ArticleBiophysical journal2012
The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Driving forces of RNA condensation revealed through coarse-grained modeling with explicit MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Modeling riboswitches: The impact of concentration of MgBiophysical journal · 2025Article
- Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.The Journal of chemical physics · 2024Article
- Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations.Scientific reports · 2024Article
- Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.The journal of physical chemistry. B · 2023Article
- Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.Journal of chemical information and modeling · 2023Article
- Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation.Biophysical journal · 2021Article
- Similarities and Differences between NaJournal of chemical theory and computation · 2021Article
- Modeling Microtubule Counterion Distributions and Conductivity Using the Poisson-Boltzmann Equation.Frontiers in molecular biosciences · 2021Article
- Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting.Biophysical journal · 2019Article
- Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations.Biophysical journal · 2019Article
- Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.Journal of the American Chemical Society · 2018Article
- Competitive Binding of MgBiophysical journal · 2018Article
- Water Dynamics in the Hydration Shells of Biomolecules.Chemical reviews · 2017Review
- MCTBI: a web server for predicting metal ion effects in RNA structures.RNA (New York, N.Y.) · 2017Article
- Unraveling MgRNA (New York, N.Y.) · 2017Article
- Counting the ions surrounding nucleic acids.Nucleic acids research · 2017Article
- Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA.Physical review letters · 2016Article
- Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods.Nucleic acids research · 2016Article
- Understanding the kinetic mechanism of RNA single base pair formation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The distributions of different cations around A-RNA are computed by Poisson-Boltzmann (PB) equation and replica exchange molecular dynamics (MD). Both the nonlinear PB and size-modified PB theories are considered. The number of ions bound to A-RNA, which can be measured experimentally, is well reproduced in all methods. On the other hand, the radial ion distribution profiles show differences between MD and PB. We showed that PB results are sensitive to ion size and functional form of the solvent dielectric region but not the solvent dielectric boundary definition. Size-modified PB agrees with replica exchange molecular dynamics much better than nonlinear PB when the ion sizes are chosen from atomistic simulations. The distribution of ions 14 Å away from the RNA central axis are reasonably well reproduced by size-modified PB for all ion types with a uniform solvent dielectric model and a sharp dielectric boundary between solvent and RNA. However, this model does not agree with MD for shorter distances from the A-RNA. A distance-dependent solvent dielectric function proposed by another research group improves the agreement for sodium and strontium ions, even for shorter distances from the A-RNA. However, Mg(2+) distributions are still at significant variances for shorter distances.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.