help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Sen, S.
Right arrow Articles by Nilsson, L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sen, S.
Right arrow Articles by Nilsson, L.

Biophys J, October 1999, p. 1782-1800, Vol. 77, No. 4

Structure, Interaction, Dynamics and Solvent Effects on the DNA-EcoRI complex in Aqueous Solution from Molecular Dynamics Simulation

Srikanta Sen and Lennart Nilsson

Center for Structural Biochemistry, Karolinska Institute, Department of Biosciences, Huddinge, Sweden

A 0.7-ns molecular dynamics simulation of the DNA-EcoRI complex in a 7.0-Å solvent shell indicated a stable behavior of the system. No significant evaporation or smearing of the solvent's outer boundary occurred. The structure and the intermolecular interactions were found to be well maintained during the simulation. The interaction pattern in the simulation was found to be very similar to that in the crystal structure. Most of the specific interactions between the DNA and the protein were found to be enhanced in the simulation compared to that in the crystal structure as a result of improved interaction geometry. The nonspecific interactions were found to be stronger than the specific ones. The specific interactions between the N7 atoms of Gua4 or Ade5 or Ade6 and the protein were found to be present over almost the entire time of the simulation, whereas hydrogen bonds involving the amino groups of the Ade5 and Ade6 with the protein were found to be relatively weaker, with lower probability and shorter lifetime. The time evolution of the root mean square deviations of the DNA and the protein were highly correlated even at the later part of the simulation, showing the tight binding between them. Several long-lived water bridges were found between the DNA backbone atoms and the protein and also between the two protein monomers, which increased the overall stability of the complex. The two protein monomers were found to interact strongly with each other. The energy of the DNA kink deformation was estimated as approximately 31 kcal/mol.

Biophys J, October 1999, p. 1782-1800, Vol. 77, No. 4
© 1999 by the Biophysical Society   0006-3495/99/10/1782/19  $2.00


This article has been cited by other articles:


Home page
 Mol. Endocrinol.Home page
P. Carlsson, K. F. Koehler, and L. Nilsson
Glucocorticoid Receptor Point Mutation V571M Facilitates Coactivator and Ligand Binding by Structural Rearrangement and Stabilization
Mol. Endocrinol., August 1, 2005; 19(8): 1960 - 1977.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
T. Castrignano, G. Chillemi, G. Varani, and A. Desideri
Molecular Dynamics Simulation of the RNA Complex of a Double-Stranded RNA-Binding Domain Reveals Dynamic Features of the Intermolecular Interface and Its Hydration
Biophys. J., December 1, 2002; 83(6): 3542 - 3552.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
T. W. Lynch and S. G. Sligar
Macromolecular Hydration Changes Associated with BamHI Binding and Catalysis
J. Biol. Chem., September 22, 2000; 275(39): 30561 - 30565.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1999 by the Biophysical Society.