Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg2+ Bound Structure in the Presence of Monovalent Ions

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• 作者：Christina Bergonzo ; Kathleen B. Hall ; Thomas E. Cheatham ; III
• 刊名：Journal of Physical Chemistry B
• 出版年：2015
• 出版时间：September 24, 2015
• 年：2015
• 卷：119
• 期：38
• 页码：12355-12364
• 全文大小：595K
• ISSN：1520-5207

文摘

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鈥?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 鈥済atekeeper鈥?or precursor to Mg²⁺ binding when those ions are present.