Anbo Hiroto, Sakuma Koya, Fukuchi Satoshi, Ota Motonori
Faculty of Engineering, Maebashi Institute of Technology, Maebashi 371-0816, Japan.
Graduate School of Informatics, Nagoya University, Nagoya 464-8601, Japan.
Biology (Basel). 2023 Jan 25;12(2):182. doi: 10.3390/biology12020182.
AlphaFold2 (AF2) is a protein structure prediction program which provides accurate models. In addition to predicting structural domains, AF2 assigns intrinsically disordered regions (IDRs) by identifying regions with low prediction reliability (pLDDT). Some regions in IDRs undergo disorder-to-order transition upon binding the interaction partner. Here we assessed model structures of AF2 based on the annotations in IDEAL, in which segments with disorder-to-order transition have been collected as Protean Segments (ProSs). We non-redundantly selected ProSs from IDEAL and classified them based on the root mean square deviation to the corresponding region of AF2 models. Statistical analysis identified 11 structural and sequential features, possibly contributing toward the prediction of ProS structures. These features were categorized into two groups: one that contained pLDDT and the other that contained normalized radius of gyration. The typical ProS structures in the former group comprise a long α helix or a whole or part of the structural domain and those in the latter group comprise a short α helix with terminal loops.
AlphaFold2（AF2）是一个能提供精确模型的蛋白质结构预测程序。除了预测结构域，AF2还通过识别预测可靠性低（pLDDT）的区域来指定内在无序区域（IDR）。IDR中的一些区域在与相互作用伙伴结合时会发生无序到有序的转变。在这里，我们基于IDEAL中的注释评估了AF2的模型结构，其中无序到有序转变的片段已被收集为可变片段（ProS）。我们从IDEAL中无冗余地选择了ProS，并根据与AF2模型相应区域的均方根偏差对其进行分类。统计分析确定了11个结构和序列特征，可能有助于预测ProS结构。这些特征分为两组：一组包含pLDDT，另一组包含归一化回转半径。前一组中的典型ProS结构包括一个长α螺旋或一个结构域的全部或部分，后一组中的典型ProS结构包括一个带有末端环的短α螺旋。
