A standard reference frame for the description of nucleic acid base-pair geometry
A standard reference frame for the description of nucleic acid base-pair geometry
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DOI：
10.1006/jmbi.2001.4987
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发表时间：
2001-10-12
影响因子：
5.6
通讯作者：
Berman, HM
中科院分区：
文献类型：
--
作者：
Olson, WK;Bansal, M;Berman, HM
需要一个共同的参照点来描述核酸结构中碱基和碱基对的三维排列。在为此目的而创建的计算机程序中使用的不同标准会导致对同一结构的解释产生冲突。[1]例如，一个结构的某些部分，根据一种计算方案看起来是“正常的”，但根据另一种计算方案看起来可能是非常不寻常的，反之亦然。因此，很难进行核酸结构的全面比较并精确定位单个结构中的独特构象特征。为了解决这些问题，一组创建和使用不同软件包的研究人员提出了下面概述的用于核酸构象分析的标准基本参考框架。这些定义建立在先前建立的定性指导原则的基础上，以指定DNA和RNA结构中碱基和碱基对的排列。2碱基坐标来源于对存储在剑桥结构数据库（CSD）中的核酸类似物的高分辨率晶体结构的调查。3选择坐标系，使互补碱基在未畸变的参考状态下形成理想的平面沃森-克里克碱基对，氢键供体-受体距离、C1 H ÁÁC 1H虚拟长度、嘌呤N9-C1 H ÁÁC 1H和嘧啶N1-C1 H ÁÁC 1H虚拟角度与相关小分子晶体结构中观察到的值一致。在这个参考框架中进行的构象分析导致解释的本地螺旋结构，基本上是独立的计算方案。来自核酸数据库（NDB）4的代表性A-DNA、B-DNA和蛋白质结合的DNA结构的碱基对参数的汇编为理解其他核酸结构提供了有用的指导。
A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures. The different standards used in computer programs created for this purpose give rise to conicting interpretations of the same structure. 1 For example, parts of a structure that appear``normal''according to one computational scheme may be highly unusual according to another and vice versa. It is thus dif® cult to carry out comprehensive comparisons of nucleic acid structures and to pinpoint unique conformational features in individual structures. In order to resolve these issues, a group of researchers who create and use the different software packages have proposed the standard base reference frames outlined below for nucleic acid conformational analysis. The de® nitions build upon qualitative guidelines established previously to specify the arrangements of bases and base-pairs in DNA and RNA structures. 2 Base coordinates are derived from a survey of high-resolution crystal structures of nucleic acid analogs stored in the Cambridge Structural Database (CSD). 3 The coordinate frames are chosen so that complementary bases form an ideal, planar Watson-Crick base-pair in the undistorted reference state with hydrogen bond donor-acceptor distances, C1 H ÁÁÁC1H virtual lengths, and purine N9-C1H ÁÁÁC1H and pyrimidineN1-C1H ÁÁÁC1H virtual angles consistent with values observed in the crystal structures of relevant small molecules. Conformational analyses performed in this reference frame lead to interpretations of local helical structure that are essentially independent of computational scheme. A compilation of base-pair parameters from representative A-DNA, B-DNA, and protein-bound DNA structures from the Nucleic Acid Database (NDB) 4 provides useful guidelines for understanding other nucleic acid structures.