Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions

Abstract

Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very 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 simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https://zenodo.org/collection/user-nmrlipids ) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.

Figure 1

Chemical structure of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC).

Figure 2

Order parameters from simulations listed in Table 1 and experiments for glycerol and choline groups. The experimental values were taken from the following publications: DMPC 303 K from ref (68), DMPC 314 K from ref (69), DPPC 322 K from ref (54), DPPC 323 K from ref (50), POPC 296 K from ref (45), and POPC 300 K from ref (35). The vertical bars shown for some of the computational values are not error bars, but demonstrate that for these systems we had at least two data sets (see Table 1); the ends of the bars mark the extreme values from the sets, and the dot marks their measurement-time-weighted average. An interactive version of this figure is available at https://plot.ly/~HubertSantuz/72/lipid-force-fieldcomparison/.

Figure 3

Order parameters for POPC glycerol and choline groups from simulations with Berger-POPC-07, MacRog, GAFFlipid, and CHARMM36 force fields (the bolded systems in Table 1) together with experimental values. The error bars of simulation data are standard errors of mean (see Methods section for details). The magnitudes for experimental order parameters are taken from Ferreira et al., the signs are based on the measurements by Hong et al.^, and Gross et al., and the R/S labeling is based on the measurements by Gally et al.

Figure 4

Rough subjective ranking of force fields based on Figure 2. Here “M” indicates a magnitude problem, “F” a forking problem; letter size increases with problem severity. Color scheme: “within experimental error” (dark green), “almost within experimental error” (light green), “clear deviation from experiments” (light red), and “major deviation from experiments” (dark red). The Σ-column shows the total deviation of the force field, when individual carbons are given weights of 0 (matches experiment), 1, 2, and 4 (major deviation). For full details of the assessment, see Supporting Information.

Figure 5

Dihedral angle distributions for g₃–g₂–g₁–O(sn-1) dihedral from different models (POPC bilayer in full hydration).

Figure 6

Dihedral angle distributions for N-β-α-O dihedral from different models (POPC bilayer in full hydration).

Figure 7

Effect of dehydration on glycerol and choline order parameters in experiments. The magnitudes of order parameters are measured for DMPC (¹H–¹³C NMR) at 314 K, for POPC (²H NMR) at 296 K, and for DOPC (²H NMR) at 303 K. The signs are based on the measurements by Hong et al.^, and Gross et al. Note that to elucidate the relative change as a function of hydration level, the simulation results were vertically shifted; the shift magnitudes for each of the force fields are listed (S_CH + shift) in the y-label.

Figure 8

Average angle between membrane normal and P–N vector as a function of hydration level calculated from different simulations.

Figure 9

Effect of cholesterol content on the glycerol backbone and choline order parameters in experiments^, and simulations with the Berger-POPC-07/Höltje-CHOL-13, CHARMM36, and MacRog force fields. The signs in the experimental values are based on the measurements by Hong et al.^, and Gross et al. In order to elucidate the relative change as a function of cholesterol content, the simulation results were vertically shifted; the shift magnitudes for each of the force fields are listed (S_CH + shift) in the y-label.