JOURNAL BROWSE
Search
Advanced SearchSearch Tips
A Theoretical Study of a Z-DNA Crystal: Structure of Counterions, Water and DNA Molecules
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
A Theoretical Study of a Z-DNA Crystal: Structure of Counterions, Water and DNA Molecules
Ho Soon Kim; Byung Jin Mhin; Chang Woo Yoon; C. X. Wang; Kwang S. Kim;
  PDF(new window)
 Abstract
To study the effect of solvents and counterions in Z-DNA crystal of d(5BrC-G-5BrC-G-5BrC-G), we performed the local energy analysis and then molecular dynamics simulations. Since counterions raise serious caging problems in crystal simulations, it is very important to search for the possible positions before simulations. For this purpose, the local energy analysis was done for the whole crystal volume. It is shown from our simulation that counterions along with water molecules play a bridging role to bind adjacent oligomers so as to form the crystal. In this crystal, each water molecule bound to Gua-N2H, either directly or indirectly, hydrates the adjacent anionic phosphate oxygen, and thus assists Gua to be in a syn position. From the simulation, the average root-mean-square deviation of allthe DNA heavy atom coordinates from the X-ray data is . The bases are less deviated from the X-ray positions than the phosphates. The temperature factors from the simulation are consistent with those from the X-ray refinement, showing that the phosphates are more mobile than the bases.
 Keywords
 Language
English
 Cited by
 References
1.
Mol. Biol., vol.67. pp.375

2.
Nature, vol.282. pp.680

3.
Nature, vol.286. pp.567

4.
Ann. Rev. Bioche., vol.53. pp.791

5.
J. Biol. Chem., vol.264. pp.7921

6.
J. Mol. Biol., vol.188. pp.707

7.
Biol. Chem., vol.261. pp.8093

8.
Science, vol.216. pp.475

9.
Waters and Ions in Biomolecular Systems, pp.11

10.
J. Mol. Biol., vol.163. pp.129

11.
Nature, vol.288. pp.129

12.
J. Phys. Chem., vol.92. pp.939

13.
Biopolymers, vol.27. pp.187

14.
J. Am. Chem. Soc., vol.107. pp.227

15.
J. Am. Chem. Soc., vol.107. pp.5504

16.
J. Phys. Chem., vol.89. pp.2870

17.
J. Comput. Chem., vol.6. pp.256

18.
Biophys. J., vol.47. pp.327

19.
J. Comput. Chem., vol.8. pp.57

20.
Biochimie, vol.67. pp.811

21.
J. Am. Chem. Soc., vol.106. pp.765

22.
Croat. Chem. Acta, vol.59. pp.369

23.
J. Biolog. Phys., vol.30. pp.49

24.
Chem. Phys. Lett., vol.156. pp.261

25.
Proc. Natl. Acad. Sci U.S.A., vol.79. pp.4040