Recent development in computer simulations of lipid bilayers

Abstract

Rapid development of computer power during the last decade has made molecular simulations of lipid bilayers feasible for many research groups, which, together with the growing general interest in investigations of these very important biological systems has lead to tremendous increase of the number of research on the computational modeling of lipid bilayers. In this review, we give account of the recent progress in computer simulations of lipid bilayers covering mainly the period of the last 5 years, and covering several selected subjects: development of the force fields for lipid bilayer simulations, studies of the role of lipid unsaturation, the effect of cholesterol and other inclusions on properties of the bilayer, and use of coarse-grained models.

Phosphatidylcholine reverse micelles on the wrong track in molecular dynamics simulations of phospholipids in an organic solvent

“…CHARMM36 force field performs very well in describing all the studied components individually or in aqueous environment, 37,38 and is currently one of the highest regarded lipid force fields, with good accuracy in water environment. [1][2][3][4] However, the FIG. 7.…”

“…Then, the box vectors and the coordinates were repeatedly scaled by the factor of 0.98 and the resulting configuration energy minimized. This was repeated until the size of the box was significantly compressed to size (∼3.7 nm) 3 . This ensured no substantial voids were left in the system.…”

“…This ensured no substantial voids were left in the system. After this, the system was allowed to expand in the NPT ensemble (barostat time constant τ p = 40 ps) until the volume reached ∼125 nm 3 corresponding to a density close to the experimental value.…”

Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study

“…26,82 Sampling problems are more important in lateral diffusion than in some other properties, because it involves large-scale motions of whole molecules rather than limited range/segmental motions (like those involved in lipid acyl chains or probe long axis orientation). For relatively short times, lipid diffusion (as perceived by MSD variation) is mainly due to conformational changes of the hydrocarbon chains rather than diffusion of the entire molecule, 26 and therefore its meaning and its relationship to experimental observables are somewhat questionable. For these reasons, we will refrain from a quantitative discussion of absolute D values, and will focus on trends of variation across the studied series instead.…”

M.DynaMix Studies of Solvation, Solubility and Permeability

“…It is not surprising that lipid membrane bilayers composed of various phosphatidylcholine lipids have been extensively studied by molecular dynamics as soon as computer hardware allowed to do such simulations. However, obtaining of reliable information on physical-chemical properties of lipid bilayers was, in many studies of the last decades, seriously limited by two factors: 1) necessity to simulate a large (of the order of few tens thousand) number of atoms during long (hundreds of nanosecond) simulation time and 2) not satisfactory reliability of the commonly available force fields to describe behaviour of lipid bilayers www.intechopen.com consistently, with respect to variation of lipid chemical structure, composition, thermodynamic conditions (Lyubartsev & Rabinovich, 2011). While solution of the first problem is determined by advances in the development of computer hardware, the issue of proper parametrization of the force field requires extensive computational work including numerous test simulation of the bilayer systems and calculations of different experimentally measured properties.…”