[Protein-analysis] Gly4-Ser linker proteolytic degradation

[patrick.stancombe at hpa.org.uk]

E.coli expression of a two domain protein is undergoing specific
proteolytic cleavage at the (Gly4-Ser)x4 linker site between them.
Tried using protease inhibitor cocktails without success. Is this a
common problem? Does anyone have suggestions to what is the cause and
what can be tried to prevent it?
Thanks