A Theoretical Study of a Z-DNA Crystal: Structure of Counterions, Water and DNA Molecules

  • Ho Soon Kim (Department of Chemistry, Pohang Institute of Science and Technology) ;
  • Byung Jin Mhin (Department of Chemistry, Pohang Institute of Science and Technology) ;
  • Chang Woo Yoon (Department of Chemistry, Pohang Institute of Science and Technology) ;
  • C. X. Wang (Department of Chemistry, Pohang Institute of Science and Technology) ;
  • Kwang S. Kim (Department of Chemistry, Pohang Institute of Science and Technology)
  • Published : 1991.04.20

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 $0.99{\AA}$ . 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

References

  1. Mol. Biol. v.67 F. M. Pohl;T. M. Jovin
  2. Nature v.282 A. H.-J. Wang;G. J. Quigley;F. J. Kolpak;J. L. Crawford;J. H. van Boom;G. van der Marel;A. Rich
  3. Nature v.286 H. Drew;H. T. Takano;S. Tanaka;K. Itakura;R. E. Dickerson
  4. Ann. Rev. Bioche. v.53 A. Rich;A. Nordheim;A. H.-J. Wang
  5. J. Biol. Chem. v.264 R. V. Gessner;C. A. Frederick;G. J. Quigley;A. Rich;A. H.-J. Wang
  6. J. Mol. Biol. v.188 B. Chevrier;A. C. Dock;B. Hartmann;M. Leng;D. Moras;M. T. Thuong;E. Westhof
  7. Biol. Chem. v.261 Schorschinsky;M. J. Behe
  8. Science v.216 R. E. Dickerson;H. R. Drew;B. M. Conner;R. M. Wing;A. V. Fratini;M. Kopka
  9. Waters and Ions in Biomolecular Systems E. Westhof
  10. J. Mol. Biol. v.163 M. L. Kopka;A. V. Fratini;H. R. Drew;R. E. Dickerson
  11. Nature v.288 S. Neidle;H. M. Berman;H. S. Shieh
  12. J. Phys. Chem. v.92 P. S. Ho;G. J. Quigley;R. F. Tilton;A. Rich
  13. Biopolymers v.27 S. Devarajan;N. Pattabiraman;R. H. Shafer
  14. J. Am. Chem. Soc. v.107 K. S. Kim;E. Clementi
  15. J. Am. Chem. Soc. v.107 K. S. Kim;E. Clementi
  16. J. Phys. Chem. v.89 K. S. Kim;H. L. Nguyen;P. K. Swaminathan;E. Clementi
  17. J. Comput. Chem. v.6 K. S. Kim
  18. Biophys. J. v.47 K. S. Kim;D. P. Vercateren;M. Welti;S. Chin;E. Clementi
  19. J. Comput. Chem. v.8 K. S. Kim;E. Clementi
  20. Biochimie v.67 E. Westhof;Th. Prange;B. Chevrier;D. Moras
  21. J. Am. Chem. Soc. v.106 S. J. Weiner;P. A. Kollman;D. A. Case;U. C. Singh;C. Ghio;G. Alagona;S. Profeta;P. Weiner
  22. Croat. Chem. Acta v.59 K. S. Kim;D. P. Vercauteren;M. Welti;S. L. Fornili;E. Clementi
  23. J. Biolog. Phys. v.30 P. K. Swaminathan;D. P. Vercauteren;K. S. Kim;E. Clementi
  24. Chem. Phys. Lett. v.156 K. S. Kim
  25. Proc. Natl. Acad. Sci U.S.A. v.79 H. Drew;S. Samson;R. E. Dickerson