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- W2901894003 abstract "Using computer simulations, we consider the balance of thermodynamic forces that collapse RNA. A model helix-junction-helix (HJH) construct is used to investigate the transition from an extended to a collapsed conformation. Conventional Molecular Dynamics and Milestoning Simulations are used to study the free energy profile of the process for two ion concentrations. We illustrate that HJH folds to a collapsed state with two types of counterions (Mg2+ and K+). By dissecting the free energy landscape into energetic and entropic contributions, we illustrate that the electrostatic forces between the RNA and the mobile ions do not drive the RNA to a collapsed state. Instead, entropy gains from water expulsion near the neighborhood of the RNA provide the stabilization free energy that tilt HJH into more compact structures. Further simulations of a three-helix hammerhead ribozyme show a similar behavior and support the idea of collapse due to increased gain in water entropy." @default.
- W2901894003 created "2018-11-29" @default.
- W2901894003 creator A5072275747 @default.
- W2901894003 creator A5081349407 @default.
- W2901894003 date "2018-11-22" @default.
- W2901894003 modified "2023-10-18" @default.
- W2901894003 title "Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix–Junction–Helix Systems" @default.
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- W2901894003 doi "https://doi.org/10.1021/jacs.8b11111" @default.
- W2901894003 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6470002" @default.
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- W2901894003 hasPublicationYear "2018" @default.
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