In X-ray study, normally the bilayer repeat distance is determined (shown as D in this paper (Nagle, J.F. and S. Tristram-Nagle, Lipid bilayer structure. Current opinion in structural biology, 2000. 10(4): p. 474-480)). However, from simulation we calculate the bilayer distance from peak to peak based on local density profile. That is D'B from above paper. Is this the correct way of doing it?
Yes, Pavel has the right idea. A D-spacing measurement gives you the repeat distance of bilayers in a stack, either in a multilamellar vesicle, or a stack of bilayers on a silicon wafer, such as in our oriented samples. The D-spacing is the combined thickness of the lipid bilayer and the water between the bilayers. It does not give you the lipid thickness directly. For fully hydrated fluctuating lipids in the fluid phase, we obtain the x-ray diffuse scattering which provides us not only material properties, such as the bending modulus, but also the structure directly. We take the square root of this intensity (form factor) and then the Fourier Transform, while fitting to a model of the lipid bilayer, where the Gaussian components are allowed to move to fit the data through the Fourier transform. It sounds complicated and it is, but our data agree nicely with MD simulations in many cases, including with peptides in the bilayer. Please read some of our papers which are available here in Research Gate or on our WEBsite: http://www.cmu.edu/biolphys/jfstn. Thank you. Stephanie
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