Phase separation behavior of mixed lipid systems at neutral and low pH: coarse-grained simulations with DMD/LIME

Abstract

We extend LIME, an intermediate resolution, implicit solvent model for phospholipids previously used in discontinuous molecular dynamics simulations of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer formation at 325 K, to the description of the geometry and energetics of 1,2-distearoyl-sn-glycero-3-phospho-L-serine (DSPS) and 1,2-dihenarachidoyl-sn-glycero-3-phosphocholine (21PC) and mixtures thereof at both neutral and low pH at 310 K. A multiscale modeling approach is used to calculate the LIME parameters from atomistic simulation data on a mixed DPPC/DSPS system at different pH values. In the model, 17 coarse-grained sites represent DSPS and 18 coarse-grained sites represent 21PC. Each of these coarse-grained sites is classified as 1 of 9 types. LIME/DMD simulations of equimolar bilayers show the following: (1) 21PC/DSPS bilayers with and without surface area restrictions separate faster at low pH than at neutral pH, (2) 21PC/DSPS systems separate at approximately the same rate regardless of whether they are subjected to surface area restrictions, and (3) bilayers with a molar ratio of 9:1 (21PC:DSPS) phase separate to form heterogeneous domains faster at low pH than at neutral pH. Our results are consistent with experimental findings of Sofou and co-workers (Bandekar et al. Mol. Pharmaceutics, 2013, 10, 152-160; Karve et al. Biomaterials, 2010, 31, 4409-4416) that more doxorubicin is released from 21PC/DSPS liposomes at low pH than at neutral pH, presumably because greater phase separation is achieved at low pH than at neutral pH. These are the first molecular-level simulations of the phase separation in mixed lipid bilayers induced by a change in pH.

Figure 1

Structure of (a) 21PC and (b) DSPS at neutral pH. At low pH, the oxygen atom in the dotted circle becomes protonated.

Figure 2

United atom and coarse-grained representations of (a) DSPS and (b) 21PC. The color scheme is black (negatively charged carboxyl group, type Ia; protonated carboxyl group, type Ib for DSPS site 1); magenta (amine group, type II for DSPS site 2); yellow (phosphate group, type III for DSPS site 3); red (ester group, type IV for DSPS site 4 and 21PC site 3); orange (ester group, type V for DSPS site 11 and 21PC site 11); cyan (alkyl tail groups, type VI for DSPS sites 5–9 and 12–16 and for 21PC sites 4–9 and 12–17); gray (terminal tail groups, type VII for DSPS sites 10 and 17 and for 21PC sites 10 and 18); purple (choline entity, type VIII for 21PC site 1); and yellow (phosphate group, type IX for 21PC site 2).

Figure 3

Snapshots (aerial images) of the bilayer formed at 1 million collisions in simulations of Systems 1 (a), 2 (c), 3 (e), 4 (g), 5 (i), and 6 (k) and at 1 billion collisions in simulations of Systems 1 (b), 2 (d), 3 (f), 4 (h), 5 (j), and 6 (l). The color scheme is lime (21PC lipids) and purple (DSPS lipids at neutral pH and low pH).

Figure 4

Normalized, time-averaged percentage of DSPS lipid molecules within a 5 Å radius of each DSPS headgroup (coarse-grained site 1 on each DSPS lipid molecule).