Journal ArticleDOI
Ions and RNA Folding
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TLDR
This review distinguishes three different kinds of ion environments that differ in the extent of direct ion-RNA contacts and the degree to which the ion hydration is perturbed, and summarizes the current understanding of the way each environment relates to the overall energetics of RNA folding.Abstract:
The problem of how ions influence the folding of RNA into specific tertiary structures is being addressed from both thermodynamic (by how much do different salts affect the free energy change of folding) and structural (how are ions arranged on or near an RNA and what kinds of environments do they occupy) points of view. The challenge is to link these different approaches in a theoretical framework that relates the energetics of ion-RNA interactions to the spatial distribution of ions. This review distinguishes three different kinds of ion environments that differ in the extent of direct ion-RNA contacts and the degree to which the ion hydration is perturbed, and summarizes the current understanding of the way each environment relates to the overall energetics of RNA folding.read more
Citations
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The structural and functional diversity of metabolite-binding riboswitches.
Adam Roth,Ronald R. Breaker +1 more
TL;DR: A diverse set of metabolite-sensing RNAs is found to exploit a variety of distinct mechanisms to regulate genes that are fundamental to metabolism.
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Effects of molecular crowding on the structures, interactions, and functions of nucleic acids.
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Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field
Haibo Yu,Troy W. Whitfield,Troy W. Whitfield,Edward Harder,Guillaume Lamoureux,Igor Vorobyov,Victor M. Anisimov,Alexander D. MacKerell,Benoît Roux +8 more
TL;DR: Structural and dynamic properties of the resulting ion models in aqueous solutions at infinite dilution are presented.
Journal ArticleDOI
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Jiří Šponer,Giovanni Bussi,Miroslav Krepl,Miroslav Krepl,Pavel Banáš,Sandro Bottaro,Richard A. Cunha,Alejandro Gil-Ley,Giovanni Pinamonti,Simón Poblete,Petr Jurečka,Nils G. Walter,Michal Otyepka +12 more
TL;DR: An in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods are covered.
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Structure and Mechanism of a Metal-Sensing Regulatory RNA
Charles E. Dann,Catherine A. Wakeman,Cecelia L. Sieling,Stephanie C. Baker,Irnov Irnov,Wade C. Winkler +5 more
TL;DR: The data demonstrate that a previously uncharacterized orphan riboswitch, renamed the "M-box," is a divalent metal-sensing RNA involved in Mg(2+) homeostasis and suggests the possibility of additional RNA-based metal sensors in modern and primordial organisms.
References
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Structure of yeast phenylalanine tRNA at 3 A resolution.
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TL;DR: The structure of a tRNA has been determined by isomorphous replacement but the interactions which maintain the tertiary structure are of a novel type and this model differs significantly from one which has recently been proposed.
Journal ArticleDOI
A guide to ions and RNA structure
TL;DR: The energetic factors that must be considered when ions interact with two different RNA environments are summarized and an important conclusion is that diffuse ions are a major factor in the stabilization of RNA tertiary structures.