Simulations of edge behavior in a mixed-lipid bilayer: fluctuation analysis.

Molecular Insight into the Mutual Interactions of Two Transmembrane Domains of Human Glycine Receptor (TM23-GlyR), with the Lipid Bilayers

Appearing as a computational microscope, MD simulation can ‘zoom in’ to atomic resolution to assess detailed interactions of a membrane protein with its surrounding lipids, which play important roles in the stability and function of such proteins. This study has employed the molecular dynamics (MD) simulations, to determine the effect of added DMPC or DMTAP molecules on the structure of D...

Coarse-grained model simulations of mixed-lipid systems: composition and line tension of a stabilized bilayer edge.

Bilayer disks and ribbons composed of a mixture of short- and long-tail phospholipids have been studied by molecular dynamics with a coarse-grained model. The effects of system composition on the edge structure, composition, and line tension were analyzed. Increases in the fraction of short-tail lipids tend to decrease the line tension (i.e., stabilize the edge) but not eliminate it. The short-...

Evidences for a new cation channel in the brain mitochondrial inner membrane

Introduction: Previous studies and our works have indicated several cation channels in the rat brain mitochondrial inner membrane. In this work, we report the single-channel characterization of a cation channel from the rat brain mitochondrial inner membrane incorporated into a planar lipid bilayer. Methods: After removing and homogenizing the adult rat brain, its supernatant was centrifuged...

Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations Supporting Material

Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ∼1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC ...