Global properties of the mapping between local amino acid sequence and local structure in proteins
Global properties of the mapping between local amino acid sequence and local structure in proteins
复制标题
DOI：
10.1073/pnas.93.12.5814
复制
发表时间：
1996-06-11
影响因子：
11.1
通讯作者：
Baker, D
中科院分区：
文献类型：
--
作者：
Han, KF;Baker, D
局部蛋白质结构预测的努力一直未能超过70%的准确率，我们通过研究在不同蛋白质中发现的相似序列片段采用相似三维结构的程度，来表征从局部序列到局部结构的映射的简并性，利用聚类分析将来自154个不同蛋白质家族的长度为3-15个残基的序列片段划分为包含具有相似序列的片段的邻域，通过比较已知结构的蛋白质中相同邻域中序列片段所采用的局部结构来评估序列到结构映射的一致性。在154个家族中，45%和28%的位置分别发生在一个和两个局部结构占主导地位的邻域中。表征第一类邻域的序列模式可能包括蛋白质中几乎所有的短序列基序，这些短序列基序始终发生在特定的局部结构中。这些模式，其中许多发生在二级结构元素之间的过渡，是一个有趣的组合，以前研究和新的图案。识别在蛋白质中的一个或少数局部结构中一致出现的序列模式应该有助于从序列预测蛋白质结构。
Local protein structure prediction efforts have consistently failed to exceed similar to 70% accuracy, We characterize the degeneracy of the mapping from local sequence to local structure responsible for this failure by investigating the extent to which similar sequence segments found in different proteins adopt similar three-dimensional structures, Sequence segments 3-15 residues in length from 154 different protein families are partitioned into neighborhoods contain ing segments with similar sequences using cluster analysis, The consistency of the sequence-to-structure mapping is assessed by comparing the local structures adopted by sequence segments in the same neighborhood in proteins of known structure. In the 154 families, 45% and 28% of the positions occur in neighborhoods in which one and two local structures predominate, respectively, The sequence patterns that characterize the neighborhoods in the first class probably include virtually all of the short sequence motifs in proteins that consistently occur in a particular local structure. These patterns, many of which occur in transitions between secondary structural elements, are an interesting combination of previously studied and novel motifs. The identification of sequence patterns that consistently occur in one or a small number of local structures in proteins should contribute to the prediction of protein structure from sequence.