PackMem

PackMem analyzes topography of lipid bilayer surfaces from molecular dynamics simulations, identifying and quantifying lipid-packing defects and surface features relevant to membrane structure and protein adsorption.

Key Features:

• Topographic Analysis: Uses a Cartesian grid system to generate detailed topographic maps of lipid bilayer surfaces derived from molecular dynamics simulations.
• Lipid-Packing Defects Identification: Detects lipid-packing defects as cavities that expose aliphatic carbons to solvent, occurring both deep within the membrane and near its surface.
• Quantification and Rationalization: Unifies previous analyses into a coherent framework to quantify and rationalize lipid-packing defects across different conditions.

Scientific Applications:

• Understanding Membrane Properties: Characterizes how lipid-packing defects influence membrane adhesive properties and control adsorption of peripheral proteins with hydrophobic insertions.
• Temperature and Composition Analysis: Quantifies how the abundance of lipid-packing defects varies with changes in temperature and bilayer composition.
• Mechanical Perturbation Response: Assesses alterations in lipid packing in response to mechanical perturbations such as membrane deformation.

Methodology:

Applies a Cartesian grid-based analysis to molecular dynamics simulation coordinates to map and quantify lipid-packing defects on the bilayer surface.