ArticleJournal of chemical theory and computation2016
Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.Journal of chemical information and modeling · 2025Article
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.Communications biology · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.bioRxiv : the preprint server for biology · 2023Article
- Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.The journal of physical chemistry. B · 2022Article
- Pore structure controls stability and molecular flux in engineered protein cages.Science advances · 2022Article
- A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors.Proteins · 2022Article
- Graph deep learning locates magnesium ions in RNA.QRB discovery · 2022Article
- Improving the speed of volumetric density map generation via cubic spline interpolation.Journal of molecular graphics & modelling · 2021Article
- Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops.International journal of molecular sciences · 2020Article
- Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting.Biophysical journal · 2019Article
- Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.Journal of structural biology · 2019Review
- Predicting RNA-Metal Ion Binding with Ion Dehydration Effects.Biophysical journal · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Competitive Binding of MgBiophysical journal · 2018Article
- Hexahydrated MgBiophysical journal · 2018Article
- Physics-based all-atom modeling of RNA energetics and structure.Wiley interdisciplinary reviews. RNA · 2017Review
- How Does MgBiophysical journal · 2017Article
- MgBiophysical journal · 2017Article
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3 authors.
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Abstract
We compare the performance of five magnesium (Mg(2+)) ion models in simulations of an RNA stem loop which has an experimentally determined divalent ion dependent conformational shift. We show that despite their differences in parametrization and resulting van der Waals terms, including differences in the functional form of the nonbonded potential, when the RNA adopts its folded conformation, all models behave similarly across ten independent microsecond length simulations with each ion model. However, when the entire structure ensemble is accounted for, chelation of Mg(2+) to RNA is seen in three of the five models, most egregiously and likely artifactual in simulations using a 12-6-4 model for the Lennard-Jones potential. Despite the simple nature of the fixed point-charge and van der Waals sphere models employed, and with the exception of the likely oversampled directed chelation of the 12-6-4 potential models, RNA-Mg(2+) interactions via first shell water molecules are surprisingly well described by modern parameters, allowing us to observe the spontaneous conformational shift from Mg(2+) free RNA to Mg(2+) associated RNA structure in unrestrained molecular dynamics simulations.
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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.