The Ubiquitin-Proteasome System, Volume 2,9783527311309

The Ubiquitin-Proteasome System, Volume 2

by ; ;
Edition: 1st
ISBN13: 9783527311309
ISBN10: 3527311300
Format: Hardcover
Pub. Date: 2006-02-10
Publisher(s): Wiley-VCH
List Price: $325.25

Buy New

Usually Ships in 3-4 Business Days
$309.76
Add to Cart

Rent Textbook

Select for Price
Add to Cart
There was a problem. Please try again later.

Used Textbook

We're Sorry
Sold Out

eTextbook

We're Sorry
Not Available

Buy from our Marketplace starting at $50.81

How Marketplace Works:

  • This item is offered by an independent seller and not shipped from our warehouse
  • Item details like edition and cover design may differ from our description; see seller's comments before ordering.
  • Sellers much confirm and ship within two business days; otherwise, the order will be cancelled and refunded.
  • Marketplace purchases cannot be returned to eCampus.com. Contact the seller directly for inquiries; if no response within two days, contact customer service.
  • Additional shipping costs apply to Marketplace purchases. Review shipping costs at checkout.

Summary

The second volume in a new series dedicated to protein degradation, this book discusses the mechanism and cellular functions of targeted protein breakdown via the ubiquitin pathway.Drawing on the combined knowledge of the world's leading protein degradation experts, this handy reference compiles information on the proteasome-mediated degradation steps of the ubiquitin pathway. In addition to proteasomal function and regulation, it also presents the latest results on novel members of the ubiquitin superfamily and their role in cellular regulation.Further volumes in the series cover the function of ubiquitin-protein ligases, and the roles of the ubiquitin pathway in regulating key cellular processes, as well as its pathophysiological disease states. Required reading for molecular biologists, cell biologists and physiologists with an interest in protein degradation.

Author Biography

<b>John Mayer</b> obtained his MS and PhD degrees from the University of Birmingham (UK). He is currently serving as Professor of Biochemistry at the School of Biomedical Sciences at Nottingham University.<br> For the past 30 years, he has investigated intracellular proteolysis and particularly the ubiquitin/proteasome system. Presently, he is particularly interested in intracellular proteolysis in relation to neurodegenerative illnesses. <p> <b>Aaron Ciechanover</b> obtained his MD from the Hebrew University in Jerusalem (Israel), and his PhD from the Technion-Israel Institute of Technology in Haifa, where he is presently serving as Professor of Biochemistry. Professor Ciechanover is known for his discovery of the first ubiquitin system mutant cell, demonstrating the role of the ubiquitin-proteasome proteolytic system in protein degradation in vivo. In 2004, he has received the Nobel Prize in Chemistry for his ground-breaking work on the ubiquitin-proteasome system. <p> <b>Martin Rechsteiner</b> is Professor of Biochemistry at the University of Utah in Salt Lake City (USA). He is interested in the proteasome component of the ubiquitin-proteasome pathway. He has identified several key regulators of proteasome function and is currently working on their structural and functional elucidation.

