Between order and disorder in protein structures: Analysis of "dual personality" fragments in proteins
Between order and disorder in protein structures: Analysis of "dual personality" fragments in proteins
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DOI：
10.1016/j.str.2007.07.012
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发表时间：
2007-09-01
期刊：
影响因子：
5.7
通讯作者：
Godzik, Adam
中科院分区：
文献类型：
--
作者：
Zhang, Ying;Stec, Boguslaw;Godzik, Adam
在其自然环境中，蛋白质的三维结构经历显著的波动，并且通常是部分或完全无序的。这种现象最近成为人们关注的焦点，因为许多蛋白质，特别是来自高等生物的蛋白质，被证明含有大的内在无序区域。这种无序区域只有在非常特定的情况下才可能变得有序，并且可以通过特定的氨基酸组成和序列特征来识别。在这里，我们认为，有序和无序之间的平衡是非常微妙的，因为许多地区非常接近有序/无序的边界。具体来说，分析蛋白质结构的实验模型的冗余集，其中重点放在不同条件和功能状态下解决的相同蛋白质的结构比较，显示了数百个片段捕获在两种状态：有序和无序。我们发现，这样的片段，我们在这里称之为“双重人格”（DP）片段，有显着的特点，区分他们从两个定期折叠和内在无序的片段。我们假设，并显示在几个例子中，这些片段往往是目标的调节，无论是通过变构或翻译后修饰。
In their natural environment, three-dimensional structures of proteins undergo significant fluctuations and are often partially or completely disordered. This phenomenon recently became the focus of much attention, as many proteins, especially from higher organisms, were shown to contain large intrinsically disordered regions. Such disordered regions may become ordered only under very specific circumstances, if at all, and can be recognized by specific amino acid composition and sequence signatures. Here, we suggest that the balance between order and disorder is much more subtle in that many regions are very close to the order/disorder boundary. Specifically, analysis of redundant sets of experimental models of protein structures, where emphasis is put on comparison of structures of identical proteins solved in different conditions and functional states, shows hundreds of fragments captured in two states: ordered and disordered. We show that such fragments, which we call here "dual personality" (DP) fragments, have distinctive features that differentiate them from both regularly folded and intrinsically disordered fragments. We hypothesize, and show on several examples, that such fragments are often targets of regulation, either by allostery or posttranslational modifications.