Protein dephosphorylation protocol

Removal of phosphate groups from proteins, before or after blotting. 

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To demonstrate specificity of an antibody for a protein in its phosphorylated state, proteins can be dephosphorylated either before SDS-PAGE or after transfer to a membrane. Dephosphorylated samples should show little or no staining compared with untreated samples.


Calf intestinal alkaline phosphatase (CIP)
CIP buffer: 100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1 mM dithiothreitol, pH to 7.9 at 25ºC
​Protease inhibitor cocktail, EDTA-free

Dephosphorylation of lysates before SDS-PAGE

  1. After lysing cells or homogenizing tissue in lysis buffer and determining the protein concentrations, set aside two samples of a lysate/homogenate that are expected to be positive for the phosphoprotein. Typically, only two lanes of a gel are needed to demonstrate the specificity of a phosphoprotein-specific antibody: one for the dephosphorylated sample and one for the control, an untreated sample. We recommend 20-30 µg of protein per lane for crude extracts.

    If possible, avoid using sodium orthovanadate (a component of RIPA lysis buffer) and EDTA in the lysis buffer: 10 mM sodium orthovanadate inhibits CIP activity (10 units) by 90% and 50 mM EDTA inactivates CIP (10 units) almost 100%. It is essential if using crude extracts that protease inhibitors are included in the CIP buffer.

  2. Resuspend protein/lysate in the CIP buffer, 1 µg protein per 10 µl 1X buffer with protease inhibitors, EDTA-free. 
  3. Add 1 unit CIP per µg of protein to the "+phosphatase" sample. CIP is typically provided as 10,000 units per ml. Incubate up to 60 min at 37°C, although shorter times and a lower temperature may be effective if proteolytic degradation is a concern. Samples can be frozen and stored at this point or processed as usual for SDS-PAGE. If desired, sodium phosphate (pH 7.4) can be added as a competitive inhibitor, at a final concentration of 10 mM.

Dephosphorylation of membranes after transfer

For an antibody that only binds its phosphoprotein target when the protein is denatured, treating the membrane with phosphatase post-transfer may be preferable to treating the non-denatured lysate with phosphatase, pre-SDS-PAGE. For a well-controlled comparison, the membrane treated with phosphatase should be a piece cut from a blot of a single gel containing a duplicate lane or lanes.

  1. Transfer gel proteins to nitrocellulose or PVDF and block the membrane with 5% BSA in TBS with 0.1% Triton X-100 for 1 hr at room temperature. Milk contains casein, a phosphoprotein which may create background staining if the antibody cross-reacts with the phosphorylated sites.
  2. Cut the membrane to obtain a piece containing at least one sample duplicated in the other piece.
  3. Place the two pieces in separate containers of the CIP buffer, 3-5 ml per container. 
  4. Add CIP to the container with the piece to be dephosphorylated.

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