RNA helicases:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2012
|
| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in enzymology
511 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | LI, 525 S., [5] Bl. Ill., graph. Darst. |
| ISBN: | 9780123965462 |
Internformat
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| 245 | 1 | 0 | |a RNA helicases |c ed. by Eckhard Jankowsky |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2012 | |
| 300 | |a LI, 525 S., [5] Bl. |b Ill., graph. Darst. | ||
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Datensatz im Suchindex
| _version_ | 1804149414521995264 |
|---|---|
| adam_text | Titel: RNA helicases
Autor: Jankowsky, Eckhard
Jahr: 2012
Contents
Contributors xiii
Preface xix
Volumes in Series xxi
1. Analysis of Duplex Unwinding by RNA Helicases Using
Stopped-Flow Fluorescence Spectroscopy
Andrea Putnam and Eckhard Jankowsky
1. Introduction 2
2. Experimental Considerations for Stopped-Flow Fluorescence
Experiments 3
3. Substrate Design and Preparation 7
4. Designing and Performing Stopped-Flow Fluorescence
Unwinding Experiments 13
5. Data Fitting and Analysis 20
Acknowledgments 24
References 24
2. Analyzing ATP Utilization by DEAD-Box RNA Helicases
Using Kinetic and Equilibrium Methods 29
Michael J. Bradley and Enrique M. De La Cruz
1. Introduction 30
2. Reagents and Equipment 31
3. Important Considerations for Initial DBP Characterization 34
4. Steady-State ATPase Measurements 39
5. Transient Kinetic Analysis of the DBP ATPase Cycle 46
6. ATP Hydrolysis Reversibility Measured by Isotope Exchange 54
7. RNA Unwinding Assays and ATPase Coupling 55
8. Kinetic Simulations 56
9. Putting It All Together: Quantitative Analysis of the DBP
ATPase Cycle 56
Acknowledgments 58
References 58
VI
Contents
3. Oxygen Isotopic Exchange Probes of ATP Hydrolysis by RNA
Helicases
David D. Hackney
1. Introduction
2. Determination of the k_2l^3 Ratio by Intermediate Exchange
During Net ATP Hydrolysis with Pyruvate Kinase and PEP
to Regenerate ATP
3. Derivatization of the Pi to Volatile Triethyl Phosphate
4. Isotopic Analysis by GC-MS
5. Fitting Intermediate Exchange Data to Obtain R=k_2/k3
6. Medium Pi = HOH Medium Exchange
7. Complication of Concurrent Medium Pi = HOH Exchange During
Net Hydrolysis
Acknowledgment
References
65
66
67
68
70
70
72
72
73
73
4. Conformational Changes of DEAD-Box Helicases Monitored
by Single Molecule Fluorescence Resonance Energy Transfer
Alexandra Z. Andreou and Dagmar Klostermeier
1. Introduction
2. Theoretical Background of smFRET
3. Preparing DEAD-box Proteins for smFRET Studies
4. smFRET Experiments and the Calculation of Corrected
smFRET Histograms
5. Extracting Distance Information from smFRET Measurements:
Distance Histograms
6. The Conformational Cycle of DEAD-Box Proteins
7. Perspective
Acknowledgments
References
75
76
80
83
87
91
94
103
104
104
5. RNA Catalysis as a Probe for Chaperone Activity of
DEAD-Box Helicases
Jeffrey P. Potratz and Rick Russell
1. Introduction
2. Catalytic Activity as a Probe of RNA Folding
3. Self-splicing as a Readout for Native State Formation
4. Substrate Cleavage as a Readout for Native State Formation
5. Other Applications of the Discontinuous Assay
Acknowledgments
References
111
112
113
115
118
124
126
127
Contents vii
6. Molecular Mechanics of RNA Translocases 131
Steve C. Ding and Anna Marie Pyle
1. Introduction 132
2. Major Examples of Monomeric RNA Translocases 134
3. Concluding Remarks 144
Acknowledgments 145
References 145
7. Analysis of Helicase-RNA Interactions Using Nucleotide Analog
Interference Mapping 149
Annie Schwartz, Makhlouf Rabhi, Emmanuel Margeat, and
Marc Boudvillain
