ArticleNucleic acids research2014
Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.The journal of physical chemistry. B · 2023Article
- Pressure pushes tRNAProceedings of the National Academy of Sciences of the United States of America · 2023Article
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
- RNA Structural Differentiation: Opportunities with Pattern Recognition.Biochemistry · 2019Review
- High-Throughput Explorations of RNA Structural Modularity.Biochemistry · 2018Article
- Article
- Tuning RNA folding and function through rational design of junction topology.Nucleic acids research · 2017Article
- Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.Scientific reports · 2017Article
- Small Molecule-Based Pattern Recognition To Classify RNA Structure.Journal of the American Chemical Society · 2017Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin.Biochemistry · 2016Review
- Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.Journal of molecular biology · 2016Article
- Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.Nucleic acids research · 2016Article
- Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.Cell reports · 2015Article
- Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.Journal of the American Chemical Society · 2015Article
- MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery.International journal of molecular sciences · 2015Review
- Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.Journal of the American Chemical Society · 2015Article
- Hierarchy of RNA functional dynamics.Annual review of biochemistry · 2014Review
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3 authors.
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Abstract
Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding.
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