20ns molecular dynamics simulation of the antennapedia homeodomain-dna complex: Water interaction and dna structure analysis

Journal of Biomolecular Structure and Dynamics

Volumn 27, Issue 4, 2010, Pages 443-455

  Roy, Sujata ^a   Thakur, Ashoke Ranjan ^b  

^a MAULANA ABUL KALAM AZAD UNIVERSITY OF TECHNOLOGY   (India)

^b WEST BENGAL STATE UNIVERSITY   (India)

Author keywords

Dynamical characteristics; Inter facial water; Protein DNA complex

Indexed keywords

ANTENNAPEDIA PROTEIN; WATER;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA DETERMINATION; DNA PROTEIN COMPLEX; DNA SEQUENCE; DNA STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN SECONDARY STRUCTURE; SIMULATION;

EUKARYOTA;

EID: 75149145555     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2010.10507329     Document Type: Article

References (41)

1. Banerjee-Basu, S., and Baxevanis, A. D., 2001. Nucleic Acids Research, 29:3258–3269.
2. Kim, B. M., Miletich, I., Mao, J., McMahon, A. P., Sharpe, P. A., and Shivdasani, R. A., 2007. Development, 34:3603–3613.
3. Pabo, C. O., and Sauer, R. T., 1992. Annual Review of Biochemistry, 61:1053–1095.
4. Gehring, W. J., Qian, Y. Q., Billeter, M., Furukubo-Tokunaga, K., Schier, A. F., Resendez-Perez, D., Affolter, M., Otting, G., and Wüthrich, K., 1994. Cell, 78:211–223.
5. Schott, J. J., Benson, D. W., Basson, C. T., Pease, W., and et al. 1998. al. Science, 281:108–111.
6. Kornberg, T. B., 1993. J Biol chem, 268:26813–26816.
7. Shi, X., Yang, X., Che, D., Chan, Z., and Cao, X., 1999. J Biol chem, 274:13711–13717.
8. Yang, X., Ji, X., Shi, X., and Cao, X., 2000. J Biol chem, 275:1065–1072.
9. Roy, S., and Sen, S. J., 2005. Biomol Struct Dyn, 22:707–718.
10. Schier, A. F., and Gehring, W. J., 1992. Nature, 356:804–807.
11. Qian, Y. U., Otting, G., Billeter, M., Müller, M., Gehring, W., and Wüthrich, K., 1993. J Mol Biol, 234:1070–1083.
12. Fraenkel, E., and Pabo, C. O., 1998. Nat Struct Biol, 5:692–697.
13. Billeter, M., Guntert, P., Luginbuhl, P., and Wuthrich, K., 1996. cell, 85:1057–1065.
14. Drenth, J., 1994. Principles of Protein X-ray crystallography Springer:New York.
15. Wuthrich, K., 1986. NMR of Proteins and Nucleic Acids New York:Wiley.
16. Wuthrich, K., 1995. NMR in Structural Biology Singapore:World Scientific.
17. Janin, Joël. 1999. Structure, 7:277–279.
18. Woda, J., Schneider, B., Patel, K., Mistry, K., and Berman, H. M., 1998. Biophys J, 75:2170–2177.
19. Schwabe, W. R. J., 1997. current Opinion in Structural Biology, 7:126–134.
20. Kosztin, D., Bishop, T. C., and Schulten, K., 1997. Biophysical J, 73:557–570.
21. Joachimiak, A., Haran, T. E., and Sigler, P. B., 1994. EMBO Journal, 13:367–372.
22. Reddy, C. K., Das, A., and Jayaram, B., 2001. J Mol Biol, 314:619–632.
23. Jayaram, B., and Jain, T., 2004. Annual Rev of Biophys and Biomol Struc, 33:343–361.
24. Gindilis, V., Goltsman, E., and Verlinsky, Y., 1998. J of Assisted Reproduction and Genetics, 15:349–357.
25. Brooks, C. L., III and Karplus, M., 1983. J Chem Phys, 79:6312–6325.
26. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M., 1983. J chem Phys, 7:926–935.
27. Daren, T. A., York, D. M., and Pedersen, L. G., 1993. J Chem Phys, 98:10089–10092.
28. Essman, U., Perela, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G., 1995. J Chem Phys, 103:8577–8593.
29. Steinbach, P. J., and Brooks, B. R., 1994. J Comp Chem, 15:667–683.
30. Auffinger, P., and Beveridge, D. L., 1995. Chem Phys Lett, 234:413
31. Cheatham, T. E., Miller, J. L., Fox, T., Darden, T., and Kollman, P. E., 1995. J Am Chem Soc, 117:4193–4194.
32. Norberg, J., and Nilsson, L., 2000. Biophys J, 79:1537–1553.
33. Hockney, R. W., 1970. Comp Phys, 9:135–211.
34. Foloppe, N., and Mackerell, A. D., Jr. 2000. J Comp Chem, 56:86–104.
35. Van Gunsteren, W. F., and Berendsen, H. J. C., 1977. Mol Phys, 34:1311–1327.
36. Ryckaert, J. P., Ciccotti, G. H., and Berendsen, H. J. C., 1997. J 35. Comput Phys, 23:327–341.
37. Duan, J., and Nilsson, L., 2002. Eur Biophys J, 31:306–316.
38. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., Lavery, R., Nelson, H. C. M., Olson, W. A., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C.-S., and et al. 1989. J Mol Biol, 205:787–791.
39. Olson and et al. 2001. J Mol Biol, 313:229–237.
40. Gutmanas, A., and Billeter, M., 2004. Proteins, 57:772
41. Olson, W. K., Gorin, A. A., Lu, X. J., Hock, L. M., and Zhurkin, V. B., 1998. Proc Natl Acad Sci USA, 95:11163–11168.