Open AccessMartini Coarse-Grained Force Field: Extension to DNA
Author(s) -
César A. López,
Andrzej J. Rzepiela,
de Alex Vries,
Lubbert Dijkhuizen,
Philippe H. Huenenberger,
Siewert J. Marrink
Publication year - 2015
Publication title -
journal of chemical theory and computation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.001
H-Index - 185
eISSN - 1549-9626
pISSN - 1549-9618
DOI - 10.1021/acs.jctc.5b00286
Subject(s) - force field (fiction) , nucleobase , dna , parameterized complexity , base pair , nucleotide , chemistry , molecule , polar , chemical physics , physics , computer science , algorithm , biochemistry , quantum mechanics , organic chemistry , gene
We systematically parameterized a coarse-grained (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 nucleobases 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.