Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl

Abstract

Molecular dynamics simulations are performed on two hydrated dipalmitoylphosphatidylcholine bilayer systems: one with pure water and one with added NaCl. Due to the rugged nature of the membrane/electrolyte interface, ion binding to the membrane surface is characterized by the loss of ion hydration. Using this structural characterization, binding of Na(+) and Cl(-) ions to the membrane is observed, although the binding of Cl(-) is seen to be slightly weaker than that of Na(+). Dehydration is seen to occur to a different extent for each type of ion. In addition, the excess binding of Na(+) gives rise to a net positive surface charge density just outside the bilayer. The positive density produces a positive electrostatic potential in this region, whereas the system without salt shows an electrostatic potential of zero.

FIGURE 1

(a) Area per headgroup as a function of time for the last 5 ns of the total 10 ns trajectory. (b) The z-component of the center of mass of the ions as a function of time for each leaflet of the bilayer. The center of the bilayer is denoted by the dotted line at z = 0.

FIGURE 2

The deuterium order parameters for hydrocarbon tails of DPPC. The error bars in the figure are calculated by dividing the 5-ns trajectory into ten 500-ps trajectories.

FIGURE 3

Electron densities as a function of the z-coordinate in both systems.

FIGURE 4

Distribution of the angle between the vector joining the phosphorus and nitrogen in the DPPC headgroup and the outward normal of the bilayer.

FIGURE 5

(a) Densities of various atoms in the system as function of the z-coordinate. Densities are averaged over two leaflets of the bilayer. (b) Number of Na⁺ and Cl⁻ ions found between the center of the bilayer and the x-y plane at position z in the system.

FIGURE 6

RDF of (a) Na⁺ with phosphorus, (b) Na⁺ with nitrogen, (c) Cl⁻ with phosphorus, and (d) Cl⁻ with nitrogen.

FIGURE 7

RDF of (a) Na⁺ with phosphate oxygens, and (b) Na⁺ with carbonyl oxygens.

FIGURE 8

Snapshot pictures showing the ion-lipid coordination.

FIGURE 9

The coordination number of various atoms around the ions. Water oxygen around Na⁺ (•), water oxygen around Cl⁻ (○), phosphate oxygens around Na⁺ (▵), and carbonyl oxygens around Na⁺ (▴).

FIGURE 10

(a) Total electrostatic potential profile of the system. The quantities are averaged over both leaflets of the bilayer. The error bars, inset, are calculated by dividing the 5-ns trajectory into five 1-ns trajectories. (b) Surface charge density σ as a function of the z-coordinate.