Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ∼1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC bilayer. Overall, the aMD simulations are found to produce significant speedup in trans–gauche isomerization and lipid lateral diffusion versus those in conventional MD (cMD) simulations. Further comparison of a 70-ns aMD run and a 300-ns cMD run of the mixed POPC:DMPC bilayer shows that the two simulations yield similar lipid mixing behaviors, with aMD generating a 2–3-fold speedup compared to cMD. Our results demonstrate that the aMD method is an efficient approach for the study of bilayer structural and dynamic properties. On the basis of simulations of the three bilayer systems, we also discuss the impact of aMD parameters on various lipid properties, which can be used as a guideline for future aMD simulations of membrane systems

Interrelationships between the phase diagrams of the two-component phospholipid bilayers.

Basic relationships between the phase diagrams, previously considered independent of each other, are described. Phase diagrams of two-component phosphatidylcholine/phosphatidylcholine (PC/PC), phosphatidylethanolamine/phosphatidylethanolamine (PE/PE), and PC/PE lipid membranes are systematically investigated by means of the Landau theory. While gradually changing the chain length of one of the components, a characteristic peritectic-miscible-azeotropic-semiazeotropic-eutectic (P-M-A-S-E) series of the phase diagram was found in the PC/PE system and a peritectic-miscible-one-component-miscible-peritectic (P-M-O-M-P) series was found in the PC/PC and PE/PE systems. These serial catastrophic changes in the phase diagrams could be explained by the fusion and birth of the mixed phase regions in the phase diagram. Finally when we constructed the superdiagrams, we obtained all of the possible series of the phase diagrams in a wide class of the two-component mixtures. Moreover, one can predict the type of the phase diagram when the components r and p contain equal-length saturated hydrocarbon chains. Depending on the relationships between the chain lengths (L, Lp) and that on the phase transition temperatures of the pure components (Tr, Tp), the system is: miscible (M), if 0 < Tr(L) - Tp(L) < 5 degrees C and L -Lp > 0, azeotropic (A), if 0 < T,(L) - Tp(L) < 5 degrees C and L -Lp < 0, peritectic (P), if T,(L) - Tp(L) > 40 degrees C and L -Lp - 0, eutectic (E), if Tr(L) - Tp(L) >40 degrees C and L - Lp <0,while it is M or P if 5 degrees C< Tr(L) - Tp(L) <40 degrees C and L - Lp>-0,and E,S,or Aif 5 degrees C < Tr(L) - Tp(L) < 40 degrees C and L,-Lp < 0

Component and state separation in DMPC/DSPC lipid bilayers: a Monte Carlo simulation study.

In this paper a two-state, two-component, Ising-type model is used to simulate the lateral distribution of the components and gel/fluid state acyl chains in dimyristoylphosphatidylcholine/distearoylphosphatidylcholine (DMPC/DSPC) lipid bilayers. The same model has been successful in calculating the excess heat capacity curves, the fluorescence recovery after photobleaching (FRAP) threshold temperatures, the most frequent center-to-center distances between DSPC clusters, and the fractal dimensions of gel clusters (Sugar, I. P., T. E. Thompson, and R. L. Biltonen, 1999. Biophys. J. 76:2099-2110). Depending on the temperature and mole fraction the population of the cluster size is either homogeneous or inhomogeneous. In the inhomogeneous population the size of the largest cluster scales with the size of the system, while the rest of the clusters remain small with increasing system size. In a homogeneous population, however, every cluster remains small with increasing system size. For both compositional and fluid/gel state clusters, threshold temperatures-the so-called percolation threshold temperatures-are determined where change in the type of the population takes place. At a given mole fraction, the number of percolation threshold temperatures can be 0, 1, 2, or 3. By plotting these percolation threshold temperatures on the temperature/mole fraction plane, the diagrams of component and state separation of DMPC/DSPC bilayers are constructed. In agreement with the small-angle neutron scattering measurements, the component separation diagram shows nonrandom lateral distribution of the components not only in the gel-fluid mixed phase region, but also in the pure gel and pure fluid regions. A combined diagram of component and state separation is constructed to characterize the lateral distribution of lipid components and gel/fluid state acyl chains in DMPC/DSPC mixtures. While theoretical phase diagrams of two component mixtures can be constructed only in the case of first-order transitions, state and component separation diagrams can be constructed whether or not the system is involved in first-order transition. The effects of interchain interactions on the component and state separation diagrams are demonstrated on three different models. The influences of state and component separation on the in-plane and off-plane membrane reactions are discussed

