Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers

Abstract

Phosphatidylglycerol (PG) is one of the important components of biological membranes, but there is a paucity of experimental data to test the accuracy of molecular dynamics (MD) simulations. This work consists of testing the accuracy of the CHARMM36 (C36) lipid force field on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) lipid bilayers. MD simulations of POPG lipid bilayers are compared to recently available X-ray and neutron scattering and deuterium NMR measurements. Overall, the C36 lipid force field accurately represents the X-ray and neutron form factors, bilayer and hydrocarbon thicknesses and chain deuterium order parameters. The surface area per lipid from MD simulations with C36 (67.7 ± 0.2 Å²) is in excellent agreement with the experimentally determined value of 66.0 ± 1.3 Å². C36 outperforms the lipid force field developed by Berger et al. [15] and suggests that past studies with this force field may result in lateral areas that are too small. Moreover, our studies give some insight into the structural model used in experiments and suggest that the functional form for the head group may not be Gaussian-like. Based on our simulations, the POPG lipid in the C36 lipid force field is well parameterised and can be used for other PG lipids and membrane models with mixed lipids.

Keywords::

• molecular simulations
• lipid bilayer
• POPG

Acknowledgements

This research was supported in part by the NSF grant MCB-1149187. The simulation work was done on the HPCC of Deepthought at the University of Maryland. We would like to thank Xiaohong Zhuang (in Dr Klauda's group) for providing details on some of the analysis. Moreover, we thank Dr Norbert KuČerka for sharing the valuable X-ray and neutron scattering data and also SIMtoEXP software to simplify the data comparison.