Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
Genes (Basel). 2021 Mar 11;12(3):399. doi: 10.3390/genes12030399.
tRNA methyltransferase 5 (Trm5) enzyme is an S-adenosyl methionine (AdoMet)-dependent methyltransferase which methylates the G37 nucleotide at the N atom of the tRNA. The free form of Trm5 enzyme has three intrinsically disordered regions, which are highly flexible and lack stable three-dimensional structures. These regions gain ordered structures upon the complex formation with tRNA, also called disorder-to-order transition (DOT) regions. In this study, we performed molecular dynamics (MD) simulations of archaeal Trm5 in free and complex forms and observed that the DOT residues are highly flexible in free proteins and become stable in complex structures. The energetic contributions show that DOT residues are important for stabilising the complex. The DOT1 and DOT2 are mainly observed to be important for stabilising the complex, while DOT3 is present near the active site to coordinate the interactions between methyl-donating ligands and G37 nucleotides. In addition, mutational studies on the Trm5 complex showed that the wild type is more stable than the G37A tRNA mutant complex. The loss of productive interactions upon G37A mutation drives the AdoMet ligand away from the 37th nucleotide, and Arg145 in DOT3 plays a crucial role in stabilising the ligand, as well as the G37 nucleotide, in the wild-type complex. Further, the overall energetic contribution calculated using MMPBSA corroborates that the wild-type complex has a better affinity between Trm5 and tRNA. Overall, our study reveals that targeting DOT regions for binding could improve the inhibition of Trm5.
tRNA 甲基转移酶 5（Trm5）酶是一种 S-腺苷甲硫氨酸（AdoMet）依赖性甲基转移酶，它将 tRNA 的 G37 核苷酸的 N 原子甲基化。游离形式的 Trm5 酶有三个固有无序区域，这些区域非常灵活，缺乏稳定的三维结构。这些区域在与 tRNA 形成复合物时获得有序结构，也称为无序到有序转变（DOT）区域。在这项研究中，我们对原核生物 Trm5 的自由形式和复合物形式进行了分子动力学（MD）模拟，观察到 DOT 残基在游离蛋白中非常灵活，在复合物结构中变得稳定。能量贡献表明，DOT 残基对于稳定复合物很重要。DOT1 和 DOT2 主要被观察到对于稳定复合物很重要，而 DOT3 位于活性位点附近，以协调供甲基配体与 G37 核苷酸之间的相互作用。此外，对 Trm5 复合物的突变研究表明，野生型比 G37A tRNA 突变体复合物更稳定。G37A 突变导致有效相互作用的丧失，使 AdoMet 配体远离第 37 个核苷酸，并且 DOT3 中的 Arg145 在稳定野生型复合物中的配体以及 G37 核苷酸方面发挥关键作用。此外，使用 MMPBSA 计算的整体能量贡献表明，野生型复合物在 Trm5 和 tRNA 之间具有更好的亲和力。总的来说，我们的研究表明，针对 DOT 区域进行结合可能会提高 Trm5 的抑制效果。
