I would not recommend attempting to purify protein dissolved in sodium carbonate buffer because the high pH may cause damage. It would be worth the time to try out different expression strains and conditions (medium, temperature) to see if you can find a combination that results in some soluble protein. You might also try adding a solubilizing domain to your construct. If those approaches don't work, there is the option of dissolving the insoluble protein in 8M urea or 6M guanidine-HCl and refolding it. But first, I suggest digging into the literature to see what methods have worked for others to produce this protein.

In addition to the great suggestions above, if your final detergent concentration is below the CMC levels you may get rid of them by ultrafiltration or dialysis. You may use urea and/or dilution to break open the micelles to filter out the detergent monomers but using urea will need a refolding process which is a bit cumbersome. There are some IEX or affinity-based resins to remove detergent (mainly SDS) but not sure of their efficacies.

Adam B Shapiro

Thankyou for your valuable suggestions, sure I will try the trouble shooting as you mentioned.

Kindly explain about the solubilizing domain in the construct it is very new to me. The protein expression vectors are not having such domains. Thank you.

İsmail Emir Akyildiz

Thankyou for your valuable suggestions.

I will try IEX or affinity-based resins to remove detergents. As u indicated refolding is difficult, hence not giving a try.

Thank you.

There are several domains that can be added to the N-terminus of the construct to improve folding and solubility. Examples are NusA and MBP.

Article Unrelated Solubility-Enhancing Fusion Partners MBP and NusA ...

Adam B Shapiro

Thankyou for your suggestions. The article will be highly helpful.