Faber Michael, Klumpp Stefan
Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov;88(5):052701. doi: 10.1103/PhysRevE.88.052701. Epub 2013 Nov 4.
RNA molecules form three-dimensional structures via base pairing that determine the function and biochemical activity of the molecule. Here we introduce a structure-based method for studying the folding dynamics of RNA secondary structures. The approach focuses on native contacts that are parametrized with standard empirical free energies. Kinetic Monte Carlo simulations for free folding of simple hairpins and complex structures such as a tRNA as well as for folding in the presence of an external force show good agreement with experimental data. A systematic comparison of simulated and experimental folding rates for various structures shows a strong correlation, indicating that the approach can predict folding rates within about an order of magnitude.
RNA分子通过碱基配对形成三维结构，这些结构决定了分子的功能和生化活性。在此，我们介绍一种基于结构的方法来研究RNA二级结构的折叠动力学。该方法聚焦于用标准经验自由能参数化的天然接触。对简单发夹结构和诸如tRNA等复杂结构的自由折叠以及在外力存在下的折叠进行的动力学蒙特卡罗模拟，与实验数据显示出良好的一致性。对各种结构的模拟折叠速率和实验折叠速率进行的系统比较显示出很强的相关性，这表明该方法能够在大约一个数量级内预测折叠速率。
