First of all it is important to know if the protein is basically soluble or not. If it is a membrane protein detergents should be included for solubilization.
If it is a soluble priotein it may be misfolded and peeleted during centrifugation.
To really adress this question more details about the protein and the extraction protocol are required.
Could be one of two things that I can think of:
1.) Cell lysis is incomplete
2.) Protein is stuck in insoluble fraction- this happens more often in recombinant protein purification, but I think the same principle applies to membrane proteins.
Do you commonly use this cell lysis prep protocol for protein successfully?
First of all it is important to know if the protein is basically soluble or not. If it is a membrane protein detergents should be included for solubilization.
If it is a soluble priotein it may be misfolded and peeleted during centrifugation.
To really adress this question more details about the protein and the extraction protocol are required.
Did you check the cell pellets for detecting proteins (using immunoblot); also you can add whole cells for blots to make sure you have the production of proteins (comparable to your another protein) is more or weak or not happened!
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