Molecular Dynamics Simulations of Kir2.2-Cholesterol Interactions

Molecular dynamics simulations for plasma-surface interactions

Molecular dynamics simulations of GPCR-cholesterol interaction: An emerging paradigm.

G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across cell membranes and represent major targets in the development of novel drug candidates. Membrane cholesterol plays an important role in GPCR structure and function. Molecular dynamics simulations have been successful in exploring the effect of cholesterol on the receptor and a general c...

Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations.

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol's molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an e...

Modeling of annexin A2—Membrane interactions by molecular dynamics simulations

The annexins are a family of Ca2+-regulated phospholipid binding proteins that are involved in membrane domain organization and membrane trafficking. Although they are widely studied and crystal structures are available for several soluble annexins their mode of membrane association has never been studied at the molecular level. Here we obtained molecular information on the annexin-membrane int...

Observation and description of phonon interactions in molecular dynamics simulations

Three-phonon interactions are identified and analyzed in nonequilibrium molecular dynamics simulations of the Lennard-Jones face-centered cubic crystal. The small simulation cells studied and the classical nature of the simulations lead to a different description of the phonon transport than the quantum-particle model. The selection process is strictly governed by the mode wave vectors. In dete...