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Conformational states of the glucocorticoid receptor DNA‐binding domain from molecular dynamics simulations
Author(s) -
Bredenberg Johan,
Nilsson Lennart
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10195
Subject(s) - molecular dynamics , zinc finger , chemistry , zinc , crystallography , glucocorticoid receptor , dna , biophysics , binding domain , stereochemistry , binding site , physics , receptor , computational chemistry , biochemistry , biology , organic chemistry , transcription factor , gene
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. Proteins 2002;49:24–36. © 2002 Wiley‐Liss, Inc.