Structure and dynamics of an RNA tetraloop: A joint molecular dynamics and NMR study
Structure and dynamics of an RNA tetraloop: A joint molecular dynamics and NMR study
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DOI：
10.1016/j.str.2005.05.015
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发表时间：
2005-09-01
期刊：
影响因子：
5.7
通讯作者：
Stock, G
中科院分区：
文献类型：
--
作者：
Koplin, J;Mu, YG;Stock, G
对RNA四环5 '-CGCUUUUGCG-3'在水溶剂中的高解链温度和显著的构象异质性进行了分子动力学模拟，并与NMR研究进行了比较。NMR数据允许的理论模型，包括力场的质量和构象采样的详细测试。由于构象的异质性的tetraloop，高温（350 K）和局部增强的采样模拟需要调用。Amber 98力场导致与实验数据的良好总体一致性。基于核磁共振数据和主成分分析的350 K的轨迹，显示的动力学结构的四环。主成分自由能表面表现出四个极小值，这对应于明确定义的构象结构，主要是由他们的基地堆叠在循环区域。没有发现糖环的运动和环基地的堆叠动力学之间的相关性。
Molecular dynamics simulations of the RNA tetraloop 5'-CGCUUUUGCG-3' with high melting temperature and significant conformational heterogeneity in explicit water solvent are presented and compared to NMR studies. The NMR data allow for a detailed test of the theoretical model, including the quality of the force field and the conformational sampling. Due to the conformational heterogeneity of the tetraloop, high temperature (350 K) and locally enhanced sampling simulations need to be invoked. The Amber98 force field leads to a good overall agreement with experimental data. Based on NMR data and a principal component analysis of the 350 K trajectory, the dynamic structure of the tetraloop is revealed. The principal component free energy surface exhibits four minima, which correspond to well-defined conformational structures that differ mainly by their base stacking in the loop region. No correlation between the motion of the sugar rings and the stacking dynamics of the loop bases is found.