333993 A Comparative Study of Gromos- and Charmm-Based Force Fields for the Simulation of Non-Hydroxy Ceramide Bilayers
The ability of the skin to regulate bodily functions and act as an effective barrier to chemical penetrants is controlled by the thin, outermost layer, known as the stratum corneum. The stratum corneum is predominantly composed of ceramides, cholesterol, and free fatty acids, however, the molecular level organization of the species and their role in maintaining the barrier function of the skin is not well understood . While molecular simulation has been used extensively to study phospholipid bilayers and has provided a wealth of structural information, in comparison far less is known about the atomic level structure and interactions of bilayers involving ceramides. Prior simulation studies of non-hydroxy sphingosine ceramides (CER-NS) have demonstrated important differences with other lipids, e.g., sphingomyelin bilayers, including reduced ordering  and reduced residence time  of water molecules at the interface, due to the absence of a large polar head group. However, most work to date has examined pre-assembled ceramide bilayers under a very limited timescale (~20 ns simulation time), making it possible that these studies are adversely influenced by the initial, assumed structure. Additionally, only one ceramide (CER-NS) of the twelve distinct ceramides known in the stratum corneum  has thus far been considered in the literature. Furthermore, while common force fields (e.g., CHARMM and GROMOS) have been tuned and validated for phospholipid bilayers, it is not yet known how these perform when applied to ceramide-based systems.
Here, the structural properties of CER-NS bilayers are examined using models derived from both the CHARMM and GROMOS force fields. Parameters from CHARMM36  are used with missing parameters and headgroup charges determined from density functional theory calculations; GROMOS-based simulations are performed using the model adapted by Berger  that has been employed in prior ceramide studies . Here, it is observed through examination of long simulation runs (>100 ns) that both force fields provide similar results at physiological conditions (T=305K), in good agreement with experimental observations. However, examination of the thermophysical behavior demonstrates that the CHARMM-based force field is better able to reproduce the experimentally determined gel-to-liquid bilayer transition temperature, differing by only ~10K, whereas GROMOS overpredicts the transition temperature by > 50K. The CHARMM-based force field is also able to resolve a secondary transition ~345K, in close agreement with experiment, where evidence of such a transition is absent in the GROMOS-based force field. This suggests that the GROMOS-based force field over-estimates the stability of the gel phase for the ceramide bilayer, which may alter results for simulations of mixtures more representative of the stratum corneum, where structural heterogeneity may be present. Finally, using the validated CHARMM-based force field, simulations of CER NS are compared to simulations of the non-hydroxy phytospingosine ceramide (CER NP) to begin to examine the role of ceramide structure; distinct structural differences are observed with regards to the prefered orientations of the C-O bonds and the structural ordering of nitrogen atoms in the lipid headgroups of the two difference species.
 Wertz, P. W., Lipids and barrier function of the skin. Acta Derm.-Venereol. 2000, 7-11.
 Pandit, S. A.; Scott, H. L., Molecular-dynamics simulation of a ceramide bilayer. J. Chem. Phys. 2006, 124 (1), 014708.
 Imai, Y.; Liu, X. L.; Yamagishi, J.; Mori, K.; Neya, S.; Hoshino, T., Computational analysis of water residence on ceramide and sphingomyelin bilayer membranes. Journal of Molecular Graphics & Modelling 2010, 29 (3), 461-469.
 Klauda, J. B.; Venable, R. M.; Freites, J. A.; O'Connor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D.; Pastor, R. W., Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. The Journal of Physical Chemistry B 2010, 114 (23), 7830-7843.
 Oliver Berger, O. E., Fritz Jahnig, Molecular Dynamics Simulations of a Fluid Bilayer of Dipalmitoylphosphatidylcholine at Full Hydration, Constant Pressure, and Constant Temperature. Biophys. J. 1997, 72, 2002-2013.
 Notman, R.; den Otter, W. K.; Noro, M. G.; Briels, W. J.; Anwar, J., The permeability enhancing mechanism of DMSO in ceramide Bilayers simulated by molecular dynamics. Biophysical Journal 2007, 93 (6), 2056-2068.