Table 1. Summary of MD Simulations.
Receptor/Oligomeric State | PDB ID | Length of Simulation | Activity of State | |
Total Time | Period Used in Analysis | |||
PXR-RXR heterodimer* | 1ILG | 30 ns | 20–30 ns | Inactive |
PXR-RXR heterotetramer* | 1ILG | 30 ns | 20–30 ns | Active-capable |
PPARγ467L-RXR heterodimer | 1RDT** | 20 ns | 10–20 ns | Inactive |
PPARγ-RXR heterodimer | 1RDT | 20 ns | 10–20 ns | Active-capable |
ERα monomer | 1ERE | 20 ns | 10–20 ns | Inactive |
ERα dimer | 1ERE | 25 ns | 15–25 ns | Active-capable |
*: All PXR simulations are based on 1ILG with residues 178–197 modeled in InsightII.
**: Single-site mutant of PPARγ generated in Pymol. There is no crystal structure of the mutant.