MOLECULAR-DYNAMICS SIMULATION IN SOLVENT OF THE ESTROGEN-RECEPTOR PROTEIN-DNA BINDING DOMAIN IN COMPLEX WITH A NONCONSENSUS ESTROGEN RESPONSE ELEMENT DNA-SEQUENCE

We investigated protein/DNA interactions, using molecular dynamics sim ulations computed between a 10 Angstom water layer model of the estrog en receptor (ER) protein DNA binding domain (DBD) amino acids and DNA of a non-consensus estrogen response element (ERE) consisting of 29 nu cleotide base pairs. This ERE nucleotide sequence occurs naturally ups tream of the Xenopus laevis Vitelligenin Al gene. The ER DBD is encode d by three exons. Namely, exons 2 and 3 which encode the two zinc bind ing motifs and a sequence of exon 4 which encodes a predicted alpha he lix. We generated a computer model of the ER DBD using atomic coordina tes derived from the average of 30 nuclear magnetic resonance (NMR) sp ectroscopy coordinate sets. Amino acids on the carboxyl end of the ER DBD were disordered in both X-ray crystallography and NMR determinatio ns and no coordinates were reported. This disordered region includes 1 0 amino acids of 3 predicted alpha helix encoded in exon 4 at the exon 3/4 splice junction. These amino acids are known to be important in D NA binding and are also believed to function as a nuclear translocatio n signal sequence for the ER protein. We generated a computer model of the predicted alpha helix consisting of the 10 amino acids encoded in exon 4 and attached this helix to the carboxyl end of the ER DBD at t he exon 3/4 splice junction site. We docked the ER DBD model within th e DNA major groove halfsites of the 29 base pair non-consensus ERE and flanking nucleotides. We constructed a solvated model with the ER DBD /ERE complex surrounded by a ten Angstrom water layer and conducted mo lecular dynamics simulations. Hydrogen bonding interactions were monit ored. In addition, van der Waals and electrostatic interaction energie s, were calculated. Amino acids of the ER DBD DNA recognition helix fo rmed both direct and water mediated hydrogen bonds at cognate codon-an ticodon nucleotide base and backbone sites within the ERE DNA right ma jor groove halfsite. Amino acids of the ER DBD exon 4 encoded predicte d alpha helix formed direct and water mediated H-bonds with base anc: backbone sites of their cognate codon-anticodon nucleotides within the minor grooves flanking the ERE DNA major groove halfsites. These inte ractions together induced bending of the DNA into the protein.