Fig 1.
Crystal structure of three states of rhodopsin and stability of our systems.
(a) Activation cycle of rhodopsin. Through several intermediate states including the Meta II state, the rhodopsin is decayed into the Opsin and the 11-trans-retinal. Crystal structures of the rhodopsin in (b) the Opsin, (c) the Meta II state, and (d) the dark-adapted rhodopsin are shown. The retinal is shown in orange VDW format. (e) The system used for MD simulations of the dark-adapted rhodopsin in a POPC lipid bilayer. The rhodopsin and lipids are shown in cartoon and cyan lines, respectively. Explicit water molecules correspond to the upper and lower transparent coatings. The blue line of the box is a periodic boundary. (f) Backbone root mean square deviations (RMSDs) of the dark-adapted rhodopsin, the Meta II state and the Opsin. We calculated the RMSDs only using helical parts of rhodopsin.
Fig 2.
Accessibility of water molecules.
Cross sectional diagrams of water accessibility with the cross section taken at the middle of the rhodopsin in (a) the dark-adapted rhodopsin, (b) the Meta II state, and (c) the Opsin. Blue surfaces represent places where water molecules have reached during last 0.8 μs in the equilibrium state (see Fig 1f). The protein molecules are depicted with each helix colored from red (the N terminus) to green (the C terminus). The retinal is shown in orange VDW format. A solvent pore can be identified in the Meta II state and the Opsin (yellow circle). However, the solvent pore does not exist in the dark-adapted rhodopsin (red circle).
Fig 3.
Configuration of the solvent pore on the cytoplasmic side with ribbon representation of the Meta II structure.
Extracted 16 trajectories of water molecules that passed through the solvent pore are shown in different colors. Residues of the NPxxY are shown as purple and in the red circle. The retinal is shown in orange VDW format. (a) Close-up view of the first narrow region and (b) the second region are shown. Only five trajectories are shown. The first narrow region comprises L128, M257, and Y306, and the second narrow region comprises F261 and Y306.
Fig 4.
Water displacements in z-coordinate within the solvent pore when one water molecule passes through the solvent pore.
The trajectory of the target water molecule is shown by a thick black line. The hydrophobic region and some internal hydration sites (from −10 to 0 Å) correspond to the area between the first and second regions. The trajectory has four characteristic states and upper snapshots express each characteristic state with the target water colored as blue. Residues of two narrow gates are shown as cyan. Positions 1, 2 and 3 are located between −10 and −5 Å, −5 and 0 Å, and 0 and 5 Å, respectively. Other 15 water displacements observed in the 1 μs MD simulation are shown in S5 Fig.
Fig 5.
Times series of the number of internal water molecules in each state.
The distributions of the internal water molecules (transparent cyan surface) are shown in the lower figures. The definition of internal water molecules is that water molecules within 7 Å of some amino acids located on the center of helixes.