Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments

0508974 - ÚFCH JH 2020 RIV US eng J - Journal Article
Owen, M. C. - Karner, A. - Šachl, Radek - Preiner, J. - Amaro, Mariana - Vácha, R.
Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments.
Journal of Physical Chemistry B. Roč. 123, č. 35 (2019), s. 7504-7517. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GA18-04871S; GA ČR GA17-03160S
Grant - others:GA MŠk(CZ) LM2015042
Institutional support: RVO:61388955
Keywords : molecular-dynamics * brain gangliosides * membrane-lipids * cholera-toxin * simulations * glycosphingolipids * conformations * glycolipids * extension * glycam06
OECD category: Physical chemistry
Impact factor: 2.857, year: 2019
Method of publishing: Limited access

The 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-GLYCAMO6 (in bilayers comprising SLIPIDS and LIPID14 lipids) force fields in bilayers comprising 1,2-dioleoyl-snglycero-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.
Permanent Link: http://hdl.handle.net/11104/0299797