Molecular dynamics study of glucocorticoid receptor-DNA binding

Thomas C. Bishop, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

Molecular dynamics simulations have been conducted to investigate the binding of the glucocorticoid receptor (GR) dimer to DNA. For this purpose simulations of the complex formed by a DNA segment and a dimer of GR-DNA binding domains (GR-DBD) have been carried out, employing an available X-ray structure. A second set of simulations was based on this structure as well, except that the DNA segment was altered to the consensus glucocorticoid response element (GRE). Simulations of a single GR-DBD and of the uncomplexed GRE served as controls. For the simulations, each system was encapsulated in an ellipsoid of water. Protein-DNA interactions, dimer interactions, and DNA structural parameters were analyzed for each system and compared. The consensus GRE is found to yield more favorable and symmetric interactions between the GR-DBDs and the GRE, explaining the ability of the GR dimer to recognize this DNA segment. Further analysis focused on deformations of the DNA that are induced by the binding of GR. The deformations observed involve a 35° bend of the DNA, an unwinding, and a displacement of the helical axis. These deformations are consistent with a mechanism for transcriptional regulation that involves a change of nucleosome packing upon GR binding. Significant protein-protein and protein-DNA interactions, both direct and water mediated, develop due to the deformations of the GRE and are indicative of an increased recognition achieved through DNA deformation. The interactions include direct interactions between the GRE and glycine-458 and serine-459, side groups which differentiate GR from other members of the nuclear hormone receptor family.

Original languageEnglish (US)
Pages (from-to)115-133
Number of pages19
JournalProteins: Structure, Function and Genetics
Volume24
Issue number1
DOIs
StatePublished - 1996

Keywords

  • DNA bending
  • DNA recognition
  • DNA unwinding
  • estrogen receptor
  • molecular dynamics
  • receptor proteins

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

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