Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany.
Nucleic Acids Res. 2010 Jan;38(2):683-94. doi: 10.1093/nar/gkp956. Epub 2009 Nov 11.
We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 A) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2'-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined.
我们呈现了一个由 cUUCGg 四联体帽封端的 14 个核苷酸 RNA 发夹的高分辨率核磁共振（NMR）溶液结构。这个短而非常稳定的 RNA 提供了一个重要的模型系统，用于使用 NMR 光谱学、分子动力学（MD）模拟和 RNA 力场开发研究 RNA 结构和动力学。通过测量和包含所有当前可访问的 NMR 参数，包括来自核 Overhauser 效应（NOE）强度的距离、依赖于扭转角的同核和异核标量偶合常数、投影角相关的交叉弛豫率和残差偶极偶合，可以实现结构的极高精度（均方根偏差为 0.3 A）。结构计算是使用 CNS 程序和 ARIA 设置和协议进行的。通过在显式水中使用 OPLS 非键相互作用和电荷力场参数进行最终细化，进一步提高了结构质量。此外，还对 2'-羟基进行了分配，并根据 NOE 接触分析了它们的构象。该结构目前定义了通过 NMR 光谱学确定 RNA 结构的精度和准确性的基准。在这里，我们讨论了各种 NMR 约束对结构质量的影响，并详细讨论了以前确定的该系统的动力学。
