Published in

Royal Society of Chemistry, Physical Chemistry Chemical Physics, 14(16), p. 6367-6375, 2014

DOI: 10.1039/c3cp53655f

Links

Tools

Export citation

Search in Google Scholar

Exploring the Electrostatic Energy Landscape for Tetraloop-Receptor Docking

Journal article published in 2013 by Zhaojian He, Yuhong Zhu, Shi-Jie Chen ORCID
This paper is available in a repository.
This paper is available in a repository.

Full text: Download

Green circle
Preprint: archiving allowed
Orange circle
Postprint: archiving restricted
Red circle
Published version: archiving forbidden
Data provided by SHERPA/RoMEO

Abstract

It has long been appreciated that Mg2+ is essential for the stabilization of RNA tertiary structure. However, the problem of quantitative prediction for the ion effect in tertiary structure folding remains. By using the virtual bond RNA folding model (Vfold) to generate RNA conformations and the newly improved tightly bound ion model (TBI) to treat ion-RNA interactions, we investigate Mg2+-facilitated tetraloop-receptor docking. For the specific construct of the tetraloop-receptor system,the theoretical analysis shows that the Mg2+-induced stabilizing force for the docked state is predominantly entropic and the major contribution comes from the entropy of the diffusive ions. Furthermore, our results show that Mg2+ ions promote tetraloop-receptor docking mainly through the entropy of the diffusive ions. The theoretical prediction agrees with experimental analysis. The method developed in this paper, which combines the theory for the (Mg2+) ion effects in RNA folding and RNA conformational sampling, may provide a useful framework for studying the ion effect in the folding of more complex RNA structures.