The cellular concentrations of certain metabolites are assiduously monitored to achieve appropriate levels of gene expression. Although proteins have long been known to act as sensors in this capacity, metabolite-binding RNAs, or riboswitches, also play an important role. More than 20 distinct classes of riboswitches have been identified to date, and insights to the molecular recognition strategies of a significant subset of these have been provided by detailed structural studies. This 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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The structural and functional diversity of metabolite-binding riboswitches.

Effects of molecular crowding on the structures, interactions, and functions of nucleic acids.

An accurate representation of ion solvation in aqueous solution is critical for meaningful computer simulations of a broad range of physical and biological processes. Polarizable models based on classical Drude oscillators are introduced and parametrized for a large set of monatomic ions including cations of the alkali metals (Li+, Na+, K+, Rb+, and Cs+) and alkaline earth elements (Mg2+, Ca2+, Sr2+, and Ba2+) along with Zn2+ and halide anions (F−, Cl−, Br−, and I−). The models are parametrized, in conjunction with the polarizable SWM4-NDP water model [Lamoureux et al. Chem. Phys. Lett. 2006, 418, 245], to be consistent with a wide assortment of experimentally measured aqueous bulk thermodynamic properties and the energetics of small ion−water clusters. Structural and dynamic properties of the resulting ion models in aqueous solutions at infinite dilution are presented.

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with 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. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the ava...

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Structure and Mechanism of a Metal-Sensing Regulatory RNA

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.

Ions and RNA Folding

Mg2+ ions are very effective at stabilizing tertiary structures in RNAs. In most cases, folding of an RNA is so strongly coupled to its interactions with Mg2+ that it is difficult to separate free energies of Mg2+– RNA interactions from the intrinsic free energy of RNA folding. To devise quantitative models accounting for this phenomenon of Mg2+-induced RNA folding, it is necessary to independently determine Mg2+–RNA interaction free energies for folded and unfolded RNA forms. In this work, the energetics of Mg2+–RNA interactions are derived from an assay that measures the effective concentration of Mg2+ in the presence of RNA. These measurements are used with other measures of RNA stability to develop an overall picture of the energetics of Mg2+-induced RNA folding. Two different RNAs are discussed, a pseudoknot and an rRNA fragment. Both RNAs interact strongly with Mg2+ when partially unfolded, but the two folded RNAs differ dramatically in their inherent stability in the absence of Mg2+ and in the free energy of their interactions with Mg2+. From these results, it appears that any comprehensive framework for understanding Mg2+-induced stabilization of RNA will have to (i) take into account the interactions of ions with the partially unfolded RNAs and (ii) identify factors responsible for the widely different strengths with which folded tertiary structures interact with Mg2+.

https://www.pnas.org/content/pnas/103/38/14003.full.pdf

Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures.

RNA molecules in monovalent salt solutions generally adopt a set of partially folded conformations containing only secondary structure, the intermediate or I state. Addition of Mg2+ strongly stabilizes the native tertiary structure (N state) relative to the I state. In this paper, a combination of experimental and computational approaches is used to estimate the free energy of the interaction of Mg2+ with partially folded I state RNAs and to consider the possibility that Mg2+ favors "compaction" of the I state to a set of conformations with a higher average charge density. A sequence variant with a drastically destabilized tertiary structure was used as a mimic of I state RNA; as measured by small-angle X-ray scattering, it adopted a progressively more compact conformation over a wide Mg2+ concentration range. Average free energies of the interaction of Mg2+ with the I state mimic were obtained by a fluorescence titration method. To interpret these experimental data further, we generated molecular models of the I state and used them in calculations with the nonlinear Poisson-Boltzmann equation to estimate the change in Mg2+-RNA interaction free energy as the average I state dimensions decrease from expanded to compact. The same models were also used to reproduce quantitatively the experimental difference in excess Mg2+ between N and I states. On the basis of these experiments and calculations, I state compaction appears to enhance Mg2+-I state interaction free energies by 10-20%, but this enhancement is at most 5% of the overall Mg2+-associated stabilization free energy for this rRNA fragment.

Importance of partially unfolded conformations for Mg2+-induced folding of RNA tertiary structure: Structural models and free energies of Mg2+ interactions

Dan Grilley

Papers

Ions and RNA Folding

Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures.

Importance of partially unfolded conformations for Mg2+-induced folding of RNA tertiary structure: Structural models and free energies of Mg2+ interactions

Abstract 2394: Structural Dynamics of a Hemolytic Protein

Abstract 2391: Determining the Effects of Poly-A Tracts and Monovalent Cations on Nucleosome Unwrapping Equilibrium