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Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids
[Image: see text] The molecular mechanics force field Slipids developed in a series of works by Jämbeck and Lyubartsev (J. Phys. Chem. B2012, 116, 3164–3179; J. Chem. Theory Comput.2012, 8, 2938–2948) generally provides a good description of various lipid bilayer systems. However, it was also found...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584372/ https://www.ncbi.nlm.nih.gov/pubmed/32926619 http://dx.doi.org/10.1021/acs.jpcb.0c06386 |
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author | Grote, Fredrik Lyubartsev, Alexander P. |
author_facet | Grote, Fredrik Lyubartsev, Alexander P. |
author_sort | Grote, Fredrik |
collection | PubMed |
description | [Image: see text] The molecular mechanics force field Slipids developed in a series of works by Jämbeck and Lyubartsev (J. Phys. Chem. B2012, 116, 3164–3179; J. Chem. Theory Comput.2012, 8, 2938–2948) generally provides a good description of various lipid bilayer systems. However, it was also found that order parameters of C–H bonds in the glycerol moiety of the phosphatidylcholine headgroup deviate significantly from NMR results. In this work, the dihedral force field parameters have been reparameterized in order to improve the agreement with experiment. For this purpose, we have computed energies for a large amount of lipid headgroup conformations using density functional theory on the B3P86/cc-pvqz level and optimized dihedral angle parameters simultaneously to provide the best fit to the quantum chemical energies. The new parameter set was validated for three lipid bilayer systems against a number of experimental properties including order parameters, area per lipid, scattering form factors, bilayer thickness, area compressibility and lateral diffusion coefficients. In addition, the order parameter dependence on cholesterol content in the POPC bilayer was investigated. It is shown that the new force field significantly improves agreement with the experimental order parameters for the lipid headgroup while keeping good agreement with other experimentally measured properties. |
format | Online Article Text |
id | pubmed-7584372 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-75843722020-10-26 Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids Grote, Fredrik Lyubartsev, Alexander P. J Phys Chem B [Image: see text] The molecular mechanics force field Slipids developed in a series of works by Jämbeck and Lyubartsev (J. Phys. Chem. B2012, 116, 3164–3179; J. Chem. Theory Comput.2012, 8, 2938–2948) generally provides a good description of various lipid bilayer systems. However, it was also found that order parameters of C–H bonds in the glycerol moiety of the phosphatidylcholine headgroup deviate significantly from NMR results. In this work, the dihedral force field parameters have been reparameterized in order to improve the agreement with experiment. For this purpose, we have computed energies for a large amount of lipid headgroup conformations using density functional theory on the B3P86/cc-pvqz level and optimized dihedral angle parameters simultaneously to provide the best fit to the quantum chemical energies. The new parameter set was validated for three lipid bilayer systems against a number of experimental properties including order parameters, area per lipid, scattering form factors, bilayer thickness, area compressibility and lateral diffusion coefficients. In addition, the order parameter dependence on cholesterol content in the POPC bilayer was investigated. It is shown that the new force field significantly improves agreement with the experimental order parameters for the lipid headgroup while keeping good agreement with other experimentally measured properties. American Chemical Society 2020-09-14 2020-10-08 /pmc/articles/PMC7584372/ /pubmed/32926619 http://dx.doi.org/10.1021/acs.jpcb.0c06386 Text en This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. |
spellingShingle | Grote, Fredrik Lyubartsev, Alexander P. Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids |
title | Optimization of Slipids Force Field Parameters Describing
Headgroups of Phospholipids |
title_full | Optimization of Slipids Force Field Parameters Describing
Headgroups of Phospholipids |
title_fullStr | Optimization of Slipids Force Field Parameters Describing
Headgroups of Phospholipids |
title_full_unstemmed | Optimization of Slipids Force Field Parameters Describing
Headgroups of Phospholipids |
title_short | Optimization of Slipids Force Field Parameters Describing
Headgroups of Phospholipids |
title_sort | optimization of slipids force field parameters describing
headgroups of phospholipids |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584372/ https://www.ncbi.nlm.nih.gov/pubmed/32926619 http://dx.doi.org/10.1021/acs.jpcb.0c06386 |
work_keys_str_mv | AT grotefredrik optimizationofslipidsforcefieldparametersdescribingheadgroupsofphospholipids AT lyubartsevalexanderp optimizationofslipidsforcefieldparametersdescribingheadgroupsofphospholipids |