Ubiquitin and Ubiquitin-like Protein Modifiers

by Mark Hochstrasser

Overview

Ubiquitination and Protein Stability - Part A Volume 618, the latest release in the Methods in Enzymology series, highlights new advances in the field, with this updated volume presenting interesting chapter written by an international board of authors. Topics of note in this new release include the Preparation of ubiquitinated nucleosomes with native and non-hydrolyzable linkages, Methods to measure ubiquitin chain length and linkage, Genetic approaches to study the yeast ubiquitin system, Enzymatic preparation of monoubiquitinated proteins, Methods to distinguish the function of ubiquitin in autophagy and the proteasome pathway, the Purification and characterization of enzyme activity of USPs, and much more. 

Product Details

ISBN-13:	9780128163597
Publisher:	Elsevier Science
Publication date:	03/07/2019
Series:	Methods in Enzymology , #618
Pages:	430
Product dimensions:	6.00(w) x 9.00(h) x (d)

About the Author

Dr. Mark W Hochstrasser is a Eugene Higgins Professor of Molecular Biophysics and Biochemistry and Professor of Molecular, Cellular, and Developmental Biology
Yale University, USA.

Table of Contents

1. Semisynthesis of ubiquitinated histone H2B with a native or nonhydrolyzable linkage
Michael Morgan, Muhammad Jbara, Ashraf Brik and Cynthia Wolberger
2. Dual-color pulse-chase ubiquitination assays to simultaneously monitor substrate priming and extension
Daniel C. Scott and Brenda A. Schulman
3. A genetic approach to study polyubiquitination in Saccharomyces cerevisiae
Fernando Meza-Gutierrez, Deniz Simsek and David P. Toczyski
4. Enzymatic preparation of monoubiquitinated FANCD2 and FANCI proteins
Viduth K. Chaugule, Connor Arkinson, Rachel Toth and Helen Walden
5. Methods to measure ubiquitin chain length and linkage
Fumiaki Ohtake, Hikaru Tsuchiya, Keiji Tanaka and Yasushi Saeki
6. Detection of ubiquitination activity and identification of ubiquitinated substrates using TR-TUBE
Yukiko Yoshida, Yasushi Saeki, Hikaru Tsuchiya and Keiji Tanaka
7. Methods to study phosphoribosylated ubiquitin ligation and removal
Jiazhang Qiu and Zhao-Qing Luo
8. Biochemical characterization of SUMO-conjugating enzymes by in vitro sumoylation assays
Nathalie Eisenhardt, Dragana Ilic, Easa Nagamalleswari and Andrea Pichler
9. Methods to study SUMO dynamics in yeast
Stefan Pabst, Lennard-Maximilian Döring, Natasha Petreska and R. Jürgen Dohmen
10. Approaches for investigating the extracellular signaling function of ISG15
Caleb D. Swaim, Larissa A. Canadeo and Jon M. Huibregtse
11. Analysis of modification and proteolytic targeting by the ubiquitin-like modifier FAT10
Annette Aichem, Annika N. Boehm, Nicola Catone, Gunter Schmidtke and Marcus Groettrup
12. Methods to analyze STUbL activity
Emma Branigan, Anna Plechanovová and Ronald T. Hay
13. Quantitative analysis of USP activity in vitro
Shreya Dharadhar, Robbert Q. Kim, Michael Uckelmann and Titia K. Sixma
14. Evaluating enzyme activities and structures of DUBs
Jonathan N. Pruneda and David Komander
15. Purification and functional characterization of the DUB domain of SdeA
Kedar Puvar, Shalini Iyer, Michael J. Sheedlo and Chittaranjan Das
16. Profiling DUBs and Ubl-specific proteases with activity-based probes
Paul P. Geurink, Gerbrand J. van der Heden van Noort, Monique P.C. Mulder, Robert C.M. Knaap, Marjolein Kikkert and Huib Ovaa
17. Assays of SUMO protease/isopeptidase activity and function in mammalian cells and tissues
Kathrin Kunz, Stefan Müller and Luca Mendler

What People are Saying About This

From the Publisher

Edited by one of the best scientists in the field, this series presents the latest updates in the field of enzymology

Editorial Reviews

Praise for the Series:
"Should be on the shelves of all libraries in the world as a whole collection." —CHEMISTRY IN INDUSTRY
"The work most often consulted in the lab." —ENZYMOLOGIA
"The Methods in Enzymology series represents the gold-standard." —NEUROSCIENCE

From the Publisher

Reviewer: Peter Kennelly, PhD (Virginia Tech)
Description: This book is volume 618 of the iconic Methods in Enzymology series devoted to publishing proven laboratory protocols in biochemistry and molecular biology from experienced practitioners. Each volume is organized around a particular theme; in this instance, the highly conserved, small, 76-amino-acid protein ubiquitin. In cells, ubiquitin and homologs such as SUMO (Small Ubiquitin-like MOdifier) are covalently attached to a broad range of proteins to modify their function. Frequently, the first ubiquitin is covalently bound by another, sometimes forming lengthy polyubiquitin chains, or additional units may bind to other sites on the protein. This modification serves a variety of purposes, such as marking a protein molecule for proteasome-mediated degradation or for signal transduction. While volume 619 of the series focuses on ubiquitin and its role in protein degradation, volume 618 tackles the newer members of this protein family and the functional landscape beyond modulating protein degradation.
Purpose: Long thought to be solely a modifier that targets proteins for degradation, ubiquitin and the enzymes responsible for its covalent attachment to target proteins have emerged as multifaceted players in the biology of the cell whose functional impact has additionally been multiplied by the discovery of additional homologs. This book seeks to provide readers with practical directions on how to employ the latest techniques used to study this dynamic protein family.
Audience: With its tight methodological focus, this book is aimed at students and scientists performing and planning to perform laboratory research on some aspect of ubiquitin or its homologs.
Features: This book addresses performance of specific assays, isolation of particular biomolecules, and genetic manipulation of ubiquitin-mediated processes. Each chapter begins with an introductory section placing each method into context with an accompanying description of the basis for its function supplemented by figures or tables illustrating representative outcomes. The number and range of methods covered is fairly broad. However, it is disappointing that none seemed to venture into one of the most new and exciting areas of ubiquitin research cited by the author in his preface: bacterial ubiquitin and (de)ubiquitinating enzymes and their role in microbial virulence. Many bacteria secrete these proteins as tools for manipulating eukaryotic hosts via perturbing their endogenous ubiquitination systems. Readers may be disappointed by the relatively sparing employment of illustrative figures, a characteristic feature of the entire series, and the lack of an index.
Assessment: This book represents a timely addition to "methods in enzymology" and upholds the standards responsible for this long-lived and standard setting series.

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