A structural census of the current population of protein sequences
A structural census of the current population of protein sequences
复制标题
DOI：
10.1073/pnas.94.22.11911
复制
发表时间：
1997-10-28
影响因子：
11.1
通讯作者：
Levitt, M
中科院分区：
文献类型：
--
作者：
Gerstein, M;Levitt, M
我们研究了不同生物体中大约 300 个已知蛋白质折叠的发生情况。为此，我们通过序列比较（或通过对没有结构同源物的二级结构类别预测）将其与已知结构进行匹配，从结构角度表征了目前已知的大部分蛋白质序列（大约 140,000 个）。总体而言，我们发现已知折叠的相当一部分存在于每个主要生物体中（例如，细菌和真核生物共享 275 个折叠中的 156 个），并且大多数常见折叠与许多非同源序列家族相关（即每个常见折叠> 10 个序列家族）。然而，不同类群的生物体具有不同特征的折叠分布，因此，例如，脊椎动物中一些最常见的折叠（例如球蛋白或锌指）在细菌中很少见或不存在。这些折叠使用的许多差异在生物学上是合理的，例如代谢酶的折叠在细菌中常见，而与细胞外运输和通讯相关的折叠在动物中常见。它们对于基于数据库的折叠识别方法也具有重要意义，表明来自植物的未知序列比来自动物的未知序列更有可能具有某种折叠（例如，TIM 桶）。
We examine the occurrence of the approximate to 300 known protein folds in different groups of organisms. To do this, we characterize a large fraction of the currently known protein sequences (approximate to 140,000) in structural terms, by matching them to known structures via sequence comparison (or by secondary-structure class prediction for those without structural homologues). Overall, we find that an appreciable fraction of the known folds are present in each of the major groups of organisms (e.g., bacteria and eukaryotes share 156 of 275 folds), and most of the common folds are associated with many families of nonhomologous sequences (i.e., >10 sequence families for each common fold). However, different groups of organisms have characteristically distinct distributions of folds, So, for instance, some of the most common folds in vertebrates, such as globins or zinc fingers, are rare or absent in bacteria, Many of these differences in fold usage are biologically reasonable, such as the folds of metabolic enzymes being common in bacteria and those associated with extracellular transport and communication being common in animals. They also have important implications for database-based methods for fold recognition, suggesting that an unknown sequence from a plant is more likely to have a certain fold (e.g., a TIM barrel) than an unknown sequence from an animal.