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  Coarse-grained molecular model for the glycosylphosphatidylinositol anchor with and without protein

Banerjee, P., Lipowsky, R., & Santer, M. (2020). Coarse-grained molecular model for the glycosylphosphatidylinositol anchor with and without protein. Journal of Chemical Theory and Computation, 16(6), 3889-3903. doi:10.1021/acs.jctc.0c00056.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-6C75-E Version Permalink: http://hdl.handle.net/21.11116/0000-0006-9126-B
Genre: Journal Article

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 Creators:
Banerjee, Pallavi1, Author              
Lipowsky, Reinhard2, Author              
Santer, Mark3, Author              
Affiliations:
1Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_1863289              
2Reinhard Lipowsky, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_1863327              
3Mark Santer, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_1863326              

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 Abstract: Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and micro-heterogeneity makes it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches, but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of GPI anchor constructed with a modified version of MARTINI force-field that is suited for modeling carbohydrates, proteins and lipids in an aqueous environment using MARTINI's polarizable water. The non-bonded interactions for sugars were re-parameterized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluoresccent protein, the accessible timescales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino-acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.

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Language(s): eng - English
 Dates: 2020-05-112020
 Publication Status: Published in print
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 Identifiers: DOI: 10.1021/acs.jctc.0c00056
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Title: Journal of Chemical Theory and Computation
  Other : J. Chem. Theory Comput.
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: 16 (6) Sequence Number: - Start / End Page: 3889 - 3903 Identifier: ISSN: 1549-9618