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Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation

View ORCID ProfileDiego Ugarte La Torre, View ORCID ProfileShoji Takada
doi: https://doi.org/10.1101/2020.09.20.305060
Diego Ugarte La Torre
1Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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Shoji Takada
1Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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  • For correspondence: takada@biophys.kyoto-u.ac.jp
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Abstract

Biological membranes have been prominent targets for coarse-grained (CG) molecular dynamics (MD) simulations. While minimal CG lipid models with three-beads per lipid and quantitative CG lipid models with >10-beads per lipid have been well studied, in between them, CG lipid models with a compatible resolution to residue-level CG protein models are much less developed. Here, we extended a previously developed three-bead lipid model into a five-bead model and parametrized it for two phospholipids, POPC and DPPC. The developed model, iSoLF, reproduced the area per lipid, hydrophobic thickness, and phase behaviors of the target phospholipid bilayer membranes at the physiological temperature. The model POPC and DPPC membranes were in liquid and gel phases, respectively, in accordance with experiments. We further examined the spontaneous formation of a membrane bilayer, the temperature dependence of physical properties, vesicle dynamics, and the POPC/DPPC two-component membrane dynamics of the CG lipid model, showing some promise. Once combined with standard Cα protein models, the iSoLF model will be a powerful tool to simulate large biological membrane systems made of lipids and proteins.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 20, 2020.
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Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation
Diego Ugarte La Torre, Shoji Takada
bioRxiv 2020.09.20.305060; doi: https://doi.org/10.1101/2020.09.20.305060
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Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation
Diego Ugarte La Torre, Shoji Takada
bioRxiv 2020.09.20.305060; doi: https://doi.org/10.1101/2020.09.20.305060

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