Packmem: a versatile tool to compute and visualize interfacial packing defects in lipid bilayers
- Gautier, Romain Université Côte d’Azur, Sophia-Antipolis, France
- Bacle, Amélie Institut Jacques Monod, Université Paris-Diderot, Sorbonne Paris Cité, France
- Tiberti, Marion L. Université Côte d’Azur, Sophia-Antipolis, France
- Fuchs, Patrick F. Institut Jacques Monod, Université Paris-Diderot, Sorbonne Paris Cité, France - Laboratoire des biomolécules, Sorbonne Université, École normale supérieure, Paris, France
- Vanni, Stefano Université Côte d’Azur, Sophia-Antipolis, France - Department of Biology, University of Fribourg, Switzerland
- Antonny, Bruno Université Côte d’Azur, Sophia-Antipolis, France
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07.08.2018
Published in:
- Biophysical Journal. - 2018, vol. 115, no. 3, p. 436–444
English
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.
- Faculty
- Faculté des sciences et de médecine
- Department
- Département de Biologie
- Language
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- English
- Classification
- Biological sciences
- License
- License undefined
- Identifiers
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- RERO DOC 323815
- DOI 10.1016/j.bpj.2018.06.025
- Persistent URL
- https://folia.unifr.ch/unifr/documents/307305
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