Calculation and analysis of low frequency normal modes for DNA

Journal of Computational Chemistry

Volumn 18, Issue 6, 1997, Pages 796-811

  Duong, Tap Ha ^a   Zakrzewska, Krystyna ^a  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

DNA; DNA bending; Flexibility; Modeling; Normal mode

Indexed keywords

EID: 0000213488     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19970430)18:6<796::AID-JCC5>3.0.CO;2-N     Document Type: Article

References (43)

1. G. Weber, Adv. Prot. Chem., 29, 1 (1975).
2. P. G. Debrunner and H. Frauenfelder, Annu. Rev. Phys. Chem., 33, 283 (1982).
3. J. A. McCammon, Rep. Prog. Phys., 47, 1 (1984).
4. R. G. Brown, S. C. Erfurth, E. W. Small, and W. L. Peticolas, Proc. Natl. Acad. Sci. USA, 69, 1467 (1972).
5. W. L. Peticolas, Meth. Enzymol., 61, 425 (1979).
6. H. D. Bartunik, P. Jolles, J. Berthou, and A. J. Dianoux, Biopolymers, 21, 43 (1982).
7. J. C. Smith, Quart. Rev. Biophys., 24, 227 (1991).
8. D. Perahia and L. Mouawad, Comput. Chem., 19, 241 (1995).
9. P. Durand, G. Trinquier, and Y. H. Sanejouand, Biopolymers, 34, 759 (1994).
10. S. Sunada and N. Go, J. Comput. Chem., 11, 328 (1995).
11. A. Kitao and N. Go, J. Comput. Chem., 12, 359 (1991).
12. A. Kitao, S. Hayward, and N. Go, Biophys. Chem., 52, 107 (1994).
13. R. Lavery and H. Sklenar, J. Biomol. Struct. Dynam., 6, 655 (1989).
14. H. Goldstein, Classical Mechanics, Addison-Wesley, Reading, MA, 1950.
15. R. Lavery, I. Parker, and J. Kendrick, J. Biomol. Struct. Dynam., 4, 443 (1986).
16. R. Lavery, H. Sklenar, K. Zakrzewska, and B. Pullman, J. Biomol. Struct. Dynam., 3, 989 (1986).
17. R. Lavery, Structure and expression, Vol. 3: DNA Bending and Curvature, W. K. Olson, R. H. Sarma, M. H. Sarma, and M. Sundaralingam, Eds., Adenine Press, New York, 1988, p. 191.
18. R. Lavery, K. Zakrzewska, and H. Sklenar, Comput. Phys. Commun., 91, 135 (1995).
19. T. Noguti and N. Go, J. Phys. Soc. Jpn., 52, 3283 (1983).
20. C. Eckart, Phys. Rev., 47, 552 (1935).
21. M. Levitt, C. Sander, and P. S. Stern, J. Mol. Biol., 181, 423 (1985).
22. R. Lavery and B. Hartman, Biophys. Chem., 60, 33 (1994).
23. H. Gabb, R. Lavery, and C. Prevost, J. Comput. Chem., 16, 667 (1995).
24. S. T. Rao, E. Westhof, and M. Sundaralingam, Acta Cryst., 37, 421 (1981).
25. G. G. Privé, U. Heinemann, S. Chadrasekharan, L. S. Kan, M. L. Kopka, and R. E. Dickerson, Science, 238, 498 (1987).
26. A. D. DiGabriele, M. R. Sanderson, and T. A. Steitz, Proc. Natl. Acad. Sci. USA, 16, 1816 (1989).
27. V. B. Zhurkin, Y. P. Lysov, and V. I. Ivanov, Nucl. Acids Res., 6, 1081 (1979).
28. W. K. Olson, A. R. Srinivasan, R. C. Maroun, R. Torres, and W. Clark, Unusual DNA Structures, R. D. Wells, and S. C. Harvey, Eds., Springer, New York, 1989, p. 207.
29. M. Suzuki and N. Yagi, Nucl. Acids Res., 23, 2083 (1995).
30. S. R. Sanghani, K. Zakrzewska, S. C. Harvey, and R. Lavery, Nucl. Acids Res. (in press).
31. A. E. Garcia, Computation of Biomolecular Structures, D. M. Soumpasis and T. M. Jovin, Eds., Springer, New York, 1992, p. 165.
32. T. M. Jovin, D. M. Soumpasis, and L. P. McIntosh, Annu. Rev. Phys. Chem., 38, 521 (1987).
33. W. L. Peticolas, Biopolymers, 18, 747 (1979).
34. T. Weidlich, S. M. Linsay, Q. Rui, A. Rupprecht, W. L. Peticolas, and G. A. Thomas, J. Biomol. Struct. Dynam., 8, 139 (1990).
35. S. Nuutero, B. S. Fujimoto, P. F. Flynn, B. R. Reid, and J. M. Schurr, Biopolymers, 34, 463 (1994).
36. T. M. Alam, J. Orban, and G. P. Drobny, Biochemistry, 30, 9229 (1991).
37. J. H. Shibata, B. S. Fujimoto, and J. M. Schurr, Biopolymers, 24, 1909 (1985).
38. A. Kintanar, W. C. Huang, D. C. Schindele, D. E. Wemmer, and G. Drobny, Biochemistry, 28, 282 (1989).
39. P. Wu, B. S. Fujimoto, and J. M. Schurr, Biopolymers, 26, 1463 (1987).
40. B. Tidor, K. K. Irikura, B. P. Brooks, and M. Karplus, J. Biomol. Struct. Dynam., 1, 231 (1983).
41. A. E. Garcia and D. M. Soumpasis, Proc. Natl. Acad. Sci. USA, 86, 3160 (1972).
42. J. Kottalam and D. A. Case, Biopolymers, 29, 1409 (1990).
43. T. Noguti and N. Go, Nature, 296, 776 (1982).