Protocol

Regulating Protein Stability in Mammalian Cells Using Small Molecules

Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA

¹Corresponding author (wandless{at}stanford.edu)

INTRODUCTION

Regulating protein stability using small molecules provides a rapid, reversible, and tunable method to study a protein of interest’s (POI) role in cells. We recently designed a small protein domain based on the 12-kDa FKBP (FK506 binding protein) that can be fused at either the carboxyl or amino terminus of a protein of interest. This destabilization domain (DD) confers instability to fusion protein partners. The method described here explains how to use a DD fusion to control the biological activity of a POI. In the absence of a small molecule ligand, the DD is unstable and directs the fusion protein for degradation. Addition of the ligand stabilizes the DD, allowing the fusion protein to accumulate in cells and the POI to exert its biological effect. The ligand is specific for the DD and has no detectable off-target effects. By utilizing the specificity of genetic fusion and the speed of small molecule binding, this technique provides an alternative to RNA interference to study a POI’s role in cells.