The significant difference between the wide and common binding conformations is in which amino acid residues are involved in the interaction and not in how decoron curvature changes to accommodate a tightly curved small fibril.
The less flexible complex had slightly higher binding, which may indicate unfavorable thermodynamic penalties to obtain binding conformation in the flexible complex.
PCBs can act on the RyR by stabilizing a high-affinity binding conformation, which results in increased intracellular calcium concentrations (Wong et al. 1997).
Several lines of evidence suggest that these substitutions altered the protein's dynamics and/or increased the relative occupancy of a conformation in which the latent binding site is exposed for peptide binding.
In the most frequent binding patterns, NQTrp has a closed conformation in which the indole and the naphthoquinone "clamp" the phenyl rings of Phe19 or Phe20 (Figures 7A C).
Complexes with mispaired dNTPs or complementary rNTPs are arrested at an earlier stage, corresponding to a partially closed fingers conformation, in which weak binding of DNA and nucleotide promote dissociation and resampling of the substrate pool.
This unexpected inactivity in the reporter gene assay suggests that bisphenol AF binding disrupts the ERβ-LBD activation conformation, in which the α-helix 12 (H12) of the receptor is normally positioned to recruit the coactivator protein conformation (Brzozowski et al. 1997; Ruff et al. 2000).
Likewise, phosphorylation of the bacterial nitrogen regulatory protein C shifts the balance of populations of the different forms of this protein from the inactive to the active form, and the PBX1 homeodomain transiently folds into a conformation in which the binding sites for DNA and the transcription factor Hox are preorganized even in the absence of ligands.
The latter is characterized by the inability of an empty MHC molecule to bind a peptide ligand, putatively caused by a conformation in which the peptide-binding site is blocked [21].
Consistent with this view, the crystal structure of the eIF4AIII-MLN51 complex in the absence of ATP, showed that eIF4AIII adopts an open conformation in which the RNA-binding site is disrupted [17].
