Paper Citing NAMD - Abstract
Klauda, Jeffery B.; Roberts, Mary F.; Redfield, Alfred G.; Brooks, Bernard R.; Pastor, Richard W.
Rotation of lipids in membranes: Molecular dynamics simulation, P-31 spin-lattice relaxation, and rigid-body dynamics
BIOPHYSICAL JOURNAL, 94:3074-3083, APR 15 2008
Molecular dynamics simulations and P-31-NMR spin-lattice (R-1) relaxation rates from 0.022 to 21.1 T of fluid phase dipalmitoylphosphatidylcholine bilayers are compared. Agreement between experiment and direct prediction from simulation indicates that the dominant slow relaxation (correlation) times of the dipolar and chemical shift anisotropy spin-lattice relaxation are similar to 10 ns and 3 ns, respectively. Overall reorientation of the lipid body, consisting of the phosphorus, glycerol, anclacyl chains, is well described within a rigid-body model. Wobble, with D-perpendicular to = 1-2 X 10(8) s(-1), is the primary component of the 10 ns relaxation; this timescale is consistent with the tumbling of a lipid-sized cylinder in a medium with the viscosity of liquid hexadecane. The value for D parallel to, the diffusion constant for rotation about the long axis of the lipid body, is difficult to determine precisely because of averaging by fast motions and wobble; it is tentatively estimated to be 1 X 10(7)s(-1). The resulting D-parallel to/D-perpendicular to approximate to 0. 1 implies that axial rotation is strongly modulated by interactions at the lipid/water interface. Rigid-body modeling and potential of mean force evaluations show that the choline group is relatively uncoupled from the rest of the lipid. This is consistent with the ratio of chemical shift anisotropy and dipolar correlation times reported here and the previous observations that P-31-NMR lineshapes are axially symmetric even in the gel phase of dipalmitoylphosphatidylcholine.
