Multi-domain proteins in the three kingdoms of life:: Orphan domains and other unassigned regions
Multi-domain proteins in the three kingdoms of life:: Orphan domains and other unassigned regions
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DOI：
10.1016/j.jmb.2005.02.007
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发表时间：
2005-04-22
影响因子：
5.6
通讯作者：
Elofsson, A
中科院分区：
文献类型：
--
作者：
Ekman, D;Björklund, ÅK;Elofsson, A
对不同生物体蛋白质组的比较研究为了解蛋白质结构域在生命王国中的分布提供了有价值的信息。早期的研究受到这样一个事实的限制，即只有大约50%的蛋白质组可以匹配到一个结构域。在这里，我们扩展了这些研究，包括定义不太明确的域定义，Pfam-B和集群域，MAS，除了Pfam-A和SCOP域。发现这些结构域家族的显著部分与Pfam-A或SCOP结构域同源。此外，我们发现，所有不匹配的Pfam-A或SCOP域的区域包含一个显着更高的分数的无序结构。这些非结构化区域可以包含在孤儿结构域中或作为结构化结构域之间的接头起作用。使用几种不同的定义，我们重新估计了不同生物体中多结构域蛋白的数量，发现几种方法都预测真核生物约有65%的多结构域蛋白，而原核生物约有40%的多结构域蛋白。然而，这些数字在很大程度上取决于未分配区域中域的截止值的确切选择。总之，所有的真核生物具有相似的分数的多结构域蛋白质和障碍，而高分数的重复结构域的区别只在多细胞真核生物。这意味着重复序列在细胞-细胞接触中的作用，而其他两个特征对细胞内功能很重要。(c)2005年由Elsevier Ltd.出版
Comparative studies of the proteomes from different organisms have provided valuable information about protein domain distribution in the kingdoms of life. Earlier studies have been limited by the fact that only about 50% of the proteomes could be matched to a domain. Here, we have extended these studies by including less well-defined domain definitions, Pfam-B and clustered domains, MAS, in addition to Pfam-A and SCOP domains. It was found that a significant fraction of these domain families are homologous to Pfam-A or SCOP domains. Further, we show that all regions that do not match a Pfam-A or SCOP domain contain a significantly higher fraction of disordered structure. These unstructured regions may be contained within orphan domains or function as linkers between structured domains. Using several different definitions we have re-estimated the number of multi-domain proteins in different organisms and found that several methods all predict that eukaryotes have approximately 65% multi-domain proteins, while the prokaryotes consist of approximately 40% multi-domain proteins. However, these numbers are strongly dependent on the exact choice of cut-off for domains in unassigned regions. In conclusion, all eukaryotes have similar fractions of multidomain proteins and disorder, whereas a high fraction of repeating domain is distinguished only in multicellular eukaryotes. This implies a role for repeats in cell-cell contacts while the other two features are important for intracellular functions. (c) 2005 Published by Elsevier Ltd.