Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems

Overview

Journal J Am Chem Soc

Publisher American Chemical Society

Specialty Chemistry

Date 2018 Nov 23

PMID 30465606

Citations 8

Authors

Clark Templeton

Ron Elber

Affiliations

Soon will be listed here.

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 (Mg 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.

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