Computational analysis of local membrane properties

• Published in: Journal of computer-aided molecular design Vol. 27; no. 10; pp. 845 - 858
• Main Authors: Gapsys, Vytautas, de Groot, Bert L., Briones, Rodolfo
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-10-2013; Springer Nature B.V
• Subjects: Animal Anatomy; CAD; Chemistry; Chemistry and Materials Science; Cholesterol - chemistry; Computer aided design; Computer Applications in Chemistry; Computer Simulation; Deuterium; Histology; Lipid Bilayers - chemistry; Lipid Bilayers - metabolism; Lipids; Membranes; Membranes - chemistry; Models, Molecular; Molecular biology; Molecular Dynamics Simulation; Morphology; Peptides; Phosphatidylcholines - chemistry; Phospholipids - chemistry; Physical Chemistry; Simulation; Molecular dynamics; Area per lipid; Order parameters; Bilayer thickness; Curvature; Membrane simulations
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-013-9684-0

In the field of biomolecular simulations, dynamics of phospholipid membranes is of special interest. A number of proteins, including channels, transporters, receptors and short peptides are embedded in lipid bilayers and tightly interact with phospholipids. While the experimental measurements report on the spatial and/or temporal average membrane properties, simulation results are not restricted to the average properties. In the current study, we present a collection of methods for an efficient local membrane property calculation, comprising bilayer thickness, area per lipid, deuterium order parameters, Gaussian and mean curvature. The local membrane property calculation allows for a direct mapping of the membrane features, which subsequently can be used for further analysis and visualization of the processes of interest. The main features of the described methods are highlighted in a number of membrane systems, namely: a pure dimyristoyl-phosphatidyl-choline (DMPC) bilayer, a fusion peptide interacting with a membrane, voltage-dependent anion channel protein embedded in a DMPC bilayer, cholesterol enriched bilayer and a coarse grained simulation of a curved palmitoyl-oleoyl-phosphatidyl-choline lipid membrane. The local membrane property analysis proves to provide an intuitive and detailed view on the observables that are otherwise interpreted as averaged bilayer properties.