Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations
Van Tilborg, Marc A. A.; Bonvin, Alexandre M. J. J.; Hård, Karl; Davis, Adrian L.; Maler, Bonnie; Boelens, Rolf; Yamamoto, Keith R.; Kaptein, R
(1995) Journal of Molecular Biology, volume 247, issue 4, pp. 689 - 700
(Article)
Abstract
The solution structure of the glucocorticoid receptor (GR) DNA-binding domain (DBD), consisting of 93 residues, has been refined from two and three-dimensional NMR data using an ensemble iterative relaxation matrix approach followed by direct NOE refinement with DINOSAUR. A set of 47 structures of the rat GR fragment Cys440-Arg510 was
... read more
generated with distance geometry and further refined with a combination of restrained energy minimization and restrained molecular dynamics in a parallel refinement protocol. Distance constraints were obtained from an extensive set of NOE build-up curves in H2O and2H2O via relaxation matrix calculations (1186 distance constraints from NOE intensities, 10 ∅ and 22 χ1dihedral angle constraints from J- coupling data were used for the calculations). The root-mean-square deviation values of the 11 best structures on the well-determined part of the protein (Cys440 to Ser448, His451 to Glu469 and Pro493 to Glu508) are 0.60 Å and 1.20 Å from the average for backbone and all heavy atoms, respectively The final structures have X-factors around 0.40 and good stereochemical qualities. The first zinc-coordinating domain of the GR DBD is very similar to the crystal structure with a root-mean-square difference of 1.4 Å. The second zinc-coordinating domain is still disordered in solution. No secondary structure element is found in this domain in the free state. As suggested by crystallographic studies on the estrogen receptor DBD-DNA and GR DBD-DNA complexes, part of this region will form a distorted helix and the D-box will undergo a conformational change upon cooperative binding to DNA.
show less
Download/Full Text
Keywords: DNA binding domain, Glucocorticoid receptor, Solution structure, Zinc finger direct NOE refinement, estrogen receptor, glucocorticoid receptor, amino acid sequence, animal cell, article, calculation, conformational transition, crystal structure, molecular dynamics, nonhuman, nuclear magnetic resonance, priority journal, protein DNA binding, protein domain, protein secondary structure, protein structure, rat, stereochemistry, Taverne
ISSN: 0022-2836
Publisher: Academic Press Inc.
(Peer reviewed)
See more statistics about this item