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Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Identifieur interne : 000108 ( Main/Exploration ); précédent : 000107; suivant : 000109

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Auteurs : Ryan L. Hayes [États-Unis] ; Jeffrey K. Noel [États-Unis] ; Ana Mandic [États-Unis] ; Paul C. Whitford [États-Unis] ; Karissa Y. Sanbonmatsu [États-Unis] ; Udayan Mohanty [États-Unis] ; José N. Onuchic [États-Unis]

Source :

Physical review letters [ 0031-9007 ] ; 2015.

RBID : PMC:4833092

Abstract

RNA is highly sensitive to the ionic environment, and typically requires Mg²⁺ to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg²⁺ ions explicitly to account for ion-ion correlations neglected by mean field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, non-limiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg²⁺ associated with the RNA, Γ₂₊, because Γ₂₊ is directly related to the Mg²⁺-RNA interaction free energy. The excellent agreement with experiment demonstrates the model captures the ionic dependence of the RNA free energy landscape.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833092

DOI: 10.1103/PhysRevLett.114.258105
PubMed: 26197147
PubMed Central: 4833092

Affiliations:

Le document en format XML

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<front><div type="abstract" xml:lang="en"><p id="P1">RNA is highly sensitive to the ionic environment, and typically requires Mg<sup>2+</sup>
 to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg<sup>2+</sup>
 ions explicitly to account for ion-ion correlations neglected by mean field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, non-limiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg<sup>2+</sup>
 associated with the RNA, Γ<sub>2+</sub>
, because Γ<sub>2+</sub>
 is directly related to the Mg<sup>2+</sup>
-RNA interaction free energy. The excellent agreement with experiment demonstrates the model captures the ionic dependence of the RNA free energy landscape.</p>
</div>
</front>
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<name sortKey="Mandic, Ana" sort="Mandic, Ana" uniqKey="Mandic A" first="Ana" last="Mandic">Ana Mandic</name>
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Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

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