Zhang Ying, Stec Boguslaw, Godzik Adam
Program in Bioinformatics and Systems Biology, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
Structure. 2007 Sep;15(9):1141-7. doi: 10.1016/j.str.2007.07.012.
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.
在其天然环境中，蛋白质的三维结构会经历显著波动，且常常部分或完全无序。这种现象最近成为了众多关注的焦点，因为许多蛋白质，尤其是高等生物中的蛋白质，被证明含有大量内在无序区域。此类无序区域可能仅在非常特殊的情况下才会变得有序，甚至根本不会有序，并且可以通过特定的氨基酸组成和序列特征来识别。在此，我们认为有序与无序之间的平衡要微妙得多，因为许多区域非常接近有序/无序边界。具体而言，对蛋白质结构实验模型冗余集的分析表明，在不同条件和功能状态下解析出的相同蛋白质的结构比较中，有数百个片段呈现出两种状态：有序和无序。我们表明，此类片段，我们在此称之为“双重人格”（DP）片段，具有独特特征，使其与规则折叠片段和内在无序片段都有所不同。我们通过几个例子进行了假设并证明，此类片段常常是变构调节或翻译后修饰的作用靶点。
