Native folded and compact intermediate states of RNA typically involve tertiary structures in the presence of divalent ions such as Mg2+ in a background of monovalent ions. In a recent study we have shown how the presence of Mg2+ impacts the transition from partially unfolded to folded states through a "push-pull" mechanism where the ion both favors and disfavors the sampling of specific phosphate-phosphate interactions (Biophysical Journal, 6: 1424-1437, 2020). To further understand the ion atmosphere of RNA in folded and partially folded states results from atomistic Umbrella Sampling and oscillating chemical potential Grand Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) simulations are used to obtain atomic-level details of the distributions of Mg2+ and K+ ions around Twister RNA. Results show the presence of 100 mM Mg2+ to lead to increased charge neutralization over that predicted by counterion condensation theory. Upon going from partially unfolded to folded states overall charge neutralization increases at all studied ion concentrations that, while associated with an increase in the number of direct ion-phosphate interactions, is fully accounted for by the monovalent K+ ions. Furthermore, K+ preferentially interacts with purine N7 atoms of helical regions in partially unfolded states thereby potentially stabilizing the helical regions. Thus, both secondary helical structures and formation of tertiary structures leads to increased counterion condensation, thereby stabilizing those structural features of Twister. Notably, it is shown that K+ can act as a surrogate for Mg2+ by participating in specific interactions with non-sequential phosphate pairs that occur in the folded state, explaining the ability of Twister to self-cleave at sub-millimolar Mg2+ concentrations.

中文翻译：

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Mg2+ 和 K+ 在 Twister 核酶折叠和稳定中的贡献和竞争

RNA 的天然折叠和紧凑中间状态通常涉及在二价离子（如 Mg2+）存在下单价离子背景下的三级结构。在最近的一项研究中，我们展示了 Mg2+ 的存在如何通过“推拉”机制影响从部分展开状态到折叠状态的转变，其中离子既支持又不支持特定磷酸盐 - 磷酸盐相互作用的采样（生物物理杂志，6： 1424-1437，2020）。为了进一步了解处于折叠和部分折叠状态的 RNA 的离子气氛，来自原子伞采样和振荡化学势的结果，使用 Grand Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) 模拟来获得 Mg2+ 和Twister RNA 周围的 K+ 离子。结果显示 100 mM Mg2+ 的存在导致电荷中和增加，超过反离子凝聚理论所预测的。从部分未折叠状态变为折叠状态后，所有研究的离子浓度下的整体电荷中和增加，虽然与直接离子-磷酸盐相互作用的数量增加有关，但完全由单价 K+ 离子解释。此外，K+ 优先与处于部分未折叠状态的螺旋区域的嘌呤 N7 原子相互作用，从而潜在地稳定螺旋区域。因此，二级螺旋结构和三级结构的形成都会导致抗衡离子凝聚增加，从而稳定 Twister 的这些结构特征。尤其，