Nuclear receptors that bind steroids have approximately a 5 % identity to the binding domain of the retinoic acid receptor.
This is insufficient for most homology modeling techniques (generally 30 % identity between homologous proteins is required to build a reasonable model). Recently, the crystal structures of the estrogen and progesterone receptors have been determined. Since the glucocorticoid (GR) and mineralocorticoid (MR) receptors have more than 50% identity (and higher similarity) to the progesterone receptor, it seems reasonable that homology modeling using a progesterone receptor as a template would produce a viable model of these receptors.
Using the progesterone receptor as a template, a model of the MR receptor was built using the COMPOSER module of SYBYL 6.6. The crude fit from COMPOSER was energy minimized using the Kollman All-Atom force field with consideration of Kollman charges. The resultant model of the MR receptor had two residues (Ala 114 and Asn 26) in the forbidden area of the Ramachandran diagram. Since Asn residues may lie outside favored regions due to hydrogen bonding with the backbone, this residue was not of major concern. The model was then annealed (using default values for ANNEAL within SYBYL) at the single residue Ala 114. This moved Ala out of the forbidden region and provided a working model of the MR receptor shown below in figure 1.
Figure 1. Shaded ribbon rendering of the MR Model. MR Model Stepped Rotation (3.17 Meg)
Ramachandran diagram from PROCHECK
of this model for MR validated at 1.5 angstroms is shown below in figure 2.
Figure 2. The Ramachandran diagram the MR model
The MR model and a companion (prepared in the same manner as the MR model), GR, is being used to evaluate experimental ligand binding data and also as a template for planning future mutational studies. An example of ligand docking with this model is shown below in figure 3.
3. A steroid (in space filling
mode, colored by atom type) within the ligand binding domain of MR.