1. Introduction 150
2. Materials and Reagents 152
3. Methods 154
4. Conclusions 166
Acknowledgments 167
References 167
8. Crystallization and X-ray Structure Determination of an
RNA-Dependent Hexameric Helicase 171
Nathan D. Thomsen and James M. Berger
1. Introduction 172
2. Biochemical Foundation 173
3. Protein Expression, Purification, and Storage 175
4. Ligand Preparation and Storage 176
5. Trapping Rho-RNA-Nucleotide Complexes 177
6. Design of a Substrate-Centric Crystal-Screening Strategy 177
7. Crystallization of Rho Bound to RNA and Adenosine Nucleotides 178
8. Conclusion 185
9. Additional Methods 186
Acknowledgment 187
References 187
9. Structural Analysis of RNA Helicases with Small-Angle
X-ray Scattering 191
Manja A. Behrens, Yangzi He, Cristiano L. P. Oliveira,
Gregers R. Andersen, Jan Skov Pedersen, and Klaus H. Nielsen
1. Introduction 192
2. Basic Principles of Solution Scattering and Initial Data Treatment 193
3. Model-Independent Analysis 194
viii Contents
4. Shape Determination Without Use of A Priori Information 198
5. Atomic Resolution Models and Solution Scattering 201
6. Using Atomic Resolution Models to Investigate
Solution Structures 203
7. Analysis of Protein Complexes 206
8. Concluding Remarks 210
Acknowledgments 210
References 210
10. Analysis of Cofactor Effects on RNA Helicases 213
Crystal Young and Katrin Karbstein
1. Introduction 214
2. How to Study Cofactors 219
3. Reagents 221
4. Protocols 224
Acknowledgments 233
References 233
11. Analysis of DEAD-Box Proteins in mRNA Export 239
Ben Montpetit, Markus A. Seeliger, and Karsten Weis
1. Introduction 240
2. Purification of Dbp5, Glel, and Nupl59 242
3. Steady-State ATPase Assay 244
4. Use of Fluorescence Polarization to Monitor RNA or
Nucleotide Binding and Release 246
5. Concluding Remarks 252
Acknowledgments 252
References 252
12. Biochemical Characterization of the RNA Helicase UPF1
Involved in Nonsense-Mediated mRNA Decay 255
Francesca Fiorini, Fabien Bonneau, and Hervé Le Hir
1. Introduction 256
2. Preparation of Active UPF1 and UPF1-UPF2 Complex 257
3. Complex Assembly 259
4. RNAse Protection Assay 264
5. ATPase Assay 266
6. Unwinding Assay 268
7. Conclusions 272
Acknowledgments 273
References 273
Contents ix
13. Identification of RNA Helicase Target Sites by UV
Cross-Linking and Analysis of cDNA 275
Markus T. Bohnsack, David Tollervey, and Sander Granneman
1. Introduction 276
2. Material 277
3. Methods 279
4. Protocol Adaptation and Trouble-Shooting 286
Acknowledgments 287
References 287
14. In Vivo Approaches to Dissecting the Function of RNA
Helicases in Eukaryotic Ribosome Assembly 289
David C. Rawling and Susan J. Baserga
1. Introduction 290
2. Experimental Strategies Used to Evaluate RB Helicases 291
3. Determining Where an RNA Helicase Acts in the RB Pathway 296
4. Elucidating the Supermolecular Context of an RB Helicase:
Protein-Protein Interaction Studies 308
References 316
15. Analysis of RNA Helicases in P-Bodies and Stress Granules 323
Angela Hilliker
1. Introduction 324
2. RNA Helicases in Cytoplasmic mRNP Granules 325
3. RNA Helicases That Affect P-Bodies or SGs 329
4. Determining Whether an RNA Helicase Can Localize to
Cytoplasmic mRNP Granules 331
5. Determining Whether an RNA Helicase Affects Cytoplasmic
mRNP Granules 337
6. Discussion and Perspective 340
Acknowledgment 341
References 341
16. DEAD-Box RNA Helicases as Transcription Cofactors 347
Frances V. Fuller-Pace and Samantha M. Nicol
1. Introduction 348
2. Analysis of Interactions Between RNA Helicases and
Transcription Factors In Vitro and in Cell Lines 349
3. Analysis of p68/p72 Sumoylation in Cell Lines 358
