My protein is disordered protein and it does not precipitate in water. However, I am confused regarding dialysis of my protein in water. Should I Dialyize my protein in water and then lyophillize it?
This is hard to predict, but most likely, structural parameters and the protein's "quinary state" will be affected to some degree outside the protein's native milieu of binding proteins and metabolites. http://www.nature.com/nrm/journal/v14/n4/full/nrm3542.html
It depends on a particular protein. Generally speaking it does not affect the structure but at time it tends to aggregate the protein.
Some proteins are quite robust and can tolerate dialysis in water and lyophilization. Others (especially highly charged ones) may undergo chemical modification or cleavage during the water dialysis. If you do not have an assay for your protein's native behavior (I assume you do not as it is disordered), then I would recommend only dialysis versus a buffer and skip the lyophilization.
I would recommend using Amicon pressure filtration or spin filters to concentrate. You can even perform dialysis in them. While there are examples of proteins that adhere to the membranes, most proteins we have dealt with (folded or unfolded) behave.
Is there a particular reason why you need to dialyze against water instead of a buffer?
I suggest that you dialyse your protein in a buffer and concentrate it using centricon tubes.
Why dialysis in water, what if the protein is an akali protein, best thing is use appropriate buffer and then either concentrate using a Millipore, centricon, or 4M sucrose solution. It is possible it has an effect on the structural parameter.
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