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  • 1
    Online Resource
    Online Resource
    Newark :John Wiley & Sons, Incorporated,
    Keywords: Proteins -- Metabolism. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (302 pages)
    Edition: 1st ed.
    ISBN: 9783527620364
    Series Statement: Protein Degradation Series
    Language: English
    Note: Intro -- Protein Degradation -- Contents -- Preface -- List of Contributors -- 1 Molecular Chaperones and the Ubiquitin-Proteasome System -- 1.1 Introduction -- 1.2 A Biomedical Perspective -- 1.3 Molecular Chaperones: Mode of Action and Cellular Functions -- 1.3.1 The Hsp70 Family -- 1.3.2 The Hsp90 Family -- 1.3.3 The Small Heat Shock Proteins -- 1.3.4 Chaperonins -- 1.4 Chaperones: Central Players During Protein Quality Control -- 1.5 Chaperones and Protein Degradation -- 1.6 The CHIP Ubiquitin Ligase: A Link Between Folding and Degradation Systems -- 1.7 Other Proteins That May Influence the Balance Between Chaperone-assisted Folding and Degradation -- 1.8 Further Considerations -- 1.9 Conclusions -- References -- 2 Molecular Dissection of Autophagy in the Yeast Saccharomyces cerevisiae -- 2.1 Introduction -- 2.2 Vacuoles as a Lytic Compartment in Yeast -- 2.3 Discovery of Autophagy in Yeast -- 2.4 Genetic Dissection of Autophagy -- 2.5 Characterization of Autophagy-defective Mutants -- 2.6 Cloning of ATG Genes -- 2.7 Further Genes Required for Autophagy -- 2.8 Selectivity of Proteins Degraded -- 2.9 Induction of Autophagy -- 2.10 Membrane Dynamics During Autophagy -- 2.11 Monitoring Methods of Autophagy in the Yeast S. cerevisiae -- 2.12 Function of Atg Proteins -- 2.12.1 The Atg12 Protein Conjugation System -- 2.12.2 The Atg8 System -- 2.12.3 The Atg1 Kinase Complex -- 2.12.4 Autophagy-specific PI3 Kinase Complex -- 2.12.5 Other Atg Proteins -- 2.13 Site of Atg Protein Functioning: The Pre-autophagosomal Structure -- 2.14 Atg Proteins in Higher Eukaryotes -- 2.15 Atg Proteins as Markers for Autophagy in Mammalian Cells -- 2.16 Physiological Role of Autophagy in Multicellular Organisms -- 2.17 Perspectives -- References -- 3 Dissecting Intracellular Proteolysis Using Small Molecule Inhibitors and Molecular Probes -- 3.1 Introduction. , 3.2 The Proteasome as an Essential Component of Intracellular Proteolysis -- 3.3 Proteasome Structure, Function, and Localization -- 3.4 Proteasome Inhibitors as Tools to Study Proteasome Function -- 3.4.1 Peptide Aldehydes -- 3.4.2 Lactacystin -- 3.4.3 Peptide Epoxyketones -- 3.4.4 Cyclic Peptides -- 3.4.5 Peptide Boronates -- 3.4.6 Peptide Vinyl Sulfones -- 3.4.7 Peptide Vinyl Sulfones as Proteasomal Activity Probes -- 3.4.8 Future Directions in the Development of Inhibitors of the Proteasome's Proteolytic Activities -- 3.5 Assessing the Biological Role of the Proteasome With Inhibitors and Probes -- 3.6 Proteasome-associated Components: The Role of N-glycanase -- 3.7 A Link Between Proteasomal Proteolysis and Deubiquitination -- 3.7.1 Reversal of Ub Modification -- 3.7.2 Ubiquitin-specific Proteases -- 3.7.3 USP Reactive Probes Correlate USP Activity With Proteasomal Proteolysis -- 3.8 Future Developments and Final Remarks -- Acknowledgments -- Abbreviations -- References -- 4 MEKK1: Dual Function as a Protein Kinase and a Ubiquitin Protein Ligase -- 4.1 Introduction -- 4.2 Types of Protein Kinases -- 4.3 Functions of Protein Kinases -- 4.4 Conclusions -- References -- 5 Proteasome Activators -- 5.1 Introduction -- 5.1.1 20S Proteasomes -- 5.1.2 The 20S Proteasome Gate -- 5.1.3 Proteasome Activators -- 5.2 11S Activators: Sequence and Structure -- 5.2.1 Amino Acid Sequences -- 5.2.2 Oligomeric State -- 5.2.3 PA28α Crystal Structure -- 5.2.4 Activation Loop -- 5.2.5 Homologue-specific Inserts -- 5.3 PA26-Proteasome Complex Structures -- 5.3.1 Binding -- 5.3.2 Symmetry Mismatch Mechanism of Gate Opening -- 5.3.3 Open-gate Stabilization by Conserved Proteasome Residues -- 5.3.4 Do Other Activators Induce the Same Open Conformation? -- 5.3.5 Differential Stimulation of Proteasome Peptidase Activities -- 5.3.6 Hybrid Proteasomes. , 5.4 Biological Roles of 11S Activators -- 5.5 PA200/Blm10p -- 5.6 Concluding Remarks and Future Challenges -- References -- 6 The Proteasome Portal and Regulation of Proteolysis -- 6.1 Background -- 6.2 The Importance of Channel Gating -- 6.3 A Porthole into the Proteasome -- 6.3.1 The Closed State -- 6.3.2 The Open State -- 6.4 Facilitating Traffic Through the Gated Channel -- 6.4.1 Regulatory Complexes -- 6.4.2 