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首页> 外文期刊>Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena >Development and validation of an empirical free energy function for calculating protein-protein binding free energy surfaces.
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Development and validation of an empirical free energy function for calculating protein-protein binding free energy surfaces.

机译：开发和验证用于计算蛋白质-蛋白质结合自由能表面的经验自由能函数。

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摘要

In a previous paper, we described a novel empirical free energy function that was used to accurately predict experimental binding free energies for a diverse test set of 31 protein-protein complexes to within approximately 1.0 kcal. Here, we extend that work and show that an updated version of the function can be used to (1) accurately predict native binding free energies and (2) rank crystallographic, native-like and non-native binding modes in a physically realistic manner. The modified function includes terms designed to capture some of the unfavorable interactions that characterize non-native interfaces. The function was used to calculate one-dimensional binding free energy surfaces for 21 protein complexes. In roughly 90% of the cases tested, the function was used to place native-like and crystallographic binding modes in global free energy minima. Our analysis further suggests that buried hydrogen bonds might provide the key to distinguishing native from non-native interactions. To the best of our knowledge our function is the only one of its kind, a single expression that can be used to accurately calculate native and non-native binding free energies for a large number of proteins. Given the encouraging results presented in this paper, future work will focus on improving the function and applying it to the protein-protein docking problem.
机译：在以前的论文中，我们描述了一种新颖的经验自由能函数，该函数可用于准确预测31种蛋白质-蛋白质复合物的多样化测试集的实验结合自由能至1.0 kcal以内。在这里，我们扩展了这项工作，并显示了该函数的更新版本可用于（1）准确地预测天然结合自由能，以及（2）以物理逼真的方式对晶体学，类天然和非天然结合模式进行排序。修改后的功能包括旨在捕获某些表征非本机接口的不利交互的术语。该函数用于计算21种蛋白质复合物的一维结合自由能表面。在大约90％的测试案例中，该函数用于将自然样和晶体学结合模式置于全局自由能最小值中。我们的分析进一步表明，埋藏的氢键可能提供了区分天然相互作用和非天然相互作用的关键。据我们所知，我们的功能是同类功能中唯一的一种，可用于精确计算大量蛋白质的天然和非天然结合自由能的单个表达式。鉴于本文提出的令人鼓舞的结果，未来的工作将集中在改善功能并将其应用于蛋白质-蛋白质对接问题上。

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