Amino acid coupling patterns in thermophilic proteins
Amino acid coupling patterns in thermophilic proteins
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DOI：
10.1002/prot.20386
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发表时间：
2005-04-01
影响因子：
2.9
通讯作者：
Hwang, JK
中科院分区：
文献类型：
--
作者：
Liang, HK;Huang, CM;Hwang, JK
结构分析可用于阐明负责增强蛋白质热稳定性的结构特征。然而，由于测序的基因组数据的快速增加，有更多的蛋白质序列比相应的三维（3D）结构。通常的基于序列的氨基酸组成分析提供了有用的，但简化的线索有关的蛋白质的热稳定性的氨基酸类型。在这项工作中，我们开发了一种统计方法来确定显着的氨基酸偶联序列模式的嗜热蛋白。氨基酸偶联序列模式被定义为被1个或多个氨基酸分隔的任何2种类型的氨基酸。使用这种方法，我们构建的p配置文件的耦合模式。p值给出了与嗜温菌相比，嗜热菌中偶联模式的相对发生的量度。我们发现，嗜热菌和嗜温菌表现出显着的偏见，在他们的氨基酸偶联模式。我们发现，这种偏见主要是由于温度的适应，而不是物种或GC含量的变化。虽然没有单一的突出的偶联模式可以充分解释蛋白质的热稳定性，但我们可以使用一组具有强统计学显著性（p值<10（-7））的氨基酸偶联模式来区分嗜热蛋白和嗜温蛋白。我们发现，基因组的最佳生长温度和耦合模式的发生之间有很好的相关性（相关系数为0.89）。此外，我们还可以利用氨基酸偶联模式将嗜热蛋白与其嗜温同源蛋白分离。这些结果可能有助于研究嗜热菌蛋白质的增强稳定性-特别是当结构信息不足时。(C)2005 Wiley-Liss，Inc.
Structural analysis is useful in elucidating structural features responsible for enhanced thermal stability of proteins. However, due to the rapid increase of sequenced genomic data, there are far more protein sequences than the corresponding three-dimensional (3D) structures. The usual sequence-based amino acid composition analysis provides useful but simplified clues about the amino acid types related to thermal stability of proteins. In this work, we developed a statistical approach to identify the significant amino acid coupling sequence patterns in thermophilic proteins. The amino acid coupling sequence pattern is defined as any 2 types of amino acids separated by I or more amino acids. Using this approach, we construct the p profiles for the coupling patterns. The p value gives a measure of the relative occurrence of a coupling pattern in thermophiles compared with mesophiles. We found that thermophiles and mesophiles exhibit significant bias in their amino acid coupling patterns. We showed that such bias is mainly due to temperature adaptation instead of species or GC content variations. Though no single outstanding coupling pattern can adequately account for protein thermostability, we can use a group of amino acid coupling patterns having strong statistical significance (p values < 10(-7)) to distinguish between thermophilic and mesophilic proteins. We found a good correlation between the optimal growth temperatures of the genomes and the occurrences of the coupling patterns (the correlation coefficient is 0.89). Furthermore, we can separate the thermophilic proteins from their mesophilic orthologs using the amino acid coupling patterns. These results may be useful in the study of the enhanced stability of proteins from thermophiles - especially when structural information is scarce. (C) 2005 Wiley-Liss, Inc.