The ubiquitin proteasome system methods and protocols - Mayor, Thibault ca. 20./21. Jh; Kleiger, Gary ca. 20./21. Jh (Springer New York, 2018)
Characterization of RING-Between-RING E3 Ubiquitin Transfer Mechanisms -- Single Turnover RING/U-Box E3-Mediated Lysine Discharge Assays -- Methods for NAD-Dependent Ubiquitination Catalyzed by Legionella pneumophila Effector Proteins -- Using In Vitro Ubiquitylation Assays to Estimate the Affinities of Ubiquitin-Conjugating Enzymes for their Ubiquitin Ligase Partners -- Competition Assay for Measuring Deubiquitinating Enzyme Substrate Affinity -- Enzymatic Assembly of Ubiquitin Chains -- Ubiquitin-Activated Interaction Traps (UBAITs): Tools for Capturing Protein-Protein Interactions -- Generating Intracellular Modulators of E3 Ligases and Deubiquitinases from Phage-Displayed Ubiquitin Variant Libraries -- Integrated Proteogenomic Approach for Identifying Degradation Motifs in Eukaryotic Cells -- A Method to Monitor Protein Turnover by Flow Cytometry and to Screen for Factors that Control Degradation by Fluorescence-Activated Cell Sorting --
- E. coli Based Selection and Expression Systems for Discovery, Characterization, and Purification of Ubiquitylated Proteins -- Strategies to Trap Enzyme-Substrate Complexes that Mimic Michaelis Intermediates during E3-Mediated Ubiquitin-Like Protein Ligation -- Small-Angle X-Ray Scattering for the Study of Proteins in the Ubiquitin Pathway -- Methods for Preparing Cryo-EM Grids of Large Macromolecular Complexes -- Recombinant Expression, Unnatural Amino-Acid Incorporation, and Site-Specific Labeling of 26S Proteasomal Subcomplexes -- Native Gel Approaches in Studying Proteasome Assembly and Chaperones -- Measuring the Overall Rate of Protein Breakdown in Cells and the Contributions of the Ubiquitin-Proteasome and Autophagy-Lysosomal Pathways -- Methods to Rapidly Prepare Mammalian 26S Proteasomes for Biochemical Analysis -- Measurement of the Multiple Activities of 26S Proteasomes -- Exploring the Regulation of Proteasome Function by Subunit Phosphorylation --
- Scalable In Vitro Proteasome Activity Assay -- Exploring the Rampant Expansion of Ubiquitin Proteomics -- Ubiquitin diGLY Proteomics as an Approach to Identify and Quantify the Ubiquitin-Modified Proteome -- Interpreting the Language of Polyubiquitin with Linkage-Specific Antibodies and Mass Spectrometry -- Dissecting Dynamic and Heterogeneous Proteasome Complexes Using In Vivo Cross-Linking Assisted Affinity Purification and Mass Spectrometry