Table of Contents

Preface XI
List of Contributors XIII
1 Molecular Chaperones and the Ubiquitin–Proteasome System
1(30)
Cam Patterson and Jörg Höhfeld
1.1 Introduction
1(1)
1.2 A Biomedical Perspective
2(1)
1.3 Molecular Chaperones: Mode of Action and Cellular Functions
3(5)
1.3.1 The Hsp70 Family
3(2)
1.3.2 The Hsp90 Family
5(2)
1.3.3 The Small Heat Shock Proteins
7(1)
1.3.4 Chaperonins
8(1)
1.4 Chaperones: Central Players During Protein Quality Control
8(1)
1.5 Chaperones and Protein Degradation
9(4)
1.6 The CHIP Ubiquitin Ligase: A Link Between Folding and Degradation Systems
13(3)
1.7 Other Proteins That May Influence the Balance Between Chaperone-assisted Folding and Degradation
16(3)
1.8 Further Considerations
19(1)
1.9 Conclusions
20(1)
References
21(10)
2 Molecular Dissection of Autophagy in the Yeast Saccharomyces cerevisiae
31(20)
Yoshinori Ohsumi
2.1 Introduction
31(1)
2.2 Vacuoles as a Lytic Compartment in Yeast
32(1)
2.3 Discovery of Autophagy in Yeast
32(2)
2.4 Genetic Dissection of Autophagy
34(2)
2.5 Characterization of Autophagy-defective Mutants
36(1)
2.6 Cloning of ATG Genes
36(1)
2.7 Further Genes Required for Autophagy
37(1)
2.8 Selectivity of Proteins Degraded
37(1)
2.9 Induction of Autophagy
38(1)
2.10 Membrane Dynamics During Autophagy
39(1)
2.11 Monitoring Methods of Autophagy in the Yeast S. cerevisiae
39(1)
2.12 Function of Atg Proteins
40(5)
2.12.1 The Atg12 Protein Conjugation System
42(1)
2.12.2 The Atg8 System
43(1)
2.12.3 The Atg1 Kinase Complex
44(1)
2.12.4 Autophagy-specific PI3 Kinase Complex
45(1)
2.12.5 Other Atg Proteins
45(1)
2.13 Site of Atg Protein Functioning: The Pre-autophagosomal Structure
45(1)
2.14 Atg Proteins in Higher Eukaryotes
46(1)
2.15 Atg Proteins as Markers for Autophagy in Mammalian Cells
47(1)
2.16 Physiological Role of Autophagy in Multicellular Organisms
47(1)
2.17 Perspectives
48(1)
References
48(3)
3 Dissecting Intracellular Proteolysis Using Small Molecule Inhibitors and Molecular Probes
51(28)
Huib Ovaa, Herman S. Overkleeft, Benedikt M. Kessler, and Hidde L. Ploegh
3.1 Introduction
51(3)
3.2 The Proteasome as an Essential Component of Intracellular Proteolysis
54(1)
3.3 Proteasome Structure, Function, and Localization
55(2)
3.4 Proteasome Inhibitors as Tools to Study Proteasome Function
57(7)
3.4.1 Peptide Aldehydes
57(2)
3.4.2 Lactacystin
59(1)
3.4.3 Peptide Epoxyketones
59(1)
3.4.4 Cyclic Peptides
60(1)
3.4.5 Peptide Boronates
60(1)
3.4.6 Peptide Vinyl Sulfones
61(1)
3.4.7 Peptide Vinyl Sulfones as Proteasomal Activity Probes
62(1)
3.4.8 Future Directions in the Development of Inhibitors of the Proteasome's Proteolytic Activities
63(1)
3.5 Assessing the Biological Role of the Proteasome With Inhibitors and Probes
64(1)
3.6 Proteasome-associated Components: The Role of N-glycanase
65(1)
3.7 A Link Between Proteasomal Proteolysis and Deubiquitination
66(2)
3.7.1 Reversal of Ub Modification
66(1)
3.7.2 Ubiquitin-specific Proteases
66(1)
3.7.3 USP Reactive Probes Correlate USP Activity With Proteasomal Proteolysis
67(1)
3.8 Future Developments and Final Remarks
68(1)
Acknowledgments
68(1)
Abbreviations
68(1)
References
69(10)
4 MEKK1: Dual Function as a Protein Kinase and a Ubiquitin Protein Ligase
79(10)
Zhimin Lu and Tony Hunter
4.1 Introduction
79(1)
4.2 Types of Protein Kinases
79(3)
4.3 Functions of Protein Kinases
82(2)
4.4 Conclusions 84 References
84(5)
5 Proteasome Activators
89(22)
Andreas Förster and Christopher P. Hill
