Max-Born-Institute, Berlin, Germany.
Max-Born-Institute, Berlin, Germany.
Biophys J. 2021 Dec 7;120(23):5322-5332. doi: 10.1016/j.bpj.2021.10.029. Epub 2021 Oct 27.
The electrostatic interaction of RNA with its aqueous environment is most relevant for defining macromolecular structure and biological function. The attractive interaction of phosphate groups in the RNA backbone with ions in the water environment leads to the accumulation of positively charged ions in the first few hydration layers around RNA. Electrostatics of this ion atmosphere and the resulting ion concentration profiles have been described by solutions of the nonlinear Poisson-Boltzmann equation and atomistic molecular dynamics (MD) simulations. Much less is known on contact pairs of RNA phosphate groups with ions at the RNA surface, regarding their abundance, molecular geometry, and role in defining RNA structure. Here, we present a combined theoretical and experimental study of interactions of a short RNA duplex with magnesium (Mg) ions. MD simulations covering a microsecond time range give detailed hydration geometries as well as electrostatics and spatial arrangements of phosphate-Mg pairs, including both pairs in direct contact and separated by a single water layer. The theoretical predictions are benchmarked by linear infrared absorption and nonlinear two-dimensional infrared spectra of the asymmetric phosphate stretch vibration which probes both local interaction geometries and electric fields. Contact pairs of phosphate groups and Mg ions are identified via their impact on the vibrational frequency position and line shape. A quantitative analysis of infrared spectra for a range of Mg-excess concentrations and comparison with fluorescence titration measurements shows that on average 20-30% of the Mg ions interacting with the RNA duplex form contact pairs. The experimental and MD results are in good agreement. In contrast, calculations based on the nonlinear Poisson-Boltzmann equation fail in describing the ion arrangement, molecular electrostatic potential, and local electric field strengths correctly. Our results underline the importance of local electric field mapping and molecular-level simulations to correctly account for the electrostatics at the RNA-water interface.
RNA 与其水环境的静电相互作用对定义大分子结构和生物功能最为重要。RNA 骨架中的磷酸基团与水环境中的离子的吸引相互作用导致带正电荷的离子在 RNA 周围的最初几个水合层中积累。这种离子气氛的静电作用以及由此产生的离子浓度分布已通过非线性泊松-玻尔兹曼方程的解和原子分子动力学（MD）模拟来描述。关于 RNA 表面的磷酸基团与离子的接触对，其丰度、分子几何形状及其在定义 RNA 结构中的作用，人们知之甚少。在这里，我们提出了一个短 RNA 双链与镁（Mg）离子相互作用的理论和实验综合研究。涵盖微秒时间范围的 MD 模拟给出了详细的水合几何形状以及磷酸-Mg 对的静电和空间排列，包括直接接触的对和通过单个水层隔开的对。理论预测通过线性红外吸收和探测局部相互作用几何形状和电场的不对称磷酸伸缩振动的非线性二维红外光谱进行基准测试。通过它们对振动频率位置和线形状的影响来识别磷酸基团和 Mg 离子的接触对。对一系列 Mg 过量浓度的红外光谱的定量分析以及与荧光滴定测量的比较表明，与 RNA 双链相互作用的 Mg 离子平均有 20-30%形成接触对。实验和 MD 结果吻合较好。相比之下，基于非线性泊松-玻尔兹曼方程的计算在正确描述离子排列、分子静电势和局部电场强度方面失败。我们的结果强调了局部电场映射和分子水平模拟对于正确描述 RNA-水界面静电作用的重要性。
