| Contributors to Volume 398 |
| Acknowledgments |
| Volumes in Series |
| E1 Enzyme / Section I： |
| High-Level Expression and Purification of Recombinant E1 Enzyme / Sylvie Beaudenon ; Jon M. Huibregtse1： |
| Expression, Purification and Characterization of the E1 for Human NEDD8, the Heterodimeric APPBP1-UBA3 Complex / Danny T. Huang ; Brenda A. Schulman2： |
| A Fluorescence Resonance Energy Transfer-Based Assay to Study SUMO Modification in Solution / Guillaume Bossis ; Katarzyna Chmielarska ; Ulrike Gartner ; Andrea Pichler ; Evelyn Stieger ; Frauke Melchior3： |
| Properties of the ISG15 E1 Enzyme UbE1L / Robert M. Krug ; Chen Zhao4： |
| E2 Enzyme / Section II： |
| Purification and Properties of the Ubiquitin-Conjugating Enzymes Cdc34 and Ubc13.Mms2 / Christopher Ptak ; Xaralabos Varelas ; Trevor Moraes ; Sean McKenna ; Michael J. Ellison5： |
| Expression, Purification, and Properties of the Ubc4/5 Family E2 Enzymes / Kevin L. Lorick ; Jane P. Jensen ; Allan M. Weissman6： |
| In Vitro Systems for Nedd8 Conjugation by Ubc12 / Tomoki Chiba7： |
| Purification and Activity Assays for Ubc9, the Ubiquitin-Conjugating Enzyme for the Small Ubiquitin-Like Modifier SUMO / Ali A. Yunus ; Christopher D. Lima8： |
| High-Througput Assay to Monitor Formation of the E2-Ubiquitin Thioester Intermediate / Patrick Hauser ; Francesco Hofmann9： |
| E3 Enzyme / Section III： |
| Expression and Evaluation of RING Finger Proteins / Yili Yang10： |
| Expression and Assay of HECT Domain Ligases / Anahita Dastur11： |
| High-Level Expression and Purification of Recombinant SCF Ubiquitin Ligases / Ti Li ; Nikola P. Pavletich ; Ning Zheng12： |
| In Vitro Reconstitution of SCF Substrate Ubiquitination with Purified Proteins / Matthew D. Petroski ; Raymond J. Deshaies13： |
| Expression and Assay of Glycoprotein-Specific Ubiquitin Ligases / Yukiko Yoshida14： |
| Affinity Purification of Mitotic Anaphase-Promoting Complex/Cyclosome on p13[superscript Suc1] / Avram Hershko15： |
| Large-Scale Purification of the Vertebrate Anaphase-Promoting Complex/Cyclosome / Franz Herzog ; Jan-Michael Peters16： |
| Purification and Assay of the Budding Yeast Anaphase-Promoting Complex / Lori A. Passmore ; David Barford ; J. Wade Harper17： |
| Enzymology of the Anaphase-Promoting Complex / Christopher W. Carroll ; David O. Morgan18： |
| Identification of Cell Cycle-Dependent Phosphorylation Sites on the Anaphase-Promoting Complex/Cyclosome by Mass Spectrometry / Karl Mechtler19： |
| Purification and Assay of Mad2: A Two-State Inhibitor of Anaphase-Promoting Complex/Cyclosome / Xuelian Luo ; Hongtao Yu20： |
| Identification, Expression, and Assay of an Oxidation-Specific Ubiquitin Ligase, HOIL-1 / Kazuhiro Iwai ; Haruto Ishikawa ; Takayoshi Kirisako21： |
| Purification and Assay of the Chaperone-Dependent Ubiquitin Ligase of the Carboxyl Terminus of Hsc70-Interacting Protein / Shigeo Murata ; Michiko Minami ; Yasufumi Minami22： |
| Methods for the Functional Genomic Analysis of Ubiquitin Ligases / Wei Li ; Sumit K. Chanda ; Ivana Micik ; Claudio A. P. Joazeiro23： |
| Proteasome / Section IV： |
| Purification of PA700, the 19S Regulatory Complex of the 26S Proteasome / George N. DeMartino24： |
| Purification and Analysis of Recombinant 11S Activators of the 20S Proteasome: Trypanosoma brucei PA26 and Human PA28[alpha], PA28[beta], and PA28[gamma] / Eugene I. Masters ; Gregory Pratt ; Andreas Forster ; Christopher P. Hill25： |
