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Martini Coarse-Grained Force Field: Extension to RNA

Uusitalo, J. J., Ingolfsson, H. I., Marrink, S. J. & Faustino, I., 25-Jul-2017, In : Biophysical Journal. 113, 2, p. 246-256 11 p.

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  • Martini Coarse-Grained Force Field: Extension to RNA

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DOI

RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network. This model, therefore, is not designed for applications involving RNA folding but rather offers a stable RNA structure for studying RNA interactions with other (bio) molecules. The RNA model is compatible with all other Martini models and opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.

Original languageEnglish
Pages (from-to)246-256
Number of pages11
JournalBiophysical Journal
Volume113
Issue number2
Publication statusPublished - 25-Jul-2017

    Keywords

  • SIGNAL RECOGNITION PARTICLE, 3D STRUCTURE PREDICTION, NUCLEIC-ACID STRUCTURE, MOLECULAR-DYNAMICS, BIOMOLECULAR SIMULATIONS, CRYSTAL-STRUCTURE, NONCODING RNA, STRANDED RNA, DNA, MODEL

ID: 46718744