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 6.5 Å. 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.
|Original language||English (US)|
|Number of pages||12|
|Journal||Biochimica et Biophysica Acta - Biomembranes|
|State||Published - Dec 1 2016|
Bibliographical noteFunding Information:
This research is supported by the NSF grant MCB-1149187 and DBI-1145652 (to JBK) and MCB-1157677 and DBI-1145987 (to WI). Part of simulations are performed using the Extreme Science and Engineering Discovery Environment (XSEDE) allocations on Stampede at Texas Advanced Computer Center (TACC) by grant number, MCB-100139 (to JBK) and MCB070009 (to WI), which are supported by National Science Foundation grant number ACI-1053575. Additional simulations and analyses are performed in the high performance computing (HPC) resource of Deepthought2 of the Division of Information Technology at the University of Maryland. We would like to thank Norbert Kučerka for sharing the valuable x-ray and neutron scattering data and also SIMtoEXP software.
© 2016 Elsevier B.V.
- Force field accuracy
- Lipid wobble
- Molecular dynamics
- Structural property