Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data
Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data
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DOI：
10.1073/pnas.0708094104
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发表时间：
2007-10-16
影响因子：
11.1
通讯作者：
Frank, Joachim
中科院分区：
文献类型：
--
作者：
Li, Wen;Frank, Joachim
转移RNA(TRNA)在核糖体内转位时，暂时处于杂交P/E状态(P/E-tRNA)。在本研究中，我们通过将游离tRNA的分子动力学模拟结果与P/E-tRNA的冷冻EM图相关联，表征了P/E-tRNA的结构及其与核糖体的相互作用。在我们的方法中，我们表明低温EM图可以被解释为构象平均。沿着分子动力学轨迹(44 ns、18 ns和18 ns)，一些快照被证明与观测到的密度非常接近。在一个典型的结构中，CCA(3‘)臂是唯一扭曲的，并且反密码环的茎环在反密码环和D茎的连接处扭结。此外，图谱显示P/E-tRNA不再与23S rRNA的螺旋H69结合，而是灵活的，16S rRNA的螺旋H68和H44的构象与X射线结构中的构象不同。因此，我们的研究提供了P/E-tRNA的结构和动态信息，并表征了它与转位核糖体的相互作用。
Transfer RNA (tRNA) transiently occupies the hybrid P/E state (P/E-tRNA) when mRNA-tRNA are translocated in the ribosome. In this study, we characterize the structure of P/E-tRNA and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free tRNA with the cryo-EM map of P/E-tRNA. In our approach, we show that the cryo-EM map may be interpreted as a conformational average. Along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of the snapshots prove to be quite close to the observed density. In a representative structure, the CCA (3') arm is uniquely twisted, and the anticoclon stem loop is kinked at the junctions to both the anticoclon loop and the D stem. In addition, the map shows that the P/E-tRNA is no longer bound to helix H69 of 23S rRNA and is flexible, and the conformations of helices H68 and h44 of 16S rRNA differ from those in the x-ray structure. Thus, our study presents structural and dynamic information on the P/E-tRNA and characterizes its interactions with the translocating ribosome.