Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
Institute for Computational Sciences and Technology, Ho Chi Minh City, Vietnam.
J Am Chem Soc. 2020 Apr 1;142(13):6103-6110. doi: 10.1021/jacs.9b12264. Epub 2020 Mar 23.
The ejection of nascent proteins out of the ribosome exit tunnel, after their covalent bond to transfer-RNA has been broken, has not been experimentally studied due to challenges in sample preparation. Here, we investigate this process using a combination of multiscale modeling, ribosome profiling, and gene ontology analyses. Simulating the ejection of a representative set of 122 proteins we find a greater than 1000-fold variation in ejection times. Nascent proteins enriched in negatively charged residues near their C-terminus eject the fastest, while nascent chains enriched in positively charged residues tend to eject much more slowly. More work is required to pull slowly ejecting proteins out of the exit tunnel than quickly ejecting proteins, according to all-atom simulations. An energetic decomposition reveals, for slowly ejecting proteins, that this is due to the strong attractive electrostatic interactions between the nascent chain and the negatively charged ribosomal-RNA lining the exit tunnel, and for quickly ejecting proteins, it is due to their repulsive electrostatic interactions with the exit tunnel. Ribosome profiling data from reveals that the presence of slowly ejecting sequences correlates with ribosomes spending more time at stop codons, indicating that the ejection process might delay ribosome recycling. Proteins that have the highest positive charge density at their C-terminus are overwhelmingly ribosomal proteins, suggesting the possibility that this sequence feature may aid in the cotranslational assembly of ribosomes by delaying the release of nascent ribosomal proteins into the cytosol. Thus, nascent chain ejection times from the ribosome can vary greatly between proteins due to differential electrostatic interactions, can influence ribosome recycling, and could be particularly relevant to the synthesis and cotranslational behavior of some proteins.
新生蛋白质在与转移 RNA 的共价键断裂后从核糖体出口隧道中排出，但由于样品制备的挑战，尚未进行实验研究。在这里，我们使用多尺度建模、核糖体分析和基因本体分析的组合来研究这个过程。通过模拟一组具有代表性的 122 种蛋白质的排出，我们发现排出时间有超过 1000 倍的差异。在其 C 末端附近带有负电荷残基的新生蛋白质排出最快，而富含正电荷残基的新生链则倾向于排出得慢得多。根据全原子模拟，从出口隧道中拉出排出缓慢的蛋白质比拉出排出快速的蛋白质需要更多的工作。能量分解表明，对于排出缓慢的蛋白质，这是由于新生链与带负电荷的核糖体 RNA 之间的强静电吸引相互作用，对于排出快速的蛋白质，这是由于它们与出口隧道的静电排斥相互作用。来自的数据表明，缓慢排出序列的存在与核糖体在终止密码子上停留的时间更长有关，这表明排出过程可能会延迟核糖体的回收。在 C 末端具有最高正电荷密度的蛋白质绝大多数是核糖体蛋白，这表明该序列特征可能通过延迟新生核糖体蛋白进入细胞质的释放，从而有助于共翻译核糖体的组装。因此，由于不同的静电相互作用，新生蛋白质从核糖体中的排出时间在不同蛋白质之间可能有很大差异，这可能会影响核糖体的回收，并且对于一些蛋白质的合成和共翻译行为可能特别重要。
