Phosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single non-bridging oxygen of the phosphate is replaced with a sulphur atom. PT can stabilize RNAs by protecting them from hydrolysis and is commonly used as tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stability and electronic structure. Here, we present Molecular Dynamics (MD) simulations, quantum mechanical (QM) calculations, and NMR spectroscopy measurements, exploring the effects of PT modifications in the structural context of the Neomycin-sensing riboswitch (NSR). The NSR is the smallest biologically functional riboswitch with a well-defined structure stabilized by a U-turn motif. Three of the signature interactions of the U-turn; an H-bond, an anion-π interaction and a potassium binding site; are formed by RNA phosphates, making the NSR an ideal model for studying how PT affects RNA structure and dynamics. By comparing with high-level QM calculations, we reveal the distinct physical properties of the individual interactions facilitated by the PT. The sulphur substitution, besides weakening the direct H-bond interaction, reduces the directionality of H-bonding while increasing its dispersion and induction components. It also reduces the induction and increases dispersion component of the anion-π stacking. The sulphur force-field parameters commonly employed in the literature do not reflect these distinctions, leading to unsatisfactory description of PT in simulations of the NSR. We show that it is not possible to accurately describe the PT interactions using one universal set of van der Waals sulphur parameters and provide suggestions for improving the force-field performance.

中文翻译：

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通过分子动力学模拟，QM / MM计算和NMR实验研究RNA结构中的硫代磷酸酯取代

硫代磷酸酯（PTs）是RNA骨架的重要化学修饰，其中磷酸的单个非桥联氧被硫原子取代。PT可以通过保护RNA免受水解来稳定RNA，通常用作探索其功能的工具。但是，尚不清楚PT对RNA稳定性和电子结构有什么基本的物理作用。在这里，我们介绍了分子动力学（MD）模拟，量子力学（QM）计算和NMR光谱测量，探讨了在新霉素感测核糖开关（NSR）的结构背景下PT修饰的影响。NSR是最小的具有生物学功能的核糖开关，具有通过掉头基序稳定的结构明确的结构。掉头的三种标志性互动；H键，阴离子-π相互作用和钾结合位点；NSR由RNA磷酸盐形成，使NSR成为研究PT如何影响RNA结构和动力学的理想模型。通过与高级质量管理计算进行比较，我们揭示了PT促进的各个相互作用的独特物理特性。硫取代除了削弱直接的氢键相互作用外，还降低了氢键的方向性，同时增加了其分散度和诱导成分。它还减少了感应并增加了阴离子-π堆积的色散分量。文献中常用的硫力场参数不能反映这些区别，从而导致在NSR模拟中对PT的描述不令人满意。