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Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Identifieur interne : 000425 ( Pmc/Corpus ); précédent : 000424; suivant : 000426

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

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

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

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PMC:4833092

Le document en format XML

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<author><name sortKey="Hayes, Ryan L" sort="Hayes, Ryan L" uniqKey="Hayes R" first="Ryan L." last="Hayes">Ryan L. Hayes</name>
<affiliation><nlm:aff id="A1">Center for Theoretical Biological Physics and Department of Physics & Astronomy, Rice University, Houston, TX</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Noel, Jeffrey K" sort="Noel, Jeffrey K" uniqKey="Noel J" first="Jeffrey K." last="Noel">Jeffrey K. Noel</name>
<affiliation><nlm:aff id="A1">Center for Theoretical Biological Physics and Department of Physics & Astronomy, Rice University, Houston, TX</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Mandic, Ana" sort="Mandic, Ana" uniqKey="Mandic A" first="Ana" last="Mandic">Ana Mandic</name>
<affiliation><nlm:aff id="A2">Department of Biomedical Engineering, University of Houston, Houston, TX</nlm:aff>
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<author><name sortKey="Whitford, Paul C" sort="Whitford, Paul C" uniqKey="Whitford P" first="Paul C." last="Whitford">Paul C. Whitford</name>
<affiliation><nlm:aff id="A3">Department of Physics, Northeastern University, Boston, MA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sanbonmatsu, Karissa Y" sort="Sanbonmatsu, Karissa Y" uniqKey="Sanbonmatsu K" first="Karissa Y." last="Sanbonmatsu">Karissa Y. Sanbonmatsu</name>
<affiliation><nlm:aff id="A4">Theoretic Biology and Biophysics, Theoretic Division, Los Alamos National Labs, Los Alamos, NM</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Mohanty, Udayan" sort="Mohanty, Udayan" uniqKey="Mohanty U" first="Udayan" last="Mohanty">Udayan Mohanty</name>
<affiliation><nlm:aff id="A5">Department of Chemistry, Boston College, Chestnut Hill, MA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Onuchic, Jose N" sort="Onuchic, Jose N" uniqKey="Onuchic J" first="José N." last="Onuchic">José N. Onuchic</name>
<affiliation><nlm:aff id="A1">Center for Theoretical Biological Physics and Department of Physics & Astronomy, Rice University, Houston, TX</nlm:aff>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Generalized Manning Condensation Model Captures the RNA Ion Atmosphere</title>
<author><name sortKey="Hayes, Ryan L" sort="Hayes, Ryan L" uniqKey="Hayes R" first="Ryan L." last="Hayes">Ryan L. Hayes</name>
<affiliation><nlm:aff id="A1">Center for Theoretical Biological Physics and Department of Physics & Astronomy, Rice University, Houston, TX</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Noel, Jeffrey K" sort="Noel, Jeffrey K" uniqKey="Noel J" first="Jeffrey K." last="Noel">Jeffrey K. Noel</name>
<affiliation><nlm:aff id="A1">Center for Theoretical Biological Physics and Department of Physics & Astronomy, Rice University, Houston, TX</nlm:aff>
</affiliation>
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<author><name sortKey="Mandic, Ana" sort="Mandic, Ana" uniqKey="Mandic A" first="Ana" last="Mandic">Ana Mandic</name>
<affiliation><nlm:aff id="A2">Department of Biomedical Engineering, University of Houston, Houston, TX</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Whitford, Paul C" sort="Whitford, Paul C" uniqKey="Whitford P" first="Paul C." last="Whitford">Paul C. Whitford</name>
<affiliation><nlm:aff id="A3">Department of Physics, Northeastern University, Boston, MA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sanbonmatsu, Karissa Y" sort="Sanbonmatsu, Karissa Y" uniqKey="Sanbonmatsu K" first="Karissa Y." last="Sanbonmatsu">Karissa Y. Sanbonmatsu</name>
<affiliation><nlm:aff id="A4">Theoretic Biology and Biophysics, Theoretic Division, Los Alamos National Labs, Los Alamos, NM</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Mohanty, Udayan" sort="Mohanty, Udayan" uniqKey="Mohanty U" first="Udayan" last="Mohanty">Udayan Mohanty</name>
<affiliation><nlm:aff id="A5">Department of Chemistry, Boston College, Chestnut Hill, MA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Onuchic, Jose N" sort="Onuchic, Jose N" uniqKey="Onuchic J" first="José N." last="Onuchic">José N. Onuchic</name>
<affiliation><nlm:aff id="A1">Center for Theoretical Biological Physics and Department of Physics & Astronomy, Rice University, Houston, TX</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Physical review letters</title>
<idno type="ISSN">0031-9007</idno>
<idno type="eISSN">1079-7114</idno>
<imprint><date when="2015">2015</date>
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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>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
  <pmc-dir>properties manuscript</pmc-dir>
  <front><journal-meta><journal-id journal-id-type="nlm-journal-id">0401141</journal-id>
<journal-id journal-id-type="pubmed-jr-id">21217</journal-id>
<journal-id journal-id-type="nlm-ta">Phys Rev Lett</journal-id>
<journal-id journal-id-type="iso-abbrev">Phys. Rev. Lett.</journal-id>
<journal-title-group><journal-title>Physical review letters</journal-title>
</journal-title-group>
<issn pub-type="ppub">0031-9007</issn>
<issn pub-type="epub">1079-7114</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26197147</article-id>
<article-id pub-id-type="pmc">4833092</article-id>
<article-id pub-id-type="doi">10.1103/PhysRevLett.114.258105</article-id>
<article-id pub-id-type="manuscript">NIHMS755796</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Generalized Manning Condensation Model Captures the RNA Ion Atmosphere</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Hayes</surname>
<given-names>Ryan L.</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Noel</surname>
<given-names>Jeffrey K.</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mandic</surname>
<given-names>Ana</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Whitford</surname>
<given-names>Paul C.</given-names>
</name>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sanbonmatsu</surname>
<given-names>Karissa Y.</given-names>
</name>
<xref ref-type="aff" rid="A4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mohanty</surname>
<given-names>Udayan</given-names>
</name>
<xref ref-type="aff" rid="A5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Onuchic</surname>
<given-names>José N.</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>1</label>
Center for Theoretical Biological Physics and Department of Physics & Astronomy, Rice University, Houston, TX</aff>
<aff id="A2"><label>2</label>
Department of Biomedical Engineering, University of Houston, Houston, TX</aff>
<aff id="A3"><label>3</label>
Department of Physics, Northeastern University, Boston, MA</aff>
<aff id="A4"><label>4</label>
Theoretic Biology and Biophysics, Theoretic Division, Los Alamos National Labs, Los Alamos, NM</aff>
<aff id="A5"><label>5</label>
Department of Chemistry, Boston College, Chestnut Hill, MA</aff>
<pub-date pub-type="nihms-submitted"><day>4</day>
<month>3</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="epub"><day>26</day>
<month>6</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="ppub"><day>26</day>
<month>6</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>15</day>
<month>4</month>
<year>2016</year>
</pub-date>
<volume>114</volume>
<issue>25</issue>
<fpage>258105</fpage>
<lpage>258105</lpage>
<pmc-comment>elocation-id from pubmed: 10.1103/PhysRevLett.114.258105</pmc-comment>
      <abstract><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>
</abstract>
</article-meta>
</front>
</pmc>
</record>

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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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Abstract

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