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Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids
Alexander Mirzoev1, Alexander P Lyubartsev
1Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-10691, Sweden.
Journal of Computational Chemistry
|April 30, 2014
Summary
We developed effective potentials for coarse-grained dimyristoylphosphatidylcholine (DMPC) lipid models, showing their concentration dependence impacts bilayer structure. Potentials from 1:30 lipid:water ratio simulations best matched experimental data for stable lipid bilayers.
Area of Science:
- Computational Biophysics and Molecular Modeling
- Soft Matter Physics and Materials Science
Background:
- Accurate coarse-grained models are crucial for simulating large-scale lipid systems.
- Effective potentials in coarse-grained models often exhibit state point dependence, affecting simulation accuracy.
Purpose of the Study:
- To derive and validate structure-based effective site-site potentials for a 10-site dimyristoylphosphatidylcholine (DMPC) lipid model.
- To investigate the dependence of these effective potentials on lipid-water concentration (state point).
- To assess the performance of derived potentials in reproducing atomistic simulation data and experimental properties of lipid bilayers.
Main Methods:
- Systematic structure-based coarse-graining applied to derive effective site-site potentials for DMPC.
- Atomistic simulations performed at four different lipid:water molar ratios to generate reference data.
- Coarse-grained simulations using derived potentials to analyze lipid bilayer properties (radial distribution functions, bond/angle distributions, area per lipid, compressibility, ordering).
Main Results:
- Effective potentials showed non-negligible dependence on the concentration used for their derivation.
- Potentials derived at low lipid concentration resulted in more condensed bilayers, while those from higher concentrations yielded more fluid-like structures.
- Potentials from simulations at a 1:30 lipid:water ratio provided the best agreement with atomistic data and experimental results, yielding stable bilayers with accurate lipid partitioning and properties.
Conclusions:
- The derived effective potentials accurately reproduce structural characteristics of DMPC lipid bilayers across various concentrations.
- The state point dependence of effective potentials is a critical factor influencing simulated lipid bilayer properties.
- The developed coarse-grained model demonstrates robustness for simulating lipid self-aggregation into various structures (bilayers, bicelles, vesicles).
