Different I(0) for Models of Same Protein

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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ChemMJW
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Different I(0) for Models of Same Protein

#1 Post by ChemMJW » 2016.06.03 22:07

Hello all,

I have a CRYSOL question I'd like to get your input on. I have 12500 computationally generated model structures for the protein I am studying. The protein has 173 residues and is comprised of two homologous beta-strand domains. In a modest concentration of urea, the N-terminal domain is unfolded, while the C-terminal domain is native-like. I have used CRYSOL to predict the scattering curve for each of the 12500 partially unfolded models of the protein. A semi-log plot of the CRYSOL predictions is attached.

You will notice that there is a broad range of I(0) values for the predictions. Is not I(0) dependent only on the number of electrons in the molecule and therefore should be the same for all 12500 models regardless of the fact that each model has a different conformation of the unfolded NTD?

If my understanding is mistaken, I am happy to be corrected. If not, is there something else going on here?

Thank you.
Attachments
fig.jpg
SAXS Curves for 12,500 Protein Models
fig.jpg (637.42 KiB) Viewed 4060 times

Alex
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Location: Planet Earth

Re: Different I(0) for Models of Same Protein

#2 Post by Alex » 2016.06.05 17:56

I(0) is proportional to the volume of the molecule, hence if you have a larger Rg/Dmax it may fluctuate somewhat.
For details, see equations 1-2 in:
http://journals.iucr.org/j/issues/2010/ ... ce5058.pdf

HTH, Alex

ckerr
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Re: Different I(0) for Models of Same Protein

#3 Post by ckerr » 2016.06.08 09:08

The I0 in vacuum (3rd column in the .int file) is proportional to the number of electrons in the molecule - this should be the same for all models of a given polypeptide. However, the overall scattering also takes into account the scattering from the displaced solvent and the higher-density solvent boundary layer.

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