Trimethylamine N-oxide (TMAO) is an osmolyte that accumulates in cells in response to osmotic stress. TMAO stabilizes proteins by the entropic stabilization mechanism, which pictures TMAO as a nanocrowder that predominantly destabilizes the unfolded state. However, the mechanism of action of TMAO on RNA is much less understood. Here, we use all-atom molecular dynamics simulations to investigate how TMAO interacts with a 12-nt RNA hairpin with a high melting temperature, and an 8-nt RNA hairpin, which has a relatively fluid native basin in the absence of TMAO. The use of the two hairpins with different free energy of stabilization allows us to probe the origin of the destabilization effect of TMAO on RNA molecules without the possibility of forming tertiary interactions. We generated multiple trajectories using all-atom molecular dynamics (MD) simulations in explicit water by employing AMBER and CHARMM force fields, both in the absence and presence of TMAO. We observed qualitatively similar RNA-TMAO interaction profiles from the simulations using the two force fields. TMAO hydrogen bond interactions are largely depleted around the paired RNA bases and ribose sugars. In contrast, we show that the oxygen atom in TMAO, the hydrogen bond acceptor, preferentially interacts with the hydrogen bond donors in the solvent exposed bases, such as those in the stem-loop and the destabilized base stacks in the unfolded state, especially in the marginally stable 8-nt RNA hairpin. The predicted destabilization mechanism through TMAO-RNA hydrogen bond interactions could be tested using two-dimensional IR spectroscopy. Since TMAO does not significantly interact with the hydroxyl group of the ribose sugars, we predict that similar results must also hold for DNA.

中文翻译：

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TMAO 通过直接氢键相互作用破坏 RNA 二级结构

三甲胺N-氧化物 (TMAO) 是一种渗透剂，它在细胞中积累以应对渗透压力。TMAO 通过熵稳定机制稳定蛋白质，该机制将 TMAO 描绘成主要破坏展开状态稳定性的纳米团簇。然而，TMAO 对 RNA 的作用机制知之甚少。在这里，我们使用全原子分子动力学模拟来研究 TMAO 如何与具有高熔化温度的 12-nt RNA 发夹和 8-nt RNA 发夹相互作用，后者在没有 TMAO 的情况下具有相对流动的天然盆地。使用具有不同稳定自由能的两个发夹使我们能够探索 TMAO 对 RNA 分子的去稳定作用的起源，而不可能形成三级相互作用。我们通过使用 AMBER 和 CHARMM 力场，在不存在和存在 TMAO 的情况下，使用显式水中的全原子分子动力学 (MD) 模拟生成了多个轨迹。我们从使用两个力场的模拟中观察到定性相似的 RNA-TMAO 相互作用曲线。TMAO 氢键相互作用在配对的 RNA 碱基和核糖周围被大量耗尽。相比之下，我们表明 TMAO 中的氧原子（氢键受体）优先与溶剂暴露碱基中的氢键供体相互作用，例如茎环中的碱基和未折叠状态下不稳定的碱基堆叠，尤其是在边缘稳定的 8-nt RNA 发夹。可以使用二维红外光谱测试通过 TMAO-RNA 氢键相互作用预测的不稳定机制。