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. 2004 Mar;86(3):1601-9.
doi: 10.1016/S0006-3495(04)74227-7.

Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl

Parag Mukhopadhyay  1 , Luca Monticelli, D Peter Tieleman
Affiliations

Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl

Parag Mukhopadhyay et al. Biophys J. 2004 Mar.

Abstract

Two 40 ns molecular dynamics simulations of a palmitoyl-oleoyl phosphatidylserine (POPS) lipid bilayer in the liquid crystalline phase with Na(+) counterions and NaCl were carried out to investigate the structure of the negatively charged lipid bilayer and the effect of salt (NaCl) on the lipid bilayer structure. Na(+) ions were found to penetrate deep into the ester region of the water/lipid interface of the bilayer. Interaction of the Na(+) ions with the lipid bilayer is accompanied by a loss of water molecules around the ion and a simultaneous increase in the number of ester carbonyl oxygen atoms binding the ion, which define an octahedral and square pyramidal geometry. The amine group of the lipid molecule is involved in the formation of inter- and intramolecular hydrogen bonds with the carboxylate and the phosphodiester groups of the lipid molecule. The area per lipid of the POPS bilayer is unaffected by the presence of 0.15M NaCl. There is a small increase in the order parameter of carbon atoms in the beginning of the alkyl chain in the presence of NaCl. This is due to a greater number of Na(+) ions being coordinated by the ester carbonyl oxygen atoms in the water/lipid interface region of the POPS bilayer.

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Figures

FIGURE 1
FIGURE 1
Chemical structure of a POPS molecule with the definition of the names and structure of the groups used in the analysis of the electron density profiles in Fig. 3.
FIGURE 2
FIGURE 2
Area per lipid as a function of time for the POPS bilayer in the presence and in the absence of NaCl.
FIGURE 3
FIGURE 3
Electron density profile of the various groups (as defined in Fig. 1) along the bilayer normal. The density profiles were averaged over the last 25 ns of the trajectories.
FIGURE 4
FIGURE 4
Radial distribution functions of various oxygen atoms with the lipid amine group (formula image) hydrogen atoms.
FIGURE 5
FIGURE 5
Radial distribution functions of various oxygen atoms with all the Na+ ions in the POPS bilayer (A), the Na+ ions in bulk water (B), and the Na+ ions in the ester region (C) of the water/lipid interface. Coordination number of various oxygen atoms around the Na+ ion as a function of distance Z from the bilayer center (D).
FIGURE 6
FIGURE 6
Snapshot of the Na+ ion coordination by lipid oxygen atoms.
FIGURE 7
FIGURE 7
Distribution of the oxygen-Na+-oxygen angle θ for the oxygen atoms in the first coordination shell of the hexa- and penta-coordinated species in the POPS bilayer with NaCl.
FIGURE 8
FIGURE 8
Distribution of the angle between the vector joining phosphorous and nitrogen in POPS and the outward normal to the bilayer for the POPS bilayer (A) in the presence of NaCl and (B) without NaCl.
FIGURE 9
FIGURE 9
Comparison of the deuterium order parameter (SCD) of the alkyl chains in the POPS bilayer in the presence and in the absence of NaCl (A, palmitoyl; B, oleoyl).
FIGURE 10
FIGURE 10
Comparison of the number of Na+ ions averaged over the two leaflets of the lipid bilayer as a function of distance Z from the bilayer center in the POPS bilayer in the presence and in the absence of NaCl.
See this image and copyright information in PMC

References

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