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Computational Methods for Understanding Riboswitches
1st Edition, Volume 553 - February 19, 2015
Editors: Shi-Jie Chen, Donald H. Burke-Aguero
Language: English
Hardback ISBN:9780128014295
9 7 8 - 0 - 1 2 - 8 0 1 4 2 9 - 5
eBook ISBN:9780128016183
9 7 8 - 0 - 1 2 - 8 0 1 6 1 8 - 3
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers computational predic…Read more
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This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers computational prediction RNA structure and dynamics, including such topics as computational modeling of RNA secondary and tertiary structures, riboswitch dynamics, and ion-RNA, ligand-RNA and DNA-RNA interactions.
Continues the legacy of this premier serial with quality chapters authored by leaders in the field
Covers computational methods and applications in RNA structure and dynamics
Contains chapters with emerging topics such as RNA structure prediction, riboswitch dynamics and thermodynamics, and effects of ions and ligands.
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists.
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Preface
Section I: RNA Structure Prediction
Chapter One. Automated 3D RNA Structure Prediction Using the RNAComposer Method for Riboswitches
Abstract
1 Introduction
2 RNA FRABASE—Opening the Route to RNAComposer
3 RNAComposer—From the RNA Secondary Structure to RNA 3D Structure
4 Predicting the Tertiary Structure of Riboswitches with RNAComposer
5 Conclusions and Perspectives
Acknowledgments
References
Chapter Two. Modeling Complex RNA Tertiary Folds with Rosetta
Abstract
1 Introduction
2 Setting the Stage for 3D Modeling Using Experimental Data
3 Making Models of RNA Tertiary Folds
4 Evaluation
5 Conclusion
Acknowledgments
References
Chapter Three. Computational Methods Toward Accurate RNA Structure Prediction Using Coarse-Grained and All-Atom Models
Abstract
1 Introduction
2 Discrete Molecular Dynamics
3 Three-Bead Model
4 Use of Hydroxyl-Radical Probing to Refine RNA Three-Dimensional Structure
5 All-Atom Structure Reconstruction
6 iFoldRNA
7 Conclusions
References
Chapter Four. Improving RNA Secondary Structure Prediction with Structure Mapping Data
Abstract
1 Introduction
2 Overview of Probing Methods
3 Improving the Accuracy of Secondary Structure Prediction Using Probing Data
4 Using SHAPE Data on a Single Sequence to Improve Secondary Structure Prediction Accuracy
5 Open Questions
6 Conclusions
References
Chapter Five. Computational Prediction of Riboswitch Tertiary Structures Including Pseudoknots by RAGTOP: A Hierarchical Graph Sampling Approach
Abstract
1 Introduction
2 Hierarchical Graph Folding Approach
3 Application to Riboswitch Structure Prediction
4 Future Challenges and Perspectives
Acknowledgments
References
Section II: RNA Dynamics and Thermodynamics
Chapter Six. Using Reweighted Pulling Simulations to Characterize Conformational Changes in Riboswitches
Abstract
1 Introduction
2 Methods and Theory
3 Results and Discussion
4 Conclusions
Acknowledgments
References
Chapter Seven. Force Field Dependence of Riboswitch Dynamics
Abstract
1 Introduction
2 Methods
3 Results and Discussion
Acknowledgments
References
Chapter Eight. Thermodynamic and Kinetic Folding of Riboswitches
Abstract
1 Introduction
2 Characterization and Prediction of Riboswitches
3 Thermodynamic RNA folding
4 RNA Folding Kinetics on Static Landscapes
5 RNA Folding Kinetics on Dynamic Landscapes
6 Conclusion
Acknowledgments
References
Chapter Nine. Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT
Abstract
1 Introduction
2 Materials and Methods
3 Results
4 Discussions
Acknowledgments
References
Chapter Ten. Using Simulations and Kinetic Network Models to Reveal the Dynamics and Functions of Riboswitches
Abstract
1 Introduction and Scope of the Review
2 Hydration Dynamics Around the Folded State: All Atom Simulations
3 Stability of Isolated Helices Control the Folding Landscapes of Purine Riboswitches
4 Folding Landscapes of SAM Riboswitch
5 Is SAM Riboswitch Under Thermodynamic Control?
6 Kinetic Network Model of Gene Regulation and the Role of Negative Feedback in Control of Transcription
7 Concluding Remarks
Acknowledgments
References
Section III: Ions, Ligands, and RNA Interactions
Chapter Eleven. Computational Methods for Prediction of RNA Interactions with Metal Ions and Small Organic Ligands
Abstract
1 Introduction
2 Computational Modeling of RNA–Ligand Complex Structures
3 MetalionRNA and LigandRNA
Acknowledgments
References
Chapter Twelve. Computational Prediction of Riboswitches
Abstract
1 Introduction
2 Riboswitches
3 Riboswitch gene finders
4 Conformational switches
5 Conclusion
6 Acknowledgments
References
Chapter Thirteen. Computational and Experimental Studies of Reassociating RNA/DNA Hybrids Containing Split Functionalities
Abstract
1 Introduction
2 Thermodynamic Prediction of Different Compositions of RNA and DNA Strand Associations
3 Sequence Design of RNA/DNA Hybrids
4 Enzyme-Assisted In Vitro Production of RNA/DNA Hybrids
5 Experimental Testing of RNA/DNA Hybrids
6 Concluding Remarks
Acknowledgments
References
Chapter Fourteen. Multiscale Methods for Computational RNA Enzymology
Abstract
1 Introduction
2 The “Problem Space” of Computational RNA Enzymology
3 Multiscale Modeling Strategy
4 Catalytic Strategies for Cleavage of the RNA Backbone
5 Modeling Ion and Nucleic Acid Interactions
6 Modeling pH-Rate Profiles for Enzymes
7 Modeling Conformational States
8 Modeling the Chemical Steps of Catalysis
9 Computing KIEs to Verify Transition State Structure
10 Conclusions
Acknowledgments
References
Author Index
Subject Index
Color Plate
No. of pages: 422
Language: English
Edition: 1
Volume: 553
Published: February 19, 2015
Imprint: Academic Press
Hardback ISBN: 9780128014295
eBook ISBN: 9780128016183
SC
Shi-Jie Chen
Shi-Jie Chen is Professor of the Department of Physics Astronomy and Department of Biochemistry and is core faculty member in the Informatics Institute at the University of Missouri-Columbia. Dr. Chen received his Ph.D. in Physics from the University of California, San Diego in 1994. He was a postdoctoral researcher at the University of California, San Francisco in 1994-9 and began his faculty appointment at the University of Missouri-Columbia in 1999. Chen has served the scientific community by his participation on multiple NIH review panels and site visit reviewer teams. He served as Associate Editor of the PLoS Computational Biology. His laboratory developed Vfold and TBI, open source and freely available web servers and software for the computational predictions of RNA structure, folding thermodynamics, and ion effects. Dr. Chen was elected to the fellow of American Physical Society in 2012.
Affiliations and expertise
Biophysics, Biochemistry and Informatics, University of Missouri-Columbia, USA
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Donald H. Burke-Aguero
Affiliations and expertise
Department of Molecular Microbiology & Immunology and Department of Biochemistry, University of Missouri, USA
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