Abstract

The ribonuclease III (RNase III) cleaves dsRNA in specific positions generating mature RNAs. RNase III enzymes play important roles in RNA processing, post-transcriptional gene expression, and defense against viral infection. The enzyme’s active site contains Mg²⁺ ions bound by a network of acidic residues and water molecules, but there is a lack of information about their specific roles. In this work, multiple steered molecular dynamics simulations at QM/MM level were performed to explore the hydrolysis reaction carried out by the enzyme. Free energy profiles modifying the features of the active site are obtained and the role of Mg²⁺ ions, the solvent molecules and the residues of the active site are discussed in detail. Our results show that Mg²⁺ ions carry out different roles in the hydrolysis process positioning the substrate for the attack from a coordinated nucleophile and activating it to perform hydrolysis reaction, cleaving the dsRNA backbone in a S_N2 substitution. In addition, water molecules present in the active site lower the energy barrier of the process.

Graphical abstract

RNase III hydrolyzes dsRNA to generate mature RNAs. For this purpose, its active site contains Mg²⁺ which has an important role during the reaction. Results show that the Mg²⁺ activates the solvent molecule that produces the nucleophilic attack and the surrounding waters contribute significantly to the hydrolysis process.

中文翻译：

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通过QM / MM模拟研究细菌RNase III对Mg2 +在dsRNA加工机制中的作用。

抽象的

核糖核酸酶III（RNase III）在特定位置切割dsRNA，生成成熟的RNA。RNase III酶在RNA加工，转录后基因表达和抗病毒感染中起着重要作用。该酶的活性位点包含由酸性残基和水分子网络结合的Mg ²⁺离子，但缺乏有关其具体作用的信息。在这项工作中，在QM / MM水平上进行了多个操纵分子动力学模拟，以探索该酶进行的水解反应。获得了改变活性位点特征的自由能分布图，并详细讨论了Mg ²⁺离子，溶剂分子和活性位点残基的作用。我们的结果表明，Mg ²⁺离子在水解过程中发挥不同的作用，从而将底物定位成从配位亲核体中进攻，并激活它以进行水解反应，从而以S _N 2取代形式裂解dsRNA主链。另外，存在于活性位点中的水分子降低了该过程的能垒。

图形概要

RNA酶III水解dsRNA以产生成熟的RNA。为此，它的活性位点含有Mg ²⁺，它在反应过程中起着重要的作用。结果表明，Mg ²⁺激活了引起亲核攻击的溶剂分子，周围的水对水解过程起了重要作用。