ArticleBiopolymers2016
Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.
Article in Biopolymers, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 49 citations in OpenAlex.
- Long-Timescale Molecular Dynamics Reveal a Coordination-Biased Conformational Selection Mechanism for Sorcin Activation.bioRxiv : the preprint server for biology · 2026Article
- Evaluating Force Matching as a Parametrization Strategy for the CHARMM36m Force Field Using Phosphorylation.The journal of physical chemistry. B · 2026Article
- In silico characterization of the gating and selectivity mechanism of the human TPC2 cation channel.The Journal of general physiology · 2025Article
- Understanding pectin cross-linking in plant cell walls.Communications biology · 2025Article
- Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field.Journal of chemical theory and computation · 2024Article
- Curvature Matters: Modeling Calcium Binding to Neutral and Anionic Phospholipid Bilayers.The journal of physical chemistry. B · 2023Article
- Redox regulation of KeLife · 2023Article
- Recalibrating the calcium trap in amino acid carboxyl groupsPhysical chemistry chemical physics : PCCP · 2023Article
- Multiscale modelling of claudin-based assemblies: A magnifying glass for novel structures of biological interfaces.Computational and structural biotechnology journal · 2022Review
- Probing the Suitability of Different CaMolecules (Basel, Switzerland) · 2021Article
- Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway.International journal of molecular sciences · 2021Article
- Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions.ACS omega · 2021Article
- NEDD8 Deamidation Inhibits Cullin RING Ligase Dynamics.Frontiers in immunology · 2021Article
- Ground-State Structures of Hydrated Calcium Ion Clusters From Comprehensive Genetic Algorithm Search.Frontiers in chemistry · 2021Article
- Influence of Calcium Binding on Conformations and Motions of Anionic Polyamino Acids. Effect of Side Chain Length.Polymers · 2020Article
- Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes.Royal Society open science · 2020Article
- Predicting the Structures of Glycans, Glycoproteins, and Their Complexes.Chemical reviews · 2018Review
- A Kirkwood-Buff derived force field for alkaline earth halide salts.The Journal of chemical physics · 2018Article
- New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.Physical chemistry chemical physics : PCCP · 2018Review
- Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016.
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