Lipid21: complex lipid membrane simulations with AMBER

CJ Dickson, RC Walker, IR Gould - Journal of chemical theory and …, 2022 - ACS Publications
Journal of chemical theory and computation, 2022ACS Publications
We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated
fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell
membrane lipid compositions, including raft-like domains. Head group torsion parameters
are revised, resulting in improved agreement with NMR order parameters, and hydrocarbon
chain parameters are updated, providing a better match with phase transition temperature.
Extensive validation runs (0.9 μs per lipid type) show good agreement with experimental …
We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell membrane lipid compositions, including raft-like domains. Head group torsion parameters are revised, resulting in improved agreement with NMR order parameters, and hydrocarbon chain parameters are updated, providing a better match with phase transition temperature. Extensive validation runs (0.9 μs per lipid type) show good agreement with experimental measurements. Furthermore, the simulation of raft-like bilayers demonstrates the perturbing effect of increasing PUFA concentrations on cholesterol molecules. The force field derivation is consistent with the AMBER philosophy, meaning it can be easily mixed with protein, small molecule, nucleic acid, and carbohydrate force fields.
ACS Publications
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