A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect

J Chem Phys. 2014 Sep 14;141(10):105102. doi: 10.1063/1.4894752.

Abstract

To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability, and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (≤45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 Å and an overall minimum RMSD of 1.9 Å from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ∼ 1.0 °C of melting temperatures, as compared with the extensive experimental data. In addition, the model could provide the ensemble of possible 3D structures for a short RNA at a given temperature/salt condition.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Models, Molecular
  • Monte Carlo Method
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • RNA Stability
  • Salts / chemistry*
  • Thermodynamics

Substances

  • Salts
  • RNA