Check first that you have a good expression level. I suggest to change the signal peptide for MBP protein or reduce the temperature of expression to 30. I would add also some protein inhibitor to the culture media during induction period with IPTG. I don't know your medium composition but if it is LB, the addition of some magnesium and glucose to 0.5 % (final) may also help. Good luck.
Hi, Giggsy, your protein may not express well in BL21 cells. This is a common obstacle in heterologous expression. In fact, your protein may not express well regardless of the signal peptide you use. Here's how you can further diagnose the expression profile of your protein.
1) Express your protein with your previous conditions or with typical starting conditions. (Induce with 1mM IPTG around OD 0.4-0.8. Induce for 3 hours.)
2) Spin down cells into pellet. Dissolve pellet in 1x PBS. Lyse cells via sonication, French press or chemical methods.
3) Spin down again at 15000xg for 10min. Collect supernatant.
4) Dissolve pellet in 8M Urea.
5) Run SDS-PAGE and stain with Coomassie. If protein is soluble and phoA signal peptide aids expression then protein will be found in the supernatant. If protein is difficult to express then you will find it in the pellet digested with urea. This indicates that the protein is expressed but forms inclusions bodies, or that the protein localizes to the membrane.
There are many tips and suggestions in this forum and others regarding expression and purification of non-soluble proteins.