Paper Citing NAMD - Abstract
Shintani, Megumi; Matsuo, Yushi; Sakuraba, Shun; Matubayasi, Nobuyuki
Interaction of naphthalene derivatives with lipids in membranes studied by the H-1-nuclear Overhauser effect and molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:14049-14060, 2012
The location, orientation, and dynamics of hydrophobic small molecules in lipid membranes are studied through combined use of solution-state H-1-NMR and MD simulation. 1-Naphthol and 1-methylnaphthalene were adopted as the small molecules with or without hydrophilic groups. The nuclear Overhauser effect (NOE) measurement was performed for large unilamellar vesicles (100 nm in diameter) composed of dimyristoylphosphatidylcholine (DMPC) and the naphthalene derivative. The transient NOE-SE (spin-echo) scheme previously reported (J. Phys. Chem. B, 2011, 115, 9106-9115) was employed to quantitatively determine the NOE cross relaxation rate constant between DMPC and the naphthalene derivative. The observed NOE shows that both the naphthalene derivatives distribute over a wide domain across the normal of the essentially planar membrane ranging from the hydrophobic core to the hydrophilic headgroup. The experimental NOE information was further refined in combination with the analysis of time correlation functions in MD simulation. It was found that 1-naphthol exhibits a slight preference for pointing its OH group toward the hydrophilic domain of the membrane and that no definite preference can be concluded for the orientation of 1-methylnaphthalene. When 1-naphthol and 1-methylnaphthalene are compared, the NOE is stronger for 1-naphthol due to the restricted motion of the OH group. The slowdown of the 1-naphthol motion is also evidenced by the H-1 spectral line width.
