Departamento de Química Física, Facultad de Química, Universidad de Murcia, Murcia, Spain.
Biophys J. 2011 Aug 17;101(4):892-8. doi: 10.1016/j.bpj.2011.06.046.
Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom, the latter contains one bead per amino acid (or nucleotide) residue, thus allowing calculations when atomic resolution is not available or coarse-grained models are preferred. We parameterized the effective hydrodynamic radius of the elements in the atomic- and residue-level models using a very large set of experimental data for translational and rotational coefficients (intrinsic viscosity and radius of gyration) for >50 proteins. We also extended the calculations to very large proteins and macromolecular complexes, such as the whole 70S ribosome. We show that with proper parameterization, the two levels of resolution yield similar and rather good agreement with experimental data. The new version of HYDROPRO, in addition to considering various computational and modeling schemes, is far more efficient computationally and can be handled with the use of a graphical interface.
在这里，我们将计算机程序 HYDROPRO 中预测刚性高分子结构的流体动力系数和其他溶液性质的能力扩展到具有较低分辨率的残基水平模型。在前一种情况下，每个非氢原子有一个珠，后一种情况下每个氨基酸（或核苷酸）残基有一个珠，从而允许在没有原子分辨率或需要使用粗粒度模型时进行计算。我们使用大量实验数据对原子和残基水平模型中元素的有效流体动力半径进行了参数化，这些数据包括>50 种蛋白质的平移和旋转系数（特性粘度和回转半径）。我们还将计算扩展到非常大的蛋白质和大分子复合物，如整个 70S 核糖体。我们表明，通过适当的参数化，这两种分辨率产生相似且相当好的与实验数据的一致性。新版本的 HYDROPRO 除了考虑各种计算和建模方案外，在计算效率上也有了很大的提高，并且可以使用图形界面进行处理。
