davesmith4398 / best_practice_membranes

Best Practices document to be submitted to the Living Journal of Computational Molecular Science
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NMR order parameters, form factor and area per molecule #3

Closed ohsOllila closed 5 years ago

ohsOllila commented 6 years ago

It is written in page 6, section 3.4, second paragraph that "Experimental reference data can be classified as either direct or indirect. Direct data includes experimentally mea- sured properties (e.g. x-ray and neutron form factors from scattering experiments), while indirect data includes proper- ties inferred from direct experimental data based on a given theoretical model (e.g. area per lipid, bilayer thickness, NMR bond order parameter, lipid diffusion coefficient)." I think that this is not fair for the NMR order parameter data. In order parameter experiments, the direct observables are 2H quadrupolar splitting or 13C dipolar coupling. These can be connected to the order parameters using quadrupolar or dipolar coupling constants, which are known empirically. Therefore, the mentioned theoretical model is not used to extract the order parameters.

On the other hand, "experimental" area per molecule and thickess are determined from form factors (or similar) scattering data using theoretical models, e.g., SDP model. Furthermore, assumptions related to the structure factors are needed in some form factor experiments.

In conclusion, I think that the NMR order parameter data is equally direct as form factor data, and definitely more direct than the area per molecule or thickness.

Form factor gives information about bilayer dimensions, while order parameters give information about sampled structures of individual lipid molecules. Therefore, the area per molecule and thickness information is better to derive from form factor using, e.g., SDP model. I think that the calculation of thickness and area per molecule from order parameter data, discussed in page 7, right paragraph, is much more approximative and should not be used in the validation of lipid models.

Finally, it should be noted that the order parameters can be used to validate also the structure of glycerol backbone and headgroup.

For more detailed discussion, see

O.H. Samuli Ollila and Georg Pabst Biochimica et Biophysica Acta (BBA) - Biomembranes Volume 1858, Issue 10, October 2016, Pages 2512-2528 https://doi.org/10.1016/j.bbamem.2016.01.019

Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions Botan et al. J. Phys. Chem. B, 2015, 119 (49), pp 15075–15088 DOI: 10.1021/acs.jpcb.5b04878