ArticleThe journal of physical chemistry. B2015
Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
67 citing papers in PubMed, 1 synthesis or guideline pooled it.
- pH-Dependent Degradation of Macrobial Environmental DNA in Water.Molecular ecology resources · 2026Pooled it
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- Nature Counts to Three: Universal Mg-Pinch Motif Polarizes the Cleaved Bond in NTP-Processing Enzymes.Journal of the American Chemical Society · 2026Article
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- MgJournal of the American Chemical Society · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Selective binding of divalent cations reshapes nucleosome mechanics and unlocks histone tail dynamics.Communications biology · 2026Article
- Force fields matter in DNA polProtein science : a publication of the Protein Society · 2026Article
- Simulating Metal Complex Formation and Ligand Exchange: Unraveling the Interplay between Entropy, Kinetics, and Mechanisms on the Chelate Effect.Journal of chemical theory and computation · 2025Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Pathways for accelerated bacterial spore killing with ohmic heating.NPJ science of food · 2025Article
- Structural and thermodynamic impact of oncogenic mutations on the nucleosome core particle.Biophysical journal · 2025Article
- Article
- Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.Journal of chemical theory and computation · 2025Article
- Complex Water Networks Visualized through 2.2-2.3 Å Cryogenic Electron Microscopy of RNA.bioRxiv : the preprint server for biology · 2025Article
- Systematic analysis of biomolecular conformational ensembles with PENSA.The Journal of chemical physics · 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
- Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.Nature communications · 2024Article
- RNA targeting and cleavage by the type III-Dv CRISPR effector complex.Nature communications · 2024Article
- Surface-Accelerated String Method for Locating Minimum Free Energy Paths.Journal of chemical theory and computation · 2024Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Divalent metal ions are of fundamental importance to the function and folding of nucleic acids. Divalent metal ion-nucleic acid interactions are complex in nature and include both territorial and site specific binding. Commonly employed nonbonded divalent ion models, however, are often parametrized against bulk ion properties and are subsequently utilized in biomolecular simulations without considering any data related to interactions at specific nucleic acid sites. Previously, we assessed the ability of 17 different nonbonded Mg(2+) ion models to reproduce different properties of Mg(2+) in aqueous solution including radial distribution functions, solvation free energies, water exchange rates, and translational diffusion coefficients. In the present work, we depart from the recently developed 12-6-4 potential models for divalent metal ions developed by Li and Merz and tune the pairwise parameters for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) binding dimethyl phosphate, adenosine, and guanosine in order to reproduce experimental site specific binding free energies derived from potentiometric pH titration data. We further apply these parameters to investigate a metal ion migration previously proposed to occur during the catalytic reaction of the hammerhead ribozyme. The new parameters are shown to be accurate and balanced for nucleic acid binding in comparison with available experimental data and provide an important tool for molecular dynamics and free energy simulations of nucleic acids where these ions may exhibit different binding modes.
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Registered trials
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