RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
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DOI：
10.1261/rna.657708
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发表时间：
2008-03-01
期刊：
影响因子：
4.5
通讯作者：
Berman, Helen M.
中科院分区：
文献类型：
--
作者：
Richardson, Jane S.;Schneider, Bohdan;Berman, Helen M.
使用所有的骨架扭转角为RNA骨架结构定义了一致的分类和命名。几个独立的分析方法的共识，46个离散的构象被确定为适当的质量过滤，多维二面角分布聚类。这些构象异构体中的大多数代表RNA结构中可识别的特征或作用。构象异构体被赋予两个字符的名称，反映了经验上发现的有利于糖-糖“套件”单元的七角δ-α-β-γ-δ组合，其中角相关性最强（e。例如，在一个实施例中，1a表示A型，5 z表示S基序的起始）。由于半核苷酸是由一个数字为δ ζ和一个字母为α β γ δ指定的，这个模块化系统也可以被解析来描述传统的核苷酸单元（例如，例如，在一个实施例中，a1）或二核苷酸（e.例如，在一个实施例中，a1 a1），其在晶体图拟合水平上特别有用。这种命名法也可以写成一个字符串，在碱基序列的两个字母之间有两个字符的系列名称（GNRA四环为N1 aG 1gN 1aR 1aA 1cN 1a），便于生物信息学比较。提供聚类平均值、标准差、坐标和示例，以及Suitename软件，该软件可根据原子坐标指定套件构象异构体名称和构象异构体匹配质量（适合性）。RNA本体论联盟将联合收割机将这个新的骨架系统与其他定义碱基对、碱基堆积和氢键关系的系统结合起来，以提供对RNA结构基序的完整描述。
A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle delta epsilon zeta alpha beta gamma delta combinations empirically found favorable for the sugar-to-sugar "suite'' unit within which the angle correlations are strongest (e. g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for delta epsilon zeta and a lowercase letter for alpha beta gamma delta, this modular system can also be parsed to describe traditional nucleotide units (e. g., a1) or the dinucleotides (e. g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.