Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.
Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.
复制标题
Varkud卫星RNA的茎环V在存在单价离子的情况下表现出Mg（2+）结构的特征。
DOI：
10.1021/acs.jpcb.5b05190
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发表时间：
2015-09-24
期刊：
影响因子：
--
通讯作者：
Cheatham TE 3rd
中科院分区：
文献类型：
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作者：
Bergonzo C;Hall KB;Cheatham TE 3rd
Varkud 卫星 RNA 含有一种自切割核酶，已被证明其功能独立于周围环境。这种 160 个核苷酸的核酶采用具有催化活性的三级结构，其中包括由茎环 I 和茎环 V (SLV) 形成的接吻发夹复合物。通过溶液 NMR 表明，分离的 SLV 的五核苷酸 5'-rUGACU 环采用 Mg2+ 依赖性 U 型转弯结构。这里通过单价和二价离子存在下的分子动力学模拟来检查这种 U 形转弯发夹。模拟在全原子水平上证实了 Mg2+ 离子在稳定环路中的作用以及暴露于溶剂的 U700 碱的作用的假设。此外，这些模拟表明，不含 Mg2+ 的茎环采用了多种结构，包括与 Mg2+ 结合的环结构类似的能量有利的结构。我们认为，当这些离子存在时，这种结构是 Mg2+ 结合的“看门人”或前体。
The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5′-rUGACU loop of the isolated SLV has been shown to adopt a Mg2+-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg2+ ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg2+-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg2+-bound loop structure. We propose this structure is a “gatekeeper” or precursor to Mg2+ binding when those ions are present.