Comparison of mesoscopic phospholipid–water models

Abstract

In this study we show how a coarse-grained model of a phospholipid can be developed and we study the parameter sets applied to the formation of a coarse-grained dimyristoyl phosphatidyl choline (DMPC) bilayer. We create a model comprising a head group of three hydrophilic beads, to which two hydrophobic tails are connected. From results obtained with molecular dynamics simulations on a single lipid in water, a bond-bending potential between three subsequent beads was added. Using a bead volume of 90 Å 3 , we reproduce the experimental values of the area per lipid and the hydrophobic thickness. There is no linear relation between the repulsion parameter a ij and the level of coarse graining. The key factor in the formation of a lipid bilayer is the difference between the water-water and the water-hydrophobic tail repulsion parameters.

Biological and synthetic membranes: What can be learned from a coarse-grained description?

“…This longer-ranged attraction, which acts only between the interface beads, is sufficient to stabilize fluid bilayer membranes at reduced temperature, k B T /ǫ = 0.9. A different path to the development of generic coarse-grained models has been pursued by Groot [ 184,185], Smit [ 186,187,188,189,190,191], Shillcock [ 142,192,193,194] and Mouritsen [ 195,196] with their co-workers. These coarse-grained models utilize ultra-soft interactions in conjunction with a dissipative particle dynamics (DPD) thermostat [ 197,198,199,200,201].…”

“…By the same token, a solvent bead corresponds to a small number of water molecules. (Attempts to map a single methyl unit onto a soft bead were rather unsuccessful [ 188] in reproducing the internal bilayer structure and resulted in a significant interdigitation of the apposed monolayers.) Typically the amphiphilic molecules consist of only a very small number of beads -one to three hydrophilic head beads and four to ten hydrophobic tail beads.…”

An implicit solvent coarse-grained lipid model with correct stress profile

“…It has been used to study protein insertion and assembly in the bilayer, as well as the properties of lipid mixtures including the addition of cholesterol, to name a few applications. Dissipative particle dynamics ͑DPD͒ simulations, which conserve local angular momentum even while employing random/frictional forces, allow for investigation of even larger length and time scales, and have been used to investigate, for example, the effects of tail stiffness on bilayer properties, 20 the effects of nonionic surfactants, 21 and the hydrophobic matching of embedded proteins. 22 It should be noted that the computational time spent on explicit solvent interactions and forces is the dominant contribution for these coarse-grained lipid model simulations.…”

Mesoscopic Simulations of Biological Membranes

“…In this contribution we summarize some of the results of our simulations. A more complete account can be found in [26][27][28][29][30][31][32][33][34].…”