Scale-invariance in miniature coarse-grained red blood cells by fluctuation analysis

iSoLF is a coarse-grained (CG) model for lipid molecules with the implicit-solvent approximation used in molecular dynamics (MD) simulations of biological membranes. Using the original iSoLF (iSoLFv1), MD simulations of lipid bilayers consisting of either POPC or DPPC and these bilayers, including membrane proteins, can be performed. Here, we improve the original model, explicitly treating the electrostatic interactions between different lipid molecules and adding CG particle types. As a result, the available lipid types increase to 30. To parameterize the potential functions of the new model, we performed all-atom MD simulations of each lipid at three different temperatures using the CHARMM36 force field and the modified TIP3P model. Then, we parameterized both the bonded and non-bonded interactions to fit the area per lipid and the membrane thickness of each lipid bilayer by using the multistate Boltzmann Inversion method. The final model reproduces the area per lipid and the membrane thickness of each lipid bilayer at the three temperatures. We also examined the applicability of the new model, iSoLFv2, to simulate the phase behaviors of mixtures of DOPC and DPPC at different concentrations. The simulation results with iSoLFv2 are consistent with those using Dry Martini and Martini 3, although iSoLFv2 requires much fewer computations. iSoLFv2 has been implemented in the GENESIS MD software and is publicly available.

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Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers

Torre

Takada

Sugita

2023

The Journal of Chemical Physics

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Scale-invariance in miniature coarse-grained red blood cells by fluctuation analysis

Abstract: The scale-invariance of a coarse-grained molecular dynamics model of a red blood cell is investigated through fluctuation analysis, justifying the use of “miniature cells” in silico.

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References 46 publications

Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers

Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers

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