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Small-molecule displacement of a cryptic degron causes conditional protein degradation

Nature Chemical Biology volume 7, pages 531–537 (2011)Cite this article

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Abstract

The ability to rapidly regulate the functions of specific proteins in living cells is a valuable tool for biological research. Here we describe a new technique by which the degradation of a specific protein is induced by a small molecule. A protein of interest is fused to a ligand-induced degradation (LID) domain, resulting in the expression of a stable and functional fusion protein. The LID domain is comprised of the FK506- and rapamycin-binding protein (FKBP) and a 19-amino-acid degron fused to the C terminus of FKBP. In the absence of the small molecule Shield-1, the degron is bound to the FKBP fusion protein and the protein is stable. When present, Shield-1 binds tightly to FKBP, displacing the degron and inducing rapid and processive degradation of the LID domain and any fused partner protein. Structure-function studies of the 19-residue peptide showed that a 4-amino-acid sequence within the peptide is responsible for degradation.

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Figure 1: Two strategies for ligand-regulated protein stability.
Figure 2: Characterization of the LID domain.
Figure 3: NMR analysis of FKBP and the LID domain.
Figure 4: Characterization of the 19-residue peptide degron.
Figure 5: LID domain regulates transcription factors.
Figure 6: Shield-1 can simultaneously stabilize and destabilize specific targets.

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Acknowledgements

This research was supported by the US National Institutes of Health (GM073046). K.M.B. gratefully acknowledges the support of a Human Frontiers Science Program fellowship. C.W.L. and the Stanford Magnetic Resonance Laboratory are supported in part by the Stanford University School of Medicine. We would like to thank J. Lee and M. Verdoes for technical assistance.

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Authors and Affiliations

  1. Department of Chemical & Systems Biology, Stanford University, Stanford, California, USA

    Kimberly M Bonger, Ling-chun Chen & Thomas J Wandless

  2. Stanford Magnetic Resonance Laboratory, Stanford University, Stanford, California, USA

    Corey W Liu

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  1. Kimberly M Bonger
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  2. Ling-chun Chen
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  3. Corey W Liu
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  4. Thomas J Wandless
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Contributions

K.M.B., L.-c.C. and T.J.W. designed the research. K.M.B. and L.-c.C. performed and analyzed the biological experiments. K.M.B. and C.W.L. performed and analyzed the NMR experiments. K.M.B. and T.J.W. wrote the manuscript.

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Correspondence to Thomas J Wandless.

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The authors declare no competing financial interests.

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Bonger, K., Chen, Lc., Liu, C. et al. Small-molecule displacement of a cryptic degron causes conditional protein degradation. Nat Chem Biol 7, 531–537 (2011). https://doi.org/10.1038/nchembio.598

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