| Purification and Assay of Proteasome Activator PA200 / Vicenca Ustrell ; Carlos Gorbea ; Martin Rechsteiner26： |
| Purification, Crystallization and X-Ray Analysis of Yeast 20S Proteasome / Michael Groll ; Robert Huber27： |
| Preparation of Hybrid (19S-20S-PA28) Proteasome Complexes and Analysis of Peptides Generated during Protein Degradation / Paolo Cascio ; Alfred L. Goldberg28： |
| Characterization of the Proteasome Using Native Gel Electrophoresis / Suzanne Elsasser ; Marion Schmidt ; Daniel Finley29： |
| Monitoring Activity and Inhibition of 26S Proteasomes with Fluorogenic Peptide Substrates / Alexei F. Kisselev30： |
| The Synthesis and Proteasomal Degradation of a Model Substrate Ub[subscript 5]DHFR / Y. Amy Lam ; Jen-Wei Huang ; Oluwafemi Showole31： |
| Assaying Degradation and Deubiquitination of a Ubiquitinated Substrate by Purified 26S Proteasomes / Rati Verma ; R. J. Deshaies32： |
| Probing the Ubiquitin/Proteasome System with Ornithine Decarboxylase, a Ubiquitin-Independent Substrate / Martin A. Hoyt ; Mingsheng Zhang ; Philip Coffino33： |
| Atomic Force Microscopy of the Proteasome / Pawel A. Osmulski ; Maria Gaczynska34： |
| Characterization of Noncompetitive Regulators of Proteasome Activity / 35： |
| Development and Use of Antiproteasome Monoclonal Antibodies / Klavs B. Hendil36： |
| Isopeptidases / Section V： |
| Preparation and Characterization of Yeast and Human Desumoylating Enzymes / Shyr-Jiann Li ; William Hankey ; Mark Hochstrasser37： |
| Purification of the COP9 Signalosome from Porcine Spleen, Human Cell Lines, and Arabidopsis thaliana Plants / Suchithra Menon ; Vicente Rubio ; Xiping Wang ; Xing-Wang Deng ; Ning Wei38： |
| Purification Method of the COP9 Signalosome from Human Erythrocytes / Bettina K. J. Hetfeld ; Dawadschargal ; Bech-Otschir ; Wolfgang Dubiel39： |
| UBP43, an ISG15-Specific Deconjugating Enzyme: Expression, Purification, and Enzymatic Assays / Keun Il Kim ; Dong-Er Zhang40： |
| Strategies for Assaying Deubiquitinating Enzymes / Sung Hwan Kang ; Jung Jun Park ; Sung Soo Chung ; Ok Sun Bang ; Chin Ha Chung41： |
| In Vitro Cleavage of Nedd8 from Cullin 1 by COP9 Signalosome and Deneddylase 1 / Kosj Yamoah ; Kenneth Wu ; Zhen-Qiang Pan42： |
| Ubiquitin-Ovomucoid Fusion Proteins as Model Substrates for Monitoring Degradation and Deubiquitination by Proteasomes / Tingting Yao ; Robert E. Cohen43： |
| Using Deubiquitinating Enzymes as Research Tools / Rohan T. Baker ; Ann-Maree Catanzariti ; Yamuna Karunasekara ; Tatiana A. Soboleva ; Robert Sharwood ; Spencer Whitney ; Philip G. Board44： |
| Functional Annotation of deubiquitinating Enzymes Using RNA Interference / Annette M. G. Dirac ; Sebastian M. B. Nijman ; Thijn R. Brummelkamp ; Rene Bernards45： |
| Author Index |
| Subject Index |
| Contributors to Volume 399 |
| Ubiquitin and Ubiquitin Derivatives |
| Chemical and Genetic Strategies for Manipulating Polyubiquitin Chain Structure / Sara Volk ; Min Wang ; Cecile M. Pickart |
| Controlled Synthesis of Polyubiquitin Chains / Shahri Raasi |
| Derivitization of the C-Terminus of Ubiquitin and Ubiquitin-Like Proteins Using Intein Chemistry: Methods and Uses / Keith D. Wilkinson ; Tudeviin Gan-Erdene ; Nagamalleswari Kolli |