5.1 Introduction
89(5)
5.1.1 20S Proteasomes
89(1)
5.1.2 The 20S Proteasome Gate
90(3)
5.1.3 Proteasome Activators
93(1)
5.2 11S Activators: Sequence and Structure
94(2)
5.2.1 Amino Acid Sequences
94(1)
5.2.2 Oligomeric State
94(1)
5.2.3 PA28α Crystal Structure
94(1)
5.2.4 Activation Loop
95(1)
5.2.5 Homologue-specific Inserts
95(1)
5.3 PA26–Proteasome Complex Structures
96(1)
5.3.1 Binding
97(6)
5.3.2 Symmetry Mismatch Mechanism of Gate Opening
98(1)
5.3.3 Open-gate Stabilization by Conserved Proteasome Residues
99(1)
5.3.4 Do Other Activators Induce the Same Open Conformation?
100(1)
5.3.5 Differential Stimulation of Proteasome Peptidase Activities
101(1)
5.3.6 Hybrid Proteasomes
102(1)
5.4 Biological Roles of 11S Activators
103(1)
5.5 PA200/Blm10p
104(1)
5.6 Concluding Remarks and Future Challenges
105(1)
References
106(5)
6 The Proteasome Portal and Regulation of Proteolysis
111(18)
Monika Bajorek and Michael H. Glickman
6.1 Background
111(3)
6.2 The Importance of Channel Gating
114(3)
6.3 A Porthole into the Proteasome
117(4)
6.3.1 The Closed State
117(2)
6.3.2 The Open State
119(2)
6.4 Facilitating Traffic Through the Gated Channel
121(2)
6.4.1 Regulatory Complexes
121(1)
6.4.2 Substrate-facilitated Traffic
122(1)
6.5 Summary. Consequences for Regulated Proteolysis
123(1)
References
124(5)
7 Ubiquity and Diversity of the Proteasome System
129(28)
Keiji Tanaka, Hideki Yashiroda, and Shigeo Murata
7.1 Introduction
129(1)
7.2 Catalytic Machine
130(6)
7.2.1 Standard Proteasome
130(3)
7.2.2 The Immunoproteasome
133(3)
7.3 Regulatory Factors
136(9)
7.3.1 PA700
137(2)
7.3.2 Rpn10
139(1)
7.3.3 Modulator
140(1)
7.3.4 PA28
141(1)
7.3.5 Hybrid Proteasomes
142(1)
7.3.6 PA200
143(1)
7.3.7 Ecm29
144(1)
7.3.8 PI31
144(1)
7.4 Proteasome Assembly
145(3)
7.4.1 Roles of Propeptides
145(1)
7.4.2 Ump1
146(1)
7.4.3 Immunoproteasome Assembly
146(1)
7.4.4 Assembly of the 26S Proteasome
147(1)
7.5 Perspectives
148(1)
References
149(8)
8 Proteasome-Interacting Proteins
157(26)
Jean E. O'Donoghue and Colin Gordon
8.1 Introduction
157(3)
8.1.1 The Proteasome
157(1)
8.1.2 Structure of the 26S Proteasome
158(1)
8.1.3 Marking Proteins for Proteasomal Degradation – the Ubiquitin System
159(1)
8.2 Regulators of the Holoenzyme and Chaperones Involved in Assembly of the Proteasome
160(2)
8.2.1 Proteasome Assembly and Integrity
160(1)
8.2.2 Regulators of the Holoenzyme
160(2)
8.3 Enzymes Controlling Ubiquitination and Deubiquitination
162(7)
8.3.1 E2 Ubiquitin-Conjugating Enzymes
162(1)
8.3.2 E3 Ubiquitin Ligases
163(2)
8.3.3 Deubiquitinating Enzymes (DUBs)
165(4)
8.4 Shuttling Proteins: Rpn10/Pus1 and UBA-UBL Proteins
169(3)
8.5 Other UBL-Containing Proteins
172(1)
8.6 VCP/p97/cdc48
173(1)
8.7 Proteasome Interactions with Transcription, Translation and DNA Repair
174(2)
8.8 Concluding Remarks
176(2)
References
178(5)
9 Structural Studies of Large, Self-compartmentalizing Proteases
183(32)
Beate Rockel, Jürgen Bosch, and Wolfgang Baumeister
9.1 Self-compartmentalization: An Effective Way to Control Proteolysis
183(2)
9.2 ATP-dependent Proteases: The Initial Steps in the Proteolytic Pathway
185(8)
9.2.1 The Proteasome
185(1)
9.2.1.1 The 20's Proteasome
185(1)
9.2.1.2 The PA28 Activator
186(1)
9.2.1.3 The 19S Cap Complex
187(1)
9.2.1.4 Archaeal and Bacterial AAA ATPases Activating the 20S Proteasome
189(1)
9.2.2 The Clp Proteases
190(3)
9.3 Beyond the Proteasome: ATP-independent Processing of Oligopeptides Released by the Proteasome
193(8)
