An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations
Copyright © 2016 Elsevier B.V. All rights reserved..
Previous MD simulations of six phosphocholine (PC) lipid bilayers demonstrated the accuracy of the CHARMM36 force field (C36FF) for PC bilayer simulation at varied temperatures (BBA-Biomembranes, 1838 (2014): 2520-2529). In this work, we further examine the accuracy of C36FF over a wide temperature range for a broader range of lipid types such as various head groups (phosphatidic acid (PA), PC, phosphoethanolamine (PE), phosphoglycerol (PG), and phosphoserine (PS)), and tails (saturated, mono-, mixed- and poly-unsaturated acyl chains with varied chain lengths). The structural properties (surface area per lipid (SA/lip), overall bilayer thickness, hydrophobic thickness, headgroup-to-headgroup thickness, deuterium order parameter (SCD), and spin-lattice relaxation time (T1)) obtained from simulations agree well with nearly all available experimental data. Our analyses indicate that PS lipids have the most inter-lipid hydrogen bonds, while PG lipids have the most intra-lipid hydrogen bonds, which play the main role in their low SA/lip in PS lipids and low thicknesses in PG lipids, respectively. PS, PE, and PA lipids have the largest contact clusters with on average 5-8 lipids per cluster, while PC and PG have clusters of 4 lipids based on a cutoff distance of 6.5Å. PS lipids have much slower lipid wobble (i.e., higher correlation time) than other head groups at a given temperature as the hydrogen bonded network significantly reduces a lipid's mobility, and the rate of lipid wobble increases dramatically as temperature increases. These in-depth analyses facilitate further understanding of lipid bilayers at the atomic level.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2016 |
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| Erschienen: |
2016 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:1858 |
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| Enthalten in: |
Biochimica et biophysica acta - 1858(2016), 12 vom: 19. Dez., Seite 3093-3104 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Zhuang, Xiaohong [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 26.10.2017 Date Revised 29.04.2018 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.bbamem.2016.09.016 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM26465885X |
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| 100 | 1 | |a Zhuang, Xiaohong |e verfasserin |4 aut | |
| 245 | 1 | 3 | |a An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations |
| 264 | 1 | |c 2016 | |
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| 500 | |a Date Completed 26.10.2017 | ||
| 500 | |a Date Revised 29.04.2018 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2016 Elsevier B.V. All rights reserved. | ||
| 520 | |a Previous MD simulations of six phosphocholine (PC) lipid bilayers demonstrated the accuracy of the CHARMM36 force field (C36FF) for PC bilayer simulation at varied temperatures (BBA-Biomembranes, 1838 (2014): 2520-2529). In this work, we further examine the accuracy of C36FF over a wide temperature range for a broader range of lipid types such as various head groups (phosphatidic acid (PA), PC, phosphoethanolamine (PE), phosphoglycerol (PG), and phosphoserine (PS)), and tails (saturated, mono-, mixed- and poly-unsaturated acyl chains with varied chain lengths). The structural properties (surface area per lipid (SA/lip), overall bilayer thickness, hydrophobic thickness, headgroup-to-headgroup thickness, deuterium order parameter (SCD), and spin-lattice relaxation time (T1)) obtained from simulations agree well with nearly all available experimental data. Our analyses indicate that PS lipids have the most inter-lipid hydrogen bonds, while PG lipids have the most intra-lipid hydrogen bonds, which play the main role in their low SA/lip in PS lipids and low thicknesses in PG lipids, respectively. PS, PE, and PA lipids have the largest contact clusters with on average 5-8 lipids per cluster, while PC and PG have clusters of 4 lipids based on a cutoff distance of 6.5Å. PS lipids have much slower lipid wobble (i.e., higher correlation time) than other head groups at a given temperature as the hydrogen bonded network significantly reduces a lipid's mobility, and the rate of lipid wobble increases dramatically as temperature increases. These in-depth analyses facilitate further understanding of lipid bilayers at the atomic level | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Research Support, U.S. Gov't, Non-P.H.S. | |
| 650 | 4 | |a Force field accuracy | |
| 650 | 4 | |a Lipid wobble | |
| 650 | 4 | |a Molecular dynamics | |
| 650 | 4 | |a Structural property | |
| 650 | 7 | |a Glycerophospholipids |2 NLM | |
| 650 | 7 | |a Lipid Bilayers |2 NLM | |
| 650 | 7 | |a Phosphatidylethanolamines |2 NLM | |
| 650 | 7 | |a Phosphatidylserines |2 NLM | |
| 650 | 7 | |a Deuterium |2 NLM | |
| 650 | 7 | |a AR09D82C7G |2 NLM | |
| 700 | 1 | |a Dávila-Contreras, Eder M |e verfasserin |4 aut | |
| 700 | 1 | |a Beaven, Andrew H |e verfasserin |4 aut | |
| 700 | 1 | |a Im, Wonpil |e verfasserin |4 aut | |
| 700 | 1 | |a Klauda, Jeffery B |e verfasserin |4 aut | |
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