Molecular dynamics simulations of ubiquinone inside a lipid bilayer

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 degreesC 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. Transitions between these two positions were absent and were presumably restricted by the barrier formed by the relatively ordered high-density region of the palmitic tails close to the lipid headgroups. The lateral diffusion of UQ-10 in the investigated time regime was found in the range of 10(-7) - 10(-1) cm(2)/s and strongly dependent on its relative position inside the membrane; in the midplane position its diffusion was more than three times faster than the diffusion of the lipids. while it was comparable with that of the lipids when the UQ-10 head was close to the membrane surface.