A New Model for Pore Formation by Cholesterol-Dependent Cytolysins
Figure 6
Flexibility of Domain 4 with respect to Domains 1–3 in MD simulations.
A. Each panel corresponds to an MD simulation. The starting conformer (cartoon representation, grey) is indicated at the left of the molecule. Cα positions taken from snapshots of the simulations are represented as dots after alignment on Domains 1–3. B. Arrows (red) indicate the directions of motion of the third slowest mode (scaled to 3.5 Å for clarity), which best describes the increased distance between Domain 2 and TMH2. The starting conformer is indicated at the left of its cartoon representation. The reasonably small fractional variance explained by the modes (11% (PFO I) and 8% (PFO IIIB), collectivity of 0.34 and 0.45 respectively) identifies a more localized nature of the motion. This suggests that such movement participates to, or enhances, the observed flexibility of Domain 4.