Substrate-facilitated Traffic -- 6.5 Summary: Consequences for Regulated Proteolysis -- References -- 7 Ubiquity and Diversity of the Proteasome System -- 7.1 Introduction -- 7.2 Catalytic Machine -- 7.2.1 Standard Proteasome -- 7.2.2 The Immunoproteasome -- 7.3 Regulatory Factors -- 7.3.1 PA700 -- 7.3.2 Rpn10 -- 7.3.3 Modulator -- 7.3.4 PA28 -- 7.3.5 Hybrid Proteasomes -- 7.3.6 PA200 -- 7.3.7 Ecm29 -- 7.3.8 PI31 -- 7.4 Proteasome Assembly -- 7.4.1 Roles of Propeptides -- 7.4.2 Ump1 -- 7.4.3 Immunoproteasome Assembly -- 7.4.4 Assembly of the 26S Proteasome -- 7.5 Perspectives -- References -- 8 Proteasome-Interacting Proteins -- 8.1 Introduction -- 8.1.1 The Proteasome -- 8.1.2 Structure of the 26S Proteasome -- 8.1.3 Marking Proteins for Proteasomal Degradation - the Ubiquitin System -- 8.2 Regulators of the Holoenzyme and Chaperones Involved in Assembly of the Proteasome -- 8.2.1 Proteasome Assembly and Integrity -- 8.2.2 Regulators of the Holoenzyme -- 8.3 Enzymes Controlling Ubiquitination and Deubiquitination -- 8.3.1 E2 Ubiquitin-Conjugating Enzymes -- 8.3.2 E3 Ubiquitin Ligases -- 8.3.3 Deubiquitinating Enzymes (DUBs) -- 8.4 Shuttling Proteins: Rpn10/Pus1 and UBA-UBL Proteins -- 8.5 Other UBL-Containing Proteins -- 8.6 VCP/p97/cdc48 -- 8.7 Proteasome Interactions with Transcription, Translation and DNA Repair -- 8.8 Concluding Remarks -- References -- 9 Structural Studies of Large, Self-compartmentalizing Proteases. , 9.1 Self-compartmentalization: An Effective Way to Control Proteolysis -- 9.2 ATP-dependent Proteases: The Initial Steps in the Proteolytic Pathway -- 9.2.1 The Proteasome -- 9.2.1.1 The 20S Proteasome -- 9.2.1.2 The PA28 Activator -- 9.2.1.3 The 19S Cap Complex -- 9.2.1.4 Archaeal and Bacterial AAA ATPases Activating the 20S Proteasome -- 9.2.2 The Clp Proteases -- 9.3 Beyond the Proteasome: ATP-independent Processing of Oligopeptides Released by the Proteasome -- 9.3.1 Tripeptidyl Peptidase II -- 9.3.2 Tricorn Protease -- 9.3.3 Tetrahedral Aminopeptidase -- 9.4 Conclusions -- Acknowledgments -- References -- 10 What the Archaeal PAN-Proteasome Complex and Bacterial ATP-dependent Proteases Can Teach Us About the 26S Proteasome -- 10.1 Introduction -- 10.2 Archaeal 20S Proteasomes -- 10.3 PAN the Archaeal Homologue of the 19S Complex -- 10.4 VAT, a Potential Regulator of Proteasome Function -- 10.5 The Use of PAN to Understand the Energy Requirement for Proteolysis -- 10.5.1 ATP Hydrolysis by PAN Allows Substrate Unfolding and Degradation -- 10.5.2 ATP Hydrolysis by PAN Serves Additional Functions in Protein Degradation -- 10.5.3 PAN and ATP Regulate Gate Opening -- 10.5.4 PAN and ATP Are Required for Translocation of Unfolded Substrates -- 10.6 Direction of Substrate Translocation -- 10.7 Degradation of Polyglutamine-containing Proteins -- 10.8 Eubacterial ATP-dependent Proteases -- 10.8.1 HslUV (ClpYQ) -- 10.8.2 ClpAP and ClpXP -- 10.9 How AAA ATPases Use ATP to Catalyze Proteolysis -- 10.10 Conclusions -- Acknowledgments -- References -- 11 Biochemical Functions of Ubiquitin and Ubiquitin-like Protein Conjugation -- Abstract -- 11.1 Introduction -- 11.1.1 The Ubiquitin Conjugation Pathway -- 11.1.2 Ubiquitin Polymers -- 11.1.3 Ubiquitin Attachment Dynamics -- 11.2 Ubls: A Typical Modification Cycle by an Atypical Set of Modifiers. , 11.2.1 Some Unusual Ubl Conjugation Features -- 11.3 Origins of the Ubiquitin System -- 11.3.1 Sulfurtransferases and Ubl Activation Enzymes -- 11.3.2 The E1-E2 Couple -- 11.4 Ubiquitin-binding Domains and Ubiquitin Receptors in the Proteasome Pathway -- 11.4.1 A Proteasome "Ubiquitin Receptor -- 11.4.2 A Plethora of Ubiquitin-binding Domains -- 11.4.3 Ubiquitin-Conjugate Adaptor Proteins -- 11.5 Ubiquitin-binding Domains and Membrane Protein Trafficking -- 11.5.1 The MVB Pathway and RNA Virus Budding -- 11.6 Sumoylation and SUMO-binding Motifs -- 11.6.1 A SUMO-binding Motif -- 11.6.2 A SUMO-induced Conformational Change -- 11.6.3 Interactions Between Different Sumoylated Proteins -- 11.7 General Biochemical Functions of Protein-Protein Conjugation -- 11.7.1 Negative Regulation by Ubl Conjugation -- 11.7.2 Positive Regulation by Ubl Conjugation -- 11.7.3 Cross-regulation by Ubls -- 11.8 Conclusions -- Acknowledgments -- References -- Index.
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  • 2
    Online Resource
    Online Resource
    Newark :John Wiley & Sons, Incorporated,
    Keywords: Proteins -- Metabolism. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (254 pages)
    Edition: 1st ed.
