ArticleProceedings of the National Academy of Sciences of the United States of America2007
Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties.Journal of chemical theory and computation · 2021Article
- Genetic Variation in the Domain II, 3' Untranslated Region of Human and Mosquito Derived Dengue Virus Strains in Sri Lanka.Viruses · 2021Article
- Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.The journal of physical chemistry letters · 2018Article
- Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.Nature communications · 2016Article
- Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids.The journal of physical chemistry. B · 2015Article
- RNA folding: A clear path to RNA catalysis.Nature chemical biology · 2015Article
- Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.RNA (New York, N.Y.) · 2015Article
- Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.Journal of computational chemistry · 2015Article
- GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.PloS one · 2015Article
- Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme.Nucleic acids research · 2015Article
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- Insights into RNA structure and function from genome-wide studies.Nature reviews. Genetics · 2014Review
- Exploring the electrostatic energy landscape for tetraloop-receptor docking.Physical chemistry chemical physics : PCCP · 2014Article
- Article
- The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations.Journal of molecular biology · 2013Article
- Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns.Biophysical journal · 2013Article
- Evolutionary evidence for alternative structure in RNA sequence co-variation.PLoS computational biology · 2013Article
- DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes.Communications in computational physics · 2013Article
- Toward a molecular understanding of RNA remodeling by DEAD-box proteins.RNA biology · 2013Review
- Evaluating our ability to predict the structural disruption of RNA by SNPs.BMC genomics · 2012Article
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5 authors.
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Abstract
We distinguish the contribution of the electrostatic environment, initial conformational ensemble, and macromolecular stability on the folding mechanism of a large RNA using a combination of time-resolved "Fast Fenton" hydroxyl radical footprinting and exhaustive kinetic modeling. This integrated approach allows us to define the folding landscape of the L-21 Tetrahymena thermophila group I intron structurally and kinetically from its earliest steps with unprecedented accuracy. Distinct parallel pathways leading the RNA to its native form upon its Mg(2+)-induced folding are observed. The structures of the intermediates populating the pathways are not affected by variation of the concentration and type of background monovalent ions (electrostatic environment) but are altered by a mutation that destabilizes one domain of the ribozyme. Experiments starting from different conformational ensembles but folding under identical conditions show that whereas the electrostatic environment modulates molecular flux through different pathways, the initial conformational ensemble determines the partitioning of the flux. This study showcases a robust approach for the development of kinetic models from collections of local structural probes.
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