Lipid21: complex lipid membrane simulations with AMBER.
File(s)lipid21_accepted_manuscript.pdf (1.85 MB) lipid21_SI_accepted.pdf (1.2 MB)
Accepted version
Supporting information
Author(s)
Dickson, Callum J
Walker, Ross C
Gould, Ian R
Type
Journal Article
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.
Date Issued
2022-02-03
Date Acceptance
2022-02-01
Citation
Journal of Chemical Theory and Computation, 2022, 18 (3)
ISSN
1549-9618
Publisher
American Chemical Society
Journal / Book Title
Journal of Chemical Theory and Computation
Volume
18
Issue
3
Copyright Statement
© 2022 American Chemical Society. This document is the Accepted Manuscript version of a Published Work that appeared in final form in J. Chem. Theory Comput., after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jctc.1c01217
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/35113553
Subjects
Chemical Physics
0307 Theoretical and Computational Chemistry
0601 Biochemistry and Cell Biology
0803 Computer Software
Publication Status
Published online
Coverage Spatial
United States
Date Publish Online
2022-02-03