Abstract
Assessment of small molecules that promote selective protein degradation (degraders) requires detailed characterization and measurement of protein levels in cells. Here we describe ratio-metric methods based on a dual fluorescent GFP/mCherry reporter system to quantify cellular protein levels. We further develop a kinetic framework for the analysis of such data. We describe two methods of generating the stable GFP-protein of interest (POI)/mCherry reporter cell lines, alternative readout methods by FACS and Laser Scanning Cytometry as well as the corresponding tools used for processing and analysis of such data. Finally, we show that the commonly used half-maximal degradation constant (DC50) or maximum degradation efficacy (Dmax) metrics are time-dependent and propose a time-invariant Michaelis-Menten-like analysis of degradation kinetics with analogous key parameters Km app and Vmax app.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Salami J, Crews CM (2017) Waste disposal-an attractive strategy for cancer therapy. Science 355(6330):1163–1167. https://doi.org/10.1126/science.aam7340
Winter GE et al (2015) DRUG DEVELOPMENT. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 348(6241):1376–1381. https://doi.org/10.1126/science.aab1433
Lai AC, Crews CM (2017) Induced protein degradation: an emerging drug discovery paradigm. Nat Rev Drug Discov 16(2):101–114. https://doi.org/10.1038/nrd.2016.211
Wilkinson KD (2005) The discovery of ubiquitin-dependent proteolysis. Proc Natl Acad Sci 102(43):15280–15282. https://doi.org/10.1073/pnas.0504842102
Fischer ES et al (2014) Structure of the DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide. Nature 512(7512):49–53. https://doi.org/10.1038/nature13527
Bondeson DP et al (2015) Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat Chem Biol 11(8):611–617. https://doi.org/10.1038/nchembio.1858
Riching KM et al (2018el) Quantitative live-cell kinetic degradation and mechanistic profiling of PROTAC mode of action. ACS Chem Biol 13(9):2758–2770. https://doi.org/10.1021/acschembio.8b00692
Nowak RP et al (2018) Plasticity in binding confers selectivity in ligand-induced protein degradation. Nat Chem Biol 14(7):706–714. https://doi.org/10.1038/s41589-018-0055-y
Gadd MS et al (2017) Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat Chem Biol 13(5):514–521. https://doi.org/10.1038/nchembio.2329
Douglass EF, Miller CJ, Sparer G, Shapiro H, Spiegel DA (2013) A comprehensive mathematical model for three-body binding equilibria. J Am Chem Soc 135(16):6092–6099. https://doi.org/10.1021/ja311795d
Carpenter AE et al (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7(10):R100. https://doi.org/10.1186/gb-2006-7-10-r100
Acknowledgments
The authors gratefully acknowledge the generous financial support of the following sources: NIH grant NCI R01CA214608 (grant to E. S. F). We would like to thank members of Fischer and Ebert Lab at Dana-Farber Cancer Institute for useful discussions on development and optimization of these protocols.
Conflict of Interest: E.S.F. is a founder, scientific advisory board (SAB), and equity holder in Civetta Therapeutics, Jengu Therapeutics (board member), and Neomorph, Inc. E.S.F. is an equity holder in C4 Therapeutics and a consultant to Novartis, Sanofi, EcoR1 capital, Deerfield and Astellas. The Fischer lab receives or has received research funding from Novartis, Ajax and Astellas.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Nowak, R.P., Yue, H., Park, E.Y., Fischer, E.S. (2021). Methods for Quantitative Assessment of Protein Degradation. In: Cacace, A.M., Hickey, C.M., Békés, M. (eds) Targeted Protein Degradation. Methods in Molecular Biology, vol 2365. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1665-9_13
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1665-9_13
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1664-2
Online ISBN: 978-1-0716-1665-9
eBook Packages: Springer Protocols