Chen Guanglin, Zhang Zhiyong
Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, PR China.
MOE Key Laboratory for Cellular Dynamics, University of Science and Technology of China, Hefei, Anhui 230026, PR China.
ACS Omega. 2024 Jul 10;9(29):32059-32065. doi: 10.1021/acsomega.4c04161. eCollection 2024 Jul 23.
Intrinsically disordered regions (IDRs), which may be functionally important, are common in proteins. However, the structures of IDRs are often missing due to their highly dynamic nature. In the study of IDRs, integrative modeling combining computational simulations and experimental data is a common approach, for which initial structures of the IDRs need to be built. However, applying this method to large protein complexes is challenging because existing structure generation tools are sometimes unsuitable for IDRs in large systems. To facilitate convenient and rapid structure generation of IDRs in large protein complexes, we developed a computational tool named IDRWalker based on self-avoiding random walks. Three protein complexes were used to illustrate the efficiency of the tool, and it was found that IDRs in more than 800 chains of the nuclear pore complex could be generated in minutes. These structures of large protein complexes with added IDRs can be further used to run computational simulations for integrative modeling.
内在无序区域（IDR）在蛋白质中很常见，可能具有重要的功能。然而，由于其高度动态的性质，IDR的结构往往缺失。在IDR的研究中，结合计算模拟和实验数据的整合建模是一种常用方法，为此需要构建IDR的初始结构。然而，将这种方法应用于大型蛋白质复合物具有挑战性，因为现有的结构生成工具有时不适用于大型系统中的IDR。为了便于在大型蛋白质复合物中方便快捷地生成IDR结构，我们基于自回避随机游走开发了一种名为IDRWalker的计算工具。使用三个蛋白质复合物来说明该工具的效率，结果发现，核孔复合物800多条链中的IDR可以在几分钟内生成。这些添加了IDR的大型蛋白质复合物结构可进一步用于运行整合建模的计算模拟。
