Overview

This volume details novel and popular approaches to decipher the Ubiquitin Code. Chapters guide readers through ubiquitin chain complexity, methods to generate non-hydrolysable ubiquitin-NEDD8, a fully synthetic method for the linear synthesis of fluorescently labelled rhodamine LC3A and LC3B, a HECT ligase-mediated ubiquitylation in vitro, a RNAi-based screening to identify DUBs, a Yuh1 activity assay, a pull-down to isolate K48 and K63 chains using specific nanobodies, identification of NeDDylated protein based in a NEDD8R74K mutant, in vivo identification of NEDDylated proteins from liver diseases, UbL-ID method to identify ubiquitin-like modified proteins, a LC3/GABARAP capturing system, and methods to isolate peptides that are closely associated with proteasomes or trapped inside the core particle of proteasomes in eukaryotic cells, among others. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.   Authoritative and cutting-edge, The Ubiquitin Code aims to to be a useful practical guide to researches to help further their study in this field. 

Full Product Details

Author:   Manuel S Rodriguez ,  Rosa Barrio
Publisher:   Springer-Verlag New York Inc.
Imprint:   Springer-Verlag New York Inc.
Edition:   1st ed. 2023
Volume:   2602
Weight:   0.693kg
ISBN:  

9781071628584

ISBN 10:   1071628585
Pages:   245
Publication Date:   30 November 2022
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   Manufactured on demand  
We will order this item for you from a manufactured on demand supplier.

Table of Contents

Part I: Chain Diversity                                                          1            Thioester and oxyester linkages in the ubiquitin system Alba Ferri-Blazquez, Ernst Jarosch and Thomas Sommer   2            Getting to the root of branched ubiquitin chains: A review of current methods and functions Anita Waltho, Thomas Sommer     Part II: Ub and UbL Chemical Tools                                                             3            Chemical synthesis of non-hydrolysable Ubiquitin(-like) hybrid chains David A. Pérez Berrocal, Gerbrand J. van der Heden van Noort and Monique P. C. Mulder   4            Total Linear Chemical Synthesis of LC3A and LC3B Yara Huppelschoten, Jens Buchardt, Thomas Eiland Nielsen and Gerbrand J. van der Heden van Noort     Part III: Methods to study Conjugating enzymes (E3s)                                                     5            A microbead-based flow cytometry assay to assess the activity of Ubiquitin and Ubiquitin-like conjugating enzymes Clara Recasens-Zorzo, Pierre Gâtel, Frédérique Brockly and Guillaume Bossis   6            Monitoring HECT ubiquitination activity in vitro Vincenzo Taibi, Simona Polo and Elena Maspero1         Part IV: Methods to study DUBs                                                                  7            RNAi-based screening for the identification of specific substrate-deubiquitinase pairs Nagore Elu, Natalia Presa and Ugo Mayor   8            Strategies for monitoring ‘ubiquitin C-terminal hydrolase 1’ (Yuh1) activity Shahaf Saad, Eden Berda, Yuval Klein, Suha Issa and Elah Pick   Part V: Methods to identify new targets and regulators                                                 9            Isolation and Mass Spectrometry Identification of K48 and K63 Ubiquitin Proteome using Chain-Specific Nanobodies Maria Gonzalez-Santamarta, Laurie Ceccato, Ana Sofia Carvalho, Jean-Christophe Rain, Rune Matthiesen and Manuel S. Rodriguez   10          A mass spectrometry-based strategy for mapping modification sites for the Ubiquitin-like modifier NEDD8 Caio A.B. Oliveira, Ekaterina Isaakova, Petra Beli and Dimitris P. Xirodimas           11          Isolation of the hepatic ubiquitome/NEDDylome by streptavidin pull-down assay in the biotinylated ubiquitin (bioUb)/biotinylated NEDD8 (bioNEDD8) transgenic mice Marina Serrano-Maciá, Teresa Cardoso Delgado and María Luz Martínez-Chantar   12          The Lambda display technology: a useful tool for the identification of ubiquitin and ubiquitin like-binding domains Elena Santonico   13          SUMO-ID: a strategy for the identification of SUMO-dependent proximal interactors Orhi Barroso-Gomila, Ugo Mayor, Rosa Barrio and James D. Sutherland   14          Analysis of ATG8 family members using LC3-Interacting Regions (LIR)-based molecular traps Grégoire Quinet, Pierre Génin, Naima Belgareh-Touzé, Oznur Ozturk, Robert Weil, Mickael M. Cohen, Renaud Legouis and Manuel S. Rodriguez   15          A computational tool for analysis of mass spectrometry data of ubiquitin enriched samples Rune Matthiesen, Manuel S. Rodriguez, and Ana Sofia Carvalho   Part VI:  to measure proteasome activity                                                                 16          In-plate and in-gel assays for the assessment of proteasome activity in Caenorhabditis elegans Eleni Panagiotidou, Anna Gioran and Niki Chondrogianni   17          Isolation of Proteasome-Trapped Peptides (PTPs) for degradome analysis Indrajit Sahu, Manisha Priyadarsini Sahoo, Oded Kleifeld and Michael H. Glickman

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