| Preparation, Characterization, and Use of Tagged Ubiquitins / Judy Callis ; Richard Ling |
| Knocking out Ubiquitin Proteasome System Function In Vivo and In Vitro with Genetically Encodable Tandem Ubiquitin / 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 / Masahiro Fujimuro ; Hideyoshi Yokosawa |
| Application of Ubiquitin Immunohistochemistry to Diagnosis of Disease / James Lowe ; Neil Hand ; John Mayer |
| Mechanism-Based Proteomics Tools Based on Ubiquitin and Ubiquitin-Like Proteins: Crystallography, Activity Profiling, and Protease Identification / Paul J. Galardy ; Hidde L. Ploegh ; Huib Ovaa |
| Ubiquitin Binding Domains |
| Identification and Characterization of Modular Domains That Bind Ubiquitin / Michael French ; Kurt Swanson ; Susan C. Shih ; Ishwar Radhakrishnan ; Linda Hicke |
| Analysis of Ubiquitin Chain-Binding Proteins by Two-Hybrid Methods / Jennifer Apodaca ; Jungmi Ahn ; Ikjin Kim ; Hai Rao |
| Quantifying Protein Protein Interactions in the Ubiquitin Pathway by Surface Plasmon Resonance / Rasmus Hartmann-Peterson ; Colin Gordon |
| Using NMR Spectroscopy to Monitor Ubiquitin Chain Conformation and Interactions with Ubiquitin-Binding Domains / Ranjani Varadan ; Michael Assfalg ; David Fushman |
| Analysis of Ubquitin-Dependent Protein Sorting Within the Endocytic Pathway in Saccharomyces cerevisiae / David J. Katzmann ; Beverly Wendland |
| Methods to Study the Proteasome |
| Preparation of Ubiquitinated Substrates by the PY Motif-Insertion Method for Monitoring 26S Proteasome Activity |
| Large- and Small-Scale Purification of Mammalian 26S Proteasomes / Yuko Hirano ; Keiji Tanaka |
| Identification and Characterization of Substrates and Ubiquitin ligases |
| Is This Protein Ubiquitinated? / Peter Kaiser ; Christian Tagwerker |
| Experimental Tests to Definitively Determine Ubiquitylation of a Substrate / Joanna Bloom ; Michele Pagano |
| Identification of Ubiquitination Sites and Determination of Ubiquitin-Chain Architectures by Mass Spectrometry / James Wohlschlegel |
| Mapping of Ubiquitination Sites on Target Proteins / Shigetsugu Hatakeyama ; Masaki Matsumoto ; Keiichi I. Nakayama |
| Identification of Substrates for F-Box Proteins / Jianping Jin ; Xiaolu L. Ang ; Takahiro Shirogane |
| Fusion-Based Strategies to Identify Genes Involved in Degradations of a Specific Substrate / Randolph Y. Hampton |
| Bi-Substrate Kinetic Analysis of an E3-Ligase-Dependent Ubiquitylation Reaction / 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 / Norman L. Lehman ; Matt van de Rijn ; Peter K. Jackson |
| Structure-Based Approaches to Create New E2-E3 Enzyme Pairs / G. Sebastian Winkler ; H. Th. Marc Timmers |
| Proteomic Analysis of Ubiquitin Conjugates in Yeast / Junmin Peng ; Dongmei Cheng |
| Genome and Proteome-wide Approaches to Identify Substrates and Enzymes |
| Two-Step Affinity Purification of Multiubiquitylated Proteins from Saccharomyces cerevisiae / Thibault Mayor |
| Identification of SUMO-Protein Conjugates / Meik Sacher ; Boris Pfander ; Stefan Jentsch |
| Identification of Ubiquitin Ligase Substrates by In Vitro Expression Cloning / Nagi G. Ayad ; Susannah Rankin ; Danny Ooi ; Michael Rape ; Marc W. Kirschner |
| In Vitro Screening for Substrates of the N-End Rule-Dependent Ubiquitylation / 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 / 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) / Antje Schafer ; Dieter H. Wolf |
