Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation

Binding of monovalent and divalent cations to two adenine–adenine platform structures from the Tetrahymena group I intron ribozyme has been studied using continuum solvent models based on the generalised Born and the finite-difference Poisson–Boltzmann approaches. The adenine–adenine platform RNA motif forms an experimentally characterised monovalent ion binding site important for ribozyme folding and function. Qualitative agreement between calculated and experimental ion placements and binding selectivity was obtained. The inclusion of solvation effects turned out to be important to obtain low energy structures and ion binding placements in agreement with the experiment. The calculations indicate that differences in solvation of the isolated ions contribute to the calculated ion binding preference. However, Coulomb attraction and van der Waals interactions due to ion size differences and RNA conformational adaptation also influence the calculated ion binding affinity. The calculated alkali ion binding selectivity for both platforms followed the order K(+) > Na(+) > Rb(+) > Cs(+) > Li(+) (Eisenman series VI) in the case of allowing RNA conformational relaxation during docking. With rigid RNA an Eisenman series V was obtained (K(+) > Rb(+) > Na(+) > Cs(+) > Li(+)). Systematic energy minimisation docking simulations starting from several hundred initial placements of potassium ions on the surface of platform containing RNA fragments identified a coordination geometry in agreement with the experiment as the lowest energy binding site. The approach could be helpful to identify putative ion binding sites in nucleic acid structures determined at low resolution or with experimental methods that do not allow identification of ion binding sites.

本研究基于广义玻恩（Generalized Born）与有限差分泊松-玻尔兹曼（finite-difference Poisson–Boltzmann）两种连续溶剂模型，对四膜虫I型内含子核酶（Tetrahymena group I intron ribozyme）的两个腺嘌呤-腺嘌呤平台结构与一价、二价阳离子的结合情况展开了研究。该腺嘌呤-腺嘌呤平台RNA基序可形成经实验表征的一价离子结合位点，该位点对核酶的折叠与功能具有重要意义。计算得到的离子结合位置与结合选择性与实验结果具有定性一致性。纳入溶剂化效应是获得与实验相符的低能结构及离子结合位置的关键因素。计算结果表明，游离离子的溶剂化差异是影响计算得到的离子结合偏好性的重要因素。不过，由离子尺寸差异与RNA构象适配所带来的库仑吸引力与范德华相互作用，同样会对计算得到的离子结合亲和力产生影响。当允许RNA在分子对接（docking）过程中发生构象松弛时，两个平台结构的计算碱金属离子结合选择性遵循K⁺ > Na⁺ > Rb⁺ > Cs⁺ > Li⁺的顺序（艾森曼序列VI，Eisenman series VI）。当RNA构象保持刚性时，得到的结合选择性对应艾森曼序列V（Eisenman series V）：K⁺ > Rb⁺ > Na⁺ > Cs⁺ > Li⁺。以包含平台结构的RNA片段表面的数百个钾离子初始结合位置为起点，开展系统性能量最小化分子对接模拟，最终确定了与实验结果相符的最低能结合位点的配位几何结构。该方法可用于在低分辨率核酸结构，或无法通过实验方法鉴定离子结合位点的核酸结构中，预测潜在的离子结合位点。