Paper Citing NAMD - Abstract
Baker, Michelle K.; Abrams, Cameron F.
Dynamics of Lipids, Cholesterol, and Transmembrane alpha-Helices from Microsecond Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13590-13600, NOV 27 2014
Extensive all-atom molecular dynamics (similar to 24 mu s total) allowed exploration of configurational space and calculation of lateral diffusion coefficients of the components of a protein-embedded, cholesterol-containing model bilayer. The three model membranes are composed of an similar to 50/50 (by mole) dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayer and contained an alpha-helical transmembrane protein (HIV-1 gp41 TM). Despite the high concentration of cholesterol, normal Brownian motion was observed and the calculated diffusion coefficients (on the order of 10(-9) cm(2)/s) are consistent with experiments. Diffusion is sensitive to a variety of parameters, and a temperature difference of similar to 4 K from thermostat artifacts resulted in 210-fold differences in diffusion coefficients and significant differences in lipid order, membrane thickness, and unit cell area. Also, the specific peptide sequence likely underlies the consistently observed faster diffusion in one leaflet. Although the simulations here present molecular dynamics (MD) an order of magnitude longer than those from previous studies, the three systems did not approach ergodicity. The distributions of cholesterol and DPPC around the peptides changed on the microsecond time scale, but not significantly enough to thoroughly explore configurational space. These simulations support conclusions of other recent microsecond MD in that even longer time scales are needed for equilibration of model membranes and simulations of more realistic cellular or viral bilayers.
