Rna Polymerases As Molecular Motors

Note: Supplemental materials are not guaranteed with Rental or Used book purchases.

ISBN: 9780854041343 | 0854041346
Cover: Hardcover
Copyright: 4/1/2009

Rent

(Recommended)

$131.73

Term

Due

Price

Semester

Dec 13

$146.36

Quarter

Aug 29

$139.05

Short Term

Jul 26

$131.73

*This item is part of an exclusive publisher rental program and requires an additional convenience fee. This fee will be reflected in the shopping cart.
Buy Used

Usually Ships in 2-4 Business Days

$149.21
Buy New

Usually Ships in 3-5 Business Days

$199.97
eBook

Available Instantly

Online: 1825 Days

Downloadable: Lifetime Access

$228.38

The cell can be viewed as a 'collection of protein machines' and understanding these molecular machines requires sophisticated cooperation between cell biologists, geneticists, enzymologists, crystallographers, chemists and physicists. To observe these machines in action, researchers have developed entirely new methodologies for the detection and the nanomanipulation of single molecules. This book, written by expert scientists in the field, analyses how these diverse fields of research interact on a specific example - RNA polymerases. RNA polymerases play a central role among all the other machines operating in the cell and are the target of a wide range of regulatory mechanisms and have also been the subject of spectacular advances in their structural understanding in recent years.

