Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 19, 2005, Pages 6783-6788

  Villa, Elizabeth ^a   Balaeff, Alexander ^a   Schulten, Klaus ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

DNA loop; Elastic rod model; Large scale protein motion; Molecular dynamics; Protein DNA interaction

Indexed keywords

LAC REPRESSOR PROTEIN; REPRESSOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; DNA BINDING; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DNA INTERACTION; PROTEIN STABILITY; SIMULATION;

COMPUTER SIMULATION; DATABASES, PROTEIN; DNA; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MODELS, STATISTICAL; NORMAL DISTRIBUTION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPRESSOR PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS; TIME FACTORS;

EID: 18744391399     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0409387102     Document Type: Article

References (32)

1. Berg, J. M., Tymoczko, J. L. & Stryer, L. (2002) Biochemistry (Freeman, New York), 5th Ed.
2. Matthews, K. S. (1992) Microbiol. Rev. 56, 123-136.
3. Schleif, R. (1992) Annu. Rev. Biochem. 61, 199-223.
4. Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A., Brennan, R. G. & Lu, P. (1996) Science 271, 1247-1254.
5. Oehler, S., Eismann, E. R., Krämer, H. & Müller-Hill, B. (1990) EMBO J. 9, 973-979.
6. Friedman, A. M., Fischmann, T. O. & Steitz, T. A. (1995) Science 268, 1721-1727.
7. Bell, C. E. & Lewis, M. (2000) Nat. Struct. Biol. 7, 209-214.
8. Edelman, L. M., Cheong, R. & Kahn, J. D. (2003) Biophys. J. 84, 1131-1145.
9. Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J. M. & Gaub, H. E. (1997) Science 276, 1109-1112.
10. Villa, E., Balaeff, A., Mahadevan, L. & Schulten, K. (2004) Multiscale Model Simul. 2, 527-553.
11. Phillips, R., Dittrich, M. & Schulten, K. (2002) Annu. Rev. Mater. Res. 32, 219-233.
12. Ayton, G., Bardenhagen, S., McMurtry, P., Sulsky, D. & Voth, G. (2001) J. Chem. Phys. 114, 6913-6924.
13. Schlick, T. (1995) Curr. Opin. Struct. Biol. 5, 245-262.
14. Olson, W. K. (1996) Curr. Opin. Struct. Biol. 6, 242-256.
15. Balaeff, A., Mahadevan, L. & Schulten, K. (1999) Phys. Rev. Lett. 83, 4900-4903.
16. Balaeff, A., Mahadevan, L. & Schulten, K. (2004) Structure (London) 12, 123-132.
17. Spronk, C. A. E. M., Bovin, A. M. J. J., Radha, P. K., Melacini, G., Boelens. R. & Kaptein, R. (1999) Struct. Folding Des. 7, 1483-1492.
18. Humphrey, W., Dalke, A. & Schulten, K. (1996) J. Mol. Graphics 14, 33-38.
19. Honig, B. & Nicholls, A. (1995) Science 268, 1144-1149.
20. Kalé, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K. & Schulten, K. (1999) J. Comp. Phys. 151, 283-312.
21. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evanseck, J., Field, M. J., Fischer, S., Gao, J., Quo, H., Ha, D., et al. (1998) J. Phys. Chem. B 102, 3586-3616.
22. Martyna, G., Tobias, D. J. & Klein, M. L. (1994) J. Chem. Phys. 101, 4177-4189.
23. Deserno, M. & Holm, C. (1998) J. Chem. Phys. 109, 7678-7693.
24. Balaeff, A., Koudella, C. R., Mahadevan, L. & Schulten, K. (2004) Philos. Trans. R. Soc. London A 362, 1355-1371.
25. Hagerman, P. J. (1988) Annu. Rev. Biophys. Biophys. Chem. 17, 265-286.
26. Strick, T. R., Allemand, J.-F., Bensimon, D., Bensimon, A. & Croquette, V. (1996) Science 271, 1835-1837.
27. Isralewitz, B., Gao, M. & Schulten, K. (2001) Curr. Opin. Struct. Biol. 11, 224-230.
28. Karplus, M. & Petsko, G. A. (1990) Nature 347, 631-639.
29. Snow, C. D., Nguyen, H., Pande, V. S. & Gruebele, M. (2002) Nature 420, 102-106.
30. Dominy, B. N. & Brooks, C. L., III (2001) J. Comp. Chem. 23, 147-160.
31. Howard, J. (2001) Mechanics of Motor Proteins and the Cytoskeleton (Sinauer. Sutherland, MA).
32. Gao, M., Craig, D., Vogel, V. & Schulten, K. (2002) J. Mol. Biol. 323, 939-950.