I am investigating a nonsense SNP mutation which is predicted to result in a protein truncated from 680 to less than 300 amino acids. We think this causes a relatively severe disease.
As far as I am aware, with such a significant truncation, we would expect nonsense-mediated decay. However, qPCR did not detect significantly altered level of expression in the relevant tissue of a case and a control (unfortunately we do not have the luxury of multiple samples/biological replicates), indicating NMD does not occur.
If this is true, I would then expect to see a massively truncated protein on a western blot. In the affected tissue lysate the protein is not detected at all, but it is in the normal lysate. The antibody immunogen was the full-length protein.
Is this unusual? Could it be due to misfolding of the truncated protein, which means that the antibody doesn't detect it, but the protein is still there?
I completely agree with Karousis that the antibody may have strong affinity with the C-terminal epitope. In addition, it has been observed that the truncated proteins are highly ubiquitinated and degraded immediately after their synthesis and therefore is not detected in western blot. You may also check the protein by immunostaining if they are forming insoluble aggregates in the cell.
Hope this helps. Best wishes.
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