I purified the insoluble fraction of a protein expressed in e.coli BL21 using buffers containing 8M urea, what is the best way to remove the urea while keeping the protein soluble?
The protein will precipitate if you remove the urea without refolding the protein, or without replacing the urea with something else to keep the unfolded protein in solution (detergent or guanidine-HCl).
Assuming you want to refold the protein, there are various methods, some of which were already mentioned by Lorenzo Briganti. Frequently, when refolding a protein, additives are used to help the protein refold, an example being arginine. There are refolding kits available that provide several common additives.
If it is necessary to form disulfide bonds, a redox buffer should be included, such as a mixture of reduced and oxidized glutathione.
You can remove the urea using Sephdex G25 and use IMAC resin for pruification of your protein of interest. Incase if you want to refold simulataneously you can follow oncolumn purification . Please check one such protocol attached.