Molecular dynamics simulation in solvent of the estrogen receptor protein DNA binding domain in complex with a non-consensus estrogen response element DNA sequence

Journal of Biomolecular Structure & Dynamics
L F HarrisP D Popken-Harris

Abstract

We investigated protein/DNA interactions, using molecular dynamics simulations computed between a 10 Angstom water layer model of the estrogen receptor (ER) protein DNA binding domain (DBD) amino acids and DNA of a non-consensus estrogen response element (ERE) consisting of 29 nucleotide base pairs. This ERE nucleotide sequence occurs naturally upstream of the Xenopus laevis Vitelligenin A1 gene. The ER DBD is encoded by three exons. Namely, exons 2 and 3 which encode the two zinc binding motifs and a sequence of exon 4 which encodes a predicted alpha helix. We generated a computer model of the ER DBD using atomic coordinates derived from the average of 30 nuclear magnetic resonance (NMR) spectroscopy coordinate sets. Amino acids on the carboxyl end of the ER DBD were disordered in both X-ray crystallography and NMR determinations and no coordinates were reported. This disordered region includes 10 amino acids of a predicted alpha helix encoded in exon 4 at the exon 3/4 splice junction. These amino acids are known to be important in DNA binding and are also believed to function as a nuclear translocation signal sequence for the ER protein. We generated a computer model of the predicted alpha helix consisting of the 10 amino aci...Continue Reading

References

Jun 20, 1978·Journal of Molecular Evolution·G L Nelsestuen
Jan 1, 1978·Biochemical Society Transactions·M J Sternberg, J M Thornton
Jan 11, 1992·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·J C LaceyG W Cook
May 1, 1992·Molecular and Cellular Biology·A M Nardulli, D J Shapiro
Aug 1, 1991·Molecular Endocrinology·N J Koszewski, A C Notides
Oct 18, 1990·Nature·M Karplus, G A Petsko
Nov 23, 1989·Nature·M Yarus, E L Christian
Aug 1, 1988·Journal of Biomolecular Structure & Dynamics·R Lavery, H Sklenar
May 1, 1989·The British Journal of Ophthalmology·M L Harris, M B Mathalone
Nov 23, 1989·Nature·M P CranageP A Kitchin
Dec 24, 1987·Cell·V KumarP Chambon
Jan 1, 1985·Annual Review of Genetics·K R Yamamoto
Jan 1, 1968·Proceedings of the National Academy of Sciences of the United States of America·C R Woese
Jul 14, 1969·Journal of Molecular Biology·C Woese
May 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·C Scheidereit, M Beato
Jan 1, 1984·Progress in Biophysics and Molecular Biology·E N Baker, R E Hubbard
Jan 1, 1984·Origins of Life·J C LaceyM A Khaled
Jan 1, 1984·Perspectives in Biology and Medicine·L B HendryL K Campbell
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Feb 1, 1995·AJR. American Journal of Roentgenology·M L Richardson
Mar 1, 1994·Biopolymers·E Stofer, R Lavery
Mar 11, 1993·Nucleic Acids Research·S MaderJ H White
Jun 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·L F HarrisD F Hickok
Jan 1, 1996·Proteins·T C Bishop, K Schulten

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Citations

Jun 13, 2006·The International Journal of Biochemistry & Cell Biology·Veena VijayanathanThresia Thomas
May 3, 2019·Journal of Neuroendocrinology·Angela M WongPaul E Micevych

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