Paper Citing NAMD - Abstract
Pedersen, Ulf R.; Peters, Gunther H.; Westh, Peter
Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation
BIOPHYSICAL CHEMISTRY, 125:104-111, JAN 2007
The structure and molecular packing density of a "mismatched" solute, 1-hexanol, in lipid membranes of dimytistoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data on comparable systems. The local density or molecular packing in DMPC-hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested a positive volume change, Delta V-m, of 4 cm(3) mol(-1) hexanol partitioned at 310 K in good accordance with experimental values. Analysis of the apparent volumes of each component in the pure and mixed states further showed that Delta V-m reflects a balance between a substantial increase in the packing density of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8) is stretched by about 4%. Concomitantly, the average lateral area per chain decreases and these two effects compensate so that the overall packing density in the outer region, where the hexanol molecules are located, remains practically constant. The core of the bilayer (C9-C13) is slightly thinned. The average lateral area per chain in this region expands, resulting in a looser packing density. The net effect in the core is a 2-3% decrease in density corresponding to a total volume increase of similar to 14 cm(3) mol(-1) hexanol partitioned. (c) 2006 Elsevier B.V. All rights reserved.
