title: An implicit divalent counterion force field for RNA molecular dynamics.
abstract: How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg(2+) screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Henke
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Chi H
authors.initials: CH
authors.lastname: Mak
mesh_terms: D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D020871:RNA Stability; D012492:Salts / Q000737:chemistry
chemical_list: D012492:Salts; D012313:RNA