Molecular dynamics simulations of ternary membrane mixture: phosphatidylcholine, phosphatidic acid, and cholesterol

Abstract

A ternary mixture of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl phosphatidic acid (POPA), and cholesterol (CHOL) works effectively for a functional conformation of nicotinic acetylcholine receptor (nAChR) that can undergo agonist-induced conformation changes, but POPC alone can stabilize only a desensitized state of nAChR. To gain insights into the lipid mixture that has strong impact to nAChR functions, we performed more than 50 ns all atom molecular dynamic (MD) simulations at 303 K on a fully hydrated bilayer consisting of 240 POPC, 80 POPA, and 80 CHOL (3:1:1). The MD simulation revealed various interactions between different types of molecular pairs that ultimately regulated lipid organization. The heterogeneous interactions among three different constituents resulted in a broad spectrum of lipid properties, including extensive distributions of average area per lipid and varied lipid ordering as a function of lipid closeness to CHOL. Higher percentage of POPA than POPC had close association with CHOL, which coincided with relatively higher ordering of POPA molecules in their acyl chains near lipid head groups. Lower fraction of gauche dihedrals was also found in the same region of POPA. Although the CHOL molecules had the effects on the enhancement of surrounding lipid order, relatively low lipid order parameters and high fraction of gauche bonds were observed in the ternary mixture. Collectively, these results suggest that the dynamical structure of the ternary system could be determinant for a functional nAChR.

Fig. 1

Structures of POPC, POPA, and CHOL molecules. Atoms selected for Voronoi tessellation are highlighted in spheres. Several atoms mentioned in the text and carbon atoms in the double bond are labeled.

Fig. 2

Top views of snapshots of the system experienced (A) 0-ns and (B) 50-ns MD simulations. Water molecules were removed for clarity. CHOL, POPA, and POPC are in red, blue and yellow, respectively.

Fig. 3

Radial distribution functions (RDF) between specified atom pairs after 1-ns (dash doted), 30-ns (short dashed), and 50-ns (solid line) simulations. (A) P1 atom of POPA vs. O3 atom of CHOL; (B) P1 atom of POPC vs. O3 atom of CHOL; (C) P1 atom of POPC vs. P1 atom of POPA; (D) O3-O3 in CHOL; (E) P1-P1 in POPC; (F) P1-P1 in POPA. The data resulted from the average over 500 simulation frames near the designated simulation time.

Fig. 4

Snapshots of various interacting pairs in the POPC-POPA-CHOL system: (A) VDW interaction of POPA and CHOL (orange). Two methyl groups on the rings of CHOL are highlighted in circle. Black sphere in POPA represents C4 atom in sn1 chain. (B) hydrogen bonding (HB) between POPA and CHOL; (C) HB between two CHOL molecules; (D) water mediated HB between CHOL molecules; (E) electrostatic interaction between headgroup oxygen of POPA (red) and nitrogen of choline group of POPC (blue); (F) Na⁺ (yellow) mediated pairing between POPA and POPC.

Fig. 5

Histograms of area per molecule for the system experienced 10-ns (grey) and 50-ns (black) MD simulations. Each histogram, with a bin size of 2.5, resulted from averaging both leaflets in 10 representative simulation snapshots over 40 ps time slabs. Individual components included POPC (●), POPA (■), CHOL (◆). For clarity, most of the symbols were not shown in the plots.

Fig. 6

Comparison of order parameters for (A) the sn1 chains of POPC (●) and POPA (■) at 50 ns and (B) POPC at a number of simulation time point: 10ns (◆), 15 ns (▼), 30 ns (▲) and 50 ns (●). The reported $S_n^{CD}$ resulted from the average over 500 simulation frames near the designated simulation time. The error bars is smaller than the symbol size.

Fig. 7

Electron density profiles averaged over the last 1-ns simulation along the bilayer normal. (A) Total simulated system (solid line), water (dashed line), POPC (●), POPA (○) and CHOL (◆); and (B) individual groups of lipids: POPC phosphorous (▼), POPA phosphorous (▽), hydroxyl oxygen of CHOL (■), C4 of POPC (●), C4 of POPA (○).