Paper Citing NAMD - Abstract
Kasson, P.M.; Pande, V.S.
Molecular dynamics simulation of lipid reorientation at bilayer edges
BIOPHYSICAL JOURNAL, 86:3744-3749, JUN 2004
Understanding cellular membrane processes is critical for the study of events such as viral entry, neurotransmitter exocytosis, and immune activation. Supported lipid bilayers are commonly used to model these membrane processes experimentally. Despite the relative simplicity of such a system, many important structural and dynamic parameters are not experimentally observable with current techniques. Computational approaches allow the development of a high-resolution model of bilayer processes. We have performed molecular dynamics simulations of dimyristoylphosphatidylcholine (DMPC) bilayers to model the creation of bilayer gaps-a common process in bilayer patterning-and to analyze their structure and dynamics. We propose a model for gap formation in which the bilayer edges form metastable micelle-like structures on a nanosecond timescale. Molecules near edges structurally resemble lipids in ungapped bilayers but undergo small-scale motions more rapidly. These data suggest that lipids may undergo rapid local rearrangements during membrane fusion, facilitating the formation of fusion intermediates thought key to the infection cycle of viruses such as influenza, Ebola, and HIV.
