RNA backbone is rotameric
RNA backbone is rotameric
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DOI：
10.1073/pnas.1835769100
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发表时间：
2003-11-25
影响因子：
11.1
通讯作者：
Richardson, JS
中科院分区：
文献类型：
--
作者：
Murray, LJW;Arendall, WB;Richardson, JS
尽管局部结构细节对于理解RNA催化和结合功能的机理很重要，但RNA骨架构象对于分析来说是相当困难的。每个残基有太多的可变扭转角，它们的原始经验分布聚类不好。本研究应用质量过滤技术（使用分辨率，晶体学B因子和全原子空间碰撞）从8，636个残基的RNA数据库的主链扭转角分布。随着噪声水平大大降低，对于潜在的角度偏好，出现了清晰的信号。α-β-γ和δ-β-ζ的半残基扭转角分布在3D中绘制和轮廓化;每个都显示了大约十几个不同的峰，然后可以成对组合以定义完整的RNA骨架构象。传统的核酸残基是从磷酸到磷酸定义的，但在这里，我们使用碱基到碱基（或糖到糖）划分为“套房”来解析RNA骨架重复序列，这既是因为大多数骨架空间冲突都在套房内，也是因为连续碱基的关系既可靠又构象重要。一个套件构象有七个变量，糖折叠指定在两端。如果在应用质量过滤器后没有至少一小簇令人信服的数据点代表，则忽略潜在的套件构象。最终的结果是一个小的42 RNA骨架构象，这应该提供有效的构象几乎所有的RNA骨架中遇到的实验结构库。
Despite the importance of local structural detail to a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to analysis. There are too many variable torsion angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor, and all-atom steric clashes) to the backbone torsion angle distributions from an 8,636-residue RNA database. With noise levels greatly reduced, clear signal appears for the underlying angle preferences. Half-residue torsion angle distributions for alpha-beta-gamma and for delta-epsilon-zeta are plotted and contoured in 3D; each shows about a dozen distinct peaks, which can then be combined in pairs to define complete RNA backbone conformers. Traditional nucleic acid residues are defined from phosphate to phosphate, but here we use a base-to-base (or sugar-to-sugar) division into "suites" to parse the RNA backbone repeats, both because most backbone steric clashes are within suites and because the relationship of successive bases is both reliably determined and conformationally important. A suite conformer has seven variables, with sugar pucker specified at both ends. Potential suite conformers were omitted if not represented by at least a small cluster of convincing data points after application of quality filters. The final result is a small library of 42 RNA backbone conformers, which should provide valid conformations for nearly all RNA backbone encountered in experimental structures.