Fig. 1
Structural characteristics of states in the lipid translocation mechanism. a Central panel: 2-D landscape representing all the trajectories of the WT nhTMEM16 (Supplementary Table 1) mapped with the tICA transformation in the space of the first two tICA eigenvectors (tICWT 1 and tICWT 2; see “Methods”). The lighter shades (green to yellow) indicate the most populated regions of the 2D space. The dynamics of the two subunits of the protein in each trajectory were analyzed separately. Microstates representing the most populated states in these simulations are indicated by the numbered circles and represent various stages in the lipid translocation process. Representative structures of microstates 1 and 3 are shown in the surrounding snapshots. In these models, TM4 and TM6 are labeled; the relevant groove residues appear in space-fill representations and are labeled (see also Supplementary Fig. 1A). The location of the initial conformation of the system (the 4WIS model) is indicated by the yellow circle marked Start. b Structural comparison of the position of groove helices TM3-TM6 (in cartoon) in microstates 1 and 3. Note the major repositioning of TMs 3 and 4 from microstate 1 (light gray) to microstate 3 (dark gray). c The probability distributions of the Cα-Cα distance between V337 and V447 residues in the ensemble of conformations from microstates 1 and 3. The vertical dashed lines represent the 8.5 Å distance cut-off used to define the occluded conformation of the groove. d The pore radius as a function of position along an axis perpendicular to the membrane (channel coordinate) for the X-ray structure of nhTMEM16 (PDBID 4WIS, red line), and for selected structures from microstate 3 (gray lines) representing 34 frames (separated from each other by at least 10 ns time interval) from the last 500 ns of a 15 μs MD simulation (WT6 in Supplementary Table 1). The EC and IC ends of the pore are indicated; Z = 0 Å corresponds to the location of the Cα atom of residue Q436 (red triangle symbol), the dot marks the position of the Cα atoms of residue Y439, and the diamond symbol that of V447. The calculations were performed with HOLE (http://www.holeprogram.org/)
