Here are some reasons why the immobilized bait partner may not pull down the interacting prey protein and some tips to improve the pulldown:
-It is possible that the prey protein is degraded: in this case, include protease inhibitors and or phosphatase inhibitors (see examples) in the lysis buffer. Also use fresh lysate or lysate frozen at -80 degrees C.
-If the interaction between bait and prey is weak or transient, such that the stringent wash conditions disrupt the interaction, you can reduce the number of washes and ionic strength of wash buffer.
-If the prey protein is expressed at a low level, apply more protein (prey) sample, increase amount of bait protein and incubation time.
-Test to see if any cofactor is essential for the interaction being studied and include this in the incubation.
-It is also possible that binding or sample preparation conditions were insufficient to maintain or allow protein interactions. In this case, try alternative buffers for sample preparation, binding or washing procedures.
-Excessive labeling (e.g., biotinylation) of the bait could sterically hinder binding to the prey protein. In this case, reduce molar excess of the biotinylation reagent used for labeling or use a reagent that targets a different functional group.
Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.
Answer Id: E13067
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