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Characterization of Mg2+ Distributions around RNA in Solution.

ABSTRACT: Binding of metal ions is an important factor governing the folding and dynamics of RNA. Shielding of charges in the polyanionic backbone allows RNA to adopt a diverse range of folded structures that give rise to their many functions within the cell. Some RNA sequences fold only in the presence of Mg2+, which may be bound via direct interactions or occupy the more diffuse "ion atmosphere" around the RNA. To understand the driving forces for RNA folding, it is important to be able to fully characterize the distribution of metal ions around the RNA. In this work, a combined Grand Canonical Monte Carlo-Molecular Dynamics (GCMC-MD) method is applied to characterize Mg2+ distributions around folded RNA structures. The GCMC-MD approach identifies known inner- and outer-shell Mg2+ coordination, while also predicting new regions occupied by Mg2+ that are not observed in crystal structures but that may be relevant in solution, including the case of the Mg2+ riboswitch, for which alternate Mg2+ binding sites may have implications for its function. This work represents a significant step forward in establishing a structural and thermodynamic description of RNA-Mg2+ interactions and their role in RNA structure and function.

SUBMITTER: Lemkul JA

PROVIDER: S-EPMC5088455 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Characterization of Mg<sup>2+</sup> Distributions around RNA in Solution.

Lemkul Justin A JA Lakkaraju Sirish Kaushik SK MacKerell Alexander D AD

ACS omega 20161026 4

Binding of metal ions is an important factor governing the folding and dynamics of RNA. Shielding of charges in the polyanionic backbone allows RNA to adopt a diverse range of folded structures that give rise to their many functions within the cell. Some RNA sequences fold only in the presence of Mg<sup>2+</sup>, which may be bound via direct interactions or occupy the more diffuse "ion atmosphere" around the RNA. To understand the driving forces for RNA folding, it is important to be able to fu ...[more]

PMID: 27819065

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Project description:Formed via aqueous carbonation of Mg2+ ions, the crystallization of magnesite (MgCO3) is a promising route to carbon capture and reuse, albeit limited by the slow precipitation of MgCO3. Although magnesite is naturally abundant, forming at low temperature conditions, its industrial production is an energy-intensive process due to the temperatures required to prevent the formation of hydrated phases. The principal difficulty in aqueous conditions arises from the very strong Mg2+···H2O interaction, with high barriers to Mg2+ dehydration. Using atomistic simulations, we have investigated the influence of 30 additive anions (X n-, n = 1-3), ranging from simple halides to more complex molecules, on the first two steps of MgCO3 aggregation from solution, as follows: Mg2+ dehydration and subsequent prenucleative Mg2+···CO3 2- pairing. We have computed the thermodynamic stabilities of solvent shared ion pairs (Mg2+···H2O···X n-) and contact ion pairs (Mg2+···X n-) to reveal the propensity of solution additives to inhibit or promote Mg2+···CO3 2- formation. We have determined the stabilization of undercoordinated hydrated Mg2+ states with a vacant coordination site to which CO3 2- can bind, subsequently initiating MgCO3 nucleation or Mg2+ incorporation into the crystal lattice. Extensive molecular dynamics simulations of electrolyte solutions containing Na2CO3 with different sources of Mg2+ (i.e., MgCl2, MgSO4, and Mg(CH3COO)2) further show that the degree of dehydration of Mg2+ and the structure of prenucleation MgCO3 clusters change depending on the counterion identity. Through a fundamental understanding of the role of solution additives in the mechanism of Mg2+ dehydration, our results help to rationalize previously reported experimental observation of the effect of solvation environments on the growth of magnesite. This understanding may contribute to identifying the solution composition and conditions that could promote the low-temperature CO2 conversion into MgCO3 at industrially relevant scales.

Dataset Information

Characterization of Mg2+ Distributions around RNA in Solution.

Publications

Characterization of Mg<sup>2+</sup> Distributions around RNA in Solution.

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