Comparative Molecular Dynamics Study of Ether- and Ester-linked Phospholipid Bilayers

Keiko Shinoda, Wataru Shinoda, Teruhiko Baba, and Masuhiro Mikami

J. Chem. Phys. 121 9648-9654 (2004).

The lipid membranes found in archaea have high bilayer stability and low permeability. The molecular structure of their constituent lipids is characterized by ether-linked, branched hydrophobic chains, whereas the conventional lipids obtained from eukaryotic or eubacterial sources have ester-linked straight chains. In order to elucidate the influence of the ether-linkage, instead of an ester-one, on the physical properties of the lipid bilayers, we have carried out comparative 10ns-molecular dynamics simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers in water, respectively. We analyze bilayer structures, hydration of the lipids, membrane dipole potentials, and free energy profiles of water and oxygen across the bilayers. We observe that the membrane dipole potential for the ether-DPhPC bilayer, which arises mainly from the ether linkage, is about half of that of the ester-DPhPC. The calculated free energy barrier for a water molecule in the ether-DPhPC bilayer system is slightly higher than that in the ester-DPhPC counterpart, which is in accord with experimental data.

Electrostatic potential profile along the bilayer normal