Modeling protein-induced configurational changes in DNA minicircles

Biopolymers

Volumn 41, Issue 4, 1997, Pages 419-430

  Martino, Jennifer A ^a   Olson, Wilma K ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRON ENERGY LEVELS; MATHEMATICAL MODELS; MOLECULAR ORIENTATION; PROTEINS; RANDOM PROCESSES; SIMULATED ANNEALING;

CONFIGURATIONAL CHANGES; DNA MINICIRCLES; HISTONE OCTAMERS; WRITHING NUMBER;

DNA;

ARTICLE; CHROMATIN; DNA BINDING; DNA DETERMINATION; DNA HELIX; DNA SEQUENCE; MINICHROMOSOME; PROTEIN BINDING; PROTEIN DNA INTERACTION;

DNA, CIRCULAR; DNA-BINDING PROTEINS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; THERMODYNAMICS;

EID: 0031553967     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(19970405)41:4<419::AID-BIP6>3.0.CO;2-P     Document Type: Article

References (62)

1. Widom, J. (1992) Proc. Natl. Acad. Sci. USA 89, 1095-1099.
2. Horowitz, R. A., Agard, D. A., Sedat, J. W. & Woodcock, C. L. (1994) J. Cell. Biol. 125, 1-10.
3. Yang, G., Leuba, S. H., Bustamante, C., Zlatanova, J. & van Holde, K. (1994) Nature Struct. Biol. 1, 761-763.
4. Wolffe, A. P. & Dimitrov, S. (1993) Crit. Rev. Eukary. Gene Expres. 3, 167-191.
5. Meersseman, G., Pennings, S. & Bradbury, E. M. (1992) EMBO J. 11, 2951-2959.
6. Clark, D. J. & Felsenfeld, G. (1992) Cell 71, 11-22.
7. Studitsky, V. M., Clark, D. J. & Felsenfeld, G. (1994) Cell 76, 371-382.
8. Studitsky, V. M., Clark, D. J. & Felsenfeld, G. (1995) Cell 83, 19-27.
9. Polach, K. J. & Widom, J. (1995) J. Mol. Biol. 254, 130-149.
10. Goulet, I., Zivanovic, Y., Prunell, A. & Révet, B. (1988) J. Mol. Biol. 200, 253-266.
11. Yao, J., Lowary, P. T. & Widom, J. (1991) Biochemistry 30, 8408-8414.
12. Zhang, P., Tobias, I. & Olson, W. K. (1994) J. Mol. Biol. 242, 271-290.
13. Olson, W. K., Westcott, T. P., Martino, J. A. & Liu, G.-H. (1996) in Mathematical Approaches to Biomolecular Structure and Dynamics, Mesirov, J. P., Schulten, K. & Sumners, D. W., Eds., Springer-Verlag, New York, pp. 195-218.
14. Thomas, G. H. & Elgin, S. C. R. (1988) EMBO J. 7, 2191-2201.
15. Schild, C., Claret, F.-X., Wahli, W. & Wolffe, A. P. (1993) EMBO J. 12, 423-433.
16. Lee, H.-L. & Archer, T. K. (1994) Mol. Cell. Biol. 14, 32-41.
17. Hao, M.-H. & Olson, W. K. (1989) Biopolymers 28, 873-900.
18. Hao, M.-H. & Olson, W. K. (1989) Macromolecules 22, 3292-3303.
19. Schlick, T. & Olson, W. K. (1992) J. Mol. Biol. 223, 1089-1119.
20. Fenley, M. O., Olson, W. K., Tobias, I. & Manning, G. S. (1994) Biophys. Chem. 50, 255-271.
21. Benham, C. J. (1983) Biopolymers 22, 2477-2495.
22. Le Bret, M. (1984) Biopolymers 23, 1835-1867.
23. Tsuru, H. & Wadati, M. (1986) Biopolymers 25, 2083-2096.
24. Olson, W. K. & Zhang, P. (1991) Methods Enzymol. 203, 403-432.
25. Zhang, P., Olson, W. K. & Tobias, I. (1991) Comp. Polym. Sci. 1, 3-17.
26. Gordon, W. J. & Reisenfeld, R. F. (1974) Computer Aided Geometric Design, Academic Press, New York, chap. 6.
