Minimization of the E. coli ribosome, aided and optimized by community science
Minimization of the E. coli ribosome, aided and optimized by community science
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DOI：
10.1093/nar/gkad1254
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发表时间：
2024-01-12
影响因子：
14.9
通讯作者：
Schepartz，Alanna
中科院分区：
文献类型：
--
作者：
Tangpradabkul，Tiyaporn;Palo，Michael;Schepartz，Alanna
核糖体是一种核糖核蛋白复合体，存在于生命的各个领域。它的作用是催化蛋白质合成，即以信使核糖核酸为模板在α-氨基酸单体之间形成酰胺键。酰胺键的形成发生在大的核糖体亚基的一个高度保守的区域内，称为肽转移酶中心(PTC)。在这里，我们描述了mini-PTC 1.1的逐步设计和特征，它是一个284个核苷酸的RNA，概括了大肠杆菌PTC的许多基本特征。Mini-PTC 1.1在生理条件下折叠成PTC样结构，即使在没有r-蛋白的情况下也是如此，并与A-位和P-位tRNA的小分子类似物结合。Mini-PTC 1.1的序列与野生Typee不同。一群公民科学家使用在线视频游戏Eterna安装了12个核苷酸的Colicore糖体。这些碱基的变化改善了mini-PTC 1.1的二级结构和三级折叠，以及它与小分子底物类似物的结合能力。在这里，来自Eterna公民科学家和RNA结构分析的组合输入为设计最小的PTC提供了一个强大的工作流程，它概括了完整核糖体的许多特征。
The ribosome is a ribonucleoprotein complex found in all domains of life. Its role is to catalyze protein synthesis, the messenger RNA (mRNA)-templated formation of amide bonds between α-amino acid monomers. Amide bond formation occurs within a highly conserved region of the large ribosomal subunit known as the peptidyl transferase center (PTC). Here we describe the step-wise design and characterization of mini-PTC 1.1, a 284-nucleotide RNA that recapitulates many essential features of theEscherichia coliPTC. Mini-PTC 1.1 folds into a PTC-like structure under physiological conditions, even in the absence of r-proteins, and engages small molecule analogs of A- and P-site tRNAs. The sequence of mini-PTC 1.1 differs from the wild typeE. coliribosome at 12 nucleotides that were installed by a cohort of citizen scientists using the on-line video game Eterna. These base changes improve both the secondary structure and tertiary folding of mini-PTC 1.1 as well as its ability to bind small molecule substrate analogs. Here, the combined input from Eterna citizen-scientists and RNA structural analysis provides a robust workflow for the design of a minimal PTC that recapitulates many features of an intact ribosome.