18 February 2016 3 705 Report

I've been purifying a fragment of GAP protein from mouse, expressed in E.coli BL21 cells. The protein has a GST tag at the N-terminus and a StrepTagII at the C-terminus. Firstly, I purify it on GST resin, and after overnight dialysis I load approx. 25 mg protein to 5 ml Streptactin resin. I incubate it 1h at 4 degrees, wash the resin and elute proteins with 2.5 mM desthiobiotin. Buffers I use contain 50 mM Tris pH 7.5, 300 mM NaCl and 5 mM BME. SDS-PAGE revealed there is basically no difference in purity before and after streptactin purification. I have a lot of low molecular weight impurities right below the band of interest.  

I used to work on the protein that had all tags at the N-terminus, but decided to move Streptag to the C-terminus, hoping that those impurities were some kind of degradation or incomplete translation products, but it didn't improve the purity. I've already tried size exclusion and ion exchange chromatography, but the separation is quite poor.

Does anyone has any suggestion of what it can be and how to tackle this problem?

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