Specific interaction between the start codon, 5'-AUG-3', and the anticodon, 5'-CAU-3', ensures accurate initiation of translation. Recent studies show that several near-cognate start codons (e.g. GUG and CUG) can play a role in initiating translation in eukaryotes. However, the mechanism allowing initiation through mismatched base-pairs at the ribosomal decoding site is still unclear at an atomic level. In this work, we propose an extended simulation-based method to evaluate free energy profiles, through computing the distance between each base-pair of the triplet interactions (d₁, d₂ and d₃) involved in recognition of start codons in eukaryotic translation pre-initiation complex. Our method provides not only the free energy penalty (ΔΔG) for mismatched start codons relative to the AUG start codon, but also the preferred pathways of transitions between bound and unbound states, which has not been described by previous studies. To verify the method, the binding dynamics of cognate (AUG) and near-cognate start codons (CUG and GUG) were simulated. Evaluated free energy profiles agree with experimentally observed changes in initiation frequencies from respective codons. This work proposes for the first time how a G:U mismatch at the first position of codon (GUG)-anticodon base-pairs destabilizes the accommodation in the initiating eukaryotic ribosome and how initiation at a CUG codon is nearly as strong as, or sometimes stronger than, that at a GUG codon. Our method is expected to be applied to study the affinity changes for various mismatched base-pairs.

中文翻译：

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真核生物核糖体预启动复合体的起始密码子识别中RNA结合动力学的自由能景观。

起始密码子5'-AUG-3'和反密码子5'-CAU-3'之间的特定相互作用确保了翻译的准确启动。最近的研究表明，几个近同源的起始密码子（例如GUG和CUG）可以在真核生物的翻译起始中发挥作用。但是，在核糖体解码位点允许通过不匹配的碱基对启动的机制在原子水平上仍不清楚。在这项工作中，我们提出了一种扩展的基于模拟的方法，通过计算三重态相互作用的每个碱基对之间的距离（d ₁，d ₂和d _3）来评估自由能分布）参与真核翻译预启动复合体中起始密码子的识别。我们的方法不仅提供免费的能量损失（ΔΔ g ^）（相对于AUG起始密码子而言）错配的起始密码子，以及结合状态和未结合状态之间过渡的首选途径，先前的研究尚未对此进行描述。为了验证该方法，模拟了同源（AUG）和近同源起始密码子（CUG和GUG）的结合动力学。评估的自由能分布与实验观察到的来自各个密码子的起始频率变化一致。这项工作首次提出了在密码子（GUG）-反密码子碱基对的第一个位置的G：U错配如何破坏起始真核生物核糖体中的调节能力，以及在CUG密码子中的起始与近乎于或有时一样强的方式比GUG密码子更强。我们的方法有望用于研究各种错配碱基对的亲和力变化。