Molecular dynamics simulation in solvent of the estrogen receptor protein dna binding domain in complex with a non-consensus estrogen response element dna sequence

Journal of Biomolecular Structure and Dynamics

Volumn 15, Issue 3, 1997, Pages 407-430

  Harris, Lester F ^a   Sullivan, Michael R ^a   Popken Harris, Pamela D ^a  

^a ABBOTT NORTHWESTERN HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; ESTROGEN RECEPTOR; SIGNAL PEPTIDE;

ALPHA HELIX; ARTICLE; BASE PAIRING; CARBOXY TERMINAL SEQUENCE; COMPUTER MODEL; DNA BINDING; DNA PROTEIN COMPLEX; DNA SEQUENCE; EXON; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA BINDING; X RAY CRYSTALLOGRAPHY; XENOPUS LAEVIS;

XENOPUS LAEVIS;

EID: 0031443464     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1997.10508956     Document Type: Article

References (61)

1. Evans, R., 1988. Science, 240:889–895.
2. Encio, I., and Detera-Wadleigh, S., 1990. J. Biol. Chem., 266:7182–7188.
3. Freedman, L. P., Luisi, B. F., Korszun, Z. R., Basavappa, R., Sigler, P. B., and Yamamoto, K., 1988. Nature (London), 334:543–546.
4. Harris, L., Sullivan, M., and Hickok, D., 1990. Computers and Mathematics with Applications, 20:25–48.
5. Yamamoto, K., 1985. A. Rev. Genet., 19:209–252.
6. Mader, S., Chambon, P., and White, J., 1993. Nucleic Acids Research, 21:1125–1132.
7. Klock, G., Strahle, U., and Schultz, G., 1988. Nature, 329:734–736.
8. Walker, P., Germond, J-E., Brown-Luedi, M., Givel, F., and Wahli, W., 1984. Nucleic Acids Res, 12:8611–8626.
9. Anolik, J., Klinge, C., Bambara, R., and Hilf, R., 1993. J. Steroid Biochem. Molec. Biol., 46:713–730.
10. Schwabe, J., Neuhaus, D., and Rhodes, D., 1990. Nature (London), 348:458–461.
11. Schwabe, J., Chapman, L., Finch, J., Rhodes, D., and Neuhaus, D., 1993. Structure, 1:187–204.
12. Schwabe, J., Chapman, L., Finch, J., and Rhodes, D., 1993. Cell, 75:567–578.
13. Schwabe, J., Chapman, L., and Rhodes, D., 1995. Structure, 3:201–213.
14. Klein-Hitpass, L., Schorpp, M., Wagner, U., and Ryffel, G., 1986. Cell, 46:1053–1061.
15. Mauer, R., and Notides, A., 1987. Molec. Cell. Biol, 7:4247–4254.
16. Harris, L., Sullivan, M., and Hickok, D., 1990. Computers and Mathematics with Applications, 20:1–23.
17. Harris, L., Sullivan, M., and Hickok, D., 1993. Proc. Natl. Acad. Sci. USA, 90:5534–5538.
18. Harris, L., Sullivan, M., Popken-Harris, P., and Hickok, D., 1994. J. Biomol. Struct, and Dyn., 12:249–270.
19. Harris, L., Sullivan, M., Popken-Harris, P., and Hickok, D., 1995. J. Biomol. Struct, and Dyn., 13:423–440.
20. Harris, L., Sullivan, M., Popken-Harris, P., and Hickok, D., 1996. Univ. of Minn. Supercomputer Research Report(UMSI 96/100)
21. Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M., 1983. J. Comput. Chem., 4:187–217.
22. Karplus, M., and Petsko, G., 1990. Nature, 347:631–639.
23. Lavery, R., and Sklenar, H., 1988. J. Biomol. Struct. Dyn., 6:63–91.
24. Stofer, E., and Lavery, R., 1994. Biopolymers, 34:337–346.
25. Baker, E., and Hubbard, R., 1984. Prog. Biophys. Mol. Biol., 44:97–179.
26. Mader, S., Kumar, V., deVerneuil, H., and Chambon, R., 1989. Nature, 338:271–274.
27. Schultz, S., Shields, G., and Steitz, T., 1991. Science, 253:1001–1007.
