I would like to have an opinion about microscopy techniques to distinguish between folded and unfolded protein molecules belonging to a same or different proteins.
Am not aware of a microscopy technique that would do the job in a straightforward way, but EM might be an option. As an alternative I would recommend using a technique like CD (circular dichroism) which can discriminate folded from unfolded proteins.
Fluorescence correlation spectroscopy can be a good option, because unfolded proteins have higher diffusion coefficients than the folded ones.
http://www.sciencedirect.com/science/article/pii/S0006349505732070
Another nice microscopic technique -very useful to explore microscopic pathways in protein unfolding- is single molecule FRET, with an adequate selection of the donor-acceptor pair.
http://www.sciencedirect.com/science/article/pii/S0959440X07002035#articles
It is a good practice in protein unfolding studies to combine the information from several techniques. As mentioned by Guus, far UV Circular Dichroism is one of the reference techniques. However, it does not always work, e.g. it is not useful to distinguish between native and SDS-induced unfolded states in membrane proteins.
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