Harris et al. Figure 5

FIGURE 5

Plots of interaction energy between ERE nucleotides and selected ER DBD amino acids from the right monomer of the 10 Angstrom water layer ER DBD/25 bp ERE model after energy minimization, heating and equilibration (0 picoseconds) and after 300 picoseconds of molecular dynamics. Amino acids are labeled using the Dayhoff one letter code. Amino acids and nucleotides are numbered as in figure 4. The sense strand is on top. Codon/anticodon nucleotides reading 5' to 3' for the respective amino acids are boxed (except in figure 5a which shows a glutamic acid codon/anticodon reading 3' to 5').


a. Glutamic acid 203 total interaction energies with ERE nucleotides. On the right a close-up view of the H-bond interaction between ERE DNA right major groove half site nucleotide base A 32 (starred in energy plot) and ER DBD amino acid E 203 after 300 picoseconds of molecular dynamics. Atoms are color coded as follows: Oxygen = red, Nitrogen = blue, Phosphorous = Yellow and Carbon = Gray. The H-bond is indicated as a dashed white line. A table detailing the individual interaction energy between selected atoms is also shown.


b. Lysine 206 total interaction energies with ERE nucleotides.


c. Lysine 210 total interaction energies with ERE nucleotides.


d. Arginine 211 total interaction energies with ERE nucleotides.


e. Glutamine 214 total interaction energies with ERE nucleotides.


f. Lysine 235 total interaction energies with ERE nucleotides.


g. Glutamine 238 total interaction energies with ERE nucleotides.