title: Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.
abstract: The dimerization free energies of RNA-RNA duplexes are fundamental values that represent the structural stability of RNA complexes. We report a comparative analysis of RNA-RNA duplex dimerization free-energy changes upon mutations, estimated from a molecular dynamics simulation and experiments. A linear regression for nine pairs of double-stranded RNA sequences, six base pairs each, yielded a mean absolute deviation of 0.55 kcal/mol and an R(2) value of 0.97, indicating quantitative agreement between simulations and experimental data. The observed accuracy indicates that the molecular dynamics simulation with the current molecular force field is capable of estimating the thermodynamic properties of RNA molecules.
authors.affiliation: Graduate School of Frontier Sciences, The University of Tokyo , 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan.
authors.forename: Shun
authors.initials: S
authors.lastname: Sakuraba
authors.affiliation: Graduate School of Frontier Sciences, The University of Tokyo , 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan.|Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
authors.affiliation: Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Tomoshi
authors.initials: T
authors.lastname: Kameda
mesh_terms: D019281:Dimerization; D056004:Molecular Dynamics Simulation; D009154:Mutation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
chemical_list: D012313:RNA
keywords: Gibbs free energy; Hamiltonian replica exchange method; free-energy perturbation; nucleic acid