Solvated MARCKS-membrane system and the computational model. (a) Schematic illustration of the MARCKS peptide residing on the inner leaflet of a vesicle. Lipids with charged (red) and polar (cyan) headgroups are distributed in the membrane. (b) 2D cross section of the computational model for (a). The domain Ω mb is the bilayer membrane modeled as a dielectric continuum without atomistic details. Distribution of lipids on membrane surfaces S t and S b follows the surface electrodiffusion equation. Mobile ions are distributed in the aqueous solution exterior and interior to the vesicle. Atomistic structure of the MARCKS peptide is retained and singular charges are distributed in Ω m . Γ is the molecular surface of the peptide, and ∂Ω is the exterior boundary of the computational domain for the Poisson equation. (c) 3D tetrahedral discretization of the entire computational domain. (d) Local refinement of the tetrahedral mesh near the MARCKS peptide.
Without an appropriate model of the lipid size the PIP2 quickly exceeds the upper limit of the concentration under the attraction of the MARCKS peptide. Blue: lipids with vanishing size; Green: lipids with an effective diameter 8.33 Å. The red line signifies the limit of the lipid concentration 0.0144/Å2. Initial average percentage of PIP2 is 1%. The scale on the vertical axis is amplified 100-fold.
(a) Accumulation of PIP2 near the MARCKS peptide; (b) The dependence of the maximum concentration of PIP2 on the initial average concentration; (c) Integration region used for counting the sequestered PIP2; and (d) Number of sequestered PIP2. The initial average concentrations of PIP2 in (a) are 1%, 5%, 10%, 20%, 30% for the green, blue, black, cyan, and maroon lines, respectively. Complete history for the simulation with initial 1% PIP2 is shown in Figure 2. In (c) the red lines represents the MARCKS peptide above the membrane surface. The integration region is not pre-determined for a conforming triangulation so its boundary is not straight. The average percentages in (d) are 0.1%, 1%, 5%, 10%, 20%, and 30%.
(a–e) Accumulation of PIP2 and PS near the MARCKS peptide and (f) the dependence of the maximum concentrations of PIP2 and PS on the initial average concentration of PS. The initial average concentrations of PS in (a–e) are 1%, 5%, 10%, 20%, 30%, respectively, with blue lines denoting PIP2 and red lines denoting PS. The scale on the vertical axis is amplified 100-fold.
Salt-dependent lipid sequestration. Maximum concentration of PIP2 decreases as salt concentration increases from 50 mM (green), 100 mM (magenta), 140 mM (blue), 200 mM (cyan) to 300 mM (red). The number of sequestered PIP2 lipids are 4.02, 3.35, 2.89, 2.16, and 1.07, respectively.
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