NMRlipids III: Quantifying intermolecular interactions in binary lipid mixtures

After trying to rationalize the data in the NMRlipids III manuscript, I think that we should emphasize more the evaluation of lipid-cholesterol interactions in binary lipid bilayer against experiments. As far as I know, the quantitative comparison of intermolecular interactions between simulations and experiments has not been done much. Therefore, the procedures in this manuscript could be useful also for other than POPC/cholesterol mixtures.

To facilitate this, I plotted the absolute values of POPC sn-1 acyl chain order parameters as a function of cholesterol concentration from experiments (Fig. 1) and different simulations (slopes*pdf, see also the SI).

Fig 1: Absolute values of sn-1 acyl chain order parameters from experiments (points). The lines are fitted to the values with 0-50 mol % of cholesterol.

The increase is approximately linear below equimolar concentration in both simulations and experiments. To compare the ordering effect of cholesterol between different simulations and experiments, I made a linear fit to the data as a function of cholesterol and plotted the slopes for each carbon segment (Fig. 2).

Fig 2: Slopes of order parameters as a function of cholesterol. Determined by fitting equation S_CH(C_chol) =k_OPC_chol + S_CH(0) to the data in Fig 1 (experiment) and slopes*pdf (currently S2-S7 in the SI).

Such a plot enables the comparison of cholesterol ordering effect between different simulations and experiments, even though the data would not be measured exactly at the same concentrations. We could also add some literature data with fewer cholesterol concentrations or other lipid media in this figure for comparison.

In addition, the quantitative quality measure for the force field quality, recently contributed by Hanne Antila, could help to evaluate the intermolecular interactions. Some preliminary results are already in the manuscript, but some details in the analysis may need refinement, see issues 65 and 64 in the MATCH repository.

The most important ToDos to progress the manuscript are listed here:

1. We need to define a appropriate quantitative quality measure to be used in this manuscript, for discussion see issues 65 and 64 in the MATCH repository.
2. The changes in cholesterol order parameters upon dilution with POPC could be also analyzed from experiments and different simulations.
3. Results from Lipid14 simulations with cholesterol model would be useful, see issue 7.
4. Additional data from the literature could be added in the figure showing acyl chain order parameters slopes (Fig. 2).
5. Figure showing form factors should be updated after all the form factors are calculated properly and the scaling method for experimental form factors is decided, see issue 18.
6. Section S1 in the supplementary information about reproducibility of CHARMM36 simulations should be written based on the discussion in issue 4. 
7. Section S3 in the supplementary information about the effect of undulations on the order parameters should be written based on the discussion in issue 16.
8. The used accuracy for the experimental acyl chain order should be decided, see issue 15.