Computational methods for understanding riboswitches:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2015
|
| Edition: | 1. ed. |
| Series: | Methods in enzymology
553 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVII, 403 S., [13] Bl. Ill., graph. Darst. |
| ISBN: | 9780128014295 |
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| 245 | 1 | 0 | |a Computational methods for understanding riboswitches |c ed. by Shi-Jie Chen ... |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2015 | |
| 300 | |a XVII, 403 S., [13] Bl. |b Ill., graph. Darst. | ||
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Record in the Search Index
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| adam_text |
CONTENTS
Contributors
xi
Preface
xv
Section I
RNA
Structure Prediction
1.
Automated
3D
RNA
Structure Prediction Using the
RNAComposer Method for Riboswitches
3
KJ. Purzycka, M. Popenda, M. Szachniuk, M. Antczak, P. Lukasiak,
J. Blazewicz, and R.W. Adamiak
1.
Introduction
4
2.
RNA FRABASE—
Opening the Route to RNAComposer
7
3.
RNAComposer—From the
RNA
Secondary Structure to
RNA
3D
Structure
8
4.
Predicting the Tertiary Structure of Riboswitches with RNAComposer
16
5.
Conclusions and Perspectives
28
Acknowledgments
31
References
31
2.
Modeling Complex
RNA
Tertiary Folds with
Rosetta
35
Clarence Yu Cheng,
Fang-Chieh Chou,
and Rhiju Das
1.
Introduction
36
2.
Setting the Stage for
3D
Modeling Using
Experimentai
Data
37
3.
Making Models of
RNA
Tertiary Folds
41
4.
Evaluation
51
5.
Conclusion
52
Acknowledgments
53
Appendix. Example Command Lines and Files for
RNA
Modeling in
Rosetta
53
References
62
3.
Computational Methods Toward Accurate
RNA
Structure
Prediction Using Coarse-Grained and All-Atom Models
65
Andrey Krokhotin
and Nikolay V. Dokholyan
1.
Introduction
66
2.
Discrete Molecular Dynamics
68
3.
Three-Bead Model
69
vi
Contents
4.
Use
of Hydroxyl-Radical Probing to Refine
RNA
Three-Dimensional Structure
75
5.
All-Atom Structure Reconstruction
85
6.
¡FoldRNA
86
7.
Conclusions
87
References
87
4.
Improving
RNA
Secondary Structure Prediction with
Structure Mapping Data
91
Michael F.
Sloma
and David H. Mathews
1.
Introduction
92
2.
Overview of Probing methods
94
3.
Improving the Accuracy of Secondary Structure Prediction Using
Probing Data
98
4.
Using SHAPE Data on a Single Sequence to Improve Secondary
Structure Prediction Accuracy
100
5.
Open Questions
105
6.
Conclusions
108
References
109
5.
Computational Prediction of Riboswitch Tertiary Structures
Including Pseudoknots by RAGTOP: A Hierarchical Graph
Sampling Approach
115
Namhee Kim, Mai
Zahraň,
and
Tamar
Schlick
1.
Introduction
116
2.
Hierarchical Graph Folding Approach
122
3.
Application to Riboswitch Structure Prediction
124
4.
Future Challenges and Perspectives
130
Acknowledgments
132
References
132
Section II
RNA
Dynamics and Thermodynamics
6.
Using Reweighted Pulling Simulations to Characterize
Conformational Changes in Riboswitches
139
Francesco Di Palma,
Francesco Colizzi, and Giovanni
Bussi
1.
Introduction
2.
Methods and Theory
142
Contents_
vii
3.
Results and Discussion
150
4.
Conclusions
159
Acknowledgments
159
References
159
7.
Force Field Dependence of Riboswitch Dynamics
163
Christian
A. Hanke
and
Holger Gohlke
1.
Introduction
164
2.
Methods
167
3.
Results and Discussion
172
Acknowledgments
188
References
188
8.
Thermodynamic and Kinetic Folding of Riboswitches
193
Stefan Badelt, Stefan Hammer,
Christoph Flamm,
and
Ivo L
Hofacker
1.
Introduction
194
2.
Characterization and Prediction of
Riboswitches 195
3.
Thermodynamic
RNA
folding
196
4.
RNA
Folding Kinetics on Static Landscapes
205
5.
RNA
Folding Kinetics on Dynamic Landscapes
208
6.
Conclusion
210
Acknowledgments
211
References
211
9.
Integrating Molecular Dynamics Simulations with Chemical
Probing Experiments Using SHAPE-FIT
215
Serdal Kirmizialtin, Scott P. Hennelly, Alexander Schug, Jose
N.
Onuchic,
and Karissa Y. Sanbonmatsu
1.
Introduction
216
2.
Materials and Methods
219
3.
Results
224
4.
Discussions
229
Acknowledgments
231
References
231
viii
_Contents
10.
