PackMem

The analysis of the structural organization of lipid bilayers is generally
performed across the direction normal to the bilayer/water interface, whereas the
surface properties of the bilayer at the interface with water are often
neglected. Here, we present PackMem, a bioinformatic tool that performs a
topographic analysis of the bilayer surface from various molecular dynamics
simulations. PackMem unifies and rationalizes previous analyses based on a
Cartesian grid. The grid allows identification of surface regions defined as
lipid-packing defects where lipids are loosely packed, leading to cavities in
which aliphatic carbons are exposed to the solvent, either deep inside or close
to the membrane surface. Examples are provided to show that the abundance of
lipid-packing defects varies according to the temperature and to the bilayer
composition. Because lipid-packing defects control the adsorption of peripheral
proteins with hydrophobic insertions, PackMem is instrumental for us to
understand and quantify the adhesive properties of biological membranes as well
as their response to mechanical perturbations such as membrane deformation.

PackMem: A Versatile Tool to Compute and Visualize Interfacial Packing Defects in Lipid Bilayers.

PackMem is a tool for analyzing and visualizing the topography of lipid bilayer surfaces to detect packing defects. The PackMem adjusts to various membrane types, force fields, and lipids.

PackMem

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