Fig 1.
Chemical structures of the di- and tetra-ether lipids simulated in this study.
DPhPC (DPH), ether-diphytanylphosphatidylcholine. TEP, di-O-biphytanyphosphatidylcholine. GDNT, glycerol dialkylnonitol tetraether, with zero (GDNT-0) or four (GDNT-4) cyclopentane rings.
Table 1.
σ and ϵ Lennard Jones parameters for ions.
Fig 2.
Structures of a DPhPC bilayer (left) and a TEP monolayer (right). Only a single unit is displayed.
Fig 3.
Deuterium order parameter (SCD) calculated along the main lipid hydrocarbon chains (sn-1/2) of DPhPC and TEP membrane models.
Table 2.
Physical properties of the simulated membranes.
Fig 4.
Structures of (A) GDNT-0 and (B) GDNT-4. Only a single unit is displayed.
Fig 5.
Deuterium order parameter (SCD) calculated along the main lipid hydrocarbon chains (sn-1/3) of GDNT membrane models.
(A) A comparison between GDNT-0 at T = 325K and TEP. (B) A comparison between GDNT-0 and GDNT-4, with different counter-ions.
Fig 6.
Total electron density profiles of the simulated membrane models along the membrane normal.
The centre of the membrane corresponds to z = 0. (A) DPhPC bilayer (solid line) vs. TEP monolayer (dotted line); (B) GDNT-0 monolayers with small (A+, solid line) and large (B+, dashed line) counter ions vs. TEP monolayer (dotted line); (C) GDNT-4 monolayers with small (solid red line) and large counter ions (dashed red line) vs. GDNT-0 monolayers with small (solid line) and large (dashed line) counter ions.
Fig 7.
Total and separate electron density profiles of GDNT-4 with neutralising charges.
The inset depicts the density of the B+ ions.
Fig 8.
The radial distribution of counterions around the lipid phosphate ions, calculated from simulations of GDNT-4 membranes.
The cumulative number of ions at a given distance from the phosphate ions is shown by the dashed lines. A value of 1 for the radial distribution function indicates the bulk distribution. For the cumulative number, values in the Y-axis are the actual number of ions within a given distance from a phosphate group.
Fig 9.
The electric potential across the membrane.
The potential is shown over the z axis for the four different simulations. The charged phosphate groups are located on the left-hand side of the figure (lower values of z). The potential is calculated with reference to the centre of the membrane, where the charge is roughly zero. Each line is an average over four simulations, where the calculation was carried out over 40 ns. The membranes are centred at x = 0 nm. Note that the (average) box length is not exactly the same due to the simulation conditions (constant pressure, variable volume).