Ubiquitin and Protein Degradation, Part A

Content: 
High‐Level Expression and Purification of Recombinant E1 Enzyme Review Article
Pages 3-8
Sylvie Beaudenon, Jon M. Huibregtse

Expression, Purification, and Characterization of the E1 for Human NEDD8, the Heterodimeric APPBP1–UBA3 Complex Review Article
Pages 9-20
Danny T. Huang, Brenda A. Schulman

A Fluorescence Resonance Energy Transfer‐Based Assay to Study SUMO Modification in Solution Review Article
Pages 20-32
Guillaume Bossis, Katarzyna Chmielarska, Ulrike Gärtner, Andrea Pichler, Evelyn Stieger, Frauke Melchior

Properties of the ISG15 E1 Enzyme UbE1L Review Article
Pages 32-40
Robert M. Krug, Chen Zhao, Sylvie Beaudenon

Purification and Properties of the Ubiquitin‐Conjugating Enzymes Cdc34 and Ubc13·Mms2 Review Article
Pages 43-54
Christopher Ptak, Xaralabos Varelas, Trevor Moraes, Sean McKenna, Michael J. Ellison

Expression, Purification, and Properties of the Ubc4/5 Family of E2 Enzymes Review Article
Pages 54-68
Kevin L. Lorick, Jane P. Jensen, Allan M. Weissman

In Vitro Systems for NEDD8 Conjugation by Ubc12 Review Article
Pages 68-73
Tomoki Chiba

Purification and Activity Assays for Ubc9, the Ubiquitin‐Conjugating Enzyme for the Small Ubiquitin‐like Modifier SUMO Review Article
Pages 74-87
Ali A. Yunus, Christopher D. Lima

High‐Throughput Assay to Monitor Formation of the E2‐Ubiquitin Thioester Intermediate Review Article
Pages 87-100
Patrick Hauser, Francesco Hofmann

Expression and Evaluation of RING Finger Proteins Review Article
Pages 103-112
Yili Yang, Kevin L. Lorick, Jane P. Jensen, Allan M. Weissman

Expression and Assay of HECT Domain Ligases Review Article
Pages 112-125
Sylvie Beaudenon, Anahita Dastur, Jon M. Huibregtse

High‐Level Expression and Purification of Recombinant SCF Ubiquitin Ligases Review Article
Pages 125-142
Ti Li, Nikola P. Pavletich, Brenda A. Schulman, Ning Zheng

In Vitro Reconstitution of SCF Substrate Ubiquitination with Purified Proteins Review Article
Pages 143-158
Matthew D. Petroski, Raymond J. Deshaies

Expression and Assay of Glycoprotein‐Specific Ubiquitin Ligases Review Article
Pages 159-169
Yukiko Yoshida

Affinity Purification of Mitotic Anaphase‐Promoting Complex/Cyclosome on p13Suc1 Review Article
Pages 170-175
Avram Hershko

Large‐Scale Purification of the Vertebrate Anaphase‐Promoting Complex/Cyclosome Review Article
Pages 175-195
Franz Herzog, Jan‐Michael Peters

Purification and Assay of the Budding Yeast Anaphase‐Promoting Complex Review Article
Pages 195-219
Lori A. Passmore, David Barford, J. Wade Harper

Enzymology of the Anaphase‐Promoting Complex Review Article
Pages 219-230
Christopher W. Carroll, David O. Morgan

Identification of Cell Cycle‐Dependent Phosphorylation Sites on the Anaphase‐Promoting Complex/Cyclosome by Mass Spectrometry Review Article
Pages 231-245
Franz Herzog, Karl Mechtler, Jan‐Michael Peters

Purification and Assay of Mad2: A Two‐State Inhibitor of Anaphase‐Promoting Complex/Cyclosome Review Article
Pages 246-255
Xuelian Luo, Hongtao Yu

Identification, Expression, and Assay of an Oxidation‐Specific Ubiquitin Ligase, HOIL‐1 Review Article
Pages 256-271
Kazuhiro Iwai, Haruto Ishikawa, Takayoshi Kirisako

Purification and Assay of the Chaperone‐Dependent Ubiquitin Ligase of the Carboxyl Terminus of Hsc70‐Interacting Protein Review Article
Pages 271-279
Shigeo Murata, Michiko Minami, Yasufumi Minami

Methods for the Functional Genomic Analysis of Ubiquitin Ligases Review Article
Pages 280-291
Wei Li, Sumit K. Chanda, Ivana Micik, Claudio A.P. Joazeiro

Purification of PA700, the 19S Regulatory Complex of the 26S Proteasome Review Article
Pages 295-306
George N. DeMartino

