Paper Citing NAMD - Abstract
Saunders, Marissa G.; Voth, Gregory A.
Comparison between Actin Filament Models: Coarse-Graining Reveals Essential Differences
STRUCTURE, 20:641-653, APR 4 2012
The interconversion of actin between monomeric and polymeric forms is a fundamental process in cell biology that is incompletely understood, in part because there is no high-resolution structure for filamentous actin. Several models have been proposed recently; identifying structural and dynamic differences between them is an essential step toward understanding actin dynamics. We compare three of these models, using coarse-grained analysis of molecular dynamics simulations to analyze the differences between them and evaluate their relative stability. Based on this analysis, we identify key motions that may be associated with polymerization, including a potential energetic barrier in the process. We also find that actin subunits are polymorphic; during simulations they assume a range of configurations remarkably similar to those seen in recent cryOEM images.