Using Simulations and Kinetic Network Models to Reveal
the Dynamics and Functions of
Ribos
witches
235
Jong-Chin Lin, Jeseong Yoon, Changbong Hyeon, and D. Thirumalai
1.
Introduction and Scope of the Review
236
2. Hydration
Dynamics Around the Folded State: All Atom Simulations
238
3.
Stability of Isolated Helices Control the Folding Landscapes of
Purine
Riboswitches
242
4.
Folding Landscapes of SAM Riboswitch
247
5.
Is SAM Riboswitch Under Thermodynamic Control?
249
6.
Kinetic Network Model of Gene Regulation and the Role of Negative
Feedback in Control of Transcription
251
7.
Concluding Remarks
255
Acknowledgments
256
References
256
Section III
Ions, Ligands, and
RNA
Interactions
11.
Computational Methods for Prediction of
RNA
Interactions
with Metal Ions and Small Organic Ligands
261
Anna Philips,
Grzegorz Łach,
and
Janusz
M.
Bujnicki
1.
Introduction
262
2.
Computational Modeling of RNA-Ligand Complex Structures
263
3.
MetalionRNA and LigandRNA
269
Acknowledgments
282
References
283
12.
Computational Prediction of Riboswitches
287
P. Clote
1.
Introduction
287
2.
Riboswitches
289
3.
Riboswitch gene finders
293
4.
Conformational switches
299
5.
Conclusion
307
Acknowledgments
307
References
307
Contents_ix
13.
Computational and Experimental Studies of Reassociating
RNA/DNA Hybrids Containing Split Functionalities
313
KiriH A. Afonin,
Eckart Bindewald,
Maria Kireeva, and Bruce A. Shapiro
1.
Introduction
314
2.
Thermodynamic Prediction of Different Compositions of
RNA
and
DNA
Strand Associations
317
3.
Sequence Design of RNA/DNA Hybrids
323
4.
Enzyme-Assisted In Vitro Production of RNA/DNA Hybrids
325
5.
Experimental Testing of RNA/DNA Hybrids
329
6.
Concluding Remarks
330
Acknowledgments
330
References
330
14.
Multiscale Methods for Computational
RNA Enzymology
335
Maria
T. Panteva,
Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak,
Erich R. Kuechler, George M.
Giambaşu, Tai-Sung
Lee, and
Darrin M.
York
1.
Introduction
336
2.
The "Problem Space" of Computational
RNA
Enzymology
338
3.
Multiscale Modeling Strategy
340
4.
Catalytic Strategies for Cleavage of the
RNA
Backbone
340
5.
Modeling Ion and Nucleic Acid Interactions
341
6.
Modeling
pH-Rate
Profiles for Enzymes
346
7.
Modeling Conformational States
351
8.
Modeling the Chemical Steps of Catalysis
356
9.
Computing KlEs to Verify Transition State Structure
361
10.
Conclusions
363
Acknowledgments
364
References
364
Author Index
375
Subject Index
395 |
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| discipline | Chemie / Pharmazie Biologie |
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| series2 | Methods in enzymology |
| spelling | Computational methods for understanding riboswitches ed. by Shi-Jie Chen ... 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2015 XVII, 403 S., [13] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 553 Computerunterstütztes Verfahren (DE-588)4139030-1 gnd rswk-swf Riboswitch (DE-588)7721130-3 gnd rswk-swf 1\p (DE-588)4143413-4 Aufsatzsammlung gnd-content Riboswitch (DE-588)7721130-3 s Computerunterstütztes Verfahren (DE-588)4139030-1 s b DE-604 Chen, Shi-Jie Sonstige oth Methods in enzymology 553 (DE-604)BV000000938 553 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027912577&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Computational methods for understanding riboswitches Methods in enzymology Computerunterstütztes Verfahren (DE-588)4139030-1 gnd Riboswitch (DE-588)7721130-3 gnd |
| subject_GND | (DE-588)4139030-1 (DE-588)7721130-3 (DE-588)4143413-4 |
| title | Computational methods for understanding riboswitches |
| title_auth | Computational methods for understanding riboswitches |
| title_exact_search | Computational methods for understanding riboswitches |
| title_full | Computational methods for understanding riboswitches ed. by Shi-Jie Chen ... |
| title_fullStr | Computational methods for understanding riboswitches ed. by Shi-Jie Chen ... |
| title_full_unstemmed | Computational methods for understanding riboswitches ed. by Shi-Jie Chen ... |
| title_short | Computational methods for understanding riboswitches |
| title_sort | computational methods for understanding riboswitches |
| topic | Computerunterstütztes Verfahren (DE-588)4139030-1 gnd Riboswitch (DE-588)7721130-3 gnd |
| topic_facet | Computerunterstütztes Verfahren Riboswitch Aufsatzsammlung |
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