镁接触离子稳定转移RNA的三级结构：二维红外光谱和理论模拟映射的静电。,The Journal of Physical Chemistry B

当前位置： X-MOL 学术 › J. Phys. Chem. B › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

镁接触离子稳定转移RNA的三级结构：二维红外光谱和理论模拟映射的静电。
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-12-07 , DOI: 10.1021/acs.jpcb.0c08966
Jakob Schauss ₁ , Achintya Kundu ₁ , Benjamin P. Fingerhut ₁ , Thomas Elsaesser ₁

Affiliation

与水合RNA相互作用的离子在定义其二级和三级结构中起着核心作用。虽然已从X射线研究中推断出离子，水分子和磷酸基团的空间排列，但在分子水平上尚未完全理解静电和其他非共价相互作用在稳定紧密折叠RNA结构中的作用。在这里，我们证明镁（Mg ²⁺）和嵌入局部水壳中的磷酸基团的接触离子对稳定了转移RNA（tRNA）的三级平衡结构。利用来自酵母的透析tRNA ^Phe和来自大肠杆菌的tRNA ，我们关注Mg ²⁺逐步将核糖磷酸二酯主链的磷酸基团附近的位点结合起来，将磷酸酯振动的线性和非线性红外光谱与分子动力学模拟和从头算起的振动频率计算相结合。每个tRNA最多可形成6个Mg ²⁺ /磷酸盐接触对，并且局部电场诱导的水分子重新定向可平衡tRNA非螺旋部分中的磷酸盐-磷酸盐排斥，从而通过静电稳定折叠结构。这样的几何形状在水分子的排列中显示出有限的亚皮秒波动，并且离子停留时间长于1μs。较高的Mg ²⁺过量的话，每个tRNA的接触离子对的数量大约为6，并且弱相互作用的离子占优势。我们的研究结果表明，在确定和稳定tRNA的三级结构中，接触离子对在离子气氛和生物分子的长距离偶联作用中占主导地位。

"点击查看英文标题和摘要"

Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations

Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of electrostatic and other noncovalent interactions in stabilizing compact folded RNA structures is not fully understood at the molecular level. Here, we demonstrate that contact ion pairs of magnesium (Mg²⁺) and phosphate groups embedded in local water shells stabilize the tertiary equilibrium structure of transfer RNA (tRNA). Employing dialyzed tRNA^Phe from yeast and tRNA from Escherichia coli, we follow the population of Mg²⁺ sites close to phosphate groups of the ribose-phosphodiester backbone step by step, combining linear and nonlinear infrared spectroscopy of phosphate vibrations with molecular dynamics simulations and ab initio vibrational frequency calculations. The formation of up to six Mg²⁺/phosphate contact pairs per tRNA and local field-induced reorientations of water molecules balance the phosphate–phosphate repulsion in nonhelical parts of tRNA, thus stabilizing the folded structure electrostatically. Such geometries display limited sub-picosecond fluctuations in the arrangement of water molecules and ion residence times longer than 1 μs. At higher Mg²⁺ excess, the number of contact ion pairs per tRNA saturates around 6 and weakly interacting ions prevail. Our results suggest a predominance of contact ion pairs over long-range coupling of the ion atmosphere and the biomolecule in defining and stabilizing the tertiary structure of tRNA.

更新日期：2021-01-28

点击分享查看原文

点击收藏

公开下载

阅读更多本刊新发论文