I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody. When using another antibody, it shows almost no ATP1A2 expression at all in one of the two cell lines. Any insights onto what might be going on here?
No, it is NOT possible that different gene sequences encode the same protein (AA sequence). Maybe other Isoforms may be encoded by different genes, However Isoforms are different proteins (e.g. see eNOS vs nNOS vs iNOS). In my opinion your antibodies exhibit different effectivity and specificity . Maybe one of the utilized antibody do not specifically detect your protein of interest (for ref. see Reproducibility crisis: Blame it on the antibodies. Baker M. Nature. 2015 May 21;521(7552):274-6. doi: 10.1038/521274a.).
They could be allelic variants. More likely possibilities include differential splicing of exons as well as different post translational modifications.
If the experiments were done at different times or if the samples were stored and performed the SDS-PAGE & WB later for the second time, there is a possibility of experimental error. It might be unlikely, yet it can happen.
As Andreas Eisenreich mentioned, the two different antibodies could exhibit different effectivity and specificity.
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