I am not sure what you did. You are trying to purify a protein by ammonium sulfate precipitation, correct? Now why do you have casein together with your protein? Is your protein excreted into the medium by your expression host and you added casein because the host grows better with casein? I have never done ammonium sulfate precipitation of growth medium but I can imagine that a lot of other proteins (from growth medium and from lysed dead cells) will precipitate. What other purification steps will you use? If your protein is tagged (His, SUMO, etc) do affinity chromatography first to reduce the background and then ammonium sulfate precipitation.

Since casein is a protein, it is not a good practice to add it when you are trying to purify a different protein. If this addition cannot be avoided, then you will have to identify a method to separate it from the protease. Here are 2 possibilities possibilities.

Hi

If you are adding casein as an inducer to the culture medium then you have two options, first; you could reduce the amount of added casein, second option is to increase incubation time, in both cases you guarantee that much if not all of added casein is metabolised.

Hope this helps      

you incubate the protease-casien  mixture in suitable buffer at optimally higher temerature where your protease activity  is not affected. Continue incubation for a few hours when protease would act in casein and make it soluble by hydrolysis.. Now you dialyse the mixture to remove degraded casein. you may add azide to prevent any microbial contamination.

For protease purification if casein is there it will precipitate when ammonium sulphate is added. You can remove it first by molecular exclusion chromatography.