Description
Book SynopsisThis 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 o
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
