I am trying to express one protein in pET-43.1 vector fused with N-terminus Nus tag but the size of the expressed protein is about 20 kDa smaller than expected. I also transformed the neat pET-43.1 vector (without insert) but in that case also size of Nus tag appears to be 40kDa on 12.5% SDS-PAGE gel. However the size of tag in pET-43.1 vector is expected to be around 60kDa.
Aberrant migration is fairly common with SDS-PAGE. The best way to convince yourself you have the right protein expressed are a) make sure the sequence of the cloned gene is ok; b) run the SDS-PAGE with the appropriate controls (the empty vector is a correct one), including lysates from induced and non-induced cultures. From what you say, the estimated MW difference between the Nus tag and the fusion protein match the expected value of your protein. Oh, make sure you identify correctly the bands of the molecular weight standards, I have seen this happen too many times... Good luck!
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