Transfer RNA (tRNA) is the most diversely modified RNA. Although the strictly conserved purine position 37 in the anticodon stem loop (ASL) undergoes a wide assortment of modifications that are phylogenetically distributed, we do not yet fully understand the roles of these modifications. To provide molecular-level details for how such modifications impact the structure and function of tRNA, molecular dynamics (MD) simulations are used to compare the structural dynamics of unmodified and modified tRNAs. A focus is placed on three hypermodified base families that include the parent i6A, t6A, and yW modifications, as well as derivatives formed through the incorporation of additional chemical substituents (such as a hydroxy, methyl, thiomethyl or peroxy group). Our data reveal that the hypermodifications exhibit significant conformational flexibility in tRNA, which can be modulated by additional chemical functionalization. Regardless of the modification family or level of chemical substitution, the hypermodifications do not affect the global tRNA three-dimensional structure or the domain-domain interactions, suggesting that there are no long-range effects of modifying the 37th position. Although the overall structure of the anticodon stem remains intact regardless of the modification considered, the anticodon loop must rearrange to accommodate the bulky, dynamic hypermodifications, which includes changes in the nucleotide glycosidic and backbone conformations, and enhanced or completely new nucleobase-nucleobase interactions compared to unmodified tRNA or tRNA containing smaller (m1G) modifications at the 37th position. Importantly, the extent of the changes in the anticodon loop is influenced by the addition of small functional groups to parent modifications, implying each substituent can further finetune tRNA structure. Although the dominant conformation of the ASL is achieved in different ways for each modification, the molecular features of all modified tRNA drive the ASL domain to adopt the functional open-loop conformation. Importantly, the impact of the hypermodifications is preserved in different sequence contexts. These findings highlight the likely role of modifications in regulating mRNA structure and translation.

中文翻译：

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tRNA 反密码子茎环第 37 位的转录后修饰：MD 模拟的结构见解

转移 RNA (tRNA) 是修饰最多样化的 RNA。尽管反密码子茎环 (ASL) 中严格保守的嘌呤位置 37 经历了系统发育分布的各种修饰，但我们尚未完全了解这些修饰的作用。为了提供此类修饰如何影响 tRNA 的结构和功能的分子水平详细信息，使用分子动力学 (MD) 模拟来比较未修饰和修饰的 tRNA 的结构动力学。重点关注三个超修饰碱基家族，包括母体 i6A、t6A 和 yW 修饰，以及通过掺入其他化学取代基（例如羟基、甲基、硫甲基或过氧基）形成的衍生物。我们的数据表明，超修饰在 tRNA 中表现出显着的构象灵活性，可以通过额外的化学功能化进行调节。无论修饰家族或化学取代水平如何，超修饰都不会影响整体 tRNA 三维结构或域与域之间的相互作用，这表明第 37 位的修饰不会产生长期影响。尽管无论考虑何种修饰，反密码子茎的整体结构都保持完整，但反密码子环必须重新排列以适应庞大的动态超修饰，其中包括核苷酸糖苷和主链构象的变化，以及与相比之下增强的或全新的核碱基-核碱基相互作用。未修饰的 tRNA 或第 37 位含有较小 (m1G) 修饰的 tRNA。重要的是，反密码子环的变化程度受到亲本修饰中添加小功能团的影响，这意味着每个取代基可以进一步微调 tRNA 结构。尽管每次修饰以不同的方式实现 ASL 的主导构象，但所有修饰的 tRNA 的分子特征都驱动 ASL 结构域采用功能性开环构象。重要的是，超修改的影响在不同的序列环境中得以保留。这些发现强调了修饰在调节 mRNA 结构和翻译中可能发挥的作用。