    ISBN: 9783527620296
    Series Statement: Protein Degradation Series
    DDC: 612.3/98
    Language: English
    Note: Intro -- Protein Degradation -- Contents -- Preface -- List of Contributors -- 1 Ubiquitin: A New Player in the Peroxisome Field -- 1.1 Introduction -- 1.2 Matrix Protein Import into Peroxisomes is Mediated by Cycling Receptors -- 1.3 Pex5p is Monoubiquitinated in Wild-type Cells, but Polyubiquitinated in Late-acting pex Mutants -- 1.4 Ubiquitination of Pex18p -- 1.5 Role for the RING Finger and AAA Peroxins in Pex5p Ubiquitination and Recycling -- 1.6 Pex5p Monoubiquitination: A Role in Receptor Recycling -- 1.7 Conclusions/Future Prospects -- Acknowledgements -- References -- 2 The Ubiquitin Proteasome System and Muscle Development -- 2.1 Introduction -- 2.2 Muscle Histology -- 2.3 UPS and Developing Muscle -- 2.3.1 Ubiquitin-dependent Degradation of MyoD -- 2.3.2 Degradation of MyoD by SCF(MAFbx) -- 2.3.3 Other Muscle Regulatory Factors -- 2.4 UPS and Organizing Muscle -- 2.4.1 Ozz-E3-dependent β-Catenin Regulation in the Muscle -- 2.4.2 Regulation of Myosin Assembly by CHN-1 and UFD-2 -- 2.5 UPS and Muscle Destruction or Degeneration -- 2.5.1 N-end Rule and Muscle Atrophy -- 2.5.2 MuRFs, E3 Enzymes in Atrophying Muscles -- 2.5.3 Atrogin-1/MAFbx Function in Muscle Atrophy -- 2.5.4 Activation of Muscle-atrophy Pathways -- 2.6 Concluding Remarks -- References -- 3 The COP9 Signalosome: Structural and Biochemical Conservation and Its Roles in the Regulation of Plant Development -- 3.1 Introduction -- 3.2 The Plant COP9 Signalosome -- 3.3 CSN Involvement in the Ubiquitin-Proteasome Pathway -- 3.4 Plant CSN Biochemical Activities -- 3.4.1 Deneddylation -- 3.4.2 Subcellular Partitioning -- 3.5 CSN Functions in Plant Development -- 3.5.1 Floral Development -- 3.5.2 Responses to Plant Hormones -- 3.5.3 Disease Resistance -- 3.5.4 Photomorphogenesis -- 3.6 Conclusions -- References -- 4 Ubiquitin and Protein Sorting to the Lysosome -- 4.1 Introduction. , 4.2 Identification of Ubiquitin as an Endosomal Sorting Signal -- 4.3 Ubiquitin-mediated Sorting at the Endosome: The MVB Sorting Machinery -- 4.3.1 Endosome-associated Ubiquitin Interacting Domains: Structure and Function -- 4.3.2 The Hrs-STAM Complex and the Endosomal Clathrin Coat -- 4.3.3 GGA and Tom1: Alternative Sorting Adapters? -- 4.3.4 The ESCRT Machinery -- 4.3.5 Vps4-SKD1 -- 4.4 Ubiquitin Ligases and Endosomal Sorting -- 4.4.1 Nedd4 Family -- 4.4.2 c-Cbl -- 4.5 Endosomal DUBs -- 4.5.1 Ubp1 and Ubp2 -- 4.5.2 Doa4 -- 4.5.3 UBPY -- 4.5.4 AMSH -- 4.6 Polyubiquitin Linkages and Endocytosis -- 4.6.1 Proteasome Involvement in Endocytic Sorting -- 4.6.2 K63-linked Ubiquitin -- 4.7 Future Directions -- Acknowledgements -- References -- 5 ISG15-dependent Regulation -- 5.1 Introduction and Overview -- 5.2 The Discovery of ISG15 -- 5.3 Structure and Properties of the ISG15 Protein -- 5.4 The ISG15 Conjugation Pathway -- 5.4.1 Activation of ISG15 by UbE1L -- 5.4.2 UbcH8 is an ISG15-specific Conjugating Enzyme -- 5.4.3 Candidate ISG15-specific Ligases -- 5.5 Regulation of Intracellular ISG15 Pools -- 5.6 Functional Roles for ISG15 -- 5.6.1 ISG15 as an Extracellular Cytokine -- 5.6.2 Role of ISG15 in the Antiviral Response -- 5.6.3 ISG15 and Early Events of Pregnancy -- 5.7 Perspective -- Acknowledgements -- References -- 6 The Role of the Ubiquitin-Proteasome Pathway in the Regulation of the Cellular Hypoxia Response -- 6.1 Overview of the Hypoxia Response -- 6.2 Players in the Hypoxia-response Signalling Pathway -- 6.2.1 Hypoxia-inducible Factors -- 6.2.2 Prolyl-hydroxylase Domain-containing Enzymes and FIH -- 6.3 pVHL-dependent Degradation of HIF-1α -- 6.4 Siah-dependent Regulation of PHD -- 6.5 Other Examples of Altered Ubiquitination During Hypoxia -- 6.5.1 p53/Mdm2 -- 6.5.2 MyoD -- 6.5.3 CREB -- 6.5.4 SUMOylation -- 6.6 Ischemia Model. , 6.7 Regulation of the Ubiquitin System in Hypoxia -- 6.8 Concluding Remarks -- References -- 7 p97 and Ubiquitin: A Complex Story -- Abstract -- 7.1 Introduction -- 7.2 Interactions of Ubiquitin, p97 and Adaptors -- 7.2.1 Ubiquitin-binding Domains and Motifs -- 7.2.2 p97 Interacts Directly With Ubiquitin -- 7.2.3 p97 Adaptor Proteins Can Also Interact With Ubiquitin -- 7.2.4 p97-p47 Structure as a General Model for UBX Domain Binding: A Level of Similarity Between UBX Domains -- 7.2.5 The Interaction of p97 With Ubiquitin Ligases -- 7.2.6 The Interactions of p97 With Deubiquitinating Enzymes -- 7.3 The Cellular Roles of