Definitions and nomenclature of nucleic acid structure parameters.
Definitions and nomenclature of nucleic acid structure parameters.
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DOI：
10.1002/j.1460-2075.1989.tb03339.x
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发表时间：
1989-01
期刊：
影响因子：
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通讯作者：
S. Diekmann
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作者：
S. Diekmann
在1988年9月10日至15日在剑桥丘吉尔学院举行的EMBO关于DNA曲率和弯曲的讲习班上，安排了两次会议，讨论用于描述核酸链和螺旋几何形状的参数的定义，以及这些参数的共同命名法。使用最广泛的螺旋分析程序库HELIB （Fratini et al., 1982; Dickerson, 1985）的缺点是，定义的平移和旋转不是完全独立的，在一定程度上取决于整体螺旋轴的选择。几个研究小组已经独立从事开发多核苷酸链几何分析的替代程序，但计算量的定义不同，即使涉及相同的参数，命名法也大不相同。EMBO工作会议涉及四个这样的编程小组和其他潜在用户，其目标是引入一套共同的概念和共同的语言，以便更容易地交流。希望本说明中商定和报告的标准将被该领域的其他人所接受，并最终得到IUPAC/IUB生物命名委员会（IUPAC/IUB生物命名联合委员会，1983年）的批准。以下要点在EMBO研讨会上达成一致：(i)程序开发的既定目标是创建一个新的和优化的程序库，用于分析和描述多核苷酸结构，特别是但不限于DNA双螺旋结构。这个通用库主要是为那些使用x射线、核磁共振或其他物理技术解决核酸结构的人以及对这些结果感兴趣的人设计的。人们认识到，理论研究将需要更详细和更专业的程序，但人们认为，首先要做的是创建一个简单、易于使用的库，计算易于理解和物理上有意义的结构参数。特别是，新的分析例程应该尽可能减少对已经使用了五年多的熟悉的HELIB库的更改，使从一个碱基对到下一个碱基对的三次旋转和三次平移在数学上独立。（ii）在尝试选择“标准”库之前，几个研究小组开发的试验程序将在未来12 - 18个月内分发给感兴趣的用户进行实际评估。程序将由以下四组提供，但如果需要，其他人也可以参与：a. Richard Lavery和Heinz Sklenar (Lavery和Sklenar， 1988) b. D.M.Soumpasis和Chang-Shung Tung (Soumpasis和Tung， 1988) c. e.f onkitzing和s.d ekkmann (von Kitzing和Diekmann， 1987) d. Manju Bansal （Bhattacharya和Bansal， 1988）每个编程参与者将把生成的例程应用于三个测试用例：序列C-G-C-G-A-A-T-T-C-G-C-G - g的Drew Native B-DNA，由Andrew H.-J提供的A-DNA结构。Wang和tRNA分子。所产生的参数表将分发给所有感兴趣的各方进行比较。（iii）所有程序都应有碱基对与单链单个碱基的选择作为用户选项。它们还应该允许相对于局部螺旋轴（从一个碱基对到下一个）以及相对于远程或全局轴进行计算。（iv）局部或碱基对坐标集的x方向应指向该碱基对的短轴，y方向指向该碱基对的长轴，z方向垂直于该碱基对的平面，为右手正交轴集。（正x、正y、正z的方向将在下面根据参数的定义进行考虑。）碱基对的长轴可以用从嘧啶的C6到嘌呤的C8的连线来定义，也可以用从C6到嘌呤上假设的C8*原子的连线来定义，选择这样C6-C8*向量与Cl‘-Cl’向量平行。（使用的选择应该明确说明。）如果需要，沿着一个碱基对的三个主要转动惯量的轴的使用可以作为一个额外的用户选择，但不应取代更简单的定义。(v)每个碱基对步骤的参数计算轴的选择应使从碱基对1到碱基对2得到的数值与从碱基对2到碱基对1得到的数值相同（仅可能有符号变化）。实现这一目的的一种方法是在碱基对本身之间选择一个局部参考轴集。商定的参数共同命名法如下，按照国际图联协建议的做法，用希腊字母表示旋转，用罗马字母表示翻译。
At an EMBO Workshop on DNA Curvature and Bending, held at Churchill College, Cambridge, on 10-15 September 1988, two sessions were scheduled on definitions of parameters used to describe the geometry of nucleic acid chains and helices, and a common nomenclature for these parameters. The most widely used library of helix analysis programs, HELIB (Fratini et al., 1982; Dickerson, 1985) suffers from the fact that the translations and rotations as defined are not fully independent and depend to a certain extent upon the choice of overall helix axis. Several research groups have been engaged independently in developing alternative programs for the geometrical analysis of polynucleotide chains, but with different definitions of quantities calculated and with widely different nomenclature even when the same parameter was involved. The EMBO work sessions involved four such programming groups and other potential users, and had as its goal the introduction of a common set of concepts and common language for greater ease of communication. It is hoped that the standards agreed upon and reported in this note will prove acceptable to others in the field, and ultimately will be approved by the IUPAC/IUB Commission on Biochemical Nomenclature (IUPAC/IUB Joint Commission on Biological Nomenclature, 1983). The following points were agreed upon at the EMBO Workshop: (i)The stated goal in program development is the creation of a new and optimized