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A combined cluster analysis further uncovered that the two GBS-bound molecules populated a shared cluster, while there was only minimal overlap with clusters populated in any of the other simulated molecules. It is rather more likely that the lever arm undergoes conformational selection from a highly heterogeneous collection of clusters in the free state to a small number of unique clusters in the functional, DNA-bound state. These insights contribute to our understanding of how DNA sequence inputs control the conformational landscape of the GR DBD, which may have consequences for the transcriptional regulation of target genes.

Cells were grown to an OD of 0. Protein was purified by nickel affinity chromatography, followed by cleavage of the His 6 -Sumo-tag using Ulp-1 enzyme. No electron density indicating the presence of nucleic acid was found anywhere in the unit cell. For consistency, all GR sequences were truncated to contain residues — human numbering. All systems were set up using xleap in AmberTools version 17 and force fields contained in Amber16 All minimizations and simulations were performed with Amber A 2-fs time step was used and all bonds between heavy atoms and hydrogens were fixed with the SHAKE algorithm For analysis, 50, evenly spaced frames were obtained from each simulation.

The k-means clustering algorithm kclust was used with a 2. This radius was selected as the optimal radius to reflect the conformational variability of the selected fragment i. To identify sampled conformations that overlap between the free and DNA-bound GR monomers in the two replicate simulations, 5, evenly spaced snapshots from each monomer 50, total were combined, RMSD fitted and clustered. Vandewalle, J. Therapeutic Mechanisms of Glucocorticoids. Trends Endocrinol.

Whitehouse, M. Anti-inflammatory glucocorticoid drugs: reflections after 60 years.

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Inflammopharmacol 19 , 1—19 Weikum, E. Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat Rev Mol Cell Biol 18 , — Meijsing, S. Science , — Hudson, W. The structural basis of direct glucocorticoid-mediated transrepression. Nat Struct Mol Biol 20 , 53—58 Surjit, M. Cell , — Nordeen, S. Structural determinants of a glucocorticoid receptor recognition element.

Luisi, B. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature , — Haerd, T. Biochemistry 29 , — Bittencourt, D. G9a functions as a molecular scaffold for assembly of transcriptional coactivators on a subset of Glucocorticoid Receptor target genes. Rogatsky, I. Alternate surfaces of transcriptional coregulator GRIP1 function in different glucocorticoid receptor activation and repression contexts. Chinenov, Y. Yang, C. Role of the N-terminal activation domain of the coiled-coil coactivator in mediating transcriptional activation by beta-catenin.

Watson, L. The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals. Nat Struct Mol Biol 20 , — Morgan, D.

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Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. Birth, P. Identification and characterization of BATF3 as a context-specific coactivator of the glucocorticoid receptor. Thomas-Chollier, M. A naturally occuring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms. Baumann, H. Refined solution structure of the glucocorticoid receptor DNA-binding domain.

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Structural analysis

Biochemistry 32 , — J Mol Biol , — Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. Solution structure of the glucocorticoid receptor DNA-binding domain. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

Nat Commun 7 , Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain suggest a role of the lever-arm mobility in transcriptional output. Mossessova, E. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast.

Mol Cell 5 , — Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate. Nat Commun 5 , Adams, P. Emsley, P. Coot: model-building tools for molecular graphics. Case, D.

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AMBER University of California , San Francisco Peters, M. Theory Comput. Ryckaert, J. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes.

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Journal of Computational Physics 23 , — Roe, D. Feig, M. Journal of Molecular Graphics and Modelling 22 , — Download references. This work was supported by a W. Keck Foundation Medical Research Grant. All authors reviewed the manuscript. Correspondence to Eric A. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Skip to main content. Subjects Computational biophysics X-ray crystallography. Abstract The glucocorticoid receptor GR is a steroid hormone receptor of the nuclear receptor family that regulates gene expression in response to glucocorticoid hormone signaling. Introduction Glucocorticoids GCs are steroid hormones that are involved in various fundamental processes at the cellular and organismal level.

Table 1 X-ray diffraction data. Full size table. Figure 1. Full size image. Figure 2. Figure 3.

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Figure 4. Figure 5. Figure 6.