Interpretation of fluctuation spectra in lipid bilayer simulations.

Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations Supporting Material

Testing procedures for extracting fluctuation spectra from lipid bilayer simulations.

To address concerns about how to obtain the height-height spectrum from simulations of biomembranes, we emulated the fluctuations in real space using exact input spectra. Two different methods that have given different results in the literature were then used to extract spectra from the emulated fluctuations that were then compared to the exact input spectra. A real space method shows systemati...

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...

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

Coarse-grained molecular dynamics simulations of lipid bilayer ribbons consisting of a mixture of lipids of different tail lengths have been performed to gain insight into bicelle mixtures. The line tension of the bilayer edge decreases as the mole fraction of short-chain lipids in the system is increased, dropping below zero between 30% and 35%. The mole fraction of short-chain lipids in the r...

Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular-dynamics simulations.

Molecular-dynamics simulations covering 30 ns of both a natural and a synthetic antimicrobial peptide in the presence of a zwitterionic lipid bilayer were performed. In both simulations, copies of the peptides were placed in an alpha-helical conformation on either side of the bilayer about 10 A (1 A=0.1 nm) from the interface, with either the hydrophobic or the positively charged face of the he...