Purification and Analysis of Recombinant 11S Activators of the 20S Proteasome: Trypanosoma brucei PA26 and Human PA28О±, PA28ОІ, and PA28Оі Review Article
Pages 306-321
Eugene I. Masters, Gregory Pratt, Andreas Förster, Christopher P. Hill

Purification and Assay of Proteasome Activator PA200 Review Article
Pages 321-329
Vicença Ustrell, Gregory Pratt, Carlos Gorbea, Martin Rechsteiner

Purification, Crystallization, and X‐Ray Analysis of the Yeast 20S Proteasome Review Article
Pages 329-336
Michael Groll, Robert Huber

Preparation of Hybrid (19S‐20S‐PA28) Proteasome Complexes and Analysis of Peptides Generated during Protein Degradation Review Article
Pages 336-352
Paolo Cascio, Alfred L. Goldberg

Characterization of the Proteasome Using Native Gel Electrophoresis Review Article
Pages 353-363
Suzanne Elsasser, Marion Schmidt, Daniel Finley

Monitoring Activity and Inhibition of 26S Proteasomes with Fluorogenic Peptide Substrates Review Article
Pages 364-378
Alexei F. Kisselev, Alfred L. Goldberg

The Synthesis and Proteasomal Degradation of a Model Substrate Ub5DHFR Review Article
Pages 379-390
Y. Amy Lam, Jen‐Wei Huang, Oluwafemi Showole

Assaying Degradation and Deubiquitination of a Ubiquitinated Substrate by Purified 26S Proteasomes Review Article
Pages 391-399
Rati Verma, R.J. Deshaies

Probing the Ubiquitin/Proteasome System with Ornithine Decarboxylase, a Ubiquitin‐Independent Substrate Review Article
Pages 399-413
Martin A. Hoyt, Mingsheng Zhang, Philip Coffino

Atomic Force Microscopy of the Proteasome Review Article
Pages 414-425
Pawel A. Osmulski, Maria Gaczynska

Characterization of Noncompetitive Regulators of Proteasome Activity Review Article
Pages 425-438
Maria Gaczynska, Pawel A. Osmulski

Development and Use of Antiproteasome Monoclonal Antibodies Review Article
Pages 439-453
Klavs B. Hendil

Preparation and Characterization of Yeast and Human Desumoylating Enzymes Review Article
Pages 457-467
Shyr‐Jiann Li, William Hankey, Mark Hochstrasser

Purification of the COP9 Signalosome from Porcine Spleen, Human Cell Lines, and Arabidopsis thaliana Plants Review Article
Pages 468-481
Suchithra Menon, Vicente Rubio, Xiping Wang, Xing‐Wang Deng, Ning Wei

Purification Method of the COP9 Signalosome from Human Erythrocytes Review Article
Pages 481-491
Bettina K.J. Hetfeld, Dawadschargal Bech‐Otschir, Wolfgang Dubiel

UBP43, an ISG15‐Specific Deconjugating Enzyme: Expression, Purification, and Enzymatic Assays Review Article
Pages 491-499
Keun Il Kim, Dong‐Er Zhang

Strategies for Assaying Deubiquitinating Enzymes Review Article
Pages 500-508
Sung Hwan Kang, Jung Jun Park, Sung Soo Chung, Ok Sun Bang, Chin Ha Chung

In Vitro Cleavage of Nedd8 from Cullin 1 by COP9 Signalosome and Deneddylase 1 Review Article
Pages 509-522
Kosj Yamoah, Kenneth Wu, Zhen‐Qiang Pan

Ubiquitin‐Ovomucoid Fusion Proteins as Model Substrates for Monitoring Degradation and Deubiquitination by Proteasomes Review Article
Pages 522-540
Tingting Yao, Robert E. Cohen

Using Deubiquitylating Enzymes as Research Tools Review Article
Pages 540-554
Rohan T. Baker, Ann‐Maree Catanzariti, Yamuna Karunasekara, Tatiana A. Soboleva, Robert Sharwood, Spencer Whitney, Philip G. Board

Functional Annotation of Deubiquitinating Enzymes Using RNA Interference Review Article
Pages 554-567
Annette M.G. Dirac, Sebastian M.B. Nijman, Thijn R. Brummelkamp, RenГ© Bernards

Series Editors
Page ii

Contributors to Volume 398
Pages xi-xvi

Acknowledgments
Page xvii

Methods in Enzymology
Pages xix-xli

Author Index
Pages 569-596

Subject Index
Pages 597-609

Table of Contents
Pages v-ix