Ubiquitin and Protein Degradation, Part B

Content: 
Chemical and Genetic Strategies for Manipulating Polyubiquitin Chain Structure Review Article
Pages 3-20
Sara Volk, Min Wang, Cecile M. Pickart

Controlled Synthesis of Polyubiquitin Chains Review Article
Pages 21-36
Cecile M. Pickart, Shahri Raasi

Derivitization of the C‐Terminus of Ubiquitin and Ubiquitin‐like Proteins Using Intein Chemistry: Methods and Uses Review Article
Pages 37-51
Keith D. Wilkinson, Tudeviin Gan‐Erdene, Nagamalleswari Kolli

Preparation, Characterization, and Use of Tagged Ubiquitins Review Article
Pages 51-64
Judy Callis, Richard Ling

Knocking out Ubiquitin Proteasome System Function In Vivo and In Vitro with Genetically Encodable Tandem Ubiquitin Review Article
Pages 64-74
Y. Saeki, E. Isono, M. Shimada, H. Kawahara, H. Yokosawa, A. Toh‐e

Production of Antipolyubiquitin Monoclonal Antibodies and Their Use for Characterization and Isolation of Polyubiquitinated Proteins Review Article
Pages 75-86
Masahiro Fujimuro, Hideyoshi Yokosawa

Application of Ubiquitin Immunohistochemistry to the Diagnosis of Disease Review Article
Pages 86-119
James Lowe, Neil Hand, R. John Mayer

Mechanism‐Based Proteomics Tools Based on Ubiquitin and Ubiquitin‐Like Proteins: Crystallography, Activity Profiling, and Protease Identification Review Article
Pages 120-131
Paul Galardy, Hidde L. Ploegh, Huib Ovaa

Identification and Characterization of Modular Domains That Bind Ubiquitin Review Article
Pages 135-157
Michael French, Kurt Swanson, Susan C. Shih, Ishwar Radhakrishnan, Linda Hicke

Analysis of Ubiquitin Chain‐Binding Proteins by Two‐Hybrid Methods Review Article
Pages 157-164
Jennifer Apodaca, Jungmi Ahn, Ikjin Kim, Hai Rao

Quantifying Protein–Protein Interactions in the Ubiquitin Pathway by Surface Plasmon Resonance Review Article
Pages 164-177
Rasmus Hartmann‐Petersen, Colin Gordon

Using NMR Spectroscopy to Monitor Ubiquitin Chain Conformation and Interactions with Ubiquitin‐Binding Domains Review Article
Pages 177-192
Ranjani Varadan, Michael Assfalg, David Fushman

Analysis of Ubiquitin‐Dependent Protein Sorting Within the Endocytic Pathway in Saccharomyces cerevisiae Review Article
Pages 192-211
David J. Katzmann, Beverly Wendland

Preparation of Ubiquitinated Substrates by the PY Motif‐Insertion Method for Monitoring 26S Proteasome Activity Review Article
Pages 215-227
Y. Saeki, E. Isono, A. Toh‐e

Large‐ and Small‐Scale Purification of Mammalian 26S Proteasomes Review Article
Pages 227-240
Yuko Hirano, Shigeo Murata, Keiji Tanaka

Is This Protein Ubiquitinated? Review Article
Pages 243-248
Peter Kaiser, Christian Tagwerker

Experimental Tests to Definitively Determine Ubiquitylation of a Substrate Review Article
Pages 249-266
Joanna Bloom, Michele Pagano

Identification of Ubiquitination Sites and Determination of Ubiquitin‐Chain Architectures by Mass Spectrometry Review Article
Pages 266-277
Peter Kaiser, James Wohlschlegel

Mapping of Ubiquitination Sites on Target Proteins Review Article
Pages 277-286
Shigetsugu Hatakeyama, Masaki Matsumoto, Keiichi I. Nakayama

Identification of Substrates for F‐Box Proteins Review Article
Pages 287-309
Jianping Jin, Xiaolu L. Ang, Takahiro Shirogane, J. Wade Harper

Fusion‐Based Strategies to Identify Genes Involved in Degradation of a Specific Substrate Review Article
Pages 310-323
Randolph Y. Hampton

Bi‐substrate Kinetic Analysis of an E3‐Ligase–Dependent Ubiquitylation Reaction Review Article
Pages 323-333
David C. Swinney, Michael J. Rose, Amy Y. Mak, Ina Lee, Liliana Scarafia, Yi‐Zheng Xu

Screening of Tissue Microarrays for Ubiquitin Proteasome System Components in Tumors Review Article
Pages 334-355
Norman L. Lehman, Matt van de Rijn, Peter K. Jackson

Structure‐Based Approaches to Create New E2–E3 Enzyme Pairs Review Article
Pages 355-366
G. Sebastiaan Winkler, H. Th. Marc Timmers

Proteomic Analysis of Ubiquitin Conjugates in Yeast Review Article
Pages 367-381
Junmin Peng, Dongmei Cheng

Two‐Step Affinity Purification of Multiubiquitylated Proteins from Saccharomyces cerevisiae Review Article
Pages 385-392
Thibault Mayor, Raymond J. Deshaies

Identification of SUMO–Protein Conjugates Review Article
Pages 392-404
Meik Sacher, Boris Pfander, Stefan Jentsch

Identification of Ubiquitin Ligase Substrates by In Vitro Expression Cloning Review Article
Pages 404-414
Nagi G. Ayad, Susannah Rankin, Danny Ooi, Michael Rape, Marc W. Kirschner