27. Bartells, R. H., Beatty, J. C. & Barsky, B. A. (1987) An Introduction to Splines for Computer Graphics and Geometric Modeling, Morgan Kauffman, Inc., Los Altos, CA, chap. 4.
28. Mortenson, M. E. (1985) Geometric Modeling, John Wiley & Sons, New York, chap. 2.
29. Kirchhoff, G. J. (1859) J. f. Reine. Angew. Math. (Crelle) 56, 285-313.
30. Landau, L. D. & Lifshitz, E. M. (1986) Theory of Elasticity, 3rd ed., Pergamon, Oxford, chap. 2.
31. Fuller, F. B. (1971) Proc. Natl. Acad. Sci. USA 68, 815-819.
32. Benham, C. J. (1977) Proc. Natl. Acad. Sci. USA 74, 2397-2401.
33. Tanaka, F. & Takahashi, H. (1985) J. Chem. Phys. 83, 6017-6026.
34. Fuller, F. B. (1978) Proc. Natl. Acad. Sci. USA 75, 3557-3561.
35. White, J. H. (1969) Am. J. Math. 91, 693-728.
36. Germond, J. E., Hirt, B., Oudet, P., Gross-Bellard, M. & Chambon, P. (1975) Proc. Natl. Acad. Sci. USA 72, 1843-1847.
37. Simpson, R. T., Thoma, F. & Brubaker, J. M. (1985) Cell 42, 799-808.
38. Zivanovic, Y., Goulet, I., Révet, B., Le Bret, M. & Prunell, A. (1988) J. Mol. Biol. 200, 267-290.
39. Eisenberg, H. (1987) Accts. Chem. Res. 20, 276-282.
40. Hagerman, P. J. (1988) Ann. Rev. Biophys. Biophys. Chem. 17, 265-286.
41. Zhurkin, V. B., Lysov, Y. P. & Ivanov, V. (1979) Nucleic Acids Res. 6, 1081-1096.
42. Kabsch, W., Sander, S. & Trifonov, E. N. (1982) Nucleic Acids Res. 10, 1097-1104.
43. Gorin, A. A., Zhurkin, V. B. & Olson, W. K. (1995) J. Mol. Biol. 247, 34-48.
44. Marini, J. C., Effron, P. N., Goodman, T. C., Singleton, C. K., Wells, R. D., Wartell, R. M. & Englund, P. T. (1984) J. Biol. Chem. 259, 8974-8979.
45. Hayes, J. J., Tullius, T. D. & Wolffe, A. P. (1990) Proc. Natl. Acad. Sci. USA 87, 7405-7409.
46. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. & Teller, E. (1953) J. Chem. Phys. 21, 1087-1092.
47. Kirkpatrick, S., Gelatt, C. D. & Vecchi, M. P. (1983) Science 220, 671-680.
48. Richmond, T. J., Finch, J. T., Rushton, B., Rhodes, D. & Klug, A. (1984) Nature 311, 532-537.
49. Le Bret, M. (1988) J. Mol. Biol. 200, 285-290.
50. Klug, A. & Lutter, L. C. (1981) Nucleic Acids Res. 9, 4267-4283.
51. Klug, A. & Travers, A. A. (1989) Cell 56, 10-11.
52. White, J. H. & Bauer, W. R. (1989) Cell 56, 9-10.
53. Klug, A. & Lutter, L. C. (1981) Nucleic Acids Res. 9, 4267-4283.
54. Furrer, P., Bednar, J. & Dubochet, J. (1995) J. Struct. Biol. 114, 177-183.
55. Bednar, J., Horowitz, R. A., Dubochet, J. & Woodcock, C. L. (1995) J. Cell Biol. 131, 1365-1376.
56. Tobias, I., Coleman, B. & Olson, W. K. (1994) J. Chem. Phys. 101, 10990-10996.
57. Crick, F. H. C. (1976) Proc. Natl. Acad. Sci. USA 73, 2639-2643.
58. Strauss, J. K. & Maher, L. J. I. (1994) Science 266, 1829-1834.
59. Buttinelli, M., Leoni, L., Sampaolese, B. & Savino, M. (1991) Nucleic Acids Res. 19, 4543-4549.
60. Hamiche, A. & Prunell, A. (1992) J. Mol. Biol. 228, 327-337.
61. Jackson, S., Brooks, W. & Jackson, V. (1994) Biochemistry 33, 5392-5403.
62. Jeffreys, H. & Jeffreys, B. S. (1946) Methods of Mathematical Physics, Cambridge University Press, Cambridge, chap. 4.