In translation, G•U mismatch in codon-anticodon decoding is an error hotspot likely due to transition of G•U from wobble (wb) to Watson-Crick (WC) geometry, which is governed by keto/enol tautomerization (wb-WC reaction). Yet, effects of the ribosome on the wb-WC reaction and its implications for decoding mechanism remain unclear. Employing quantum-mechanical/molecular-mechanical umbrella sampling simulations using models of the ribosomal decoding site (A site) we determined that the wb-WC reaction is endoergic in the open, but weakly exoergic in the closed A-site state. We extended the classical ‘induced-fit’ model of initial selection by incorporating wb-WC reaction parameters in open and closed states. For predicted parameters, the non-equilibrium exoergic wb-WC reaction is kinetically limited by the decoding rates. The model explains early observations of the WC geometry of G•U from equilibrium structural studies and reveals discrimination capacity for the working ribosome operating at non-equilibrium conditions. The equilibration of the exoergic wb-WC reaction counteracts the equilibration of the open-closed transition of the A site, constraining the decoding accuracy and potentially explaining the persistence of the G•U as an error hotspot. Our results unify structural and mechanistic views of codon-anticodon decoding and generalize the ‘induced-fit’ model for flexible substrates.

中文翻译：

---

翻译中G•U互变异构的计算研究揭示了错误率的约束

在翻译中，密码子-反密码子解码中的 G•U 错配是一个错误热点，这可能是由于 G•U 从摆动 (wb) 过渡到 Watson-Crick (WC) 几何，这是由酮/烯醇互变异构 (wb-WC反应）。然而，核糖体对 wb-WC 反应的影响及其对解码机制的影响仍不清楚。使用核糖体解码位点（A 位点）模型进行量子力学/分子力学伞形采样模拟，我们确定 wb-WC 反应在开放时是吸能的，但在封闭的 A 位点状态下是弱放能的。我们通过在打开和关闭状态下结合 wb-WC 反应参数来扩展初始选择的经典“诱导拟合”模型。对于预测参数，非平衡放热 wb-WC 反应在动力学上受到解码速率的限制。该模型解释了从平衡结构研究中对 G•U WC 几何形状的早期观察结果，并揭示了在非平衡条件下工作的核糖体的辨别能力。放热 wb-WC 反应的平衡抵消了 A 位点的开闭过渡的平衡，限制了解码的准确性，并可能解释 G•U 作为错误热点的持续存在。我们的结果统一了密码子-反密码子解码的结构和机制观点，并概括了柔性基板的“诱导拟合”模型。放热 wb-WC 反应的平衡抵消了 A 位点的开闭过渡的平衡，限制了解码的准确性，并可能解释 G•U 作为错误热点的持续存在。我们的结果统一了密码子-反密码子解码的结构和机制观点，并概括了柔性基板的“诱导拟合”模型。放热 wb-WC 反应的平衡抵消了 A 位点的开闭过渡的平衡，限制了解码的准确性，并可能解释 G•U 作为错误热点的持续存在。我们的结果统一了密码子-反密码子解码的结构和机制观点，并概括了柔性基板的“诱导拟合”模型。