I'm doing a multi-step purification to purify a protein (or proteins!) responsible for a particular biochemical activity. I do not know the identity of the protein, so I am doing the purification by following the activity only. Here is my purification table.
_____Step_____________________Total protein_____Specific activity ____Yield____Fold_________
Processed crude fraction___________57.6______________35___________ ____100_______=1_____
Ammonium sulfate___________________36.9______________74____ ___________87________2.13____
Phenyl sepharose___________________6.64_____________1560_ _____________29________44.9____
Heparin sepharose_________________0.46_____________2215___ __________2.5________63.8____
Gel filtration____________________0.082_____________23 56_____________1.9 _______67.8____
As you can see, something funky is happening with the Hydroxyapatite column, because the specific activity does not increase at that step. I am stumped as to what that can mean. Is the hydroxyapatite column fractionating out a cofactor or another protein that is necessary for activity? This is my first time doing a purification like this. Is a yield of 1.9% considered colossally shitty? It seems I am losing the most yield at the Phenyl sepharose step -- does that mean I should eliminate that column from my purification?Any help is appreciated! Thanks in advance!