Dynamics of Forward and Backward Translocation of mRNA in the Ribosome

Translocation of the mRNA-tRNA complex in the ribosome, which is catalyzed by elongation factor EF-G, is one of critical steps in the elongation cycle of protein synthesis. Besides this conventional forward translocation, the backward translocation can also occur, which can be catalyzed by elongation factor LepA. However, the molecular mechanism of the translocation remains elusive. To understand the mechanism, here we study theoretically the dynamics of the forward translocation under various nucleotide states of EF-G and the backward translocation in the absence of and in the presence of LepA. We present a consistent explanation of spontaneous forward translocations in the absence of EF-G, the EF-G-catalyzed forward translocations in the presence of a non-hydrolysable GTP analogue and in the presence of GTP, and the spontaneous and LepA-catalyzed backward translocation. The theoretical results provide quantitative explanations of a lot of different, independent experimental data, and also provide testable predictions.

核糖体中mRNA-tRNA复合物的移位过程（由延伸因子EF-G催化）是蛋白质合成延伸循环中的关键步骤之一。除这一常规正向移位外，还可发生反向移位，该过程可由延伸因子LepA催化。然而，此类移位的分子机制仍未明确。为解析该机制，本文从理论层面研究了EF-G处于不同核苷酸结合状态下的正向移位动力学，以及无LepA和存在LepA时的反向移位动力学。本研究对无EF-G时的自发正向移位、存在不可水解GTP类似物时及存在GTP时EF-G催化的正向移位，以及自发反向移位和LepA催化的反向移位给出了统一的解释。本理论结果可对诸多独立的不同实验数据提供定量阐释，同时还提出了可验证的预测。