28. Leidig, F., Baxter, J., and Eberhardt, N., 1990. Transactions of the Association of American Physicians, 103:154–162.
29. Nardulli, A., and Shapiro, D., 1992. Mol. Cell. Biol., 12:2037–2042.
30. Martinez, E., and Wahli. 1989. EMBO J, 8:3781–3791.
31. Kumar, V., and Chambon, P., 1988. Cell, 55:145–156.
32. Koszewski, N., and Notides, A., 1991. Molec. Endocr., 5:1129–1136.
33. Harris, L., Sullivan, M., Popken-Harris, P., and Hickok, D., 1996. The World Wide Web Journal of Biology (http://epress.com/w3jbio)
34. Harris, L., Sullivan, M., and Hickok, D., 1993. Univ. of Minn. Supercomputer Research Report UMSI 93/74
35. Scheidereit, C., Geisse, S., Westphal, H., and Beato, M., 1983. Nature, 304:749–752.
36. Payvar, F., DeFranco, D., Firestone, G., Edgar, B., Wrange, O., Okret, S., Gustafsson, J., and Yamamoto, K., 1983. Cell, 35:381–392.
37. Scheidereit, C., and Beato, M., 1984. Proc. Natl Acad. Sci. USA, 81:3029–3034.
38. Buetti, E., and Kuhnel, B., 1986. J. Mol. Biol., 190:379–389.
39. Hollenberg, S., and Evans, R., 1988. Cell, 55:899–906.
40. Chalepakis, G., Postma, J., and Beato, M., 1988. Nucleic Acids Res., 16:10237–10247.
41. Bishop, T., and Schulten, K., 1996. Proteins, 24:115–133.
42. Petz, L., Nardulli, A., Jongsook, K., Horwitz, K., Freedman, L., and Shapiro, D., 1997. J. Steroid Biochem. Molec. Biol., 60:1–2. 31–41
43. Prendergast, P., Pan, Z., and Edwards, D., 1996. Molecular Endocrinology, 10:4–407. 393
44. Harris, L., Sullivan, M., and Hickok, D., 1989. Univ. of Minn. Supercomputer Research Report UMSI 89/168
45. Luisi, B., Xu, W., Otwinowski, Z., Freedman, L., Yamamoto, K., and Sigler, P., 1991. Nature, 352:497–502.
46. Harris, L., Sullivan, M., Popken-Harris, P., and Hickok, D., 1996. Biol. Struct, and Dyn., Proc. of the Ninth Corv.,:61–82.
47. Woese, C., 1969. J. Mol. Biol., 43:235–240.
48. Woese, C., 1968. Proc. Natl. Acad. Sci. USA, 59:110–117.
49. Hendry, L., Bransome, E., Jr, Hutson, M., and Campbell, L., 1984. Perspect. Biol. Med., 27:623–651.
50. Hendry, L., Mahesh, V., Bransome, E., Jr, Hutson, M., and Campbell, L., 1995. The World Wide Web Journal of Biology (http://epress.com/w3jbio)
51. Lacey, J., and Mullins, D., Jr. 1983. Origins of Life, 13:3–42.
52. Lacey, J., and Mullins, D., Jr. 1984. Origins of Life, 14:505–511.
53. Lacey, J., Wickramasinghe, N., and Cook, G., 1992. Origins of Life, 22:243–275.
54. Yarus, M., and Christian, E., 1989. Nature, 342:349–350.
55. Yarus, M., 1991. New Biologist, 3:183–189.
56. Nelsestuen, G., 1978. J. Mol Evol., 11:19–120.
57. Nelsestuen, G., 1979. Biochemistry, 18:2843–2846.
58. Smith, T., and Waterman, M., 1981. J. Mol. Biol., 147:195–197.
59. Dayhoff, M., 1978. Atlas of protein sequence and structure. Silver Spring, MD:National Biomedical Research Foundation.
60. Kumar, V., Green, S., Stack, G., Berry, M., Jin, J.-R., and Chambon, P., 1987. Cell, 51:941–951.
61. Quanta is a molecular modeling and display tool developed by Molecular Simulations Inc., (200 Fifth Avenue, Waltham, Massachusetts 02254) which allows the construction of molecular models of DNA sequences, point mutations of existing models, and the modeling of small peptides with a selected secondary structure