Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations.

ABSTRACT: Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-electron microscopy (cryo-EM) densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities using experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our

SUBMITTER: Ansell TB 

PROVIDER: S-EPMC8515805 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature