title: RNA pseudo-knots simulated with a one-bead coarse-grained model.
abstract: We present a revised version of a Monte Carlo simulation model for RNA molecules that was introduced in a previous communication [O. Taxilaga-Zetina, P. Pliego-Pastrana, and M. D. Carbajal-Tinoco, Phys. Rev. E 81, 041914 (2010)]. The basic model consists of a series of knowledge-based pair potentials that were obtained from the statistical analysis of large RNAs belonging to the Protein Data Bank. These effective interactions are then used to dress a polymeric chain that reproduces relatively simple secondary structures (e.g., small hairpins). In order to describe more complicated three-dimensional structures such as pseudo-knots, here we include orientational information for the interaction between nucleotides forming hydrogen bonds, as in the case of the Watson-Crick base pairs. As a result, the simulated molecules obtained through the modified model are now consistent with their corresponding experimental configurations.
authors.affiliation: Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D.F., Mexico.
authors.forename: Oscar
authors.initials: O
authors.lastname: Taxilaga-Zetina
authors.affiliation: Área Académica de Matemáticas y Física, ICBI, Universidad Autónoma del Estado de Hidalgo, Carr. Pachuca Tulancingo Km 4.5, 42182 Pachuca Hgo., Mexico.
authors.forename: Patricia
authors.initials: P
authors.lastname: Pliego-Pastrana
authors.affiliation: Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D.F., Mexico.
authors.forename: Mauricio D
authors.initials: MD
authors.lastname: Carbajal-Tinoco
mesh_terms: D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA