I agree with Thelymitra pulchella. Your protein may be aggregating into inclusion body form. For avoiding this situation, you may need some advises, such as 1) fusion of the target protein with a more soluble partner, typically a bacterial protein; 2) co-expression of folding catalysts and chaperones; 3) expression under culture conditions which reduce the translation rates or affect the intracellular environment; and 4) modification of the protein sequence.
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