Folding of a small RNA hairpin based on simulation with replica exchange molecular dynamics.
Folding of a small RNA hairpin based on simulation with replica exchange molecular dynamics.
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DOI：
10.1021/jp904573r
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发表时间：
2010-04
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影响因子：
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通讯作者：
Guanghong Zuo;Wenfei Li;Jian Zhang;Jin Wang;Wei Wang
中科院分区：
文献类型：
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作者：
Guanghong Zuo;Wenfei Li;Jian Zhang;Jin Wang;Wei Wang
利用分子动力学模拟方法研究了小RNA四环发夹结构的折叠过程，旨在了解这种小而快的RNA折叠器的折叠机理。我们的研究结果表明，这种RNA发夹结构尽管尺寸很小，但却具有非常复杂的折叠行为。发现折叠跃迁具有低协同性。而不是两个状态的折叠，观察到四个主要状态，包括天然状态，中间，未折叠状态，和错误折叠状态。错折叠态主要由非天然氢键稳定，并且更紧凑。观察到两种潜在的折叠途径，其中两个碱基对以不同的顺序形成，并且内侧碱基对在末端碱基对之前形成的途径更有利，并且主导RNA发夹的折叠。
The folding of a small RNA tetraloop hairpin is studied based on intensive molecular dynamics simulation, aiming to understand the folding mechanism of this small and fast RNA folder. Our results showed that this RNA hairpin has very complicated folding behavior in spite of its small size. It is found that the folding transition has low cooperativity. Instead of a two-state folding, four major states are observed, including the native state, the intermediate, the unfolded state, and the misfolded state. The misfolded state is mainly stabilized by the non-native hydrogen bonds, and is more compact. Two potential folding pathways, in which two basepairs formed with different order, are observed, and the pathway with the inboard basepair formed before the terminal one is much more favorable, and dominates the folding of the RNA hairpin.