I am expressing a protein in E.coli using the pGex system. The fusion
protein is expressed in high yield and can be purified using GST-agaroase.
When I cleave my protein from the gst (using thrombin) on the GST-agarose
I get a product that runs as a single band by SDS page plus a few minor
contaminants. If I run this product on an IEF gel I see multiple bands and
likewise if I try to purify this by ion exchange I get multiple peaks.
Each of these peaks from the ion exchange run at the same hight on SDS
PAGE and all are detected by my antibody in western blot. Could anyone
explain what is happening.