Geometric nomenclature and classification of RNA base pairs
Geometric nomenclature and classification of RNA base pairs
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DOI：
10.1017/s1355838201002515
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发表时间：
2001-04-01
期刊：
影响因子：
4.5
通讯作者：
Westhof, E
中科院分区：
文献类型：
--
作者：
Leontis, NB;Westhof, E
非沃森-克里克碱基对介导负责RNA-RNA自组装和RNA-蛋白质识别的特异性相互作用。一个明确的和描述性的命名与明确定义的和非重叠的参数是必要的，以简明扼要地传达有关RNA碱基对的结构信息。定义应反映潜在的分子结构和相互作用，从而促进新RNA结构的自动注释、分类和比较。我们提出了一个分类的基础上观察到的平面边到边，RNA碱基之间的氢键相互作用涉及三个不同的边缘之一：沃森-克里克边缘，Hoogsteen边缘，糖边缘（其中包括2 '-OH，也被称为浅槽边缘）。碱基可以在相对于糖苷键的两个方向（相对于氢键的顺式或反式）中的任一个方向上相互作用。这产生了12种基本几何类型，其中至少有两个H键连接碱基，对于每种几何类型，可以容易地推导出链的相对取向。12种几何形状中有11种的高分辨率实例目前可用。分叉对，其中一个碱基的单个环外羰基或氨基直接接触第二个碱基的边缘，和水插入对，其中每个碱基上的单个官能团直接相互作用，是两个标准几何形状之间的中间体。该命名法有利于识别每个几何结构中碱基对之间的等排关系，从而有利于识别同源序列比较中的重复性三维基序。提出了在二级结构图上显示非Watson-Crick相互作用的图形约定，并举例说明了该分类法在RNA三级基序同源建模中的实用性。
Non-Watson-Crick base pairs mediate specific interactions responsible for RNA-RNA self-assembly and RNA-protein recognition. An unambiguous and descriptive nomenclature with well-defined and nonoverlapping parameters is needed to communicate concisely structural information about RNA base pairs. The definitions should reflect underlying molecular structures and interactions and, thus, facilitate automated annotation, classification, and comparison of new RNA structures. We propose a classification based on the observation that the planar edge-to-edge, hydrogen-bonding interactions between RNA bases involve one of three distinct edges: the Watson-Crick edge, the Hoogsteen edge, and the Sugar edge (which includes the 2'-OH and which has also been referred to as the Shallow-groove edge). Bases can interact in either of two orientations with respect to the glycosidic bonds, cis or trans relative to the hydrogen bonds. This gives rise to 12 basic geometric types with at least two H bonds connecting the bases, For each geometric type, the relative orientations of the strands can be easily deduced. High-resolution examples of 11 of the 12 geometries are presently available. Bifurcated pairs, in which a single exocyclic carbonyl or amino group of one base directly contacts the edge of a second base, and water-inserted pairs, in which single functional groups on each base interact directly, are intermediate between two of the standard geometries. The nomenclature facilitates the recognition of isosteric relationships among base pairs within each geometry, and thus facilitates the recognition of recurrent three-dimensional motifs from comparison of homologous sequences, Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram, The utility of the classification in homology modeling of RNA tertiary motifs is illustrated.