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The Ubiquitin Proteasome System

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Cover of 'The Ubiquitin Proteasome System'

Table of Contents

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    Book Overview
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    Chapter 1 Characterization of RING-Between-RING E3 Ubiquitin Transfer Mechanisms
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    Chapter 2 Single-Turnover RING/U-Box E3-Mediated Lysine Discharge Assays
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    Chapter 3 Methods for NAD-Dependent Ubiquitination Catalyzed by Legionella pneumophila Effector Proteins
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    Chapter 4 Using In Vitro Ubiquitylation Assays to Estimate the Affinities of Ubiquitin-Conjugating Enzymes for Their Ubiquitin Ligase Partners
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    Chapter 5 Competition Assay for Measuring Deubiquitinating Enzyme Substrate Affinity
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    Chapter 6 Enzymatic Assembly of Ubiquitin Chains
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    Chapter 7 Ubiquitin-Activated Interaction Traps (UBAITs): Tools for Capturing Protein-Protein Interactions
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    Chapter 8 Generating Intracellular Modulators of E3 Ligases and Deubiquitinases from Phage-Displayed Ubiquitin Variant Libraries
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    Chapter 9 Integrated Proteogenomic Approach for Identifying Degradation Motifs in Eukaryotic Cells
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    Chapter 10 A Method to Monitor Protein Turnover by Flow Cytometry and to Screen for Factors that Control Degradation by Fluorescence-Activated Cell Sorting
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    Chapter 11 E. coli-Based Selection and Expression Systems for Discovery, Characterization, and Purification of Ubiquitylated Proteins
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    Chapter 12 Strategies to Trap Enzyme-Substrate Complexes that Mimic Michaelis Intermediates During E3-Mediated Ubiquitin-Like Protein Ligation
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    Chapter 13 Small-Angle X-Ray Scattering for the Study of Proteins in the Ubiquitin Pathway
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    Chapter 14 Methods for Preparing Cryo-EM Grids of Large Macromolecular Complexes
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    Chapter 15 Recombinant Expression, Unnatural Amino Acid Incorporation, and Site-Specific Labeling of 26S Proteasomal Subcomplexes
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    Chapter 16 Native Gel Approaches in Studying Proteasome Assembly and Chaperones
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    Chapter 17 Measuring the Overall Rate of Protein Breakdown in Cells and the Contributions of the Ubiquitin-Proteasome and Autophagy-Lysosomal Pathways
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    Chapter 18 Methods to Rapidly Prepare Mammalian 26S Proteasomes for Biochemical Analysis
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    Chapter 19 Measurement of the Multiple Activities of 26S Proteasomes
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    Chapter 20 Exploring the Regulation of Proteasome Function by Subunit Phosphorylation
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    Chapter 21 Scalable In Vitro Proteasome Activity Assay
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    Chapter 22 Exploring the Rampant Expansion of Ubiquitin Proteomics
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    Chapter 23 Ubiquitin diGLY Proteomics as an Approach to Identify and Quantify the Ubiquitin-Modified Proteome
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    Chapter 24 Interpreting the Language of Polyubiquitin with Linkage-Specific Antibodies and Mass Spectrometry
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    Chapter 25 Dissecting Dynamic and Heterogeneous Proteasome Complexes Using In Vivo Cross-Linking-Assisted Affinity Purification and Mass Spectrometry
Attention for Chapter 13: Small-Angle X-Ray Scattering for the Study of Proteins in the Ubiquitin Pathway
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Chapter title
Small-Angle X-Ray Scattering for the Study of Proteins in the Ubiquitin Pathway
Chapter number 13
Book title
The Ubiquitin Proteasome System
Published in
Methods in molecular biology, September 2018
DOI 10.1007/978-1-4939-8706-1_13
Pubmed ID
Book ISBNs
978-1-4939-8705-4, 978-1-4939-8706-1
Authors

Jean-François Trempe, Kalle Gehring, Trempe, Jean-François, Gehring, Kalle

Abstract

Small-angle X-ray scattering (SAXS) is an invaluable complement to other biophysical methods used to interrogate the structure and dynamics of proteins. Here, we describe the standard experimental protocol used in our laboratory to analyze proteins in the ubiquitin pathway. The method addresses buffer selection, data collection using an in-house X-ray source, diagnostic tests to assess data quality, and computational approaches to interpret SAXS data.

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Mendeley readers

The data shown below were compiled from readership statistics for 5 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 5 100%

Demographic breakdown

Readers by professional status Count As %
Professor 1 20%
Student > Ph. D. Student 1 20%
Professor > Associate Professor 1 20%
Student > Doctoral Student 1 20%
Unknown 1 20%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 1 20%
Chemistry 1 20%
Unknown 3 60%