Paper Citing NAMD - Abstract
Imai, Yosuke; Liu, Xinli; Yamagishi, Junya; Mori, Kenichi; Neya, Saburo; Hoshino, Tyuji
Computational analysis of water residence on ceramide and sphingomyelin bilayer membranes
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:461-469, NOV 2010
Many physical chemical properties of lipid membranes, for example, the thickness, phase state, order parameter, and fluidity, can be understood straightforwardly. Water residence on a membrane is, however, an exception. To tackle this problem, we have performed molecular dynamics simulations of the distribution of water normal to the surface of several lipid membranes and from this deduced the associated water residence time. Our analysis of the results clearly indicates that lipid membranes have hydration shells on their surface, just as a solute in an aqueous solution does, and that the water residence time can be estimated from the potential for the mean force field derived from the distribution function of the water. We have done this atomic-scale analysis for ceramide bilayers and contrasted the calculation results with those for sphigomyelin bilayers, revealing that sphingomyelin bilayers can retain water molecules longer than ceramide bilayers and that the total number of water molecules retained on the membrane surface of sphingomyelin is larger than that for ceramide. In addition, we find that not only polar atoms of lipid molecules, such as oxygen, but also non-polar atoms, such as carbon, influence the motion of water on the membranes. (C) 2010 Elsevier Inc. All rights reserved.
