I wouldn't say it is impossible, but it will be tricky. Since both proteins presumably have secondary structure, you can measure the CD spectrum of each individually, and of the mixture. Subtracting the CD spectrum of sepF from the CD spectrum of the mixture should give you the spectrum of FtsZ in the presence of sepF. Importantly, this assumes that there is no change in the CD spectrum of sepF when it binds to FtsZ. If both proteins are altered, this subtractive method won't work.
An additional problem is keeping the absorbance of the mixture low enough to get a good measurement of the far UV CD spectrum.
Finally, unless there is a major change in the secondary structure, which is not very likely, it may be challenging to notice it in the CD spectrum.
assuming that only one protein is changing secondary structure upon interaction of two proteins carries the risk of being misleading. The only situation I would consider this kind of comparison meaningful is when an intrinsically unfolded protein gains structure upon binding to a second protein.
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