Paper Citing NAMD - Abstract
Tobias, Douglas J.; Sengupta, Neelanjana; Tarek, Nlounir
Hydration dynamics of purple membranes
FARADAY DISCUSSIONS, 141:99-116, 2009
Protein motions occur over many decades of time, from femtoseconds to seconds and longer. Fast (ps ns) protein motion enabled by water dynamics on the surfaces of protein molecules is generally believed to be required for biological function. The coupling between water and protein dynamics for soluble proteins in aqueous solution is relatively well understood, while the couplings between protein, lipid, and water dynamics in membranes are only beginning to be unravelled. We report a molecular dynamics simulation study of the dynamics of water hydrating purple membranes (PM). We validate our simulations by comparing the temperature and hydration dependence of crystal lattice parameters and water and protein/lipid dynamics with neutron diffraction and spectroscopic data. We proceed to examine the temperature dependence of several time-dependent quantities describing different aspects of water dynamics, and identify and characterize the correlations between water dynamics and the motion of the protein and lipid components of PM. Our results point to a correlation between the solvation dynamics of lipid molecules and the dynamics of the both the protein and lipid components.
