Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase

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

Volumn 100, Issue 1, 2003, Pages 68-73

  Huang, Niu ^a   Banavali, Nilesh K ^a   MacKerell Jr , Alexander D ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE 5 METHYLTRANSFERASE; DNA; METHYLTRANSFERASE; PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; DNA METHYLATION; DNA STRUCTURE; ENERGY; ENERGY TRANSFER; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 0037422594     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0135427100     Document Type: Article

References (44)

1. Nakao, M. (2001) Gene 278, 25-31.
2. Roberts, R. J. & Halford, S. S. (1993) in Nucleases, eds. Linn, S. M., Lloyd, R. S. & Roberts, R. J. (Cold Spring Harbor Lab. Press, Plainview, NY).
3. Plass, C. & Soloway, P. D. (2002) Eur. J. Hum. Genet. 10, 6-16.
4. Goodman, J. I. & Watson, R. E. (2002) Annu. Rev. Pharmacol. Toxicol.
5. Esteller, M. & Herman, J. G. (2002) J. Pathol. 196, 1-7.
6. Roberts, R. J. (1995) Cell 82, 9-12.
7. Roberts, R. J. & Cheng, X. (1998) Annu. Rev. Biochem. 67, 181-198.
8. Cheng, X. & Roberts, R. J. (2001) Nucleic Acids Res. 29, 3784-3795.
9. Patel, P. H., Suzuki, M., Adman, E., Shinkai, A. & Loeb, L. A. (2001) J. Mol. Biol. 308, 823-837.
10. Schneider, T. D. (2001) Nucleic Acids Res. 29, 4881-4891.
11. Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. (1994) Cell 76, 357-369.
12. Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E. & Tainer, J. A. (1996) Nature 384, 87-92.
13. Stivers, J. T., Pankiewiez, K. W. & Watanabe, K. A. (1999) Biochemistry 38, 952-963.
14. Banavali, N. K. & MacKerell, A. D., Jr. (2002) J. Mol. Biol. 319, 141-160.
15. Varnai, P. & Lavery, R. (2002) J. Am. Chem. Soc. 124, 7272-7273.
16. Klimasauskas, S., Szyperski, T., Serva, S. & Wuthrich, K. (1998) EMBO J. 17, 317-324.
17. Wu, J. C. & Santi, D. V. (1987) J. Biol. Chem. 262, 4778-4786.
18. Lindstrom, W. M., Jr., Flynn, J. & Reich, N. O. (2000) J. Biol. Chem. 275, 4912-4919.
19. Vilkaitis, G., Merkiene, E., Serva, S., Weinhold, E. & Klimasauskas, S. (2001) J. Biol. Chem. 276, 20924-20934.
20. Karplus, M. & Petsko, G. A. (1990) Nature 347, 631-639.
21. Boczko, E. M. & Brooks, C. L., III (1995) Science 269, 393-396.
22. Berneche, S. & Roux, B. (2001) Nature 414, 73-77.
23. McQuarrie, D. A. (1976) Statistical Mechanics (Harper & Row, New York).
24. McCammon, J. A. & Karplus, M. (1979) Proc. Natl. Acad. Sci. USA 76, 3585-3589.
25. Sheikhnejad, G., Brank, A., Christman, J. K., Goddard, A., Alvarez, E., Ford, H., Jr., Marquez, V. E., Marasco, C. J., Sufrin, J. R., O'Gara, M. & Cheng, X. (1999) J. Mol. Biol. 285, 2021-2034.
26. Humphrey, W., Dalke, A. & Schulten, K. (1996) J. Mol. Graphics 14, 33-38.
27. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) J. Comput. Chem. 4, 187-217.
28. MacKerell, A. D., Jr., Brooks, B., Brooks, C. L., III, Nilsson, L., Roux, B., Won, Y. & Karplus, M. (1998) in Encyclopedia of Computational Chemistry, eds. Schleyer, P. v. R., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer, H. F., III, & Schreiner, P. R. (Wiley, New York), Vol. 1, pp. 271-277.
29. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evanseck, J., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) J. Phys. Chem. 102, B3586-B3616.
30. Foloppe, N. & MacKerell, A. D., Jr. (2000) J. Comput. Chem. 21, 86-104.
31. MacKerell, A. D., Jr., & Banavali, N. (2000) J. Comput. Chem. 21, 105-120.
32. Jorgensen, W. L. (1983) J. Phys. Chem. 87, 5304-5312.
33. Beglov, D. & Roux, B. (1997) J. Phys. Chem. 101, 7821-7826.
34. Cheng, X., Kumar, S., Posfai, J., Pflugrath, J. W. & Roberts, R. J. (1993) Cell 74, 299-307.
35. O'Gara, M., Roberts, R. J. & Cheng, X. (1996) J. Mol. Biol. 263, 597-606.
36. Steinbach, P. J. & Brooks, B. R. (1994) J. Comput. Chem. 15, 667-683.
37. Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. (1977) J. Comput. Phys. 23, 327-341.
38. Nosé, S. (1984) J. Chem. Phys. 81, 511-519.
39. Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A. & Rosenberg, J. M. (1992) J. Comput. Chem. 13, 1011-1021.
40. Crouzy, S., Baudry, J., Smith, J. C. & Roux, B. (1999) J. Comput. Chem. 20, 1644-1658.
41. Elcock, A. H. & McCammon, J. A. (1996) J. Am. Chem. Soc. 118, 3787-3788.
42. Cheng, X. & Blumenthal, R. M. (1996) Structure (London) 4, 639-645.
43. Klimasauskas, S. & Roberts, R. J. (1995) Nucleic Acids Res. 23, 1388-1395.
44. Wang, P., Nicklaus, M. C., Marquez, V. E., Brank, A. S., Christman, J., Banavali, N. K. & MacKerell, A. D., Jr. (2000) J. Am. Chem. Soc. 122, 12422-12434.