Geometrical properties of gel and fluid clusters in DMPC/DSPC bilayers: Monte Carlo simulation approach using a two-state model.

In this paper the geometrical properties of gel and fluid clusters of equimolar dimyristoylphosphatidylcholine/distearoylphosphatidylcholine (DMPC/DSPC) lipid bilayers are calculated by using an Ising-type model (Sugar, I. P., T. E. Thompson, and R. L. Biltonen. 1999. Biophys. J. 76:2099-2110). The model is able to predict the following properties in agreement with the respective experimental data: the excess heat capacity curves, fluorescence recovery after photobleaching (FRAP) threshold temperatures at different mixing ratios, the most frequent center-to-center distance between DSPC clusters, and the fractal dimension of gel clusters. In agreement with the neutron diffraction and fluorescence microscopy data, the simulations show that below the percolation threshold temperature of gel clusters many nanometer-size gel clusters co-exist with one large gel cluster of size comparable with the membrane surface area. With increasing temperature the calculated effective fractal dimension and capacity dimension of gel and fluid clusters decrease and increase, respectively, within the (0, 2) interval. In the region of the gel-to-fluid transition the following geometrical properties are independent from the temperature and the state of the cluster: 1) the cluster perimeter linearly increases with the number of cluster arms at a rate of 8.2 nm/arm; 2) the average number of inner islands in a cluster increases with increasing cluster size, S, according to a power function of 0.00427 x S(1.3); 3) the following exponential function describes the average size of an inner island versus the size of the host cluster, S: 1 + 1.09(1 - e(-0.0072xS)). By means of the equations describing the average geometry of the clusters the process of the association of clusters is investigated

The lateral distribution of pyrene-labeled sphingomyelin and glucosylceramide in phosphatidylcholine bilayers.

The lateral distribution of N-[10(1-pyrenyl)decanoyl]-sphingomyelin (PyrSPM) and N-[10(1-pyrenyl)decanoyl]-glucocerebroside (PyrGlcCer) was studied in multilamellar vesicles of 1,2-dipalmitoyl-, 1,2-dimyristoyl-, and 1-palmitoyl-2-oleoyl-phosphatidylcholine (DPPC, DMPC, and POPC, respectively) under anaerobic conditions by determining the excimer-to-monomer fluorescence intensity ratio (E/M) as a function of temperature. The E/M(T) curves for PyrSPM and PyrGlcCer in the three phosphatidylcholine matrices are qualitatively similar to the curves reported for 1-palmitoyl-2-[10-(1-pyrenyl)decanoyl]-phosphatidylcholine (PyrPC) in the same three matrix phospholipids (Hresko, R. C., I. P. Sugár, Y. Barenholz, and T. E. Thompson, 1986, Biochemistry, 25:3813-3823). However, there is independent evidence to suggest that sphingomyelin and glucocerebroside are organized in POPC, DPPC, and DMPC in a more complex manner than is PyrPC. In an effort to examine further the relationship between the lateral distribution of the labeled lipid and the shape of an E/M(T) curve, E/M vs. temperature simulations were carried out together with an analysis of the equation that relates E/M to the system parameters. The results indicate that information about the lateral distribution of the pyrene-labeled lipid can be obtained from an E/M(T) curve only for those systems in which the gel to liquid crystalline phase transition temperature of the matrix lipid is higher than that of the pyrene-labeled lipid. However, very little can be known about the system from an E/M(T) curve if the matrix lipid has the lower phase transition temperature