Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C–H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to ‘reality’. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
- Form factor
- Neutron scattering
- Order parameter
- X-ray scattering
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Project Members, N. L. (Creator), Botan, A. (Creator), Favela-Rosales, F. (Creator), Fuchs, P. F. J. (Creator), Javanainen, M. (Creator), Kanduc, M. (Creator), Kulig, W. (Creator), Lamberg, A. (Creator), Loison, C. (Creator), Lyubartsev, A. (Creator), Miettinen, M. (Creator), Monticelli, L. (Creator), Määttä, J. (Creator), Ollila, S. (Creator), Retegan, M. (Creator), Róg, T. (Creator), Santuz, H. (Creator), Tynkkynen, J. (Creator), Girych, M. (Creator), Ferreira, T. M. (Creator), Topgaard, D. (Creator) & [...] (Other), 2015