Structural significance of conformational preferences and ribose ring puckering of newly discovered hyper modified nucleotide, 5’-monophosphate 2-methylthio cyclic N⁶-threonylcarbamoyladenosine (p-ms²ct⁶A) have been investigated using quantum chemical semi-empirical RM1 and molecular dynamics simulation techniques. Automated geometry optimization of most stable structure of p-ms²ct⁶A has also been carried out with the help of abinitio (HF SCF, DFT) as well as semi empirical quantum chemical (RM1, AM1, PM3, and PM6) methods. Most stable structure of p-ms²ct⁶A is stabilized by intramolecular interactions between N(3)…HC(2’), N(1)…HC(16), O(13)…HC(15), and O(13)…HO(14). The torsion angles alpha (α) and beta (β) show the significant characteristic patterns with the involvement of intramolecular hydrogen bonding to provide stability to the p-ms²ct⁶A. Further, molecular dynamics simulations of p-ms²ct⁶A revealed the role of ribose sugar ring puckering i.e. C2’-endo and C3’-endo on the structural dynamics of ms²ct⁶A side chain. The modified nucleotide p-ms²ct⁶A periodically prefers both the C2’-endo and C3’-endo sugar with ‘anti’ and ‘syn’ conformations. This property of p-ms²ct⁶A could be useful to recognize the starting ANN codons. All atom explicit MD simulation of anticodon loop (ACL) of tRNA^Lys of Bacillus subtilis containing ms²ct⁶A at 37th position showed the U-turn feature, base stacking ability with other adjacent bases and hydrogen bonding interactions similar to the isolated base p-ms²ct⁶A. The ribose sugar puckering contributes to the orientation of the side chain conformation of p-ms²ct⁶A. Thus, the present study could be helpful to understand the structure-function relationship of the hypermodified nucleoside, ms²ct⁶A in recognition of the proper codons AAA/AAG during protein biosynthesis.

已使用量子化学半经验 RM1 和分子动力学研究了新发现的超修饰核苷酸 5'-单磷酸 2-甲硫基环状 N ⁶ -苏氨酰氨基甲酰腺苷 (p-ms ² ct ⁶ A) 的构象偏好和核糖环褶皱的结构意义模拟技术。在 abinitio（HF SCF、DFT）以及半经验量子化学（RM1、AM1、PM3 和 PM6）方法的帮助下，还对最稳定的 p-ms ² ct ^{6 A 结构进行了自动几何优化。}p-ms ² ct ^{6的最稳定结构}A 通过 N(3)…HC(2')、N(1)…HC(16)、O(13)…HC(15) 和 O(13)…HO(14) 之间的分子内相互作用稳定。扭转角 alpha (α) 和 beta (β) 显示出显着的特征模式，其中涉及分子内氢键，为 p-ms ² ct ^{6 A 提供稳定性。此外，p-ms 2} ct ⁶ A的分子动力学模拟揭示了核糖环褶皱即C2'-endo和C3'- endo对ms ² ct ⁶ A侧链的结构动力学的作用。修饰的核苷酸 p-ms ² ct ⁶ A 周期性地偏好C2'-endo和具有“反”和“顺”构象的C3'-内切糖。p-ms ² ct ⁶ A 的这一特性可用于识别起始 ANN 密码子。在第 37 位含有 ms ² ct ⁶ A的枯草芽孢杆菌tRNA ^Lys的反密码子环 (ACL) 的所有原子显式 MD 模拟显示了 U 形转弯特征、与其他相邻碱基的碱基堆叠能力以及与分离的碱基 p 相似的氢键相互作用-ms ² ct ⁶ A. 核糖褶皱有助于 p-ms ² ct ^{6侧链构象的方向}A. 因此，本研究有助于理解超修饰核苷 ms ² ct ⁶ A 的结构-功能关系，以识别蛋白质生物合成过程中的正确密码子 AAA/AAG。