Targeted Protein Degradation: Methods and Protocols

Part I Methods to Discover and Characterize Ligands for Targets and/or Ligases.

1. Protein Ligand Interactions Using Surface Plasmon Resonance

Nichole O'Connell

2. High-Throughput Detection of Ligand-Protein Binding using a SplitLuc Cellular Thermal Shift Assay

Tino W. Sanchez, Ashley Owens, Natalia J. Martinez, Eric Wallgren, Anton Simeonov, and Mark J. Henderson

3. Proteins and their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3

Danielle Allison Brackenridge and Liam James McGuffin

4. Evaluating ligands for ubiquitin ligases using affinity beads

Jennifer Dobrodziej, Hanqing Dong, Kurt Zimmermann, and Christopher M. Hickey

Part II Approaches to Study Ligase: Degrader: Target Ternary Complexes.

5. Mechanistic and Structural Features of PROTAC Ternary Complexes

Ryan Casement, Adam Bond, Conner Craigon, and Alessio Ciulli

6. MST and TRIC Technology to Reliably Study PROTAC Binary and Ternary Binding In Drug Development

Tanja Bortoschik, Andreas Zoephel, Klaus Rumpel, Alessio Ciulli, and Charles Heffern

7. An in vitro Pull-down Assay of the E3 ligase: PROTAC: Substrate Ternary Complex to Identify Effective PROTACs

Daniel P. Bondeson, Blake E. Smith, and Alexandru D. Buhimschi

8. Kinetic detection of E3: PROTAC: Target Ternary Complexes using NanoBRET technology in Live Cells

Sarah D. Mahan, Kristin M. Riching, Marjeta Urh, and Danette L. Daniels

Part III Approaches and Tools to Understand Ubiquitylation and Proteasomal Degradation

9. Inducing Ubiquitylation and Protein Degradation as a Drug Development Strategy

Kamaldeep S. Dhami and XiaoDong Huang

10. Methodological Versatility of Tandem Ubiquitin Binding Entities (TUBEs) for Understanding Poly-ubiquitination and its Various Chains

Katie J. Sheets, Patrick H. Gross, Myra J. Zerr, and Dahmane Ouazia, and Karteek Kadimisetty

11. Global Mass Spectrometry-Based Analysis of Protein Ubiquitination Using K-e-GG Remnant Antibody Enrichment

Alissa J. Nelson, Yiying Zhu, Jian Min Ren, and Matthew P. Stokes

12. Determination of Proteasomal Unfolding Ability

by Christina M. Hurley and Daniel A. Kraut

Part IV Methods for Evaluating Protein Degrader Function

13. Methods for Quantitative Assessment of Protein Degradation

Radoslaw P. Nowak, Hong Yue, Emily Y. Park, and Eric S. Fischer

14. A High Throughput method to prioritize PROTAC intracellular target engagement and cell permeability using NanoBRET

by James D. Vasta, Cesear R. Corona, and Matthew B. Robers

15. Profiling CELMoD Mediated Degradation of Cereblon Neosubstrates

by Joel W. Thompson, Thomas Clayton, Gody Khambatta, Leslie A. Bateman, Christopher W. Carroll, Philip P. Chamberlain, and Mary E. Matyskiela

16. Global Proteome Profiling to Assess Changes in Protein Abundance using