We compare the order parameters predicted for the hydrocarbon segments in lipid bilayer headgroup region by the Berger molecular dynamics simulation model to those measured by Nuclear Magnetic Resonance (NMR) experiments. We first show resultsfor a fully hydrated POPC bilayer, and then focus on changes of the order parameters as a function of hydration level, NaCl and CaCl2 concentrations, and cholesterol content. The experimental headgroup order parameters are never reproduced. This indicates that under all of these conditions the used model is unable to correctly reproduce the headgroup structure. Consequently, many of the conclusions drawn over the years from this modelmight be erroneous. This manuscript has not beensubmitted to any journal, instead its contents are discussed at nmrlipids.blogspot.fi.
Phospholipids are essential building blocks of biological membranes. Despite of vast amount of accurate experimental data the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulation model would automatically resolve the structures giving an interpretation of experimental results, if the model would reproduce the experimental data. In this work we compare the C-H bond vector order parameters for glycerol backbone and choline headgroup between 14 different atomistic resolution models and experiments in fully hydrated lipid bilayer. The current models are not accurately enough to resolve the structure. However, closer inspection of three best performing models (CHARMM36, GAFFlipid and MacRog) suggest that improvements in the sampled dihedral angle distributions would potentilly lead to the model which would resolve the structure. Despite of the inaccuracy in the fully hydrated structures, the response to the dehydration, i.e. P-N vector tilting more parallel to membrane normal, is qualitatively correct in all models. The CHARMM36 and MacRog models describe the interactions between lipids and cholesterol better than Berger/H\"oltje model. This work has been, and continues to be, progressed and discussed through the blog: nmrlipids.blogspot.fi. Everyone is invited to join the discussion and make contributions through the blog. The manuscript will be eventually submitted to an appropriate scientific journal. Everyone who has contributed to the work through the blog will be offered coauthorship. For more details see: nmrlipids.blogspot.fi.
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We compare the order parameters predicted for the hydrocarbon segments in lipid bilayer headgroup region by the Berger
Phospholipids are essential building blocks of biological membranes. Despite of vast amount of accurate experimental data the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution
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to those measured by Nuclear Magnetic Resonance (NMR) experiments. We first show resultsfor a fully hydrated POPC bilayer, and then focus on changes of the order parameters as a function of hydration level, NaCl and CaCl2 concentrations, and cholesterol content. The experimental headgroup order parameters are never reproduced. This indicates that under all of these conditions the used model is unable to correctly reproduce the headgroup structure. Consequently, many of the conclusions drawn over the years from this modelmight be erroneous. This manuscript has not beensubmitted to any journal, instead its contents are discussed at
would automatically resolve the structures giving an interpretation of experimental results, if the model would reproduce the experimental data. In this work we compare the C-H bond vector order parameters for glycerol backbone and choline headgroup between 14 different atomistic resolution models and experiments in fully hydrated lipid bilayer. The current models are not accurately enough to resolve the structure. However, closer inspection of three best performing models (CHARMM36, GAFFlipid and MacRog) suggest that improvements in the sampled dihedral angle distributions would potentilly lead to the model which would resolve the structure. Despite of the inaccuracy in the fully hydrated structures, the response to the dehydration, i.e. P-N vector tilting more parallel to membrane normal, is qualitatively correct in all models. The CHARMM36 and MacRog models describe the interactions between lipids and cholesterol better than Berger/H\"oltje model. This work has been, and continues to be, progressed and discussed through the blog: nmrlipids.blogspot.fi. Everyone is invited to join the discussion and make contributions through the blog. The manuscript will be eventually submitted to an appropriate scientific journal. Everyone who has contributed to the work through the blog will be offered coauthorship. For more details see: