Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations
Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations
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RAM 变构激活人类 mRNA 帽甲基转移酶 (RNMT) 的机制：加速分子动力学模拟的见解
DOI：
10.1101/558502
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发表时间：
2019
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影响因子：
--
通讯作者：
Bueren-Calabuig J
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文献类型：
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作者：
Bueren-Calabuig J
RNA鸟嘌呤- n7甲基转移酶（RNMT）与RNMT激活蛋白（RAM）在新生RNA聚合酶II转录本的5 '端催化形成n7甲基化的鸟嘌呤帽结构。mRNA帽保护初级转录物免受外切酶的侵害，并招募介导RNA加工、输出和翻译的帽结合复合物。通过微秒标准和加速分子动力学模拟，我们首次提供了RAM对RNMT变构调控的详细分子机制。我们发现RAM选择了最适合结合底物（AdoMet和帽）的RNMT活性位点构象，从而增强了它们的亲和力。此外，我们的研究结果强烈提示了帽结合促进后续AdoMet结合的可能情况，这与之前提出的合作结合模型一致。通过网络社区分析，我们揭示了潜在的远程变构网络和路径，这些网络和路径对RAM的变构调节至关重要。我们的发现补充并解释了之前关于RNMT活性的实验数据。此外，本研究提供了最完整的cap和AdoMet结合姿势和酶活性位点内相互作用的描述。这一信息对于将RNMT视为有希望的抗癌靶点的药物发现工作至关重要。
The RNA guanine-N7 methyltransferase (RNMT) in complex with RNMT-activating miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5′ end of nascent RNA polymerase II transcripts. The mRNA cap protects the primary transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. By using microsecond standard and accelerated molecular dynamics simulations, we provide for the first time a detailed molecular mechanism of allosteric regulation of RNMT by RAM. We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. Furthermore, our results strongly suggest the likely scenario in which the cap binding promotes the subsequent AdoMet binding, consistent with the previously suggested cooperative binding model. By employing the network community analyses, we revealed the underlying long-range allosteric networks and paths that are crucial for allosteric regulation by RAM. Our findings complement and explain previous experimental data on RNMT activity. Moreover, this study provides the most complete description of the cap and AdoMet binding poses and interactions within the enzyme’s active site. This information is critical for the drug discovery efforts that consider RNMT as a promising anti-cancer target.