Nola, and H. J. C. Berendsen, Proteins 35, 283 (1999).
28. D. Ben-Avraham, Phys. Rev. B 47, 559 (1993).
29. N. Go, T. Noguti, and T. Nishikawa, Proc. Natl. Acad. Sci. U.S.A. 80, 3696 (1983).
30. B. Brooks and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 80, 6571 (1983).
31. K. Hinsen and G. R. Kneller, J. Chem. Phys. 111, 10766 (1999).
32. M. A. Balsera, W. Wriggers, Y. Oono, and K. Schulten, J. Phys. Chem. 100, 2567 (1996).
33. B. Hess, Phys. Rev. E 62, 8438 (2000).
34. B. Hess, Phys. Rev. E 65, 031910 (2002).