p97 and Ubiquitin -- 7.3.1 ERAD -- 7.3.1.1 The ERAD Pathway -- 7.3.1.2 Recognition of ERAD Substrates -- 7.3.1.3 Translocation into the Cytosol -- 7.3.1.4 Mono/diubiquitin Conjugation -- 7.3.1.5 Polyubiquitination by E4 Factors -- 7.3.1.6 Release from the ER Membrane -- 7.3.1.7 Transport to the Proteasome -- 7.3.1.8 The Proteasome in ERAD -- 7.3.2 Other Ubiquitin-dependent Processes That Involve p97 -- 7.3.2.1 p97 and the Degradation of Cytoplasmic Substrates -- 7.3.2.2 p97 and the Proteasome in Transcription-factor Processing -- 7.3.2.3 p97 and Other Ubiquitin-binding Adaptors -- 7.3.2.4 p97 and Ubiquitin in Membrane Fusion -- 7.4 The Action of p97 -- 7.4.1 p97 as a Chaperone -- 7.4.2 p97 and NSF: SNARE Disassembly Machines -- 7.4.3 p97 Liberates Polyubiquitinated Substrates from the ER Membrane -- 7.4.4 p97 as a Segregase -- 7.5 When Things Go Wrong: p97 in Disease -- 7.6 Conclusions -- Acknowledgments -- References -- 8 Cdc48 (p97) and Its Cofactors -- 8.1 Introduction -- 8.2 Cdc48 Cofactors -- 8.2.1 Cofactor Families -- 8.2.1.1 UBX Domain Proteins -- 8.2.1.2 Ufd1/Npl4 -- 8.2.1.3 Other Cofactors -- 8.2.2 Cofactor Functions -- 8.2.2.1 Substrate-recruiting Cofactors -- 8.2.2.2 Substrate-processing Cofactors. , 8.2.2.3 Additional Functions of Cofactors -- 8.3 Cellular Functions -- 8.3.1 Cdc48(Ufd1/Npl4) -- 8.3.1.1 Protein-degradation Pathways -- 8.3.1.2 Cell Cycle Regulation -- 8.3.2 Cdc48(Shp1) -- 8.3.2.1 Membrane Fusion -- 8.3.2.2 Protein Degradation -- 8.3.3 Further Functions -- 8.4 Outlook -- Acknowledgements -- References -- 9 Deubiquitinating Enzymes, Cell Proliferation, and Cancer -- 9.1 Introduction -- 9.1.1 Ubiquitination -- 9.1.2 Deubiquitination -- 9.2 DUBs, Oncogenes, and Cell Transformation -- 9.2.1 USP6/Tre-2/Tre-17 -- 9.2.2 Unp/Usp4/Usp15 -- 9.2.3 DUBs and NFκB Signalling -- 9.2.4 USP7/HAUSP and p53 -- 9.2.5 USP33/VDU1, USP20/VDU2, and von Hippel-Lindau Disease -- 9.2.6 USP1, Fanconi Anaemia, and DNA Repair -- 9.2.7 DUBs Associated with BRCA1 and BRCA2 -- 9.2.8 The Cytokine-inducible DUB-1/DUB-2/USP17 Family and Regulation of Cell Growth -- 9.3 Conclusions and Perspectives -- References -- Index.
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  • 3
    Online Resource
    Online Resource
    Newark :John Wiley & Sons, Incorporated,
    Keywords: Cell Physiology. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (260 pages)
    Edition: 1st ed.
    ISBN: 9783527620302
    Series Statement: Protein Degradation Series
    Language: English
    Note: Intro -- Protein Degradation -- Contents -- Preface -- List of Contributors -- 1 Ubiquitin Signaling and Cancer Pathogenesis -- 1.1 Introduction -- 1.1.1 Ubiquitin Signaling Networks -- 1.1.2 Ubiquitin-like Proteins -- 1.2 Ubiquitin in Cancer Pathogenesis -- 1.2.1 Ubiquitin in Cell Cycle Control -- 1.2.2 Ubiquitin in the NF-κB Pathway -- 1.2.3 Ubiquitin as a Signal in DNA Repair -- 1.2.3.1 p53 Pathway -- 1.2.3.2 BRCA1 and FANCD2 -- 1.2.3.3 PCNA and TLS Polymerases -- 1.2.4 Ubiquitin Networks in Angiogenesis -- 1.2.5 Ubiquitin Networks in Receptor Endocytosis -- 1.3 Targeting Ubiquitin Networks in Cancers -- 1.3.1 Targeting Interactions between E3s and their Substrates -- 1.3.2 Targeting the Proteasome -- 1.3.3 Other Approaches -- 1.4 Conclusions and Future Perspectives -- 2 Regulation of the p53 Tumor-suppressor Protein by Ubiquitin and Ubiquitin-like Molecules -- 2.1 Functional Domains of p53 -- 2.2 The Family of Ubiquitin-like Molecules -- 2.3 E3 Ligases for p53 -- 2.4 Modification of p53 with Ubiquitin -- 2.5 Requirements for Mdm2-mediated Ubiquitination of p53 -- 2.6 Regulation of p53 Ubiquitination -- 2.6.1 E2 Conjugating Enzymes -- 2.6.2 Interacting Proteins -- 2.6.3 By Other Post-translational Modifications -- 2.7 De-ubiquitination of p53 -- 2.8 SUMO-1/sentrin/smpt3 -- 2.9 NEDD8/Rub1 -- 2.10 Therapeutic Intervention through the Ubiquitin Pathway -- 3 The Ubiquitin-Proteasome System in Epstein-Barr Virus Infection and Oncogenesis -- 3.1 Introduction -- 3.2 Viral Interference with the Ubiquitin-Proteasome System -- 3.3 The EBV Life Cycle -- 3.4 EBV and the Ubiquitin-Proteasome System -- 3.4.1 EBNA1 -- 3.4.2 EBNA6 (EBNA3C) -- 3.4.3 LMP1 -- 3.4.4 LMP2 -- 3.4.5 BZLF1 (Zta) and BRLF1 (Rta) -- 3.4.6 BPLF1 -- 3.5 EBV-associated Malignancies -- 3.6 Concluding Remarks -- 4 HECT Ubiquitin-protein Ligases in Human Disease -- 4.1 Introduction. , 4.2 Definition of HECT E3s -- 4.3 Human HECT E3s and their Role in Disease -- 4.4 E6-AP -- 4.4.1 E6-AP and Cervical