Amy Y. Shih, Ilia G. Denisov, James C. Phillips, Stephen G. Sligar, and Klaus
Schulten.
Molecular dynamics simulations of discoidal bilayers assembled from
truncated human lipoproteins.
Biophysical Journal, 88:548-556, 2005.
(PMC: 1305032)
SHIH2005
Human apolipoprotein A-1 (apo A-1) is the major protein component of high-density
lipoproteins. The apo A-1 lipid-binding domain was used as a template for the synthesis
of amphipathic helical proteins termed membrane scaffold proteins, employed to self-
assemble soluble monodisperse discoidal particles called Nanodiscs. In these particles,
membrane scaffold proteins surround a lipid bilayer in a belt-like fashion forming bilayer
discs of discrete size and composition. Here we investigate the structure of Nanodiscs
through molecular dynamics simulations in which Nanodiscs were built from scaffold
proteins of various lengths. The simulations showed planar or deformed Nanodiscs
depending on optimal length and alignment of the scaffold proteins. Based on mean
surface area per lipid calculations, comparison of small angle x-ray scattering curves, and
the relatively planar shape of Nanodiscs made from truncated scaffold proteins, one can
conclude that the first 17 to 18 residues of the 200-residue apo A-1 lipid-binding domain
are not involved in formation of the protein "belts'' surrounding the lipid bilayer. To
determine whether the addition of an integral membrane protein has an effect on the
overall structure of a Nanodisc, bacteriorhodopsin was embedded into a Nanodisc and
simulated using molecular dynamics, revealing a planar disk with a slightly rectangular
shape.
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