Harris et al. Figure 6

FIGURE 6

Closeup views of amino acid-nucleotide interactions between ERE nucleotides and selected ER DBD amino acids from the right monomer of the ER DBD/25 bp ERE model at various time steps during solvated molecular dynamics (see Table I). Interactions involving amino acids from the exon 2 encoded DNA recognition alpha helix and the exon 3 encoded beta strand are shown. Atoms on amino acids, nucleotides, and water molecules which form direct and water mediated DNA/protein H-bonds are highlighted with VDW surfaces. Hydrogen bonds are indicated with white dashed lines. Water molecules are colored blue-gray; amino acids and nucleotides are colored as described in figure 3.


a. A direct hydrogen bond between amino acid E 203 and its codon nucleotide (reading 3' to 5') A 32 at the H61 base site. Water mediated hydrogen bonds between amino acid E 203 and codon nucleotide (reading 3' to 5') A 31 at the O2P backbone site and the codon nucleotide G 33 (reading 3' to 5') at the O6 Watson-Crick H-bond site are also shown.

b. Direct H-bonds between amino acid K 206 and codon nucleotide A 32 at N7 base site and the O2P backbone site are shown. A water mediated hydrogen bond with codon nucleotide G 33 at the O6 Watson-Crick H-bond site is also shown.


c. A direct H-bond between amino acid K 210 and codon nucleotide G 33 at the N7 site. Water mediated H-bonds with codon nucleotide G 33 at the O6 Watson-Crick H-bond site, the N7 site and at the O2P backbone site are also shown.

d. Direct hydrogen bonds between R 211 and its non-codon nucleotide G16 at the O6 Watson-Crick H- bond site and the N7 site. A water mediated hydrogen bond with non-codon nucleotide T34 at the O4 Watson-Crick H-bond site is also shown.


e. Direct H-bonds between K 235 and its codon nucleotide G 39 phosphate backbone O2P atom are shown.
f. A direct H-bond between Q 238 and its anticodon nucleotide T 15 at the O2P backbone site. Water mediated H- bonds with anti-codon nucleotide T14 at the O2P backbone site and the sugar O3 site are also shown.