You might try to replace guanidinium hydrchloride by urea either directly for solubilization of the inclusion bodies or after solubilization with GdnHCl and then exchange GdnHCl with urea by dialysis.

(I don't see why GdnHCl should harm the disulfide bonds or thiolate.)

Thank you very much.

Where did you produce this protein?

E.coli SHuffle strain from NEB

Does it have reducing or oxidizing production conditions?

yes. It is Genetically Engineered 

Ok, i see that you do not understand what i am asking. Anyway you should change induction or growth conditions to express the protein as a soluble entity. 

What Omar might be suggesting: try other expression conditions to prevent the formation of inclusion bodies, that is (as explained) expression as soluble protein. Lower temperature, 'softer' induction, shorter expression time (different strain).

Dear Ulrich,

I have already tried 0.01,0.1,0.5 and 0.7 mM IPTG and 16C,20C,25C and 37C temperature. Shuffle strain is specialized to include disulfide bonds and I co-transformed with pRARE that includes all the rare codons.

OK... For solubilization of inclusion bodies and refolding/oxidation you might browse the papers by Raines Rudolph, Elisabeth Schwarz and/or Hauke Lilie, all from Martin Luther University Halle-Wittenberg.

Dear Ulrich Arnold,

I have used 5 % sarcosyl to dissolve the protein and it worked.

Sarkosyk, as mentioned above, will work for recovery.  And so will Gdm-HCl at high molar concentrations, and even SDS. However, your biggest problem will  be folding the purified protein into its native state. Many non-natural disulfide bonds are likely to form during  the process and these will have to be broken with a reducing agent prior to folding the protein correctly, including having all sulfhydryls in their correct redox form. If you are lucky, the right combination of reduced and oxidized glutathione will help fold it. Otherwise, it will required a lot of guesswork, trial and error, and some folding protocols to get the protein folded correctly.