If I were you, I would answer a couple more questions first:
When you say you express a lot of protein, is it right to assume that
it is soluble, and you're not losing it (or much of it) in the
It should be easy to tell if your protein is binding to your resin or not.
Assay the flow-through from your column, or else take a sample of the
resin (if you can) before and after adding your extract, boil the
samples with SDS-PAGE loading buffer and run them on SDS-PAGE.
I think it's critical to know if your protein is either not binding to
your resin, or not coming off the resin, before trying to solve your