I express my target protein which cloned into a pet28a with a his tag and expressed in a BL 21. After induction of 1 mM IPTG and expressed at 37 ℃ for 3 h, it was lysed with lysis buffer ( 50 mM NaH2PO4, 500 mM NaCl, 10 mM imidizole) and sonicated with pulse 6 second ON and 6 second OFF For 6 Minutes with 35% amplitude. It could be easily detected by SDS-PAGE, however, after centrifugation at 13,000 rpm for 10 min, the target protein could not be detected in the supernatant.
First of all you need to add sufficient volume of lysis buffer to the cells(1 g of dry wheght cell to 20 ml of lysis buffer). Second perfom your centrifugation at min 15,000 g for at least 20 min. After all take a 1 sample from supernatant(20 mkl), dissolve unsoluble fraction in your lisis buffer + 8M Urea, perfom new centrifugation and take 2 sample(20 mkl). Compare samples 1 and 2 on SDS PAGE, in your protein of interest in 1 lane - it is soluble, if in 2nd - unsoluble(inclusion bodies or bad lisis buffer).
I agree with Koptev, but also have an alternate approach that we use frequently in my lab. We also express our proteins in BL21 cells and use His-Tag protein purification. For optimal protein production in these cells, you should grow the cells at 37 C an monitor the optical density (OD) to make sure the cells are in log-phase (OD between 0.6 and 1.0) before inducing them with IPTG. If you don't, you are going to get sub-optimal yields. Once your OD is in the right range, you then induce with 1 M IPTG and move them to 30 C, which is a temperature that promotes protein production rather than growth. I typically will induce and leave the protein expression to go overnight (3 hours may not be sufficient). The next morning, you want to pellet the cells, discard the LB, then re-suspend the pellet in the binding buffer for your His-Tag purification protocol (we use this one [see attached]). Vortex that thoroughly before adding Lysozyme (from chicken white) at 1 mg/mL of re-suspended pellet and vortexing again--this tends to be quite effective and I've never needed to use any sort of lysis buffer (which can get expensive for large scale protein synthesis, quite honestly). I then typically let this sit on ice for 1 hour before using a tip sonicator at 35-40% amplitude cycling at 2 seconds-"on"-2 seconds-"off" (for 4 min total). I then spin this down at >10,000 rpm for 15 min, and the lysate supernatant contains the desired protein at pretty high yield. Take that and use it with His-Tag purification and you should be set.
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