I over-expressed HA tagged mammalian protein (27KD) in 3 different cell lines; however, I saw the over expressed protein (exogenous) behaves differently than the endogenous protein in the all cell lines that I used. For instance, the exogenous protein expression level depends on other protein expression or proteosome inhibitor. I checked DNA sequence of the protein and there were no problems. The exogenous protein can be detected by Western blotting using either anti-HA or anti-protein antibody. 

Is there any ideas why the over expressed protein behaves differently than the endogenous protein? Any ideas or suggestions would be appreciated.

Ahmed

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