Figure 3.

Dynamics of biologically distinguished structural motifs. (Center) Rhodopsin is shown as a rainbow cartoon embedded in a lipid bilayer. The bottom view shows the protein’s cytoplasmic face. (a) Illustration showing retinal (white spheres) in its binding pocket and rotamer toggle residues: Phe261^6.44 (pale yellow), Trp265^6.48 (pale violet), and Tyr268^6.51 (dark red). (b) Histograms of the population of ${\chi }_1$ torsion angles for each of the three toggle switch residues. Data is colored by the simulation ensemble. (Note: a version of this figure with error bars is depicted in Fig. S8.) (c) Close-up view of the NPxxY motif. (d) The ionic lock. Arg135^3.50 and Glu247^6.30 are shown forming a salt bridge (left) as in the inactive crystal structure (PDB ID: 1U19) or in an open conformation (right) as in the active crystal structure (PDB ID: 3PXO). (e) NPxxY motif versus ionic lock dynamics. The NPxxY RMSD from the inactive crystal structure (y axis) is shown versus the ionic lock distance (x axis). Every frame (sampled at a rate of 1 ns) is shown colored according to ensemble. To see this figure in color, go online.