期刊
PHYSICAL REVIEW LETTERS
卷 114, 期 25, 页码 -出版社
AMER PHYSICAL SOC
DOI: 10.1103/PhysRevLett.114.258105
关键词
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资金
- NSF [PHY-1427654, MCB-1214457, PHY-1216435]
- NIH [1R01GM110310-01A1]
- Welch Foundation [C-1792]
- NSF CAREER Award [MCB-1350312]
- National Institutes of Health [1R01GM110310-01A1]
- John Simon Guggenheim Memorial Foundation
- CPRIT Scholar in Cancer Research
- Cancer Prevention and Research Institute of Texas
- Cyberinfrastructure for Computational Research - NSF [CNS-0821727]
- Division Of Physics
- Direct For Mathematical & Physical Scien [1427654] Funding Source: National Science Foundation
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [1214457] Funding Source: National Science Foundation
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, nonlimiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg2+ associated with the RNA, Gamma(2+), because Gamma(2+) is directly related to the Mg2+-RNA interaction free energy. The excellent agreement with experiment demonstrates that the model captures the ionic dependence of the RNA free energy landscape.
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