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首页> 外文期刊>Journal of Molecular Biology >Symmetric K(+) and Mg(2+) Ion-binding Sites in the 5S rRNA Loop E Inferred from Molecular Dynamics Simulations.
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Symmetric K(+) and Mg(2+) Ion-binding Sites in the 5S rRNA Loop E Inferred from Molecular Dynamics Simulations.

机译：从分子动力学模拟推断5S rRNA环E中对称的K（+）和Mg（2+）离子结合位点。

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Potassium binding to the 5S rRNA loop E motif has been studied by molecular dynamics at high (1.0 M) and low (0.2 M) concentration of added KCl in the presence and absence of Mg(2+). A clear pattern of seven deep groove K(+) binding sites or regions, in all cases connected with guanine N7/O6 atoms belonging to GpG, GpA, and GpU steps, was identified, indicating that the LE deep groove is significantly more ionophilic than the equivalent groove of regular RNA duplexes. Among all, two symmetry-related sites (with respect to the central G.A pair) were found to accommodate K(+) ions with particularly long residence times. In a preceding molecular dynamics study by Auffinger et al. in the year 2003, these two sites were described as constituting important Mg(2+) binding locations. Altogether, the data suggest that these symmetric sites correspond to the loop E main ion binding regions. Indeed, they are located in the deep groove of an important ribosomal protein binding motif associated with a fragile pattern of non-Watson-Crick pairs that has certainly to be stabilized by specific Mg(2+) ions in order to be efficiently recognized by the protein. Besides, the other sites accommodate monovalent ions in a more diffuse way pointing out their lesser significance for the structure and function of this motif. Ion binding to the shallow groove and backbone atoms was generally found to be of minor importance since, at the low concentration, no well defined binding site could be characterized while high K(+) concentration promoted mostly unspecific potassium binding to the RNA backbone. In addition, several K(+) binding sites were located in positions equivalent to water molecules from the first hydration shell of divalent ions in simulations performed with magnesium, indicating that ion binding regions are able to accommodate both mono- and divalent ionic species. Overall, the simulations provide a more precise but, at the same time, a more intricate view of the relations of this motif with its ionic surrounding.
机译：钾结合到5S rRNA环E主题已经通过分子动力学研究了在存在和不存在Mg（2+）的情况下高浓度（1.0 M）和低浓度（0.2 M）所添加的KCl。在所有情况下，与属于GpG，GpA和GpU步骤的鸟嘌呤N7 / O6原子连接的七个深沟K（+）结合位点或区域的清晰模式被鉴定，这表明LE深沟比离子化的亲离子性强得多规则RNA双链体的等价凹槽。其中，发现两个对称相关位点（相对于中心G.A对）可容纳具有特别长停留时间的K（+）离子。在先前的Auffinger等人的分子动力学研究中。在2003年，这两个站点被描述为构成重要的Mg（2+）绑定位置。总而言之，数据表明这些对称位点对应于环E主离子结合区。的确，它们位于重要的核糖体蛋白结合基序的深沟中，该基序与非沃森-克里克对的脆弱模式有关，必须通过特定的Mg（2+）离子对其进行稳定处理才能有效地识别它们。蛋白。此外，其他位点以更扩散的方式容纳一价离子，指出它们对该基序的结构和功能的重要性较低。通常发现离子与浅沟和主链原子的结合次要重要性不高，因为在低浓度下，没有可明确定义的结合位点，而高K（+）浓度则促进了钾离子与RNA主链的大部分非特异性结合。此外，在用镁进行的模拟中，几个K（+）结合位点位于与二价离子的第一个水合壳中的水分子等效的位置，这表明离子结合区能够容纳一价和二价离子物种。总体而言，模拟提供了该主题与其离子周围环境之间关系的更精确但更复杂的视图。

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