Resolution-exchanged simulations reveal ribosomal frameshifting via subunit rolling. Chang et al.

We are interested in modeling the perturbed dynamics of the ribosome upon encountering a stable mRNA pseudoknot (human telomerase dU177 variant), and how the resulting conformational changes lead to programmed ribosomal frameshifting.

First, all of the missing subunits of the non-rotated- and rotated-state ribosomes were modeled (provided here as PDB files). The intrinsic dynamics of these ribosome structures were obtained with anisotropic network model (ANM; codes available on https://github.com/Yuan-Yu/bioStructureM).

Second, the pseudoknot structure was pulled into the mRNA entrance of the ribosome with steered molecular dynamics (SMD) simulations (trajectory provided here). The interaction forces between the pseudoknot and the mRNA entrance were calculated from SMD simulations, and combined with intrinsic dynamics from ANM using linear response theory (LRT; codes available on https://github.com/Yuan-Yu/bioStructureM). Interestingly, a rolling motion of 30S was observed.

Finally, the tRNAs and their surroundings of the rolled structure were equilibrated with MD simulations. After equilibration, production runs of MD simulations revealed spontaneous tRNA slippage (trajectory provided here), indicating that pseudoknot-induced subunit rolling is the motion that triggers programmed ribosomal frameshifting.

本研究致力于模拟核糖体在遭遇稳定的mRNA假结（人类端粒酶dU177变异体）时产生的扰动动力学，以及由此引发的构象变化如何导致程序化核糖体移码。首先，对非旋转态和旋转态核糖体中缺失的亚基进行了建模（此处提供PDB文件）。利用各向异性网络模型（ANM；代码可在https://github.com/Yuan-Yu/bioStructureM上获取）获得了这些核糖体结构的固有动力学。其次，通过导向分子动力学（SMD）模拟将假结结构拉入核糖体的mRNA入口（此处提供轨迹）。从SMD模拟中计算了假结与mRNA入口之间的相互作用力，并利用线性响应理论（LRT；代码可在https://github.com/Yuan-Yu/bioStructureM上获取）将其与ANM的固有动力学相结合。有趣的是，观察到30S亚基的滚动运动。最后，利用分子动力学（MD）模拟对滚动结构的tRNA及其周围环境进行平衡。平衡后，MD模拟的生产运行揭示了自发的tRNA滑动（此处提供轨迹），表明假结诱导的亚基滚动是触发程序化核糖体移码的运动。