Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
Commun Biol. 2023 Apr 7;6(1):379. doi: 10.1038/s42003-023-04751-z.
Helicases are motor enzymes found in every living organism and viruses, where they maintain the stability of the genome and control against false recombination. The DEAH-box helicase Prp43 plays a crucial role in pre-mRNA splicing in unicellular organisms by translocating single-stranded RNA. The molecular mechanisms and conformational transitions of helicases are not understood at the atomic level. We present a complete conformational cycle of RNA translocation by Prp43 in atomic detail based on molecular dynamics simulations. To enable the sampling of such complex transition on the millisecond timescale, we combined two enhanced sampling techniques, namely simulated tempering and adaptive sampling guided by crystallographic data. During RNA translocation, the center-of-mass motions of the RecA-like domains followed the established inchworm model, whereas the domains crawled along the RNA in a caterpillar-like movement, suggesting an inchworm/caterpillar model. However, this crawling required a complex sequence of atomic-scale transitions involving the release of an arginine finger from the ATP pocket, stepping of the hook-loop and hook-turn motifs along the RNA backbone, and several others. These findings highlight that large-scale domain dynamics may be controlled by complex sequences of atomic-scale transitions.
解旋酶是存在于所有生物体和病毒中的运动酶，它们可以维持基因组的稳定性并防止错误重组。DEAH-box 解旋酶 Prp43 通过转运单链 RNA 在单细胞生物中剪接前体 RNA 中发挥关键作用。解旋酶的分子机制和构象转变在原子水平上尚不清楚。我们基于分子动力学模拟，以原子细节呈现了 Prp43 介导的 RNA 转位的完整构象循环。为了在毫秒时间尺度上对这种复杂转变进行采样，我们结合了两种增强采样技术，即模拟淬火和基于晶体学数据的自适应采样。在 RNA 转位过程中，RecA 样结构域的质心运动遵循既定的尺蠖模型，而结构域则以毛毛虫样的运动在 RNA 上爬行，表明存在尺蠖/毛毛虫模型。然而，这种爬行需要一系列复杂的原子尺度转变，包括精氨酸指从 ATP 口袋释放、钩环和钩转模体沿着 RNA 骨架移动以及其他几个转变。这些发现表明，大规模结构域动力学可能受到复杂的原子尺度转变序列的控制。
