FIGURE 5.
MD simulations show that PC has restricted phosphate accessibility. Upper, MD simulations showing that adding N-methyl groups to PE reduces the solvent-accessible surface areas (SASA) of the phosphate group: PE (red), CH3-PE (magenta), (CH3)2-PE (brown), and PC (black). The solvent-accessible surface areas were calculated using varying probe radii for the last 20 ns of 40-ns MD simulations of 1188 lipids. Water (radius of 1.4 Å), Arg (guanidinium group radius of ∼2.5 Å), and the fVIIa GLA domain ω-loop (radius of ∼8 Å) are shown to compare the results with the approximate sizes of functional groups that could interact with the phosphate groups. Lower, visual comparison of phosphate exposure in the bilayer simulations. Phosphate is black; the remainder of the lipid is white.