Fig 1.
Crystal structure models of PR LBD.
(A), holo-form agonistic conformation of PR LBD. (B), antagonistic conformation of PR LBD. Helix 12 and the co-peptide are green and magenta color, while for ligands (progesterone and asoprisnil), carbon atoms are cyan; oxygen atoms are red and nitrogen atoms are blue.
Fig 2.
RMSDs and RMSFs data obtained from normal MD simulations.
(A), The RMSDs of the first repeat trajectory for the 4 systems in Table 1, green and black for apo-1a28 and holo-1a28 simulations, red and blue for apo-2ovh and holo-2ovh simulations. (B), RMSDs of progesterone (P4) (green) and Asoprisnil (blue) in the PR LBD-ligand complexes. The RMSFs of the apo-1a28/holo-1a28 simulation (C) and apo-2ovh/holo-2ovh simulations (D), where residues’ index with rather large RMSF values are indicated. The secondary structures of LBD are displayed at top of panel C and D, whereas “H” indicates an α-helix.
Fig 3.
The frequency distribution of the crossing angle between helix 11 and helix 3.
(A), the helix 11-helix 3 cross angle frequency distribution in apo-1a28 and holo-1a28 simulations. (B), the helix 11-helix 3 cross angle frequency distribution in apo-2ovh and holo-2ovh simulations.
Fig 4.
The interaction and distance relative distributions between residues in loop 786–808 and loop 703–712.
(A), the overview of three important loops (green color) in holo-form crystal agonistic conformation (PDB ID 1A28). (B), the detailed view of the interactions between the residues in loop 703–712 and loop 786–808; the LBD structure is the last frame of a 100 ns trajectory of holo-1a28 simulation system; the yellow dashed lines indicate close contacts between atoms, the numeric labels are distances in unit of angstrom. (C), the relative distribution of the side-chain distance between Lys790 and Asp709 in apo-form and holo-form agonistic conformations. (D), the relative distribution of the distance between the Lys790 side-chain and the Pro708 backbone oxygen atom. In panel A and B, carbon atoms in the ligand progesterone are in green, oxygen atoms are in red color.
Fig 5.
The overall cross-correlation networks in simulation systems apo-1a28 (A), holo-1a28 (B), apo-2ovh (C) and holo-2ovh (D). If two residues are correlated or anti-correlated, they are linked by lines. Different cross-correlation co-efficiency (ccc) is indicated by color. Anti-correlation is blue (-0.4 < = ccc<0.2), yellow (0.2< = ccc<0.4), orange (0.4< = ccc<0.6) and red (ccc> = 0.6) are used for correlations. The cross-correlation maps of these 4 systems are provided in S2 Fig.
Fig 6.
Free energy along the ΔRMSD coordination and the low free energies representative structures.
(A), the free energy along the one dimensional coordination together with error bars. (B), the representative structure (gray color) in the local minimum 1, where ΔRMSD = -1.3 nm. (C), 10 representative intermediate structures in a local minimum 2 (the ΔRMSD range 0.3 nm to 0.5 nm). In panel B and C, the PR LBD crystal agonistic conformation (green) and the crystal antagonist conformation (cyan) are also superimposed with the representative structures.
Fig 7.
The free energy surface (FES) map constructed by metadynamics simulations.
8 major basins of local minima are labeled together with the positions of two crystal structure models (Ref-1: 2OVH; Ref-2: 1A28) indicated by red triangle marks. The color key at right side of the figure indicates the free energy scales in unit of kJ/mol. The iso-surface lines are given every 10 kJ/mol.
Table 1.
Interaction pairs involving residues in the helix-loop-helix segment in metadynamics low energy structures.
Fig 8.
Representiave structures of local minima 1 and 2 sampled in the metadynamics simulation.
(A), the representative structure mL1 (pink) superimposed with crystal agonistic and antagonistic models. (B), the detailed view of interaction networks around the helix 11, loop 895–908 and helix 12. (C), the representative structure mL2.3 superimposed with crystal agonistic and antagonistic models. (D), the detail interaction network between residues in helix-loop-helix segment. The crystal agonistic (PDB ID 1A28) and antagonistic (PDB ID 2OVH) conformations are colored as green and cyan in the helix-loop-helix region. The yellow dashed lines indicate close contacts between residue atoms.
Fig 9.
The interactions and distance distribution of Met908/Met909 and Glu723 and the cross angle between helix 11 and helix 3.
(A), the frequency distribution of the backbone nitrogen atoms of Met908 and Met909 to Glu723 side-chain oxygen atoms distance. (B), the two distinct interaction patterns at the two distance frequency distribution peaks, if the distance between Met908, Met909 and Glu723 is 0.43 nm colored by green, if the distance is 0.6 nm, colored by cyan; the structures were extracted from clustering analysis based on the distance from the apo-form agonistic normal MD simulations. (C), the three states of helix 11 observed in apo-form antagonistic simulations. State 1 (marine) has a ~75° cross angle between helix 11 and helix 3, while the angles for state 2 (green) and state 3 (orange) are about 55° and 40°, respectively. State 1 and state 3 are from structural models of aL2 and aL3 (S3B Fig), while state 2 is the crystal antagonistic model (PDB ID 2OVH). (D and E), PMF maps of the helix 11-helix 3 cross angle in apo-2ovh and holo-2ovh simulations.
Fig 10.
Overlay of apo-form ERα LBD with PR LBD and the π-cation interaction in NR LBDs.
(A), ERα LBD (cyan, PDB ID 1A52) has a relatively shorter helix 12 and doesn’t has a extended C terminal tail, whereas PR LBD (green, PDB ID 1A28) has a longer helix 12 and a C terminal tail. (B), conserved arginine (in helix 9) and phenylalanine (in C terminal tail) are shown as sticks, whereas other parts are shown as cartoon. Green, PR LBD agonistic conformation (PDB ID 1A28); cyan, PR LBD antagonistic conformation (PDB ID 2OVH); marine, AR LBD agonistic conformation (PDB ID 4OEA); orange, GR LBD agonistic conformation (PDB ID 3K23).
Table 2.
The setup of the 4 systems in normal MD simulations of PR LBD.