ArticleJournal of the American Chemical Society2019
Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory.
Article in Journal of the American Chemical Society, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking.Journal of chemical information and modeling · 2026Article
- Ion NMR for Biomolecular Systems.Journal of molecular biology · 2025Review
- 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
- Exploring the potential of structure-based deep learning approaches for T cell receptor design.PLoS computational biology · 2024Article
- Structure and dimerization properties of the plant-specific copper chaperone CCH.Scientific reports · 2024Article
- Exploring the Potential of Structure-Based Deep Learning Approaches for T cell Receptor Design.bioRxiv : the preprint server for biology · 2024Article
- On Water Arrangements in Right- and Left-Handed DNA Structures.Molecules (Basel, Switzerland) · 2024Review
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- Influence of MgACS omega · 2023Article
- How a highly acidic SH3 domain folds in the absence of its charged peptide target.Protein science : a publication of the Protein Society · 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
- Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations.NAR genomics and bioinformatics · 2022Article
- Computational Study of the pH-Dependent Ionic Environment around β-Lactoglobulin.The journal of physical chemistry. B · 2022Article
- Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations.Biophysical journal · 2022Article
- RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.The journal of physical chemistry. B · 2022Article
- Dynamics of Cations around DNA and Protein as Revealed byAnalytical chemistry · 2022Article
- Integral equation models for solvent in macromolecular crystals.The Journal of chemical physics · 2022Article
- Insights into the binding mode of AS1411 aptamer to nucleolin.Frontiers in molecular biosciences · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Site binding of ions and water shapes nucleic acids folding, dynamics, and biological function, complementing the more diffuse, nonspecific "territorial" ion binding. Unlike territorial binding, prediction of site-specific binding to nucleic acids remains an unsolved challenge in computational biophysics. This work presents a new toolset based on the 3D-RISM molecular solvation theory and topological analysis that predicts cation and water site binding to nucleic acids. 3D-RISM is shown to accurately capture alkali cations and water binding to the central channel, transversal loops, and grooves of the Oxytricha nova's telomeres' G-quadruplex ( Oxy-GQ), in agreement with high-resolution crystallographic data. To improve the computed cation occupancy along the Oxy-GQ central channel, it was necessary to refine and validate new cation-oxygen parameters using structural and thermodynamic data available for crown ethers and ion channels. This single set of parameters that describes both localized and delocalized binding to various biological systems is used to gain insight into cation occupancy along the Oxy-GQ channel under various salt conditions. The paper concludes with prospects for extending the method to predict divalent cation binding to nucleic acids. This work advances the forefront of theoretical methods able to provide predictive insight into ion atmosphere effects on nucleic acids function.
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