A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties |
| |
Authors: | Xiaohong Zhuang Judah R. Makover Wonpil Im Jeffery B. Klauda |
| |
Affiliation: | 1. Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA;2. Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66047, USA;3. Center for Bioinformatics, The University of Kansas, Lawrence, KS 66047, USA |
| |
Abstract: | Although lipid force fields (FFs) used in molecular dynamics (MD) simulations have proved to be accurate, there has not been a systematic study on their accuracy over a range of temperatures. Motivated by the X-ray and neutron scattering measurements of common phosphatidylcholine (PC) bilayers (Ku?erka et al. BBA. 1808: 2761, 2011), the CHARMM36 (C36) FF accuracy is tested in this work with MD simulations of six common PC lipid bilayers over a wide range of temperatures. The calculated scattering form factors and deuterium order parameters from the C36 MD simulations agree well with the X-ray, neutron, and NMR experimental data. There is excellent agreement between MD simulations and experimental estimates for the surface area per lipid, bilayer thickness (DB), hydrophobic thickness (DC), and lipid volume (VL). The only minor discrepancy between simulation and experiment is a measure of (DB − DHH) / 2 where DHH is the distance between the maxima in the electron density profile along the bilayer normal. Additional MD simulations with pure water and heptane over a range of temperatures provide explanations of possible reasons causing the minor deviation. Overall, the C36 FF is accurate for use with liquid crystalline PC bilayers of varying chain types and over biologically relevant temperatures. |
| |
Keywords: | Lipid bilayer Molecular dynamics Force field accuracy Bilayer structure |
本文献已被 ScienceDirect 等数据库收录! |
|