Ribozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries along independent MD simulations with different protonation states of the active site basic species reveals that only the canonical system, with no additional protonation changes, renders reactive conformations. A change in the coordination sphere of the Mg²⁺ ion has been observed during the simulations, which allows proposing a mechanism to explain the unique mode of action of the pistol ribozyme by comparison with other ribozymes. The present results are at the center of the debate originated from recent experimental and theoretical studies on pistol ribozyme.

核酶是一种巨大的复杂生物催化剂，由 RNA 和蛋白质的组合组成。尽管如此，小核酶（自切割核酶）的数量减少了，它们仅由 RNA 形成，显然它们存在于原始生物系统的细胞中。揭示这些“化石”酶的细节不仅有助于理解生命的起源，而且有助于开发新的简化的人工酶。本文提出了通过经典 MD 模拟和 QM/MM 混合计算进行的手枪核酶反应性的计算研究，以阐明其催化机制。沿着具有不同活性位点基本物种质子化状态的独立 MD 模拟的几何结构分析表明，只有规范系统，没有额外的质子化变化，呈现反应性构象。Mg 配位范围的变化在模拟过程中观察到²⁺离子，这允许提出一种机制来解释手枪核酶与其他核酶相比的独特作用模式。目前的结果是源自最近关于手枪核酶的实验和理论研究的争论的中心。