A series of snapshots from 600 picoseconds of molecular dynamics. In figures 5A - 5C the structures of
the DNA and protein are represented with ribbon models and bonds generated using the solid modelling
module from QUANTA (24). Figure 5D was generated using RIBBONS (54).
A. A computer model of
the GR DBD from NMR structure determination with putative flanking alpha helices attached docked at a
29bp DNA sequence of MMTPRGR1. The DNA and protein residues are color coded as in figures 1 and 2
above. 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. (click he
for PDB coordinates)
C. The structure of the DNA/protein complex after energy minimization, heating, equilibration and 600
picoseconds of dynamics.
D. A close-up view of the GRE DNA right major groove half site nucleotides, (sense strand -
5' 15-ACTGTTCTTAA-25 3') showing nucleotide base orientations after 505 picoseconds of dynamics in
complex with the GR DBD (only the DNA is shown in this model).