4. Analysis of Transcriptional Coactivator/Corepressor Activity
of p68 and p72 361
x Contents
5. Summary 363
Acknowledgments 365
References 365
17. DEAD-Box RNA Helicases in Gram-Positive RNA Decay 369
Peter Redder and Patrick Linder
1. Introduction 369
2. Measuring mRNA Decay 371
3. Phenotypic Readouts 377
4. Concluding Remarks 381
Acknowledgments 381
References 381
18. RNA Helicases in Cyanobacteria: Biochemical and
Molecular Approaches 385
George W. Owttrim
1. Introduction 386
2. Preparation of Cyanobacterial Extracts 387
3. Alteration of RNA Helicase Expression in Cyanobacteria 390
4. Northern Analysis of Transcript Levels 394
5. Western Analysis of Protein Levels 396
6. Cellular Ultrastructure and In Situ RNA Helicase Localization 397
Acknowledgments 400
References 400
19. Determination of Host RNA Helicases Activity
in Viral Replication 405
Amit Sharma and Kathleen Boris-Lawrie
1. Introduction 406
2. Methods Used To Study Cell-Associated RNA Helicase
in Cultured Mammalian Cells 409
3. Biochemical and Biophysical Methods to Study RNA Helicase 417
4. Methods Used to Study Virion-Associated RNA Helicase
in Cultured Mammalian Cells 423
5. Concluding Remarks 430
Acknowledgments 431
References 431
Contents xi
20. Inhibitors of Translation Targeting Eukaryotic Translation
Initiation Factor 4A 437
Regina Cencic, Gabriela Galicia-Vâzquez, and Jerry Pelletier
1. Introduction 438
2. Small Molecule Inhibitors of RNA Helicases 441
3. Small Molecule Inhibitors of elF4A ATPase Activity 444
4. Conclusions 455
Acknowledgments 456
References 456
21. Identification and Analysis of Inhibitors Targeting the
Hepatitis C Virus NS3 Helicase 463
Alicia M. Hanson, John J. Hernandez, William R. Shadrick, and
David N. Frick
1. Introduction 464
2. The Need for Additional HCV Drug Targets 465
3. Targeting the NS3 Helicase 466
4. HTS for HCV Helicase Inhibitors 467
5. Expression and Purification of NS3h 469
6. The Molecular Beacon-Based Helicase Assay (MBHA) 470
7. An RNA-Based Split Beacon Helicase Assay (SBHA) 477
8. Discussion 479
Acknowledgments 480
References 480
Author Index 485
Subject Index 513
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| indexdate | 2024-07-10T00:22:39Z |
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| isbn | 9780123965462 |
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| spelling | RNA helicases ed. by Eckhard Jankowsky 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2012 LI, 525 S., [5] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 511 Helicasen (DE-588)4159496-4 gnd rswk-swf RNS (DE-588)4076759-0 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content RNS (DE-588)4076759-0 s Helicasen (DE-588)4159496-4 s Methode (DE-588)4038971-6 s b DE-604 Jankowsky, Eckhard Sonstige oth Methods in enzymology 511 (DE-604)BV000000938 511 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025222351&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | RNA helicases Methods in enzymology Helicasen (DE-588)4159496-4 gnd RNS (DE-588)4076759-0 gnd Methode (DE-588)4038971-6 gnd |
| subject_GND | (DE-588)4159496-4 (DE-588)4076759-0 (DE-588)4038971-6 (DE-588)4143413-4 |
| title | RNA helicases |
| title_auth | RNA helicases |
| title_exact_search | RNA helicases |
| title_full | RNA helicases ed. by Eckhard Jankowsky |
| title_fullStr | RNA helicases ed. by Eckhard Jankowsky |
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| title_short | RNA helicases |
| title_sort | rna helicases |
| topic | Helicasen (DE-588)4159496-4 gnd RNS (DE-588)4076759-0 gnd Methode (DE-588)4038971-6 gnd |
| topic_facet | Helicasen RNS Methode Aufsatzsammlung |
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