Harris et al. Figure 7

FIGURE 7

A series of snapshots from 300 picoseconds of molecular dynamics. In figures 7A - 7C the structures of the DNA and protein are represented with ribbon models and bonds generated using the solid modelling module from QUANTA (13). Figure 7D was generated using RIBBONS (38).


a. A computer model of the ER DBD from x-ray crystallographic structure determination docked at a 25bp DNA sequence of VITA1ERE. The DNA and protein residues are color coded as in figure 3. The 10 angstrom water layer is also shown with water molecules colored light blue-grey.


b. The ribbon structures and bonds of the DNA and protein (with water molecules removed for visual clarity) are shown for the model at the start of the computations, prior to energy minimization, heating and equilibration.


c. The structure of the DNA/protein complex after energy minimization, heating, equilibration and 300 picoseconds of dynamics.


d. A close-up view of the ERE DNA right major groove half site nucleotides, showing nucleotide base orientations after 300 picoseconds of dynamics in complex with the ER DBD (only the DNA is shown in this model).


e. A close-up view of six nucleotides from the ERE DNA right major groove half site, sense: TGACTT 15-20 and antisense AAGTCA 31-36, showing nucleotide base orientations after 300 picoseconds of dynamics in complex with the ER DBD (only the DNA is shown in this model). The structure of the DNA and H-bonds were generated using the solid modeling module from QUANTA. Click on the image to view an interactive molecule of this structure.