jp9b05095_si_001.pdf (380.61 kB)
Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments
journal contribution
posted on 2019-08-23, 22:14 authored by Michael C. Owen, Andreas Karner, Radek Šachl, Johannes Preiner, Mariana Amaro, Robert VáchaThe
great physiological relevance of glycolipids is being increasingly
recognized, and glycolipid interactions have been shown to be central
to cell–cell recognition, neuronal plasticity, protein–ligand
recognition, and other important processes. However, detailed molecular-level
understanding of these processes remains to be fully resolved. Molecular
dynamics simulations could reveal the details of the glycolipid interactions,
but the results may be influenced by the choice of the employed force
field. Here, we have compared the behavior and properties of GM1,
a common, biologically important glycolipid, using the CHARMM36, OPLS,
GROMOS, and Amber99-GLYCAM06 (in bilayers comprising SLIPIDS and LIPID14
lipids) force fields in bilayers comprising 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids and compared the results to atomic
force microscopy and fluorescence resonance energy transfer experiments.
We found discrepancies within the GM1 behavior displayed between the
investigated force fields. Based on a direct comparison with complementary
experimental results derived from fluorescence and AFM measurements,
we recommend using the Amber99-GLYCAM force field in bilayers comprising
LIPID14 or SLIPIDS lipids followed by CHARMM36 and OPLS force fields
in simulations. The GROMOS force field is not recommended for reproducing
the properties of the GM1 head group.
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Keywords
GM 1 behaviorMolecular dynamics simulationsOPLS force fieldsglycero -3-phosphocholine lipidsGM 1 head groupSLIPIDSforce fieldsLIPID 14 lipidsGROMOS force fieldAFMAmber 99-GLYCAM force fieldbilayerforce Field Comparisonglycolipid interactionsFRETfluorescence resonance energy transfer experimentsDOPC Bilayer ValidatedCHARMM
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