Shi Ya-Zhou, Wang Feng-Hua, Wu Yuan-Yan, Tan Zhi-Jie
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.
J Chem Phys. 2014 Sep 14;141(10):105102. doi: 10.1063/1.4894752.
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.
为了弥合RNA序列与三维（3D）结构之间的差距，人们提出了一些计算模型来预测RNA的3D结构。然而，现有的模型很少考虑偏离室温/体温和高盐（1M NaCl）的条件，因此通常很难预测热力学和盐效应。在本研究中，我们提出了一种用于RNA的含隐式盐的粗粒度模型，以预测3D结构、稳定性和盐效应。该模型结合蒙特卡罗模拟退火算法和粗粒度力场，能将46个经过测试的RNA（≤45 nt，包括假结）从其序列折叠成类似天然的结构，与实验结构相比，总体平均RMSD为3.5 Å，总体最小RMSD为1.9 Å。对于30个RNA发夹，与大量实验数据相比，本模型还能对稳定性和盐效应给出可靠的预测，熔解温度的平均偏差约为1.0 °C。此外，该模型可以在给定的温度/盐条件下为短RNA提供可能的3D结构集合。