| Mechanism-Based Proteomics Tools Based on Ubiquitin and Ubiquitin-Like Proteins: Synthesis of Active-Site Directed Probes |
| Real Time/Non-Invasive Technologies / Section VI： |
| Application and Analysis of the GFP[superscript u] Family of Ubiquitin-Proteasome System Reporters / Neil F. Bence ; Eric J. Bennett ; Ron R. Kopito |
| Monitoring of Ubiquitin-Dependent Proteolysis with Green Fluorescent Protein Substrates / Victoria Menendez-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 / Shimon Gross ; David Piwnica-Worms |
| Bioluminescent Imaging of Ubiquitin Ligase Activity: Measuring Cdk2 Activity In Vivo Through Changes in p27 Turnover / Guo-Jun Zhang ; Willam G. Kaelin, Jr. |
| Monitoring the Distribution and Dynamics of Proteasomes in Living Cells / Tom A.M. Groothuis ; Eric A.J. Reits |
| Small Molecule Inhibitors / Section VII： |
| Identifying Small Molecules Inhibitors of the Ubiquitin-Proteasome Pathway in Xenopus Egg Extracts / Adrian Salic ; Randall W. King |
| Development and Characterization of Proteasome Inhibitors / Kyung Bo Kim ; Fabiana N. Fonseca ; Craig M. Crews |
| Screening for Selective Small Molecule Inhibitors of the Proteasome Using Activity-Based Probes / Matthew Bogyo |
| Development of E3-Substract (MDM2-p53)-Binding Inhibitors: Structural Aspects / David C. Fry ; Bradford Graves ; Lyubomir T. Vassilev |
| Druggability of SCF Ubiquitin Ligase-Protein Interfaces / Timothy Cardozo ; Ruben Abagyan |
| Overview on Approaches for Screening for Ubiquitin Ligase Inhibitors / Yi Sun |
| A Homogeneous FRET Assay System for Multiubiquitin Chain Assembly and Disassembly / Tarikere L. Gururaj ; 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 / David H. Stewart |
| Quantitative Assays for Mdm2 Ubiquitin Ligase Activity and Other Ubiquitin-Utilizing Enzymes for Inhibitor Discovery / Kurt R. Auger ; Robert A. Copeland ; Zhihong Lai46： |
| High-Throughput Screening for Inhibitors of the Cks1-Skp2 Interaction / Kuo-Sen Huang47： |
| In Vitro SCF[superscript beta-Trcp1]-Mediated I[kappa]B[alpha] Ubiquitination Assay for High-Throughput Screen / Shuichan Xu ; Palka Patel ; Mahan Abbasian ; David Giegel ; Weilin Xie ; Frank Mercurio ; Sarah Cox48： |
| High-Throughput Screening for Inhibitors of the E3 Ubiquitin Ligase APC / Julie Sheung ; Christina Coquilla49： |
| Generally Applicable Technologies / Section VIII： |
| The Split-Ubiquitin Sensor: Measuring Interactions and Conformational Alterations of Proteins In Vivo / Christoph Reichel ; Nils Johnsson50： |
| Ubiquitin Fusion Technique and Related Methods / Alexander Varshavsky51： |
| Heat-Inducible Degron and the Making of Codintional Mutants / R. Jurgen Dohmen52： |
| Ectopic Targeting of Substrates to the Ubiquitin Pathway / Jianxuan Zhang ; Pengbo Zhou53： |
| Chimeric Molecules to Target Proteins for Ubiquitination and Degradation / Kathleen M. Sakamoto54： |
| Contributors to Volume 398 |
| Acknowledgments |
| Volumes in Series |
| E1 Enzyme / Section I： |
| High-Level Expression and Purification of Recombinant E1 Enzyme / Sylvie Beaudenon ; Jon M. Huibregtse1： |
| Expression, Purification and Characterization of the E1 for Human NEDD8, the Heterodimeric APPBP1-UBA3 Complex / Danny T. Huang ; Brenda A. Schulman2： |
