The mechanism by which genetic information was copied prior to the evolution of ribozymes is of great interest because of its importance to the origin of life. The most effective known process for the nonenzymatic copying of an RNA template is primer extension by a two-step pathway in which 2-aminoimidazole-activated nucleotides first react with each other to form an imidazolium-bridged intermediate that subsequently reacts with the primer. Reaction kinetics, structure-activity relationships, and X-ray crystallography have provided insight into the overall reaction mechanism, but many puzzles remain. In particular, high concentrations of Mg are required for efficient primer extension, but the mechanism by which Mg accelerates primer extension remains unknown. By analogy with the mechanism of DNA and RNA polymerases, a role for Mg in facilitating the deprotonation of the primer 3′-hydroxyl is often assumed, but no catalytic metal ion is seen in crystal structures of the primer-extension complex. To explore the potential effects of Mg binding in the reaction center, we performed atomistic molecular dynamics simulations of a series of modeled complexes in which a Mg ion was placed in the reaction center with inner-sphere coordination with different sets of functional groups. Our simulations suggest that coordination of a Mg ion with both O3′ of the terminal primer nucleotide and the pro- nonbridging oxygen of the reactive phosphate of an imidazolium-bridged dinucleotide would help to pre-organize the structure of the primer/template substrate complex to favor the primer-extension reaction. Our results suggest that the catalytic metal ion may play an important role in overcoming electrostatic repulsion between a deprotonated O3′ and the reactive phosphate of the bridged dinucleotide and lead to testable predictions of the mode of Mg binding that is most relevant to catalysis of primer extension.

中文翻译：

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模拟预测非酶引物延伸反应中心中优选的 Mg2+ 配位

在核酶进化之前遗传信息的复制机制因其对生命起源的重要性而引起人们极大的兴趣。 RNA模板非酶复制最有效的已知方法是通过两步途径进行引物延伸，其中2-氨基咪唑激活的核苷酸首先相互反应形成咪唑桥中间体，随后与引物反应。反应动力学、结构-活性关系和 X 射线晶体学已经提供了对整个反应机制的深入了解，但仍然存在许多谜团。特别是，有效的引物延伸需要高浓度的 Mg，但 Mg 加速引物延伸的机制仍不清楚。通过与 DNA 和 RNA 聚合酶的机制类比，通常认为 Mg 在促进引物 3'-羟基去质子化中发挥作用，但在引物延伸复合物的晶体结构中没有看到催化金属离子。为了探索镁在反应中心结合的潜在影响，我们对一系列模型配合物进行了原子分子动力学模拟，其中镁离子被放置在反应中心，并与不同的官能团组进行内球配位。我们的模拟表明，Mg 离子与末端引物核苷酸的 O3' 和咪唑鎓桥联二核苷酸的活性磷酸盐的亲非桥接氧的配位将有助于预先组织引物/模板底物复合物的结构有利于引物延伸反应。我们的结果表明，催化金属离子可能在克服去质子化的 O3' 和桥联二核苷酸的反应性磷酸盐之间的静电排斥方面发挥重要作用，并导致对与引物延伸催化最相关的 Mg 结合模式进行可测试的预测。