The effect of backbone on the small-world properties of protein contact maps
The effect of backbone on the small-world properties of protein contact maps
复制标题
骨架对蛋白质接触图小世界特性的影响
DOI：
10.1088/1478-3975/4/4/l01
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发表时间：
2007-12-01
期刊：
影响因子：
2
通讯作者：
Casadio, R.
中科院分区：
文献类型：
--
作者：
Bartoli, L.;Fariselli, P.;Casadio, R.
在过去的几年中，当蛋白质由残基间蛋白质接触定义的无向图表示时，蛋白质的小世界行为已被广泛描述。通过采用这种表示，可以计算蛋白质结构的平均聚类系数（C）和特征路径长度（L），并且发现它们的值与以小世界拓扑为特征的图的值相似。在这篇评论中，我们分析了大量非冗余蛋白质结构（1753），并表明通过随机模拟蛋白质崩溃，蛋白质链的共价结构对残基间接触图的小世界行为有显着贡献。当生成蛋白质图时，施加类似于主干连接引起的约束，它们的特征路径长度和聚类系数与使用真实接触图计算的结果没有区别，表明 L 和 C 值不能用于“蛋白质指纹识别”。此外，我们验证了这些结果独立于所选的蛋白质表示、残基组成和蛋白质二级结构。
In the last years, small-world behavior has been extensively described for proteins, when they are represented by the undirected graph defined by the inter-residue protein contacts. By adopting this representation it was possible to compute the average clustering coefficient (C) and characteristic path length (L) of protein structures, and their values were found to be similar to those of graphs characterized by small-world topology. In this comment, we analyze a large set of non-redundant protein structures (1753) and show that by randomly mimicking the protein collapse, the covalent structure of the protein chain significantly contributes to the small-world behavior of the inter-residue contact graphs. When protein graphs are generated, imposing constraints similar to those induced by the backbone connectivity, their characteristic path lengths and clustering coefficients are indistinguishable from those computed using the real contact maps showing that L and C values cannot be used for 'protein fingerprinting'. Moreover we verified that these results are independent of the selected protein representations, residue composition and protein secondary structures.