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DOI	10.1073/pnas.2020837118
	Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA
	Hori N.; Denesyuk N.A.; Thirumalai D.
发表日期	2021
ISSN	00278424
卷号	118 期号:10
英文摘要	Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+ concentration between 0 and 30 mM. The Mg2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Coarse-grained simulation; Divalent ions; Ribosome assembly; RNA folding; Three-way junction
语种	英语
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/180396
作者单位	Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States; School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
推荐引用方式 GB/T 7714	Hori N.,Denesyuk N.A.,Thirumalai D.. Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA[J],2021,118(10).
APA	Hori N.,Denesyuk N.A.,&Thirumalai D..(2021).Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA.Proceedings of the National Academy of Sciences of the United States of America,118(10).
MLA	Hori N.,et al."Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA".Proceedings of the National Academy of Sciences of the United States of America 118.10(2021).