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Lipid21: Complex Lipid Membrane Simulations with AMBER.

ABSTRACT: 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.

SUBMITTER: Dickson CJ

PROVIDER: S-EPMC9007451 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Lipid21: Complex Lipid Membrane Simulations with AMBER.

Dickson Callum J CJ Walker Ross C RC Gould Ian R IR

Journal of chemical theory and computation 20220203 3

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 goo ...[more]

PMID: 35113553

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