| Literature DB >> 20095587 |
Ulf R Pedersen1, Günther H Peters, Thomas B Schrøder, Jeppe C Dyre.
Abstract
This paper reports all-atom computer simulations of five phospholipid membranes (DMPC, DPPC, DMPG, DMPS, and DMPSH) with focus on the thermal equilibrium fluctuations of volume, energy, area, thickness, and chain order. At constant temperature and pressure, volume and energy exhibit strong correlations of their slow fluctuations (defined by averaging over 0.5 ns). These quantities, on the other hand, do not correlate significantly with area, thickness, or chain order. The correlations are mainly reported for the fluid phase, but we also give some results for the ordered (gel) phase of two membranes, showing a similar picture. The cause of the observed strong correlations is identified by splitting volume and energy into contributions from tails, heads, and water, and showing that the slow volume-energy fluctuations derive from van der Waals interactions of the tail region; they are thus analogous to the similar strong correlations recently observed in computer simulations of the Lennard-Jones and other simple van der Waals type liquids (U. R. Pedersen et al., Phys. Rev. Lett. 2008, 100, 015701). The strong correlations reported here confirm one crucial assumption of a recent theory for nerve signal propagation proposed by Heimburg and Jackson (T. Heimburg and A. D. Jackson, Proc. Natl. Acad. Sci. 2005, 102, 9790-9795).Entities:
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Year: 2010 PMID: 20095587 PMCID: PMC2820308 DOI: 10.1021/jp9086865
Source DB: PubMed Journal: J Phys Chem B ISSN: 1520-5207 Impact factor: 2.991
Overview of Simulation Details and Results
| system (phase) | ||||||
|---|---|---|---|---|---|---|
| DMPC-f (fluid) | 151 | 121 | 128 | 330.0 | 329.0 ± 1.6 | 33 |
| DMPC-g (ordered) | 65 | 36 | 64 | 286.0 | 285.3 ± 2.0 | 33 |
| DPPC-f (fluid) | 180 | 124 | 72 | 325.0 | 324.0 ± 2.1 | 29 |
| DPPC-g (ordered) | 78 | 48 | 64 | 304.0 | 303.2 ± 2.1 | 33 |
| DMPG (fluid) | 149 | 49 | 128 | 330.0 | 329.0 ± 1.6 | 33 |
| DMPS (fluid) | 139 | 49 | 128 | 340.0 | 339.0 ± 1.7 | 36 |
| DMPSH (fluid) | 136 | 35 | 128 | 340.0 | 339.1 ± 1.6 | 37 |
tsim, total simulation time in nanoseconds; tprod, length of production run in nanoseconds (only membranes in quasi-equilibrium, i.e., with no detectable drift in the area per molecule, were included in the data analysis); Nlipid, number of lipid molecules; T, thermostat temperature in kelvin; Tactual, average temperature and standard deviation of fluctuations; Nwater/Nlipid, number of water molecules per lipid molecule.
R, energy−volume correlation coefficient (see eq 1). The bar indicated a 0.5 ns average. The uncertainty is estimated from the DMPC-f and DPPC-f trajectories as described in the text (67% confidence interval); γ, energy−volume scaling factor in units of 10−4 mL/J (see eq 11); R, energy−“energy of tail region” correlation coefficient; R, energy−area correlation coefficient; R, volume−area correlation coefficient; R, area−“chain order parameter” correlation coefficient; R, energy−“chain order parameter” correlation coefficient; R, volume−“chain order parameter” correlation coefficient.
Figure 1Snapshots of DMPC membranes in the fluid phase (DMPC-f; panel A) and in the ordered phase (DMPC-g; panel B). The red atoms are the oxygen atoms of water molecules; hydrogen atoms were removed for visual clarity (but included in the simulations). Acyl chains are colored green. The frame indicates the periodic boundary box.
Figure 2Correlations in the slow thermal equilibrium fluctuations of volume and energy (top) and correlation matrix for the DMPC-f membrane (bottom). The normalized fluctuations of volume and potential energy shown are averaged over time intervals of 0.5 ns. Data are shifted and scaled such that the average value is zero and the standard deviation is unity. A significant correlation is observed and quantified by the correlation coefficient, R = 0.77. This strong correlation can be associated with the tail region, as seen by the similarities with Figure 5. The bottom panel represents the absolute values of the elements of the correlation matrix of energy, volume, membrane area, thickness, and the average chain order parameter, where dark red illustrates strong correlation. Membrane area, thickness, and average chain order parameter are strongly correlated, but these quantities only correlate weakly with energy and volume. Similar results are found for the other fluid membranes (except for DMPC-g and DMPS where the energy−volume correlation is only 0.47 and 0.59, respectively); see Table 1.
Figure 5Normalized fluctuations of Voronoi volume and van der Waals energy of the tail region of the DMPC-f membrane, V̅t(t) and U̅tLJ(t). V̅t(t) and U̅tLJ(t) are shifted and scaled so the average value is zero and the standard deviation is unity. The correlation is strong with a correlation coefficient of 0.87 (justifying eq 9). Note the similarity with Figure 2A; thus, slow V−U fluctuations are dominated by the tail region.
Figure 3Time-dependent correlation coefficient of volume−energy Γ(t) (left) and area−energy Γ(t) (right). The fast fluctuations of volume and energy, t < 10−2 ns, only correlate weakly, whereas the slow fluctuations, t ≃ 1 ns, correlate strongly. Area and energy fluctuations are only weakly correlated in the investigated time regime.
Figure 4Time-dependent auto- and cross-correlation function of volume and energy terms of the DMPC-f membrane. Panel A: Volume correlation functions of the tail, head, and water regions (eq 4). Slow volume fluctuations are dominated by the tail region. The shot-time tail−water anticorrelation is probably an artifact of the way the Voronoi polyhedron is constructed (related to the tail−water interface, see text for details). Panel B: Correlation functions of energies of the three regions (eq 8). Again, slow fluctuations are dominated by the tail region. Panel C: Energy correlations split into intramolecular, Lennard-Jones (LJ), and Coulombic energies (eq 7 with x = tail).