Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.
Molecular dynamics simulations (MD) have been performed on variant crystal and NMR-derived structures of the glucocorticoid receptor DNA-binding domain (GR DBD). A loop region five residues long, the so-called D-box, exhibits significant flexibility, and transient perturbations of the tetrahedral geometry of two structurally important Cys4 zinc finger are seen, coupled to conformational changes in the D-box. In some cases, one of the Cys ligands to zinc exchanges with water, although no global distortion of the protein structure is observed. Thus, from MD simulation, dynamics of the D-box could partly be explained by solvent effects in conjunction with structural reformation of the zinc finger.
Bredenberg
Johan
J
Karolinska Institutet, Department of Bioscience at NOVUM, Center for Structural Biochemistry, Huddinge, Sweden.
Nilsson
Lennart
L
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003198:Computer Simulation; D003545:Cysteine / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011965:Receptors, Glucocorticoid / Q000737:chemistry*; D014867:Water / Q000737:chemistry; D015032:Zinc / Q000737:chemistry; D016335:Zinc Fingers
D004268:DNA-Binding Proteins; D008024:Ligands; D011965:Receptors, Glucocorticoid; D014867:Water; D015032:Zinc; D003545:Cysteine