T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
Biophys J. 2018 Feb 27;114(4):856-869. doi: 10.1016/j.bpj.2018.01.002.
Hydrodynamic properties are useful parameters for estimating the size and shape of proteins and nucleic acids in solution. The calculation of such properties from structural models informs on the solution properties of these molecules and complements corresponding structural studies. Here we report, to our knowledge, a new method to accurately predict the hydrodynamic properties of molecular structures. This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods. It works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids. Because of its simplicity and speed, the method should be useful for the modification of computer-generated, intrinsically disordered protein ensembles and ensembles of flexible, but folded, molecules in which rapid calculation of experimental parameters is needed. The convex hull method is implemented in a Python script called HullRad. The use of the method is facilitated by a web server and the code is freely available for batch applications.
水动力性质是估计溶液中蛋白质和核酸大小和形状的有用参数。从结构模型计算这些性质可以了解这些分子的溶液性质，并补充相应的结构研究。在这里，我们报告了一种新的方法，可以准确预测分子结构的水动力性质。该方法使用凸包模型来估计分子的水动力体积，其速度比常见方法快几个数量级。它对折叠蛋白质和构象异质蛋白质的混合物以及核酸都适用良好。由于其简单性和速度，该方法应该对计算机生成的固有无序蛋白质混合物以及需要快速计算实验参数的柔性但折叠分子的混合物的修饰有用。凸包方法在一个名为 HullRad 的 Python 脚本中实现。该方法通过一个网络服务器使用更加方便，并且代码可免费用于批处理应用。
