Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China.
Int J Mol Sci. 2020 Mar 11;21(6):1926. doi: 10.3390/ijms21061926.
Riboswitches are naturally occurring RNA aptamers that control the expression of essential bacterial genes by binding to specific small molecules. The binding with both high affinity and specificity induces conformational changes. Thus, riboswitches were proposed as a possible molecular target for developing antibiotics and chemical tools. The adenine riboswitch can bind not only to purine analogues but also to pyrimidine analogues. Here, long molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) computational methodologies were carried out to show the differences in the binding model and the conformational changes upon five ligands binding. The binding free energies of the guanine riboswitch aptamer with C74U mutation complexes were compared to the binding free energies of the adenine riboswitch (AR) aptamer complexes. The calculated results are in agreement with the experimental data. The differences for the same ligand binding to two different aptamers are related to the electrostatic contribution. Binding dynamical analysis suggests a flexible binding pocket for the pyrimidine ligand in comparison with the purine ligand. The 18 μs of MD simulations in total indicate that both ligand-unbound and ligand-bound aptamers transfer their conformation between open and closed states. The ligand binding obviously affects the conformational change. The conformational states of the aptamer are associated with the distance between the mass center of two key nucleotides (U51 and A52) and the mass center of the other two key nucleotides (C74 and C75). The results suggest that the dynamical character of the binding pocket would affect its biofunction. To design new ligands of the adenine riboswitch, it is recommended to consider the binding affinities of the ligand and the conformational change of the ligand binding pocket.
核糖开关是一类天然存在的 RNA 适体，通过与特定的小分子结合来控制细菌必需基因的表达。这种结合具有高亲和力和特异性，会诱导构象变化。因此，核糖开关被认为是开发抗生素和化学工具的潜在分子靶标。腺嘌呤核糖开关不仅可以与嘌呤类似物结合，还可以与嘧啶类似物结合。在这里，我们进行了长分子动力学 (MD) 模拟和分子力学泊松-玻尔兹曼表面面积 (MM-PBSA) 计算方法学研究，以展示在结合 5 种配体时结合模型和构象变化的差异。我们将 C74U 突变复合物的鸟嘌呤核糖开关适体的结合自由能与腺嘌呤核糖开关 (AR) 适体复合物的结合自由能进行了比较。计算结果与实验数据一致。对于同一配体与两种不同适体的结合，差异与静电贡献有关。结合动力学分析表明，与嘌呤配体相比，嘧啶配体的结合口袋具有更大的灵活性。总共 18 μs 的 MD 模拟表明，配体未结合和配体结合的适体在开放和关闭状态之间均会发生构象转变。配体结合明显会影响构象变化。适体的构象状态与两个关键核苷酸（U51 和 A52）的质心与另外两个关键核苷酸（C74 和 C75）的质心之间的距离有关。结果表明，结合口袋的动力学特性会影响其生物功能。为了设计新的腺嘌呤核糖开关配体，建议考虑配体的结合亲和力和配体结合口袋的构象变化。
