Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, New Hampshire 03824, United States.
J Phys Chem B. 2024 Apr 4;128(13):3157-3166. doi: 10.1021/acs.jpcb.4c00522. Epub 2024 Mar 27.
The N-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 the configuration is more favorable than the configuration 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.
N6-甲基腺苷修饰是 RNA 分子中最丰富的转录后修饰之一。我们使用分子动力学模拟和变分自由能计算，研究了在腺嘌呤单核苷酸和 RNA 发夹结构中引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 构象比 构象更稳定，稳定能差为 2.05 ± 0.15 kcal/mol。甲基化的不利影响是由于甲基与嘌呤环上的一个氮原子之间的空间位阻。然后，我们在含有 AUCG 四核苷酸的 RNA 发夹结构中探测了甲基化的影响，该四核苷酸被“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，但与未甲基化的四核苷酸相比，甲基化的四核苷酸表现出增强的构象灵活性。这种增加的灵活性与两个碱基（A6 和 U7）的向外翻转有关，它们彼此形成堆积相互作用，并与四核苷酸中的 C8 和 G9 碱基相互作用，导致与 RNA/阅读器蛋白复合物中相似的构象。因此，甲基化诱导的构象灵活性可能有助于阅读器蛋白对 RNA 的识别。
