G◦U(T) mismatch has the highest contribution to the error rate of base pair recognition in replication, as well as in codon-anticodon decoding in translation. Recently, this effect was unambiguously linked to keto/enol tautomerization, which enables the Watson-Crick (WC) geometry of the base pair. Structural studies of the ribosome revealing G◦U in the WC geometry in the closed state of the A-site challenge the classical induced-fit model of decoding and currently lack a physicochemical explanation. Using computational and theoretical methods, we herein address effects of the ribosomal A-site on the wobble↔WC tautomerization reaction in G◦U (wb-WC reaction), and the consequent implications for the decoding mechanism in translation. The free energy change of the wb-WC reaction in the middle codon-anticodon position was calculated with quantum-mechanical/molecular-mechanical (QM/MM) umbrella sampling simulations. The wb-WC reaction was endoergic in the open A-site, but exoergic in the closed state. This effect can be explained in part by the decreased polarity of the closed A-site. We developed a model of initial selection in translation that incorporates the wb-WC reaction parameters in the open and closed states of the A-site. In the new model the exoergic wb-WC reaction is kinetically restricted by the decoding rates, which explains the observations of the WC geometry at equilibrium conditions. Moreover, the model reveals constraints imposed by the exoergic wb-WC reaction on the decoding accuracy: its equilibration counteracts the favorable contribution from equilibration of the open-closed transition. The similarity of the base-pair recognition mechanism in DNA polymerases allows extending this model to replication as well. Our model can be a step towards a general recognition model for flexible substrates

中文翻译：

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互变异构化限制了密码子-反密码子解码的准确性

G？U（T）不匹配对复制中以及翻译中密码子-反密码子解码中碱基对识别的错误率有最大的贡献。最近，这种效应明确地与酮/烯醇互变异构相关，这使碱基对的沃森-克里克（WC）几何形状成为可能。核糖体的结构研究揭示了在A位点封闭状态下WC几何中的G？U挑战了经典的诱导拟合模型，目前尚缺乏理化解释。使用计算和理论方法，我们在这里讨论核糖体A位点对G？U中的摆动WC互变异构反应（wb-WC反应）的影响，以及由此对翻译中的解码机制的影响。wb-WC反应在中间密码子-反密码子位置的自由能变化是通过量子力学/分子力学（QM / MM）伞式采样模拟计算的。wb-WC反应在开放的A位点是内能的，但在封闭状态下是能位的。可以通过封闭的A位置极性降低来部分解释这种效果。我们开发了翻译的初始选择模型，该模型在A站点的打开和关闭状态下结合了wb-WC反应参数。在新模型中，放热的wb-WC反应在动力学上受到解码速率的限制，这解释了在平衡条件下WC几何结构的观察结果。此外，该模型揭示了放热wb-WC反应对解码精度的限制：它的平衡抵消了开放-封闭式过渡的平衡所带来的有利贡献。DNA聚合酶中碱基对识别机制的相似性也允许将该模型扩展到复制。我们的模型可以迈向柔性基材通用识别模型的一步