Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India.
J Phys Chem B. 2023 Nov 2;127(43):9267-9281. doi: 10.1021/acs.jpcb.3c03941. Epub 2023 Oct 18.
Riboswitches sense various ions in bacteria and activate gene expression to synthesize proteins that help maintain ion homeostasis. The crystal structure of the aptamer domain (AD) of the fluoride riboswitch shows that the F ion is encapsulated by three Mg ions bound to the ligand-binding domain (LBD) located at the core of the AD. The assembly mechanism of this intricate structure is unknown. To this end, we performed computer simulations using coarse-grained and all-atom RNA models to bridge multiple time scales involved in riboswitch folding and ion binding. We show that F encapsulation by the Mg ions bound to the riboswitch involves multiple sequential steps. Broadly, two Mg ions initially interact with the phosphate groups of the LBD using water-mediated outer-shell coordination and transition to a direct inner-shell interaction through dehydration to strengthen their interaction with the LBD. We propose that the efficient binding mode of the third Mg and F is that they form a water-mediated ion pair and bind to the LBD simultaneously to minimize the electrostatic repulsion between three Mg bound to the LBD. The tertiary stacking interactions among the LBD nucleobases alone are insufficient to stabilize the alignment of the phosphate groups to facilitate Mg binding. We show that the stability of the whole assembly is an intricate balance of the interactions among the five phosphate groups, three Mg, and the encapsulated F ion aided by the Mg solvated water. These insights are helpful in the rational design of RNA-based ion sensors and fast-switching logic gates.
核糖开关可感知细菌中的各种离子，并激活基因表达，合成有助于维持离子平衡的蛋白质。氟化物核糖开关的适体结构域 (AD) 的晶体结构表明，F 离子被结合在位于 AD 核心的配体结合域 (LBD) 上的三个 Mg 离子所包裹。该复杂结构的组装机制尚不清楚。为此，我们使用粗粒度和全原子 RNA 模型进行了计算机模拟，以连接涉及核糖开关折叠和离子结合的多个时间尺度。我们表明，Mg 离子结合到核糖开关上对 F 的包裹涉及多个连续步骤。大致而言，最初有两个 Mg 离子通过水介导的外壳配位与 LBD 的磷酸基团相互作用，并通过去水作用转变为直接的内壳相互作用，以增强与 LBD 的相互作用。我们提出，第三个 Mg 和 F 的有效结合模式是它们形成水介导的离子对，并同时与 LBD 结合，以最小化与 LBD 结合的三个 Mg 之间的静电排斥。仅 LBD 核碱基之间的三级堆积相互作用不足以稳定磷酸基团的排列，以促进 Mg 结合。我们表明，整个组装体的稳定性是由五个磷酸基团、三个 Mg 和被包裹的 F 离子之间的相互作用以及 Mg 溶剂化水的辅助之间的复杂平衡决定的。这些见解有助于基于 RNA 的离子传感器和快速开关逻辑门的合理设计。
