1. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping.
- Author
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Henke, Paul S. and Mak, Chi H.
- Subjects
- *
THERMODYNAMICS , *FREE energy (Thermodynamics) , *RNA , *COMPUTER simulation , *ALGORITHMS , *PROTEIN folding , *MATHEMATICAL models - Abstract
The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterionmediated free energy conclusively directs folding into a compact structure. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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