I am performing structural characterization for a couple proteins in my lab. Protein 1 and protein 2 were found to have a Dmax of 190 and 140 angstroms, respectively. On the other hand, my DLS measurements show a Z average of 10nm for both proteins. From Pr Distribution, Protein 1 is thought to have a dumbell type arrangement from looking at an widened curve from 35 to 80 angstroms, with a dmax of approximately 190 angstroms. From Pr distribution, protein 2 is thought to have a globular structure with a diameter of 70 angstroms and dmax of approximately 140. The mass of both proteins is 113 kDa.
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DLS and SAXS results showed no aggregation of samples.
Reviewing the literature shows that both SAXS and DLS work in the size range my proteins are expected to be in. What I am having issues with is rationalizing the discrepancy between the two experiments. SAXS shows a significant difference between proteins, whereas DLS both undervalues SAXS results and shows no difference between protein 1 and 2. I trust SAXS results more, as I am able to extract flexibility and rough protein shape from scattering data. I cannot do this with simple DLS information. Although I expanded more in my write up of these results, at the base level, it seems shaky without more concrete comparisons to literature. Would anyone happen to know of any experiments comparing the two methods and/or how my measurements are no aligning between the two experiments?
Thank you!