Figure 3.
Results of atomistic MD simulations
The upper row (A–C) and (G) correspond to MTCH2 simulated at 310 K, while the lower row (D–F) corresponds to MTCH2 simulated at 330 K.
(A and D) Cartoon structure of MTCH2 at the start of the simulation (in gray) overlaid with the structure of MTCH2 at the end of the 3 μs (A) or 1.5 μs (D) atomistic simulation (in orange). Note that the α-helical segments of the protein were quite stable and they did not significantly reorient or reposition during either of the simulations. This suggests that the predicted structure is stable and the protein cavity and the scrambling pathway remain open.
(B and E) Root-mean-square deviation (RMSD) of the MTCH2 backbone (black) and backbone of α-helices forming the cavity (blue) during the simulation. Note that most of the RMSD calculated for the protein backbone comes from the fluctuations in the loops of MTCH2, as the RMSD for α-helices never reaches 0.3 nm.
(C and F) Simulation snapshots showing several lipids (colored in yellow, orange, red, and purple) translocating along the scrambling pathway of MTCH2. The protein is shown as a molecular surface colored according to the character of its residues (hydrophilic = green, hydrophobic = white, positively charged = blue, negatively charged = red). Bulk lipids are depicted as gray beads (phosphate group) with hydrophobic tails omitted for clarity. Water is represented only schematically as a blue gradient, omitting the presence of water in the cavity of the protein for visual clarity.
(G) Free energy profiles of lipid flip-flop in a proteinless POPC membrane (black) and along the MTCH2 scrambling pathway (purple) calculated at T 310 K. As with Martini simulations, the presence of MTCH2 significantly reduces the flip-flop free energy barrier. Note that the calculation error based on the profile asymmetry is relatively high but still below 5 kJ mol−1. See Figure S3 for detailed view of free energy calculations convergence.