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

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.

Authors:
; ; ;  [1]
  1. Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072 (China)
Publication Date:
OSTI Identifier:
22308390
Resource Type:
Journal Article
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 141; Journal Issue: 10; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9606
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; ANNEALING; BODY TEMPERATURE; COMPARATIVE EVALUATIONS; MELTING POINTS; MONTE CARLO METHOD; RNA; SALTS; SIMULATION; STABILITY; THERMODYNAMICS

Citation Formats

Shi, Ya-Zhou, Wang, Feng-Hua, Wu, Yuan-Yan, and Tan, Zhi-Jie, E-mail: zjtan@whu.edu.cn. A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect. United States: N. p., 2014. Web. doi:10.1063/1.4894752.
Shi, Ya-Zhou, Wang, Feng-Hua, Wu, Yuan-Yan, & Tan, Zhi-Jie, E-mail: zjtan@whu.edu.cn. A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect. United States. doi:10.1063/1.4894752.
Shi, Ya-Zhou, Wang, Feng-Hua, Wu, Yuan-Yan, and Tan, Zhi-Jie, E-mail: zjtan@whu.edu.cn. Sun . "A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect". United States. doi:10.1063/1.4894752.
@article{osti_22308390,
title = {A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect},
author = {Shi, Ya-Zhou and Wang, Feng-Hua and Wu, Yuan-Yan and Tan, Zhi-Jie, E-mail: zjtan@whu.edu.cn},
abstractNote = {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.},
doi = {10.1063/1.4894752},
journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 10,
volume = 141,
place = {United States},
year = {2014},
month = {9}
}