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  Computational analysis of local membrane properties.

Gapsys, V., de Groot, B. L., & Briones, R. (2013). Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design, 27(10), 845-858. doi:10.1007/s10822-013-9684-0.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-CD30-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CB48-E
Genre: Journal Article

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 Creators:
Gapsys, V.1, Author              
de Groot, B. L.1, Author              
Briones, R.1, Author              
Affiliations:
1Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              

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Free keywords: Membrane simulations; Molecular dynamics; Area per lipid; Order parameters ; Curvature; Bilayer thickness
 Abstract: 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.

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Language(s): eng - English
 Dates: 2013-10-23
 Publication Status: Published online
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 Rev. Method: Peer
 Identifiers: DOI: 10.1007/s10822-013-9684-0
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Title: Journal of Computer-Aided Molecular Design
Source Genre: Journal
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Pages: - Volume / Issue: 27 (10) Sequence Number: - Start / End Page: 845 - 858 Identifier: -