How accurate are the calculated form factors from simulations?

[ohsOllila]

I think that from statistical point of view accuracy is quite high, however I am not sure about the effect of undulations etc. Any kind of information from full exaplanation with citations to the hints of relevant literature are helpful here.

[GeorgPabst]

Check for papers by Kucerka and Katsaras groups. They put out several papers on bilayer structure using the SDP (scattering density profile) model. They usually compare to MD simulations. Often they have to fix the lipid area in the simulations to get a reasonable agreement.

[heftber]

As far as I know, SIMtoEXP takes into account undulations, but unfortunately I don't know how it really works anymore. But perhaps we can also ask Norbert, as this is probably the fastest way to get sophisticated information about the Programme.

[ohsOllila]

I have red now from the literature that there is, indeed, undulation correction included. It seemed to me that is typically done for the experimental data but I will take a closer look when I write the section.

[GeorgPabst]

Experimental data is typically not corrected for undulations. I remember only one paper (a review article by Nagle and Tristram-Nagle, BBA, 2000), which corrected the experimental areas per lipid for undulations. The effect was very small though (I think on the order of 1% or less), i.e. smaller than then the error from data fitting high resolution data (~2%) and much smaller than the spread of area values found in literature.

[ohsOllila]

In this paper there is the undulation correction for the form factor (http://dx.doi.org/10.1529/biophysj.104.056606):
"There is, however, an important undulation correction.
Because undulations tilt the local orientation of the bilayers
with respect to the z axis, the average thickness of each bilayer
along the z direction is larger than if the bilayer were perfectly
flat (see section 7.1 in Nagle and Tristram-Nagle, 2000).
Previously, this undulation correction was made after obtaining
an electron density profile by reducing the width of the
bilayer by a geometric factor that depends on the measured
KC (Liu and Nagle, 2004). In this article we perform the
equivalent undulation correction before fitting to an electron
density profile by expanding the qz scale for the F(qz) data by
the same correction factor, which was 1.014 for DMPC and
1.019 for DLPC."

[GeorgPabst]

This correction is typically neglected, except for the Nagle's maybe. The calculation of the correction factor depends on parameters such as the bending rigidity, which have significant experimental uncertainties. Thus within experimental error the correction factor equals 1. See also the good comparison between the form factor data from different labs and geometries.

[ibrahim-mohd]

Form factor is one of the most important structural quantities for lipid bi layer and is one of the parameters that the force fields are optimized to reproduce in almost all popular forcefields, CHARMM , AMBER and Slipids. Therefore for the standard lipids like DOPC, POPC, DPPC etc, the simulation obtained form factors are pretty close to experiments. Form factor is obtained simply form the Fourier transform of the electron density as implemented here:

https://github.com/ibrahim-mohd/Small-angle-X-ray-Form-factor-from-simulations

For larger lipid bi-layers i.e > 300 lipids per mono layer, undulations smear out the electron density and hence need to be corrected. Such corrections are implemented here:

https://github.com/ibrahim-mohd/undulation-corrected-density-for-lipid-bilayers