Showing papers by "Stephen J. Tucker published in 2013"
TL;DR: Using a multiscale approach that combines coarse-grained and atomistic molecular dynamics simulations, the binding site for the anionic phospholipid phosphatidylinositol 4,5-bisphosphate (PIP(2) on the Kir2.2 inwardly rectifying (Kir) potassium channel is predicted.
Abstract: Protein–lipid interactions regulate many membrane protein functions. Using a multiscale approach that combines coarse-grained and atomistic molecular dynamics simulations, we have predicted the binding site for the anionic phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) on the Kir2.2 inwardly rectifying (Kir) potassium channel. Comparison of the predicted binding site to that observed in the recent PIP2-bound crystal structure of Kir2.2 reveals good agreement between simulation and experiment. In addition to providing insight into the mechanism by which PIP2 binds to Kir2.2, these results help to establish the validity of this multiscale simulation approach and its future application in the examination of novel membrane protein–lipid interactions in the increasing number of high-resolution membrane protein structures that are now available.
62 citations
TL;DR: A multi-scale approach, consisting of sequential coarse-grained and atomistic molecular dynamics simulations of Kir2.2 embedded in a phospolipid/PIP2 bilayer, proves the predictive power of this computational approach for the study of protein interactions with PIP2 and possibly other modulatory lipids.
1 citations