In Vitro Screening for Substrates of the N‐End Rule–Dependent Ubiquitylation Review Article
Pages 415-432
Ilia V. Davydov, John H. Kenten, Yassamin J. Safiran, Stefanie Nelson, Ryan Swenerton, Pankaj Oberoi, Hans A. Biebuyck

Genome‐Wide Surveys for Phosphorylation‐Dependent Substrates of SCF Ubiquitin Ligases Review Article
Pages 433-458
Xiaojing Tang, Stephen Orlicky, Qingquan Liu, Andrew Willems, Frank Sicheri, Mike Tyers

Yeast Genomics in the Elucidation of Endoplasmic Reticulum (ER) Quality Control and Associated Protein Degradation (ERQD) Review Article
Pages 459-468
Antje Schäfer, Dieter H. Wolf

Mechanism‐Based Proteomics Tools Based on Ubiquitin and Ubiquitin‐Like Proteins: Synthesis of Active Site‐Directed Probes Review Article
Pages 468-478
Huib Ovaa, Paul J. Galardy, Hidde L. Ploegh

Application and Analysis of the GFPu Family of Ubiquitin‐Proteasome System Reporters Review Article
Pages 481-490
Neil F. Bence, Eric J. Bennett, Ron R. Kopito

Monitoring of Ubiquitin‐Dependent Proteolysis with Green Fluorescent Protein Substrates Review Article
Pages 490-511
Victoria Menéndez‐Benito, Stijn Heessen, Nico P. Dantuma

Monitoring Proteasome Activity In Cellulo and in Living Animals by Bioluminescent Imaging: Technical Considerations for Design and Use of Genetically Encoded Reporters Review Article
Pages 512-530
Shimon Gross, David Piwnica‐Worms

Bioluminescent Imaging of Ubiquitin Ligase Activity: Measuring Cdk2 Activity In Vivo Through Changes in p27 Turnover Review Article
Pages 530-549
Guo‐Jun Zhang, William G. Kaelin Jr.

Monitoring the Distribution and Dynamics of Proteasomes in Living Cells Review Article
Pages 549-563
Tom A.M. Groothuis, Eric A.J. Reits

Identifying Small Molecule Inhibitors of the Ubiquitin‐Proteasome Pathway in Xenopus Egg Extracts Review Article
Pages 567-585
Adrian Salic, Randall W. King

Development and Characterization of Proteasome Inhibitors Review Article
Pages 585-609
Kyung Bo Kim, Fabiana N. Fonseca, Craig M. Crews

Screening for Selective Small Molecule Inhibitors of the Proteasome Using Activity‐Based Probes Review Article
Pages 609-622
Matthew Bogyo

Development of E3‐Substrate (MDM2‐p53)–Binding Inhibitors: Structural Aspects Review Article
Pages 622-633
David C. Fry, Bradford Graves, Lyubomir T. Vassilev

Druggability of SCF Ubiquitin Ligase–Protein Interfaces Review Article
Pages 634-653
Timothy Cardozo, Ruben Abagyan

Overview of Approaches for Screening for Ubiquitin Ligase Inhibitors Review Article
Pages 654-663
Yi Sun

A Homogeneous FRET Assay System for Multiubiquitin Chain Assembly and Disassembly Review Article
Pages 663-682
Tarikere L. Gururaja, Todd R. Pray, Raymond Lowe, Guoqiang Dong, Jianing Huang, Sarkiz Daniel‐Issakani, Donald G. Payan

Assays for High‐Throughput Screening of E2 and E3 Ubiquitin Ligases Review Article
Pages 682-701
John H. Kenten, Ilia V. Davydov, Yassamin J. Safiran, David H. Stewart, Pankaj Oberoi, Hans A. Biebuyck

Quantitative Assays of Mdm2 Ubiquitin Ligase Activity and Other Ubiquitin‐Utilizing Enzymes for Inhibitor Discovery Review Article
Pages 701-717
Kurt R. Auger, Robert A. Copeland, Zhihong Lai

High‐Throughput Screening for Inhibitors of the Cks1–Skp2 Interaction Review Article
Pages 717-728
Kuo‐Sen Huang, Lyubomir T. Vassilev

In Vitro SCFβ‐Trcp1–Mediated IκBα Ubiquitination Assay for High‐Throughput Screen Review Article
Pages 729-740
Shuichan Xu, Palka Patel, Mahan Abbasian, David Giegel, Weilin Xie, Frank Mercurio, Sarah Cox

High‐Throughput Screening for Inhibitors of the E3 Ubiquitin Ligase APC Review Article
Pages 740-754
Jianing Huang, Julie Sheung, Guoqiang Dong, Christina Coquilla, Sarkiz Daniel‐Issakani, Donald G. Payan

The Split‐Ubiquitin Sensor: Measuring Interactions and Conformational Alterations of Proteins In Vivo Review Article
Pages 757-776
Christoph Reichel, Nils Johnsson

Ubiquitin Fusion Technique and Related Methods Review Article
Pages 777-799
Alexander Varshavsky

Heat‐Inducible Degron and the Making of Conditional Mutants Review Article
Pages 799-822
R. JГјrgen Dohmen, Alexander Varshavsky

Ectopic Targeting of Substrates to the Ubiquitin Pathway Review Article
Pages 823-833
Jianxuan Zhang, Pengbo Zhou

Chimeric Molecules to Target Proteins for Ubiquitination and Degradation Review Article
Pages 833-847
Kathleen M. Sakamoto

Series Editors
Page ii

Contributors to Volume 399
Pages xi-xvi

Acknowledgments
Page xvii

Methods in Enzymology
Pages xix-xli

Author Index
Pages 849-888

Subject Index
Pages 889-907

Table of Contents
Pages v-x