Journal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Volume 134, Issue 29, Pages 12043-12053Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ja301454u
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Funding
- Center for Theoretical Biological Physics
- LANL Laboratory Research and Development
- National Science Foundation (NSF) [PHY-0822283, MCB-1051438]
- Cancer Prevention and Research Institute of Texas
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1214457] Funding Source: National Science Foundation
- Direct For Mathematical & Physical Scien
- Division Of Physics [1308264] Funding Source: National Science Foundation
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Experiments demonstrate that Mg2+ is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg2+ action on RNA is not well understood. We investigate the interplay between RNA and Mg2+ at atomic resolution through ten 2-mu s explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this time scale. Simulations reveal that outer-sphere coordinated Mg2+ ions fluctuate on the same time scale as the RNA, and that their dynamics couple. Locally, Mg2+ association affects RNA conformation through tertiary bridging interactions; globally, increasing Mg2+ concentration slows RNA fluctuations. Outer sphere Mg2+ ions responsible for these effects account for 80% of Mg2+ in our simulations These ions are transiently bound to the RNA, maintaining interactions, but shuttled from site to site. Outer sphere Mg2+ are separated from the RNA by a single hydration shell, occupying a thin layer 3-5 angstrom from the RNA. Distribution functions reveal that outer sphere Mg2+ are positioned by electronegative atoms, hydration layers, and a preference for the major groove. Diffusion analysis suggests transient outer sphere Mg2+ dynamics are glassy. Since outer-sphere Mg2+ ions account for most of the Mg2+ in our simulations, these ions may change the paradigm of Mg2+ RNA interactions. Rather than a few inner sphere ions anchoring the RNA structure surrounded by a continuum of diffuse ions, we observe a layer of outer sphere coordinated Mg2+ that is transiently bound but strongly coupled to the RNA.
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