FIGURE 5

Closeup views of amino acid-nucleotide interactions between GRE nucleotides and selected GR DBD amino acids from the right monomer of the GR DBD/29 bp GRE model at various time steps during solvated molecular dynamics. Interactions involving amino acids from the exon 3 encoded DNA recognition alpha helix, the exon 4 encoded beta strand and the exon 5 encoded predicted alpha helix are shown. Atoms on amino acids, nucleotides, and water molecules which form direct and water mediated DNA/protein H-bonds are highlighted with dot surfaces. Hydrogen bonds are indicated with white dashed lines. Water molecules are colored light blue; amino acids and nucleotides are colored as described in figure 2.

(a) Hydrogen bonds between amino acid K 461 and codon nucleotide A 37 at the N7 base site (bi-dentate H-bond), and codon nucleotide G 38 at O6 Watson -Crick H-bond site and N7 base site are shown. Direct Hydrogen bonds between K 461 and H 451 and Y 452 are also shown. Likewise, direct H-bonds between amino acid K 465 and anticodon (reading 3'to 5') nucleotide T 20 at O4 Watson -Crick H-bond site and codon nucleotide G 38 at O6 Watson -Crick H-bond site are shown.

(b) The Van der Waals interaction between V 462 and its codon nucleotide T 19 is shown. Hydrogen bonds between R 466 and its codon nucleotide A 39 at N7 base site (direct) and phosphate backbone O1P atom (water mediated), and non-codon T 19 O4 Watson -Crick H-bond site are also shown. In addition, a water mediated H-bond between the sidechains of Arg 466 and E 469 occurs. Using the same water molecule, E 469 also forms a H-bond with its codon nucleotide A 39 phosphate backbone O1P atom.

(c) Hydrogen bonds between Q 471 and codon nucleotide A 40 (reading 3' to 5') at the H61base site can be seen. Also shown are both direct and water mediated H-bonds between Q 471 and anticodon nucleotide G 18 at O6 Watson -Crick H-bond site (direct), and N7 base site (water mediated). Likewise a direct H-bond between N 473 and the phosphate backbone O1P of its anticodon nucleotide T 17 (reading 3' to 5') is shown. In addition, water mediated H-bonds between L 475 and its codon nucleotide T 17 at the phosphate backbone O1P is shown.

(d) A water mediated Hydrogen bond between R 510 and its codon nucleotide A 37 phosphate backbone O2P is shown. Likewise, a direct H-bond between K 513 and its codon nucleotide A36 at the phosphate backbone O2P, and a water mediated Hydrogen bond with its codon nucleotide A27 at the phosphate backbone O2P are shown. In addition, a direct H-bond between K 517 and its codon nucleotide A36 at the phosphate backbone O2P atom and a water mediated H-bond with its codon nucleotide A27 at the sugar backbone O3' site are shown.