Cancer (Cancer of the Uterine Cervix) -- 4.4.2 E6-AP and Angelman Syndrome -- 4.5 HECTH9 -- 4.6 HECT E3s with WW Domains -- 4.6.1 Nedd4/Nedd4-2 -- 4.6.1.1 Nedd4/Nedd4-2 and Liddle's Syndrome -- 4.6.1.2 Nedd4 and Retrovirus Budding -- 4.6.2 Itch and the Immune Response -- 4.6.3 Smurfs -- 4.6.3.1 Smurfs and Cancer -- 4.6.3.2 Smurfs and Bone Homeostasis -- 4.7 Concluding Remarks -- 5 Ubiquitin-independent Mechanisms of Substrate Recognition and Degradation by the Proteasome -- 5.1 Introduction -- 5.2 Ubiquitin-independent Proteasome Substrates -- 5.2.1 Ornithine Decarboxylase -- 5.2.2 p21(Waf1/Cip1) -- 5.2.3 Retinoblastoma Protein -- 5.2.4 p53 and p73 -- 5.2.5 Human Thymidylate Synthase -- 5.2.6 Rpn4 -- 5.2.7 NF-κB and IκBα -- 5.2.8 Steroid Receptor Co-activator-3 -- 5.2.9 c-Jun -- 5.3 Mechanisms of Ubiquitin-independent Degradation -- 5.4 Conclusion -- 6 Endoplasmic Reticulum Protein Quality Control and Degradation -- 6.1 Introduction -- 6.2 ER-import, Folding and the Unfolded Protein Response -- 6.3 General Principles and Components of ERQD (Endoplasmic Reticulum Quality Control and Protein Degradation) -- 6.4 Mechanism of ERQD -- 6.5 "Overflow" Degradation Pathways: ER-to-Golgi Transport and Autophagocytosis -- 6.6 The Retrotranslocation Channel -- 6.7 Metazoan ERQD -- 7 Interactions between Viruses and the Ubiquitin-Proteasome System -- 7.1 Introduction -- 7.2 Overview of Viruses and the Ubiquitin-Proteasome System -- 7.2.1 Proteolysis -- 7.2.2 Viruses and the ERAD Pathway -- 7.2.3 Membrane Protein Trafficking and Endosomal Sorting -- 7.2.4 Viral Entry and Egress -- 7.2.5 Transcriptional Regulation -- 7.2.6 Cell Cycle Control -- 7.2.7 Cell Signaling -- 7.3 Viruses and E3 Ubiquitin-Protein Ligases. , 7.3.1 ICP0 - A Viral RING E3 Ligase in HSV Activation -- 7.3.2 Preventing the Release of Interferon -- 7.3.3 Viral E3 Ligases Ubiquitinate and Dispose of Critical Immune Receptors -- 7.3.4 Degradation of MHC Class I Molecules by the mK3 Protein of MHV-68 Virus -- 7.3.5 Degradation of Immunoreceptors by Kaposi's Sarcoma-associated Herpesvirus -- 7.3.6 Viral SCF E3 Ligases -- 7.3.7 HIV Vif and APOBEC Function -- 7.3.8 Viral Recruitment of E3 Ligases -- 7.4 Conclusions -- 8 The Ubiquitin-Proteasome System in Parkinson's Disease -- 8.1 Introduction -- 8.2 Protein Handling in the CNS -- 8.3 The UPS and Protein Mishandling in PD -- 8.4 Parkin -- 8.5 UCH-L1 -- 8.6 α-Synuclein -- 8.7 Dardarin/LRRK2 -- 8.8 PINK1 -- 8.9 DJ-1 -- 8.10 Proteasomal Dysfunction in Sporadic PD -- 8.10.1 Altered Proteasomal Function -- 8.10.2 Role of Proteasomal Dysfunction in the Neurodegenerative Process -- 8.10.3 The Cause of Proteasomal Dysfunction -- 8.11 Conclusion -- 9 The Molecular Pathway to Neurodegeneration in Parkin-Related Parkinsonism -- 9.1 Introduction -- 9.2 Parkin is an E3 Ubiquitin Ligase -- 9.2.1 Parkin and the Ubiquitin-Proteasome System -- 9.2.2 Proteasome-independent Role of Parkin -- 9.2.3 Multiple Monoubiquitination is Mediated by Parkin -- 9.2.4 Modulators of Parkin E3 Activity -- 9.3 Substrates of Parkin -- 9.3.1 Parkin Substrates and their Recognition Mechanisms -- 9.3.2 The Link between Substrate Accumulation and Cell Death: Pael-R -- 9.3.2.1 Pael-R and Endoplasmic Reticulum Stress -- 9.3.2.2 Pael-R Overexpressing Animals and Dopaminergic Neurodegeneration -- 9.3.3 The Link between Substrate Accumulation and Cell Death: CDC-rel1, Synphilin-1, Cyclin E and p38 -- 9.4 The Animal Models of AR-JP -- 9.4.1 Drosophila Model of AR-JP -- 9.4.2 Parkin-null Drosophila and Drosophila -- 9.4.3 Mouse Model of AR-JP -- 9.4.4 The Problems with Animal Models of AR-JP. , 9.5 Future Directions -- 10 Parkin and Neurodegeneration -- 10.1 Introduction -- 10.2 AR JP and Parkin -- 10.2.1 ARJP: Introduction -- 10.2.2 PARKIN: The Gene -- 10.2.3 PARKIN: Localization and Regulation -- 10.3 Parkin in the Ubiquitin-Proteasome Pathway -- 10.3.1 The Ubiquitin-Proteasome Pathway -- 10.3.2 PARKIN: An E3 Ubiquitin Ligase -- 10.3.3 Parkin and Lewy Bodies -- 10.3.4 Parkin Substrates -- 10.4 Parkin in Neuroprotection -- 10.4.1 Toxic Parkin Substrates -- 10.4.2 Stress-mediated Toxicity -- 10.5 Parkin and Other PD-linked Genes -- 10.5.1 α-Synuclein -- 10.5.2 DJ-1 -- 10.5.3 LRRK2 -- 10.6 Mechanisms of Parkin Dysfunction -- 10.6.1 Pathogenic Mutations -- 10.6.2 Cellular Regulators of Parkin -- 10.6.3 Post-translational Regulation of Parkin -- 10.7 Animal Models of Parkin Deficiency -- 10.7.1 Drosophila Models -- 10.7.2 Mouse Models -- 10.8 Concluding Remarks -- Index.
