Cheng Peng, Peng Junhui, Zhang Zhiyong
Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
Biophys J. 2017 Apr 11;112(7):1295-1301. doi: 10.1016/j.bpj.2017.02.024.
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well. The tool has been validated with a protein and an RNA system, i.e., the tandem WW domains of formin-binding protein 21 and the aptamer domain of SAM-1 riboswitch, respectively. These Python scripts are user-friendly and can be easily modified if a different simulation engine is preferred.
生物分子的构象灵活性可能在其生物学功能中发挥关键作用。小角X射线散射（SAXS）是一种非常流行的用于表征生物分子灵活性的技术。它可用于借助计算机模拟确定生物分子在溶液中的可能结构集合。在本文中，我们展示了一个用Python编写的工具，该工具可迭代运行多个独立的增强采样模拟，如放大的集体运动和加速分子动力学，以及一种集合优化方法，以驱使生物分子趋向于一个能很好拟合SAXS数据的集合。该工具已分别通过一个蛋白质和一个RNA系统进行了验证，即formin结合蛋白21的串联WW结构域和SAM-1核糖开关的适体结构域。这些Python脚本对用户很友好，如果更喜欢不同的模拟引擎，也可以轻松修改。
