Protein bipartivity and essentiality in the yeast protein-protein interaction network
Protein bipartivity and essentiality in the yeast protein-protein interaction network
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DOI：
10.1021/pr060106e
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发表时间：
2006-09-01
影响因子：
4.4
通讯作者：
Estrada, Ernesto
中科院分区：
文献类型：
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作者：
Estrada, Ernesto
蛋白质-蛋白质相互作用网络（Protein-protein interaction networks，PIN）是由一些高度连接的蛋白质与大量连接较少的蛋白质连接而成的。已经发现必需蛋白质在这些高度连接的蛋白质中更丰富。在这里，我们证明了去除PIN中的蛋白质将证明对酵母是致命的可能性与蛋白质的双性缺乏相关。一个蛋白质是二分的，如果它可以以这样一种方式划分，有两组蛋白质与组间，但没有组内，相互作用。在最小二分蛋白质中发现的必需蛋白质的丰度明显超过在最相关的蛋白质中发现的丰度。例如，在按缺乏双偶性排名的前50种蛋白质中，62%是必需蛋白质。然而，对于根据相互作用数量排名的蛋白质，这一比例仅为38%。在识别必需蛋白质方面，蛋白质双产性还超过了酵母PIN中蛋白质中心性的另外5个指标，并使随机选择的必需蛋白质数量增加了一倍。我们提出了一个可能的机制，在酵母PIN的基础上的复制发散方案的基本蛋白质的演变。我们的结论是，从一个nonbipartite目标进化的复制蛋白也将是nonbipartite的概率很高。因此，这些新的副本从nonbipartite（必要的）目标将以高概率是必不可少的。
Protein-protein interaction networks (PINs) are structured by means of a few highly connected proteins linked to a large number of less-connected ones. Essential proteins have been found to be more abundant among these highly connected proteins. Here we demonstrate that the likelihood that removal of a protein in a PIN will prove lethal to yeast correlates with the lack of bipartivity of the protein. A protein is bipartite if it can be partitioned in such a way that there are two groups of proteins with intergroup, but not intragroup, interactions. The abundance of essential proteins found among the least bipartite proteins clearly exceeds that found among the most connected ones. For instance, among the top 50 proteins ranked by their lack of bipartivity 62% are essential proteins. However, this percentage is only 38% for proteins ranked according to their number of interactions. Protein bipartivity also surpasses another 5 measures of protein centrality in yeast PIN in identifying essential proteins and doubles the number of essential proteins selected at random. We propose a possible mechanism for the evolution of essential proteins in yeast PIN based on the duplication-divergence scheme. We conclude that a replica protein evolving from a nonbipartite target will also be nonbipartite with high probability. Consequently, these new replicas evolving from nonbipartite (essential) targets will with high probability be essential.