9.3.1 Tripeptidyl Peptidase II
193(3)
9.3.2 Tricorn Protease
196(4)
9.3.3 Tetrahedral Aminopeptidase
200(1)
9.4 Conclusions
201(1)
Acknowledgments
202(1)
References
202(13)
10 What the Archaeal PAN–Proteasome Complex and Bacterial ATP-dependent Proteases Can Teach Us About the 26S Proteasome 215(34)
Nadia Benaroudj, David Smith, and Alfred L. Goldberg
10.1 Introduction
215(2)
10.2 Archaeal 20S Proteasomes
217(5)
10.3 PAN the Archaeal Homologue of the 19S Complex
222(5)
10.4 VAT, a Potential Regulator of Proteasome Function
227(1)
10.5 The Use of PAN to Understand the Energy Requirement for Proteolysis
227(5)
10.5.1 ATP Hydrolysis by PAN Allows Substrate Unfolding and Degradation
228(1)
10.5.2 ATP Hydrolysis by PAN Serves Additional Functions in Protein Degradation
229(2)
10.5.3 PAN and ATP Regulate Gate Opening
231(1)
10.5.4 PAN and ATP Are Required for Translocation of Unfolded Substrates
232(1)
10.6 Direction of Substrate Translocation
232(2)
10.7 Degradation of Polyglutamine-containing Proteins
234(1)
10.8 Eubacterial ATP-dependent Proteases
235(3)
10.8.1 HslUV (ClpYQ)
235(2)
10.8.2 ClpAP and ClpXP
237(1)
10.9 How AAA ATPases Use ATP to Catalyze Proteolysis
238(1)
10.10 Conclusions
239(1)
Acknowledgments
240(1)
References
240(9)
11 Biochemical Functions of Ubiquitin and Ubiquitin-like Protein Conjugation 249(30)
Mark Hochstrosser
Abstract
249(1)
11.1 Introduction
249(3)
11.1.1 The Ubiquitin Conjugation Pathway
250(1)
11.1.2 Ubiquitin Polymers
251(1)
11.1.3 Ubiquitin Attachment Dynamics
251(1)
11.2 Ubls: A Typical Modification Cycle by an Atypical Set of Modifiers
252(3)
11.2.1 Some Unusual Ubl Conjugation Features
254(1)
11.3 Origins of the Ubiquitin System
255(4)
11.3.1 Sulfurtransferases and Ubl Activation Enzymes
256(1)
11.3.2 The E1–E2 Couple
257(2)
11.4 Ubiquitin-binding Domains and Ubiquitin Receptors in the Proteasome Pathway
259(2)
11.4.1 A Proteasome "Ubiquitin Receptor"
259(1)
11.4.2 A Plethora of Ubiquitin-binding Domains
259(1)
11.4.3 Ubiquitin Conjugate Adaptor Proteins
260(1)
11.5 Ubiquitin-binding Domains and Membrane Protein Trafficking
261(3)
11.5.1 The MVB Pathway and RNA Virus Budding
263(1)
11.6 Sumoylation and SUMO-binding Motifs
264(4)
11.6.1 A SUMO-binding Motif
265(1)
11.6.2 A SUMO-induced Conformational Change
266(1)
11.6.3 Interactions Between Different Sumoylated Proteins
267(1)
11.7 General Biochemical Functions of Protein–Protein Conjugation
268(3)
11.7.1 Negative Regulation by Ubl Conjugation
269(1)
11.7.2 Positive Regulation by Ubl Conjugation
270(1)
11.7.3 Cross-regulation by Ubls
270(1)
11.8 Conclusions
271(1)
Acknowledgments
272(1)
References
272(7)
Index 279

An electronic version of this book is available through VitalSource.

This book is viewable on PC, Mac, iPhone, iPad, iPod Touch, and most smartphones.

By purchasing, you will be able to view this book online, as well as download it, for the chosen number of days.

Digital License

You are licensing a digital product for a set duration. Durations are set forth in the product description, with "Lifetime" typically meaning five (5) years of online access and permanent download to a supported device. All licenses are non-transferable.

More details can be found here.

A downloadable version of this book is available through the eCampus Reader or compatible Adobe readers.

Applications are available on iOS, Android, PC, Mac, and Windows Mobile platforms.

Please view the compatibility matrix prior to purchase.