Another theory is that trace amounts of Ni may leech off the column during purification and coordinate with multiple His-tags on the pure protein, causing them to aggregate.
For sure. We had a case where a protein would precipitate after post-Ni-NTA dialysis. The precipitate would go back into solution if resuspended in the presence of imidazole or EDTA/EGTA. Inclusion of a bit of EDTA into fractions and dialysis solution completely eliminated precipitation.
Dima
