Adaptation of protein surfaces to subcellular location
Adaptation of protein surfaces to subcellular location
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DOI：
10.1006/jmbi.1997.1498
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发表时间：
1998-02-20
影响因子：
5.6
通讯作者：
Rost, B
中科院分区：
文献类型：
--
作者：
Andrade, MA;O'Donoghue, SI;Rost, B
在体内，蛋白质存在于截然不同的物理化学环境中，并且从体外研究中，我们知道蛋白质结构对环境非常敏感。然而，蛋白质结构的理论研究往往忽视这种复杂性。在本文中，我们通过按亚细胞位置对蛋白质进行分组并研究每个位置特有的结构特性来解决这个问题。我们假设，在整个进化过程中，每个亚细胞位置都保持着特有的生理化学环境，并且每个位置的蛋白质都适应了这些环境。如果是这样，我们预计不同位置的蛋白质结构将表现出特征差异，特别是在直接暴露于环境的表面。为了检验这一假设，我们检查了所有具有已知三维结构的真核蛋白质，并且已知其亚细胞位置是核、细胞质或细胞外。与之前的研究一致，我们发现总氨基酸成分携带识别亚细胞位置的信号。该信号几乎完全是由于表面残留物造成的。只要知道哪些残基位于蛋白质表面，表面残基信号通常足够强，足以准确预测亚细胞位置。结果表明如何提高序列预测位置的准确性。我们得出的结论是，蛋白质表面显示出对其亚细胞位置的适应。这些适应的本质表明了蛋白质在适应特定的物理化学环境时可能使用的几个原则；这些原则可能对蛋白质设计有用。 (C) 1998 学术出版社有限公司。
In vivo, proteins occur in widely different physio-chemical environments, and, from in vitro studies, we know that protein structure can be very sensitive to environment. However, theoretical studies of protein structure have tended to ignore this complexity. Ln this paper, we have approached this problem by grouping proteins by their subcellular location and looking at structural properties that are characteristic to each location. We hypothesize that, throughout evolution, each subcellular location has maintained a characteristic physio-chemical environment, and that proteins in each location have adapted to these environments. If so, we would expect that protein structures from different locations will show characteristic differences, particularly at the surface, which is directly exposed to the environment. To test this hypothesis, we have examined all eukaryotic proteins with known three-dimensional structure and for which the subcellular location is known to be either nuclear, cytoplasmic, or extracellular. In agreement with previous studies, we find that the total am;no acid composition carries a signal that identifies the subcellular location. This signal was due almost entirely to the surface residues. The surface residue signal was often strong enough to accurately predict subcellular location, given only a knowledge of which residues are at the protein surface. The results suggest how the accuracy of prediction of location from sequence can be improved. We concluded that protein surfaces show adaptation to their subcellular location. The nature of these adaptations suggests several principles that proteins may have used in adapting to particular physio-chemical environments; these principles may be useful for protein design. (C) 1998 Academic Press Limited.