Paper Citing NAMD - Abstract
Lupyan, Dmitry; Mezei, Mihaly; Logothetis, Diomedes E.; Osman, Roman
A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP2
BIOPHYSICAL JOURNAL, 98:240-247, JAN 20 2010
Phosphoinositides like phosphatidylinositol 4,5-bisphosphate (PIP2) are negatively charged lipids that play a pivotal role in membrane trafficking, signal transduction, and protein anchoring. We have designed a force field for the PIP2 headgroup using quantum mechanical methods and characterized its properties inside a lipid bilayer using molecular dynamics simulations. Macroscopic properties such as area/headgroup, density profiles, and lipid order parameters calculated from these simulations agree well with the experimental values. However, microscopically, the PIP2 introduces a local perturbation of the lipid bilayer. The average PIP2 headgroup orientation of 45 degrees relative to the bilayer normal induces a unique, distance-dependent organization of the lipids that surround PIP2. The headgroups of these lipids preferentially orient closer to the bilayer normal. This perturbation creates a PIP2 lipid microdomain with the neighboring lipids. We propose that the PIP2 lipid microdomain enables the PIP2 to function as a membrane-bound anchoring molecule.
