It's better to describe my question with an example :
Suppose that we have a protein solution and SEC (size exclusion chromatography) indicates that it has 10% of aggregated form and SDS-PAGE shows that it has 60% of native form and 40% of unfolded form. Now, since the SDS-PAGE doesn't show the amount of aggregated form (because of its high molecular weight, it can't move in gel) and excludes it, can we conclude that :
Aggregated form = 10%
Native form = 0.6 x ( 100 -10 ) = 54%
Unfolded form = 0.4 x ( 100 -10 ) = 36% ???
It is difficult to do this. First, I am not sure how you have ~40% of your protein in the solution in the unfolded form. How was the SDS-PAGE gel run? (SDS can unfold your protein). If the SDS-PAGE gel was run under native conditions then from the data provided, you may make that claim. If you really want to find these values SEC-MALS is the equipment I would recommend.
You probably need to define what you mean by folded and unfolded better. Does unfolded mean a particular partially unfolded state or complete unfolding of the protein (by urea for example)?
We take our samples from the middle of a refolding process, where some of completely unfolded proteins ( inclusion bodies that were solved by urea ) are folded, some of them are still unfolded and of course some are aggregated. The SDS-PAGE test is performed in the non-reduced mode.
First, theoretically, SDS-PAGE is an analytical technique made to analyse denatured proteins. If you put SDS-containing laemmli buffer with you protein and heat it, it will unfold, and SDS will bind your protein and prevent it from folding back to its native state. This is the reason why the shape of the protein isn't (or at least only fewly) a parameter influencing migration in SDS-PAGE compared to native PAGE. Knowing this, you only look at unfolded proteins in SDS-PAGE...
Second, you told you used non-reducing conditions for your samples. So, if you used only one purified protein for your experiment, and you see several bands on you gel, it is likely to be because of the creation of disulfide bridges between protein chains giving multimers (or of course a protein degradation, which is also possible).
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