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Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids
[Image: see text] An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on kn...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2012
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320744/ https://www.ncbi.nlm.nih.gov/pubmed/22352995 http://dx.doi.org/10.1021/jp212503e |
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author | Jämbeck, Joakim P. M. Lyubartsev, Alexander P. |
author_facet | Jämbeck, Joakim P. M. Lyubartsev, Alexander P. |
author_sort | Jämbeck, Joakim P. M. |
collection | PubMed |
description | [Image: see text] An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions. |
format | Online Article Text |
id | pubmed-3320744 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-33207442012-04-06 Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids Jämbeck, Joakim P. M. Lyubartsev, Alexander P. J Phys Chem B [Image: see text] An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions. American Chemical Society 2012-02-21 2012-03-15 /pmc/articles/PMC3320744/ /pubmed/22352995 http://dx.doi.org/10.1021/jp212503e Text en Copyright © 2012 American Chemical Society http://pubs.acs.org This is an open-access article distributed under the ACS AuthorChoice Terms & Conditions. Any use of this article, must conform to the terms of that license which are available at http://pubs.acs.org. |
spellingShingle | Jämbeck, Joakim P. M. Lyubartsev, Alexander P. Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids |
title | Derivation and Systematic
Validation of a Refined
All-Atom Force Field for Phosphatidylcholine Lipids |
title_full | Derivation and Systematic
Validation of a Refined
All-Atom Force Field for Phosphatidylcholine Lipids |
title_fullStr | Derivation and Systematic
Validation of a Refined
All-Atom Force Field for Phosphatidylcholine Lipids |
title_full_unstemmed | Derivation and Systematic
Validation of a Refined
All-Atom Force Field for Phosphatidylcholine Lipids |
title_short | Derivation and Systematic
Validation of a Refined
All-Atom Force Field for Phosphatidylcholine Lipids |
title_sort | derivation and systematic
validation of a refined
all-atom force field for phosphatidylcholine lipids |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320744/ https://www.ncbi.nlm.nih.gov/pubmed/22352995 http://dx.doi.org/10.1021/jp212503e |
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