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  • 4
    Online Resource
    Online Resource
    Newark :John Wiley & Sons, Incorporated,
    Keywords: Proteins -- Metabolism. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (395 pages)
    Edition: 1st ed.
    ISBN: 9783527605569
    Series Statement: Protein Degradation Series
    Language: English
    Note: Intro -- Protein Degradation -- Contents -- Preface -- List of Contributors -- 1 Brief History of Protein Degradation and the Ubiquitin System -- 1.1 Introductory Remarks -- 1.2 Protein Degradation - Does It Exist? -- 1.3 Discovery of the Role of Ubiquitin in Protein Degradation -- 1.4 Identification of Enzymes of the Ubiquitin-mediated Proteolytic System -- 1.5 Discovery of Some Basic Cellular Functions of the Ubiquitin System -- 1.6 Concluding Remarks -- References -- 2 N-terminal Ubiquitination: No Longer Such a Rare Modification -- Abstract -- 2.1 Background -- 2.2 Results -- 2.3 Discussion -- Acknowledgments -- References -- 3 Evolutionary Origin of the Activation Step During Ubiquitin-dependent Protein Degradation -- Abbreviations -- Abstract -- 3.1 Introduction -- 3.1.1 Activation of Ubiquitin and Ubiquitin-like Proteins -- 3.1.2 Molybdenum Cofactor Biosynthesis -- 3.2 The Crystal Structure of MoaD Reveals the Ubiquitin Fold -- 3.3 Structural Studies of the MoeB-MoaD Complex -- 3.3.1 Structure of MoeB -- 3.3.2 The MoeB-MoaD Interface -- 3.3.3 Structure of MoeB-MoaD with Bound ATP -- 3.3.4 Structure of the MoaD Adenylate -- 3.3.5 Fate of the Adenylate -- 3.4 Structure of the NEDD8 Activator -- 3.4.1 Overall Structure of the NEDD8-E1 -- 3.4.2 Comparison with the MoaD-MoeB Complex -- 3.4.3 Conformational Changes during the Formation of the Acyl Adenylate -- Summary -- Acknowledgments -- References -- 4 RING Fingers and Relatives: Determinators of Protein Fate -- 4.1 Introduction and Overview -- 4.1.1 Historical Perspective -- 4.2 RING Fingers as E3s -- 4.2.1 General Considerations -- 4.2.2 Structural Analysis and Structure-Function Relationships -- 4.2.2.1 RING finger-E2 Interactions -- 4.2.3 Other Protein-Protein Interaction Motifs in RING finger Proteins -- 4.2.4 Variations on the RING Finger -- 4.2.5 High-order Structure of RINGs - TRIMs. , 4.3 RING Fingers in Cell Signaling -- 4.3.1 Siahs -- 4.3.2 IAPs -- 4.3.3 TRAFs -- 4.3.4 Cbls -- 4.4 Multi RING finger Proteins -- 4.4.1 Mindbomb and TRIADs -- 4.4.2 Parkin and Parkinson's Disease -- 4.4.2.1 Parkin Substrates -- 4.4.2.2 Parkin Animal Models -- 4.4.2.3 Possible Pathogenic Mechanisms in ARJP -- 4.5 Regulation of p53 by Mdm2 and other RING finger Proteins -- 4.5.1 Mdm2 -- 4.5.2 Pirh2 -- 4.5.3 MdmX -- 4.5.4 Arf and Other Modulators of Mdm2 Activity -- 4.5.5 Other Potential Mdm2 Substrates -- 4.5.6 Mdm2 and Therapeutic Intervention in Cancer -- 4.6 Conclusion - Perspective -- Acknowledgments -- References -- 5 Ubiquitin-conjugating Enzymes -- 5.1 Introduction -- 5.2 Historical Background -- 5.3 What is an E2? -- 5.4 Functional Diversity of Ubiquitin-conjugating Enzymes -- 5.4.1 Functions Related to Proteasome Proteolysis -- 5.4.2 Endocytosis and Trafficking -- 5.4.3 Non-proteolytic Functions -- 5.4.4 E2s of Uncertain Function -- 5.4.5 E2 Enzymes and Disease -- 5.5 E2 Enzymes Dedicated to Ubiquitin-like Proteins (UbLs) -- 5.6 The Biochemistry of E2 Enzymes -- 5.6.1 E1 Interaction -- 5.6.2 Interactions with Thiol-linked Ubiquitin -- 5.6.3 E3 Interactions -- 5.6.3.1 RING E3/E2 Interactions -- 5.6.3.2 U-box E3/E2 Interactions -- 5.6.3.3 HECT E3/E2 Interactions -- 5.6.4 E2/Substrate Interactions -- 5.6.5 E2 Catalysis Mechanism -- 5.7 Functional Diversification of the E2 Fold -- 5.8 Concluding Remarks -- References -- 6 The SCF Ubiquitin E3 Ligase -- 6.1 Introduction -- 6.2 Discovery of the SCF Complex -- 6.3 The Components of the SCF Complex -- 6.3.1 Roc1/Rbx1/Hrt1 -- 6.3.2 Cullin-1 (Cul1) -- 6.3.3 Skp1 -- 6.3.4 F-box Proteins -- 6.4 E2-conjugating Enzymes for the SCF E3 Ligases -- 6.5 Substrates and Substrate Recognition -- 6.5.1 Skp2 and Its Substrates -- 6.5.2 β-Trcp and Its Substrates -- 6.5.3 Yeast Cdc4 and Its Substrates. , 6.6 Structure of the SCF E3 Ligase Complex -- 6.7 Regulation of SCF Activity -- 6.8 The SCF Complex and the Related Cullin-containing Ubiquitin E3 Ligase -- 6.9 Perspectives -- References -- 7 The Structural Biology of Ubiquitin-Protein Ligases -- 7.1 Introduction -- 7.2 The Two Major Classes of Ubiquitin-Protein Ligases -- 7.3 Mechanistic