Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling
Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling
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DOI：
10.1021/jacs.9b12264
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发表时间：
2020-04-01
影响因子：
15
通讯作者：
O'Brien, Edward P.
中科院分区：
文献类型：
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作者：
Nissley, Daniel A.;Vu, Quyen V.;O'Brien, Edward P.
由于样品制备的挑战，新生蛋白质在其与转移RNA的共价键被破坏后从核糖体出口通道中排出尚未进行实验研究。在这里，我们调查这个过程中使用的多尺度建模，核糖体分析，和基因本体分析的组合。模拟一组代表性的122 E.大肠杆菌蛋白质，我们发现喷射时间的变化超过1000倍。在其C末端附近富含带负电荷残基的新生蛋白质喷射最快，而富含带正电荷残基的新生链往往喷射得慢得多。根据全原子模拟，将缓慢喷射的蛋白质拉出出口隧道比快速喷射的蛋白质需要更多的工作。能量分解揭示，对于缓慢排出蛋白质，这是由于新生链和带负电荷的核糖体-RNA之间的强吸引静电相互作用衬出口隧道，而对于快速排出蛋白质，这是由于它们与出口隧道的排斥静电相互作用。核糖体分析数据来自E.大肠杆菌的研究表明，缓慢喷射序列的存在与核糖体在终止密码子上花费更多时间相关，表明喷射过程可能会延迟核糖体再循环。在其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质，这表明这种序列特征可能通过延迟新生核糖体蛋白质释放到胞质溶胶中来帮助核糖体的共翻译组装。因此，由于静电相互作用的差异，核糖体的新生链喷射时间在蛋白质之间可能存在很大差异，可以影响核糖体回收，并且可能与某些蛋白质的合成和共翻译行为特别相关。
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 E. coli 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 E. coli 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.