Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models
Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models
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DOI：
10.1016/j.bpj.2011.06.046
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发表时间：
2011-08-17
影响因子：
3.4
通讯作者：
Garcia de la Torre, J.
中科院分区：
文献类型：
--
作者：
Ortega, A.;Amoros, D.;Garcia de la Torre, J.
在这里，我们将预测刚性大分子结构的流体动力学系数和其他溶液特性的能力从原子级结构（在计算机程序 HYDROPRO 中实现）扩展到具有较低残基级分辨率的模型。在前一种情况下，每个非氢原子有一个珠子，而后者每个氨基酸（或核苷酸）残基有一个珠子，因此可以在原子分辨率不可用或优选粗粒度模型时进行计算。我们使用大量超过 50 种蛋白质的平移和旋转系数（特性粘度和回转半径）实验数据，对原子级和残基级模型中元素的有效流体动力学半径进行了参数化。我们还将计算扩展到非常大的蛋白质和大分子复合物，例如整个 70S 核糖体。我们表明，通过适当的参数化，两个分辨率水平与实验数据产生相似且相当好的一致性。新版本的 HYDROPRO 除了考虑各种计算和建模方案外，计算效率更高，并且可以使用图形界面进行处理。
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.