Molecular Dynamics Simulations of Ubiquinone inside a Lipid Bilayer

Abstract

A series of multiple nanosecond molecular dynamics simulations has been carried out for a dipalmitoylphosphatidylcholine lipid bilayer system in water solution, with ubiquinone (UQ) freely moving inside the bilayer. The focus is on the mobility and the preferential positions of the quinone molecule. Two different tail lengths have been used in the simulations to investigate the effect of the long tail, attached to the quinone-ring. The lateral diffusion rate in the nanosecond time scale, obtained for 2,3-dimethoxy-5-ethyl-6-methyl-1,4-benzoquinone (short tail, denoted UQ-et) was at 60 °C found to be roughly the same as that for the lipids. The headgroup of UQ-et preferred a location between the 4th and the 10th carbon atom in the palmitic chains of the lipids. For UQ-10 (10 unit long isoprenoid tail), two preferred positions of the headgroup were found in separate simulations with different initial configurations for the quinone; one close to the lipid headgroups, the other in the membrane midplane. Trans...