Molecular dynamics simulation of a phospholipid membrane.
We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in future simulations. This goal being reached it is then further possible to gain insight in to those properties that are experimentally more difficult to access. The system studied is dipalmitoylphosphatidylcholine/water, consisting of 5408 atoms. Using original force field parameters the membrane turned out to approach a gel-like state. With slight changes of the parameters, the system adopted a liquid-crystalline state. Separate 80 ps runs were performed on both the gel and liquid-crystalline systems. Comparison of MD results with reliable experimental data (bilayer repeat distance, surface area per lipid, tail order parameters, atom distributions) showed that our simulations, especially the one in the liquid-crystalline phase, can serve as a realistic model for a phospholipid membrane. Further analysis of the trajectories revealed valuable information on various properties. In the liquid-crystalline phase, the interface turns out to be quite diffuse, with water molecules penetrating into the bilayer to the position of the carbonyl groups. The 10-90% width of the interface turns out to be 1.3 nm and the width of the hydrocarbon interior 3.0 nm. The headgroup dipoles are oriented at a small angle with respect to the bilayer plane. The resulting charge distribution is almost completely cancelled by the water molecules. The electron density distribution shows a large dip in the middle of the membrane. In this part the tails are more flexible. The mean life time between dihedral transitions is 20 ps. The average number of gauche angles per tail is 3.5. The occurrence of kinks is not a significant feature.
Egberts
E
E
Department of Biophysical Chemistry, University of Groningen, The Netherlands.
Marrink
S J
SJ
Berendsen
H J
HJ
D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry; D003198:Computer Simulation; D003460:Crystallization; D004058:Diffusion; D006838:Hydrocarbons / Q000737:chemistry; D008567:Membranes, Artificial; D008968:Molecular Conformation; D010713:Phosphatidylcholines / Q000737:chemistry; D010743:Phospholipids / Q000737:chemistry*; D013696:Temperature; D014867:Water / Q000737:chemistry
D006838:Hydrocarbons; D008567:Membranes, Artificial; D010713:Phosphatidylcholines; D010743:Phospholipids; D014867:Water; D015060:1,2-Dipalmitoylphosphatidylcholine