There and Back Again: A Structural Atlas of RNAP	p. 1
From Promoter Recognition to Promoter Escape
Where it all Begins: An Overview of Promoter Recognition and Open Complex Formation
Gene Expression as a Driver of Life	p. 13
Escherichia coli RNA Polymerase	p. 14
Promoters and Core Promoter Elements	p. 17
Biochemistry: It Works with RNA Polymerase!	p. 19
Biochemistry of Promoter Regulation	p. 22
A Word about the Intracellular Environment	p. 26
Coupling Transcription to Changes in a Complex Environment	p. 27
A Global View of the RNA Polymerase Economy	p. 30
The Real World, Emergency Procedures and RNA Polymerase	p. 32
This is just the Beginning!	p. 33
References	p. 34
Opening the DNA at the Promoter; The Energetic Challenge
Introduction	p. 38
Structural Characterization	p. 42
Crystal Structure of the Holoenzyme	p. 42
Crystal Structure of the Holoenzyme with Fork-junction DNA	p. 43
Structural Model of the Open Complex	p. 45
Physical Characterization and Structure of the Intermediates	p. 47
Finding the Promoter. Induced fit and Indirect Sequence Recognition	p. 48
Formation of the Closed Complex	p. 49
On a Unique Structure of the Closed Complex	p. 49
Role of Upstream Contacts for the Stability of the Closed Complex and in Leading the Complex Towards Subsequent Isomerization	p. 50
The First Isomerization Step. The role of Sigma, Formation of Specific Interactions	p. 51
Upstream Contacts	p. 51
Nucleation of the Single Stranded Region and its Propagation	p. 52
Phasing of -10 and -35 Regions, the Role of the Spacer	p. 54
Probing Possible Sequential Linear Pathways by the use of Temperature	p. 54
Specific Protein Domains Destabilize the Intermediates in the Pathway	p. 57
Overstabilization is sometimes used as a Regulatory Mechanism	p. 59
Formation of Transcriptionally Active Open Complex and the Rate-limiting Step: Protein Conformational Changes or DNA Melting?	p. 60
A Rugged Energy Landscape	p. 61
Summary and Conclusions	p. 62
Acknowledgements	p. 63
References	p. 63
Intrinsic In vivo Modulators: Negative Supercoiling and the Constituents of the Bacterial Nucleoid
Introduction	p. 69
DNA Superhelicity - Structures and Implications	p. 69
Structure of the Bacterial Nucleoid	p. 72
Supercoiling Utilization	p. 75
Promoter Structure and DNA Supercoiling	p. 78
Role of RNA Polymerase Composition	p. 80
Exchange of ¿ Factors	p. 81
Auxiliary Subunits	p. 82
Role of ppGpp	p. 82
Model and Implications	p. 82
Causality	p. 85
Cooperation with Nucleoid Associated Proteins	p. 86
Conversion of Supercoil Energy into Genomic Transcript Patterns	p. 87
Conclusions	p. 88
References	p. 88
Transcription by RNA Polymerases: From Initiation to Elongation, Translocation and Strand Separation
Introduction	p. 96
Transition from the Initiation to the Elongation Phase	p. 98
T7 RNA Polymerase	p. 98
Multi-subunit RNA Polymerases	p. 103
Translocation and Strand Separation	p. 103
T7 RNA Polymerase	p. 103
Multi-subunit Cellular RNAPs	p. 108
Additional Similarities between Single and Multi-subunit Polymerases	p. 112
Acknowledgements	p. 113
References	p. 113
Single-molecule FRET Analysis of the Path from Transcription Initiation to Elongation
Introduction	p. 115
Methodology: FRET and ALEX Spectroscopy	p. 117
Transcription Mechanisms Addressed using Single-molecule FRET and ALEX	p. 124
Fate of Initiation Factor ¿70 in Elongation	p. 126
Mechanism of Initial Transcription	p. 133
Kinetic Analysis of Initial Transcription and Promoter Escape	p. 141
Comparison of FRET Approaches with Magnetic-trap Approaches	p. 142
Future Prospects	p. 145
Summary	p. 147
Acknowledgements	p. 148
References	p. 148
Real-time Detection of DNA Unwinding by Escherichia coli RNAP: From Transcription Initiation to Termination
Introduction	p. 157
Twist Deformations at the Promoter	p. 158
Magnetic Trapping and Supercoiling of a Single DNA Molecule	p. 159
General Features of the Magnetic Trap	p. 159
Calibrating the DNA Sensor	p. 161
Characterization of RPo at two Canonical Promoters	p. 166
Structural Characterization of RPo	p. 167
Kinetic Analysis of RPo	p. 168
Effect of Environmental Variables on Kinetics of RPo	p. 171
Promoter Escape by DNA Scrunching	p. 172
Characterization of DNA Scrunching during Abortive Initiation	p. 173
Characterization of DNA Scrunching during Promoter Escape	p. 176
Future Directions	p. 182
References	p. 183
Transcription Elongation and Termination
Interlude The Engine and the Brake
Introduction	p. 191
The Engine	p. 193
Mechano-chemical Coupling at the Catalytic Site	p. 194
Coupling between Translocation and Topology	p. 200
The Brake	p. 201
Conclusions	p. 202
References	p. 204
Substrate Loading, Nucleotide Addition, and Translocation by RNA Polymerase
Basic Mechanisms of Transcript Elongation by RNA Polymerase	p. 206
Active-site Features of an Elongation Complex	p. 207
The Nucleotide Addition Cycle	p. 207
Pyrophosphorolysis and Transcript Cleavage	p. 208
Regulation of Transcript Elongation by Pauses	p. 211
Structural Basis of NTP Loading and Nucleotide Addition	p. 212
Bridge-helix-centric Models of Nucleotide Addition and Translocation	p. 213
Central Role of the Trigger Loop in Nucleotide Addition and Pausing	p. 216
A Trigger-loop Centric Mechanism for Substrate Loading and Catalysis	p. 217
Models of Translocation: Power-stroke versus Brownian Ratchet	p. 219
Key Distinctions between Power-stroke and Brownian Ratchet Models	p. 220
Power-stroke Models	p. 221
Brownian Ratchet Models	p. 221
Technical Outlook in Detecting the Precise Translocation Register	p. 222
Kinetic Models of Nucleotide Addition	p. 223
Allosteric NTP Binding Model	p. 223
NTP-driven Translocation Model	p. 226
Two-pawl Ratchet Model	p. 226
Biophysical Models for Transcript Elongation	p. 227
Technological Advances in Studies of Transcript Elongation	p. 228
Concluding Remarks	p. 228
References	p. 229
Regulation of RNA Polymerase through its Active Center
Introduction	p. 236
Regulatory Checkpoints of the RNAP Active Center	p. 237
Versatility of the Active Center. How many Metals are Enough?	p. 237
Delivery of NTPs to the Active Center. How many Channels are Enough?	p. 238
Nucleotide Selection. How many Steps are Enough?	p. 241
Regulators that Target the RNAP Active Center	p. 244
Small-molecule Effectors of RNAP	p. 244
Regulation of RNAP by Proteins that Bind in the Secondary Channel	p. 250
Transcript Proofreading	p. 254
Transcriptional Proofreading through Pyrophosphorolysis	p. 255
Proofreading by Transcript Cleavage Factors	p. 256
Transcript-assisted Proofreading. A New Class of Ribozymes?	p. 257
Conclusions	p. 258
Acknowledgements	p. 259
References	p. 259
Kinetic Modeling of Transcription Elongation
Introduction	p. 263
Background	p. 265
Mechano-chemical Coupling of Transcription	p. 266
NTP Incorporation Cycle	p. 266
NTP Incorporation Pathway in a Simple Brownian Ratchet Model	p. 266
NTP Incorporation Pathways in more Elaborate Brownian Ratchet Models	p. 267
NTP Incorporation Pathway in a Power-stroke Model	p. 269
Elongation Kinetics	p. 270
Force-dependent Elongation Kinetics	p. 271
Sequence-dependent RNAP Kinetics	p. 274
Thermodynamic Analysis of the TEC	p. 274
Sequence-dependent NTP Incorporation Kinetics in Brownian Ratchet Models	p. 275
Model Predictions of Pause Locations, Kinetics and Mechanisms	p. 277
Acknowledgements	p. 278
References	p. 278
Mechanics of Transcription Termination
Introduction	p. 281
Structure/Function Overview of the Elongation Complex (EC)	p. 282
Mechanism of Intrinsic Termination	p. 283
The Pausing Phase	p. 285
The Termination Phase	p. 287
Mechanism of Rho Termination	p. 294
Summary	p. 295
Concluding Remarks	p. 296
References	p. 296
Conclusion Past, Present, and Future of Single-molecule Studies of Transcription
Introduction	p. 302
RNA Polymerase as a Molecular Machine: Past and Present	p. 303
Technical Developments in Optical Tweezers	p. 307
A Look into the Future	p. 309
References	p. 312
Subject Index	p. 315
Table of Contents provided by Ingram. All Rights Reserved.

Please wait while the item is added to your bag...

FREE SHIPPING

Amazon no longer offers textbook rentals. We do!

Rna Polymerases As Molecular Motors

Summary

Table of Contents

Supplemental Materials