Figure 1.
Structural Features of the PXR-RXR Heterotetramer.
(A) A model of the PXR (blue, magenta, green)-RXR (yellow) heterotetramer highlights the PXR homodimer interface and the ten-stranded intermolecule β-sheet formed between the two monomers. PXR residues Trp-223 and Tyr-225 central to homodimerization are rendered in yellow with transparent CPK spheres. The α-helices 3, 3′, 4 and αAF (green) create the AF-2 surfaces that bind leucine-rich coactivator peptides like SRC-1 (orange) using a charge clamp (Lys-259, Glu-427) and other residues (light pink). (B) Schematics of the oligomeric NR complexes examined in this paper.
Table 1.
Summary of MD Simulations.
Figure 2.
Conservation of Total Energy During PXR-RXR Simulations.
Total energy (kcal/mol), used as a measure of overall simulation stability, remains relatively constant during the course of both the PXR-RXR heterodimer (A) and PXR-RXR heterotetramer (B) simulations, particularly during the final 10 ns used for analysis (boxed). Both the total energy (grey diamonds) and a running average (black line) are shown.
Figure 3.
Highly Correlated Motion in the PXR-RXR Heterotetramer.
(A) Covariance analysis of the PXR LBD in the PXR-RXR heterodimer and heterotetramer. Residue-residue correlation coefficient values range from blue (anticorrelated, –0.9) to red (correlated, +1), with uncorrelated residue pairs in yellow. Secondary structure is provided from right-to-left, and bottom-to-top. (B) Clustering of correlated PXR LBD residues from the PXR-RXR heterodimer simulation. Eleven clusters were identified, five with a correlation cutoff (CC) of 0.6, five with a CC of 0.7, and one with a CC of 0.8. (C) Clustering of correlated PXR LBD residues from the PXR-RXR heterotetramer simulation. Three clusters were identified, one each with CCs of 0.6, 0.7, and 0.8. Clusters are colored by the maximum correlation coefficient at which they are observed.
Figure 4.
Correlated AF-2 Domain Motions in the PXR-RXR Heterotetramer.
Vectors describing the motions of PXR LBD α-helices from the heterotetramer (A) and heterodimer (B) simulations show the active-capable heterotetramer PXR LBD exhibits more overall correlated motion as well as correlation between AF-2 surface helices. Each helix eigenvector (shown by an arrow) is the sum of the α-carbon eigenvectors in that helix. All arrows were generated using the same scalar magnifications of motion vectors and are presented on the same scale. As such, they represent relative, rather than absolute, movements.
Table 2.
θ Angle Analysis of α-carbons of PXR LBD.
Figure 5.
Quasiharmonic and Normal Mode Analyses.
Angles between motion vectors for all residue pairs in the PXR-RXR heterodimer and heterotetramer. Motion vectors were identified by quasiharmonic analysis (QHA, using the first two modes; (A) and by normal mode analysis (NMA, using the first 14 nontrivial modes; (B). In the plots, green represents angles close to zero (correlated), while yellow indicates angles close to 180° (anticorrelated).
Figure 6.
AF-2 Surface Motions in PPARγ and ERα Complexes.
Similar to Figure 4, the active-capable PPARγ-RXR heterodimer and ERα homodimer complexes exhibit correlated motions in their AF-2 surfaces during MD trajectories (A, C), while inactive states of both receptors exhibit reduced AF-2 surface correlation (B, D).
Table 3.
θ Angle Analysis of α-carbons of PPARγ LBD.
Table 4.
θ Angle Analysis of α-carbons of ERα LBD.