Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop
Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop
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DOI：
10.1021/acs.jpcb.4c00522
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发表时间：
2024-03-27
影响因子：
3.3
通讯作者：
Vashisth，Harish
中科院分区：
文献类型：
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作者：
Levintov，Lev;Vashisth，Harish
N6-甲基腺苷修饰是核糖核酸分子中含量最丰富的转录后修饰之一。利用分子动力学模拟和炼金术自由能计算，我们研究了在腺嘌呤单核苷酸和RNA发夹结构中加入这种修饰的结构和能量影响。在单核苷酸水平上，我们发现合成构型比反构型有利2.05±0.15千卡/摩尔。甲基化的不利影响是由于嘌呤环上的甲基和氮原子之间的空间重叠。然后，我们探索了包含AUCG四环的RNA发夹结构中甲基化的影响，该四环被“阅读器”蛋白(YTHDC1)识别，以促进长非编码RNA的转录沉默。虽然甲基化对发夹茎没有显著的构象影响，但与未甲基化的四环相比，甲基化的四环显示出更强的构象灵活性。灵活性的增加与两个碱基(A6和U7)的向外翻转有关，这两个碱基相互作用，并与四元环中的C8和G9碱基形成堆积作用，导致了类似于RNA/阅读器蛋白复合体中的构象。因此，甲基化诱导的构象灵活性可能有助于阅读器蛋白识别RNA。
The N6-methyladenosine modification is one of the most abundant post-transcriptional modifications in ribonucleic acid (RNA) molecules. Using molecular dynamics simulations and alchemical free-energy calculations, we studied the structural and energetic implications of incorporating this modification in an adenine mononucleotide and an RNA hairpin structure. At the mononucleotide level, we found that thesynconfiguration is more favorable than theanticonfiguration by 2.05 ± 0.15 kcal/mol. The unfavorable effect of methylation was due to the steric overlap between the methyl group and a nitrogen atom in the purine ring. We then probed the effect of methylation in an RNA hairpin structure containing an AUCG tetraloop, which is recognized by a “reader” protein (YTHDC1) to promote transcriptional silencing of long noncoding RNAs. While methylation had no significant conformational effect on the hairpin stem, the methylated tetraloop showed enhanced conformational flexibility compared to the unmethylated tetraloop. The increased flexibility was associated with the outward flipping of two bases (A6 and U7) which formed stacking interactions with each other and with the C8 and G9 bases in the tetraloop, leading to a conformation similar to that in the RNA/reader protein complex. Therefore, methylation-induced conformational flexibility likely facilitates RNA recognition by the reader protein.