Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.
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DOI：
10.1021/ja301454u
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发表时间：
2012-07-25
影响因子：
15
通讯作者：
Sanbonmatsu, Karissa Y.
中科院分区：
文献类型：
--
作者：
Hayes, Ryan L.;Noel, Jeffrey K.;Mohanty, Udayan;Whitford, Paul C.;Hennelly, Scott P.;Onuchic, Jose N.;Sanbonmatsu, Karissa Y.
实验表明，Mg 2+对RNA系统的结构和功能至关重要，但Mg 2+作用于RNA的详细分子机制还不清楚。我们调查RNA和Mg 2+之间的相互作用，在原子分辨率通过10个2微秒明确的溶剂分子动力学模拟的SAM-I核糖开关与不同的离子浓度。包括三个茎环的结构在这个时间尺度上非常稳定。模拟结果表明，外层协调镁离子的波动在相同的时间尺度上的RNA，和他们的动力学耦合。局部，Mg 2+协会影响RNA构象通过三级桥接相互作用;全球范围内，增加Mg 2+浓度减缓RNA波动。在我们的模拟中，负责这些效应的外层Mg 2+离子占Mg 2+的80%。这些离子与RNA短暂结合，维持相互作用，但从一个位点穿梭到另一个位点。外层Mg ~（2+）与RNA之间被一层水化壳隔开，在离RNA 3- 5 μ m处占据一薄层。分布函数表明，外层Mg ~（2+）被电负性原子和水化层所占据，并优先进入主沟。扩散分析表明，瞬态外层Mg 2+动力学是玻璃态的。由于在我们的模拟中，外层Mg 2+离子占Mg 2+的大部分，这些离子可能会改变Mg 2 +-RNA相互作用的范例。而不是几个内球离子锚定的RNA结构周围的一个连续的扩散离子，我们观察到一层外层协调Mg 2+是短暂的绑定，但强烈耦合到RNA。
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 microsecond explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this timescale. 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 3-5Å from the RNA. Distribution functions reveal outer sphere Mg2+ are positioned by electronegative atoms, hydration layers, and have 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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DOI：
10.1073/pnas.80.12.3696
发表时间：
1983-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
GO, N;NOGUTI, T;NISHIKAWA, T
通讯作者：
NISHIKAWA, T
DOI：
10.1039/c0cp00111b
发表时间：
2010-07-28
期刊：
Physical chemistry chemical physics : PCCP
影响因子：
--
作者：
Dupradeau FY;Pigache A;Zaffran T;Savineau C;Lelong R;Grivel N;Lelong D;Rosanski W;Cieplak P
通讯作者：
Cieplak P
影响因子：
2.9
作者：
Grilley, Dan;Misra, Vinod;Draper, David E.
通讯作者：
Draper, David E.
影响因子：
8.6
作者：
Das, R;Mills, TT;Pollack, L
通讯作者：
Pollack, L
DOI：
10.1073/pnas.92.15.6675
发表时间：
1995-07-18
影响因子：
11.1
作者：
ANGELL, CA
通讯作者：
ANGELL, CA