Dataset Information

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

ABSTRACT: 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 Mg(2+)-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 Mg(2+) ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg(2+)-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg(2+)-bound loop structure. We propose this structure is a "gatekeeper" or precursor to Mg(2+) binding when those ions are present.

SUBMITTER: Bergonzo C

PROVIDER: S-EPMC4634716 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

Bergonzo Christina C Hall Kathleen B KB Cheatham Thomas E TE

The journal of physical chemistry. B 20150914 38

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 Mg(2+)-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the p ...[more]

PMID: 26328924

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Dataset Information

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

Publications

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

Similar Datasets

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