Figure 4
Comparison of the structural and dynamic properties of the phospholipid bilayer in simulations of the CYP 2C9-POPC membrane system conducted with the LIPID14 + ff14SB and the GAFF-LIPID + ff99SB parameters. Computed time averaged C-H (deuterium) order parameters for the Sn1 (solid lines) and Sn2 (dashed lines) chains (a) and electron density profiles (b) for simulations with LIPID14 + ff14SB (black) and GAFF-LIPID + ff99SB (grey) parameters. The electron density profiles computed for the last 50 ns of the simulations are shown for the protein+phospholipid system (upper lines) and for the water molecules (lower lines). The profiles peak at 0.43 e/Å3 for the head groups and drop below 0.3 e/Å3 for the methylene groups in the tail region48. The thickness of the bilayer is lower for GAFF-LIPID + ff99SB and the electron density is less depleted in the middle of the bilayer. The asymmetry in the electron density distribution around the bilayer center is due to the interaction of the protein globular domain on the positive side of the z-axis of the bilayer. The decomposition of the electron density profile into different segments of the membrane bilayer, water and protein is shown in (c) and the variation in the bilayer thickness over the simulated bilayer (d) for LIPID14 + ff14SB (upper panels) and GAFF-LIPID + ff99SB (lower panels). A similar shape of the trough in the profile is seen in all systems simulated with LIPID14 + ff14SB, whereas for GAFF-LIPID + ff99SB, a broader trough is visible. The plots in Fig. 4A–C were generated using Xmgrace (plasma-gate.weizmann.ac.il/Grace/)38. Fig. 4D was generated using g_lomepro v1.0.2 (www3.mpibpc.mpg.de/groups/de_groot/g_lomepro.html)50.
