Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 11, Issue 8, Pages 3932-3945Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.5b00286
Keywords
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Funding
- Emil Aaltonen foundation
- Rubicon grant from The Netherlands Organization for Scientific Research (NWO)
- University of Calgary Eyes High postdoctoral fellowship
- NWO
- Natural Sciences and Engineering Research Council of Canada
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We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nudeobases between polar and nonpolar solvents as well as base base potential of mean force calculations. The bonded interactions are fit to single-stranded DNA (ssDNA) atomistic simulations and an elastic network is used to retain double-stranded DNA (dsDNA) and other specific DNA conformations. We present the implementation of the Martini DNA model and demonstrate the properties of individual bases, ssDNA as well as dsDNA, and DNA-protein complexes. The model opens up large-scale simulations of DNA interacting with a wide range of other (bio)molecules that are available within the Martini framework.
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