ArticleThe journal of physical chemistry. B2011
A coarse-grained model of DNA with explicit solvation by water and ions.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics.Journal of biomechanical engineering · 2018Article
- Structure and conformational dynamics of scaffolded DNA origami nanoparticles.Nucleic acids research · 2017Article
- Structural Characterization of Bubbles Formed in DNA Melting: A Monte Carlo Simulation Study.ACS omega · 2017Article
- Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments.Scientific reports · 2016Article
- Close encounters with DNA.Journal of physics. Condensed matter : an Institute of Physics journal · 2014Review
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.Journal of chemical theory and computation · 2014Article
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- The power of coarse graining in biomolecular simulations.Wiley interdisciplinary reviews. Computational molecular science · 2014Article
- More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization.The Journal of chemical physics · 2014Article
- An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization.The Journal of chemical physics · 2013Article
- Article
- Gas-phase hydration thermochemistry of sodiated and potassiated nucleic acid bases.Journal of the American Society for Mass Spectrometry · 2012Article
- Coarse-Grained Molecular Models of Water: A Review.Molecular simulation · 2012Article
- The ABCs of molecular dynamics simulations on B-DNA, circa 2012.Journal of biosciences · 2012Review
- Moving beyond Watson-Crick models of coarse grained DNA dynamics.The Journal of chemical physics · 2011Article
- A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.The Journal of chemical physics · 2011Article
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3 authors.
Funding
Abstract
Solvation by water and ions has been shown to be vitally important for biological molecules, yet fully atomistic simulations of large biomolecules remain a challenge due to their high computational cost. The effect of solvation is the most pronounced in polyelectrolytes, of which DNA is a paradigmatic example. Coarse-grained (CG) representations have been developed to model the essential physics of the DNA molecule, yet almost without exception, these models replace the water and ions by implicit solvation in order to significantly reduce the computational expense. This work introduces the first coarse-grained model of DNA solvated explicitly with water and ions. To this end, we combined two established CG models; the recently developed mW-ion model [DeMille, R. C.; Molinero, V. J. Chem. Phys. 2009, 131, 034107], which reproduces the structure of aqueous ionic solutions without electrostatic interactions, was coupled to the three-sites-per-nucleotide (3SPN) CG model of DNA [Knotts, T. A., IV; et al. J. Chem. Phys. 2007, 126, 084901]. Using atomistic simulations of d(CGCGAATTCGCG)(2) as a reference, we optimized the coarse-grained interactions between DNA and solvent to reproduce the solvation structure of water and ions around CG DNA. The resulting coarse-grained model of DNA explicitly solvated by ions and water (mW/3SPN-DNA) exhibits base-pair specificity and ion-condensation effects and it is 2 orders of magnitude computationally more efficient than atomistic models. We describe the parametrization strategy and offer insight into how other CG models may be combined with a coarse-grained solvent model such as mW-ion.
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