Godwin Ryan C, Macnamara Lindsay M, Alexander Rebecca W, Salsbury Freddie R
Department of Physics and Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27106, United States.
Department of Biochemistry, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina 27106, United States.
ACS Omega. 2018 Sep 30;3(9):10668-10678. doi: 10.1021/acsomega.8b00280. Epub 2018 Sep 5.
The fidelity of protein synthesis is largely dominated by the accurate recognition of transfer RNAs (tRNAs) by their cognate aminoacyl-tRNA synthetases. Aminoacylation of each tRNA with its cognate amino acid is necessary to maintain the accuracy of genetic code input. Aminoacylated tRNA functions in both initiation and elongation steps during protein synthesis. As a precursor to the investigation of a methionyl-tRNA synthetase-tRNA complex, presented here are the results of molecular dynamics (MD) for single nucleotide substitutions in the D-loop of tRNA (G15A, G18A, and G19A) probing structure/function relationships. The core of tRNA likely mediates an effective communication between the tRNA anticodon and acceptor ends, contributing an acceptor stem rearrangement to fit into the enzyme-active site. Simulations of tRNA were performed for 1 μs four times each. The MD simulations showed changes in tRNA flexibility and long-range communication most prominently in the G18A variant. The results indicate that the overall tertiary structure of tRNA remains unchanged with these substitutions; yet, there are perturbations to the secondary structure. Network-based analysis of the hydrogen bond structure and correlated motion indicates that the secondary structure elements of the tRNA are highly intraconnected, but loosely interconnected. Specific nucleotides, including U8 and G22, stabilize the mutated structures and are candidates for substitution in future studies.
蛋白质合成的保真度在很大程度上取决于其同源氨酰 - tRNA合成酶对转运RNA（tRNA）的准确识别。每个tRNA与其同源氨基酸的氨酰化对于维持遗传密码输入的准确性是必要的。氨酰化的tRNA在蛋白质合成的起始和延伸步骤中均发挥作用。作为对甲硫氨酰 - tRNA合成酶 - tRNA复合物研究的前奏，本文展示了对tRNA D环中单个核苷酸取代（G15A、G18A和G19A）进行分子动力学（MD）研究以探索结构/功能关系的结果。tRNA的核心可能介导了tRNA反密码子和受体末端之间的有效通讯，促使受体茎重排以适应酶活性位点。对tRNA进行了四次每次1微秒的模拟。MD模拟显示，在G18A变体中，tRNA的灵活性和长程通讯变化最为显著。结果表明，这些取代后tRNA的整体三级结构保持不变；然而，二级结构受到了扰动。基于网络的氢键结构和相关运动分析表明，tRNA的二级结构元件内部高度连接，但相互之间连接松散。包括U8和G22在内的特定核苷酸稳定了突变结构，是未来研究中取代的候选对象。