Questions About E3 Function -- 7.4 The E6AP HECT Domain in Complex With UbcH7 -- 7.5 The c-Cbl-UbcH7 Complex -- 7.6 The SCF E3 Superfamily -- 7.6.1 The VHL-ElonginC-ElonginB-Hif1 α Complex -- 7.6.2 Skp1-Skp2 Complex -- 7.6.3 SCF(Skp2) Structure -- 7.6.4 Skp1-βTrCP1-β-Catenin Peptide and Skp1-Cdc4-CyclinE Peptide Complexes -- 7.6.5 Model of the SCF in Complex With E2 and Substrates -- 7.6.6 Mechanism of RING E3-mediated Catalysis -- 7.7 The Mms2-Ubc13 Complex -- 7.8 The RanGAP1-Ubc9 Complex -- 7.9 Summary and Perspective -- Acknowledgments -- References -- 8 The Deubiquitinating Enzymes -- 8.1 Introduction -- 8.2 Structure and In Vitro Specificity of DUB Families -- 8.2.1 Ubiquitin C-terminal Hydrolases (UCH) -- 8.2.2 Ubiquitin-specific Processing Proteases (UBP/USP) -- 8.2.3 Ubiquitin-like Specific Proteases (ULP) -- 8.2.4 OTU DUBs -- 8.2.5 JAMM Isopeptidases -- 8.3 DUB Specificity -- 8.3.1 Recognition of the Ub-like Domain -- 8.3.2 Recognition of the Gly-Gly Linkage -- 8.3.3 Recognition of the Leaving Group -- 8.3.4 Substrate-induced Conformational Changes -- 8.4 Localization of DUBs -- 8.5 Probable Physiological Roles for DUBs -- 8.5.1 Proprotein Processing -- 8.5.2 Salvage Pathways: Recovering Mono-ubiquitin Adducts and Recycling Polyubiquitin -- 8.5.3 Regulation of Mono-ubiquitination -- 8.5.4 Processing of Proteasome-bound Polyubiquitin -- 8.6 Finding Substrates and Roles for DUBs -- 8.7 Roles of DUBs Revealed in Disease -- 8.7.1 NF-κB Pathway -- 8.7.2 Neural Function -- 8.8 New Tools for DUB Analysis. , 8.8.1 Active-site-directed Irreversible Inhibitors and Substrates -- 8.8.2 Non-hydrolyzable Polyubiquitin Analogs -- 8.9 Conclusion -- References -- 9 The 26S Proteasome -- Abstract -- 9.1 Introduction -- 9.2 The 20S Proteasome -- 9.2.1 Structure -- 9.2.2 Enzyme Mechanism and Proteasome Inhibitors -- 9.2.3 Immunoproteasomes -- 9.3 The 26S Proteasome -- 9.3.1 The Ubiquitin-Proteasome System -- 9.3.2 Ultrastructure of the 26S Proteasome and Regulatory Complex -- 9.3.3 The 19S Regulatory Complex -- 9.3.4 ATPases of the RC -- 9.3.5 The non-ATPase Subunits -- 9.3.6 Biochemical Properties of the Regulatory Complex -- 9.3.6.1 Nucleotide Hydrolysis -- 9.3.6.2 Chaperone-like Activity -- 9.3.6.3 Proteasome Activation -- 9.3.6.4 Ubiquitin Isopeptide Hydrolysis -- 9.3.6.5 Substrate Recognition -- 9.4 Substrate Recognition by Proteasomes -- 9.4.1 Degradation Signals (Degrons) -- 9.4.2 Ubiquitin-dependent Recognition of Substrates -- 9.4.3 Substrate Selection Independent of Ubiquitin -- 9.5 Proteolysis by the 26S Proteasome -- 9.5.1 Presumed Mechanism -- 9.5.2 Contribution of Chaperones to Proteasome-mediated Degradation -- 9.5.2.1 Substrate Binding to the 26S Proteasome -- 9.5.2.2 Translocation of the Polypeptide Substrate to the Central Proteolytic Chamber -- 9.5.3 Processing by the 26S Proteasome -- 9.6 Proteasome Biogenesis -- 9.6.1 Subunit Synthesis -- 9.6.2 Biogenesis of the 20S Proteasome -- 9.6.3 Biogenesis of the RC -- 9.6.4 Post-translational Modification of Proteasome Subunits -- 9.6.5 Assembly of the 26S Proteasome -- 9.7 Proteasome Activators -- 9.7.1 REGs or PA28s -- 9.7.1.1 REGs -- 9.7.1.2 PA200 -- 9.7.1.3 Hybrid Proteasomes -- 9.7.2 ECM29 -- 9.8 Protein Inhibitors of the Proteasome -- 9.9 Physiological Aspects -- 9.9.1 Tissue and Subcellular Distribution of Proteasomes -- 9.9.2 Physiological Importance -- Summary -- References. , 10 Molecular Machines for Protein Degradation -- 10.1 Introduction -- 10.2 The ATP-dependent Protease HslVU -- 10.2.1 HslVU Physiology and Biochemistry -- 10.2.2 HslV Peptidase -- 10.2.3 HslU ATPase -- 10.2.4 The HslVU-Protease Complex -- 10.2.4.1 Allosteric Activation -- 10.2.5 A Comparison of HslVU with ClpXP and ClpAP -- 10.2.6 HslVU Peptidase as a Model for the Eukaryotic 26S Proteasome? -- 10.3 The Yeast 20S Proteasome -- 10.3.1 The Proteasome, a Threonine Protease -- 10.3.2 Inhibiting the Proteasome -- 10.3.3 Access to the Proteolytic Chamber -- 10.4 The Tricorn Protease and its Structural and Functional Relationship with Dipeptidyl Peptidase IV -- 10.4.1 Architecture of the Tricorn Protease -- 10.4.2 Catalytic Residues and Mechanism -- 10.4.3 Substrate Access and Product Egress Through β-propellers -- 10.4.4 Structural and Functional Relationship of Tricorn and DPIV -- 10.5 The DegP Protease Chaperone: A Molecular Cage with Bouncers -- 10.5.1 The DegP Protomer, a PDZ Protease -- 10.5.2 The Two Forms of the DegP Hexamer -- 10.5.3 DegP, a Chaperone -- 10.5.4 The Protease Form -- 10.5.5 Working Model for an ATP-independent Heat-shock Protein -- Acknowledgment -- References -- 11 Proteasome Regulator, PA700 (19S Regulatory Particle) -- 11.1 Overview -- 11.2 Structure -- 11.2.1 Component Subunits of PA700/19S RP -- 11.2.2 Non-universal Subunits of PA700/19S RP -- 11.2.3 General Architecture of PA700/19S RP: The Base and the Lid -- 11.3 Post-translational Modifications of PA700 -- 11.3.1 Overview -- 11.3.2 Phosphorylation of PA700/19S RP -- 11.3.3 Glycosylation of PA700/19S RP -- 11.4 Function of PA700/19S RP -- 11.4.1 A Model for PA700 Regulation of Proteasome Function -- 11.4.2 Roles of ATPase Activity in PA700 Function -- 11.4.3 Proteasome Activation by PA700 -- 11.4.4 Polyubiquitin-chain Binding -- 11.4.5 Unfolding/Modification of Substrates. , 11.4.6 Translocation of Substrates from PA700/19S RP to the Proteasome.
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  • 5
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 75 (1971), S. 4056-4059 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1471-4159
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Abstract: We have shown by northern analyses that the expression of the mouse polyubiquitin C gene is increased several fold in the brains of mice infected with both the ME7 and 87V strains of scrape. Expression of the polyubiquitin gene does not change significantly, compared with controls, until the later stages of disease progression when there is a 2.5-fold increase in ME7-infected brains and a 1.8-fold increase in 87V-infected brains. The patterns of changes of expression of the polyubiquitin genes in brains infected with the two strains of scrapie resemble those of accumulation of ubiquitin-conjugate-positive structures in the brain that are detected immunohisto chemically. A similar increase in the expression of a heatshock protein 70 gene also occurs.
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  • 7
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 81 (1959), S. 5125-5128 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 76 (1954), S. 6330-6335 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of neurochemistry 19 (1972), S. 0 
    ISSN: 1471-4159
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: The activities of mitochondrial hexokinase and adenylate kinase have been measured in various osmotic conditions. Sucrose, potassium chloride and ammonium acetate were used as solutes. The total hexokinase activity of mitochondrial suspensions increased steadily with decreasing osmolarity of the sucrose or salt solutions. The hexokinase activity of mitochondrial suspensions in water was 93 per cent of that measured in the presence of Triton X-100.The increase in hexokinase activity was irreversible even after very short exposure (90 s) to hypo-osmotic conditions. Total adenylate kinase activity was not affected by osmotic conditions. Adenylate kinase activity increased hyperbolically in supernatants prepared from mitochondrial suspensions with decreasing osmolarity of the sucrose or salt solutions. Besides monitoring adenylate kinase leakage as a measure of outer mitochondrial membrane disruption, mitochondrial swelling was followed by measurement of the turbidity of mitochondrial suspensions at 520 nm. The data has been interpreted in terms of binding of some hexokinase to the inner mitochondrial membrane.
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  • 10
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 62 (1991), S. 360-363 
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: This study investigated the direct imaging of low intensity x-rays by a room-temperature charge coupled device (CCD). Commercial CCD evaluation kits read out the information and provided initial processing of the data. The extraction of the signal from noise was achieved using NIM modules rather than by storing and numerically analyzing the data. Due to the fast processing at standard TV rates, the storage of the data required conversion of the signal from a timing to a pulse height analysis (PHA) spectrum. The tested CCDs were found to have lower efficiency relative to the proportional counter for the range of photon energies (1.5–8.0 keV) studied but had higher spatial resolution than gas-filled position-sensitive detectors. Application of CCDs for x-ray energy dispersive detectors is described.
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