Thomas C. Bishop and Klaus Schulten.
Molecular dynamics study of a sequence specific protein-DNA
interaction.
In G. Wipff, editor, Computational Approaches in Supramolecular
Chemistry, pp. 419-439. Kluwer Academic Publishers, Boston, 1994.
BISH94
The crystal structure of the DNA-binding domain of the glucocorticoid receptor complexed with DNA has been made available to us by Sigler et al [1]. The glucocorticoid receptor binds as a dimer to DNA, and the receptor dimer recognizes a specific sequence of DNA through nucleotide interactions in the major groove. The target DNA consists of a palindrome or near palindrome of hexameric half-sites separated by a three base pair sequence of DNA. To increase the stability of the system for the following molecular dynamics study, the protein and DNA have been encapsulated in an ellipsoid of water consisting of approximately 3,000 water molecules. Energy minimization, equilibration and dynamics have conducted and the following properties of the system have been evaluated: DNA parameters (including major and minor groove width, twist and bending of the helical axis); interactions between the receptors and DNA, and the correlation to bending; and orientation of the alpha helix axes of the receptor in comparison to DNA helical axis.
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