library of routines for the analysis and description of polynucleotide structure, especially but not exclusively the DNA double helix. This general purpose library is intended mainly for those who solve nucleic acid structures using X-rays, NMR or other physical techniques and those who are interested in these results. It is recognized that theoretical studies will require more elaborate and more specialized programs, but it is felt that the first order of business is the creation of a simple, easily used library calculating easily understood and physically meaningful structure parameters. In particular, the-new analysis routines should involve the least possible change from the familiar HELIB library that has been in use for more than five years, consonant with making the three rotations and three translations leading from one base pair to the next mathematically independent. (ii) Trial programs developed by several research groups are to be circulated to interested users over the next 12 18 months for practical evaluation, before any attempt is made to select a 'standard' library. Programs will be contributed by the following four groups, but others may participate if desired: a. Richard Lavery and Heinz Sklenar (Lavery and Sklenar, 1988) b. D.M.Soumpasis and Chang-Shung Tung (Soumpasis and Tung, 1988) c. E.von Kitzing and S.Diekmann (von Kitzing and Diekmann, 1987) d. Manju Bansal (Bhattacharya and Bansal, 1988) Each of the programming participants will apply the resulting routines to three test cases: the Drew Native B-DNA of sequence C-G-C-G-A-A-T-T-C-G-C-G, an A-DNA structure to be supplied by Andrew H.-J.Wang and a tRNA molecule. The tables of parameters generated will be circulated to all interested parties for comparison. (iii) All programs should have as a user option the choice of base pairs versus individual bases of a single strand. They should also allow calculations to be carried out relative to local helix axes (from one base pair to the next), and relative to a long-range or global axis. (iv) The x direction of a local or base pair coordinate set should point along the short axis of the base pair, the y direction along the long axis and the z direction perpendicular to the plane of the pair, in a right-handed orthogonal axial set. (Directions of positive x, y and z are considered below, following defintions of parameters.) The long axis of a base pair can be defined either by the line from the C6 of a pyrimidine to the C8 of a purine, or alternatively by the line from C6 to a hypothetical C8* atom on the purine, chosen so that the C6-C8* vector is parallel to the Cl'-Cl' vector. (The choice used should be stated explicitly.) If desired, employment of axes along the three principal moments of inertia of a base pair may be incorporated as an extra user option, but should not replace the simpler defintions. (v) Axes for calculating parameters of each base pair step should be chosen so that the same numerical values result (with only a possible change of sign) when going from base pair 1 to base pair 2, as from base pair 2 to 1. One way in which this can be accomplished is by choosing a local reference axis set intermediate between those of the base pairs themselves. (vi) The agreed-upon common nomenclature of parameters is as follows, using Greek letters for rotations and Roman letters for translations in accordance with IUPAC recommended practice.