I am trying to express a recombinant protein which is a cysteine protease in E.coli expression system since a very long time but it is not expressing efficiently as it should be. I have used different strains e.g., BL21, Rosetta & Codon plus also used different conditions for culture and different IPTG concentrations but nothing works.

Can it be because of the presence of signal peptide or and other inhibitory domains which are usually present in protease proteins. My protein contains one signal peptide from 1-21 position and a Propeptide from 23-91 which I have predicted from Signal 4.1 server and NCBI conserved domain search sites.

I am expressing complete protein sequence including signal peptide. Do I have to express only mature form?