Survey of the geometric association of domain-domain interfaces
Survey of the geometric association of domain-domain interfaces
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DOI：
10.1002/prot.20693
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发表时间：
2005-12-01
影响因子：
2.9
通讯作者：
Ison, JC
中科院分区：
文献类型：
--
作者：
Kim, WK;Ison, JC
考虑到最复杂的对接方法的有限成功和系统对接所需的计算量，编目所有已知的接口可能是预测蛋白质三级和四级结构的替代基础。我们根据域-域关联的几何形状对域接口进行分类。通过应用一种简单而有效的称为“界面标签聚类”的方法，从蛋白质四级结构服务器和蛋白质数据库中收集了4,000多种不同类型的结构域界面。给定一对相互作用的结构域，我们定义“面”为每个结构域中相互作用的残基的集合，并且将这对相互作用的面定义为“界面”。“我们研究了界面的几何形状如何与相互作用的蛋白质家族网络相关，例如两个家族之间可能有多少不同的结合方向，或者当家族具有来自不同家族的不同相互作用伙伴时，家族是否使用不同的表面或相同的表面。我们发现，平均有1.2-1.9不同类型的接口之间的相互作用域和大量的家庭对关联在多个方向。一般来说，当家庭有不同的互动伙伴时，家庭倾向于为每个伙伴使用不同的面孔。每个面都高度特定于其交互伙伴和绑定方向。界面残基的相对位置在相同类型的界面内通常是保守的，即使在远距离同源物之间也是如此。分类结果见http://www.biotec.tu-dresden.de/-wkim/补充资料。
Considering the limited success of the most sophisticated docking methods available and the amount of computation required for systematic docking, cataloging all the known interfaces may be an alternative basis for the prediction of protein tertiary and quaternary structures. We classify domain interfaces according to the geometry of domain-domain association. By applying a simple and efficient method called "interface tag clustering," more than 4,000 distinct types of domain interfaces are collected from Protein Quaternary Structure Server and Protein Data Bank. Given a pair of interacting domains, we define "face" as the set of interacting residues in each single domain and the pair of interacting faces as an "interface." We investigate how the geometry of interfaces relates to a network of interacting protein families, such as how many different binding orientations are possible between two families or whether a family uses distinct surfaces or the same surface when the family has diverse interaction partners from various families. We show there are, on average, 1.2-1.9 different types of interfaces between interacting domains and a significant number of family pairs associate in multiple orientations. In genera, a family tends to use distinct faces for each partner when the family has diverse interaction partners. Each face is highly specific to its interaction partner and the binding orientation. The relative positions of interface residues are generally well conserve within the same type of interface even between remote homologs. The classification result is available at http://www.biotec.tu-dresden.de/-wkim/ supplement.