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首页> 外文期刊>Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena >Towards molecular dynamics simulation of large proteins with a hydration shell at constant pressure.
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Towards molecular dynamics simulation of large proteins with a hydration shell at constant pressure.

机译：在恒定压力下使用水合壳对大型蛋白质进行分子动力学模拟。

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摘要

Molecular dynamics simulation of a large protein in explicit water with periodic boundary conditions is extremely demanding in terms of computation time. Consequently, we have sought approximations of the solvent environment that model its important features. Here, we describe our SAPHYR (Shell Approximation for Protein HYdRation) model in which the protein is surrounded by a shell of water molecules maintained at constant pressure. In addition to the usual pairwise interatomic interactions, these water molecules are subjected to forces approximating van der Waals and dipole-dipole interactions with the implicit surrounding bulk solvent. The SAPHYR model is tested for a system of one argon atom in water and for the protein ubiquitin, and then applied to cytochrome P450cam, a protein with over 400 residues. The results demonstrate that structural and dynamic properties of the simulated systems are improved by use of the SAPHYR model, and that this model provides a significant computational saving over simulations with periodic boundary conditions.
机译：就计算时间而言，在具有周期性边界条件的显性水中对大蛋白进行分子动力学模拟非常需要。因此，我们寻求了模拟其重要特征的溶剂环境的近似值。在这里，我们描述了我们的SAPHYR（蛋白质HYdRation的壳近似）模型，其中蛋白质被保持在恒定压力下的水分子壳包围。除了通常的成对原子间相互作用之外，这些水分子还受到近似范德华力和与隐性周围本体溶剂偶极-偶极相互作用的作用力。测试了SAPHYR模型中水中一个氩原子的系统和泛素蛋白的含量，然后将其应用于细胞色素P450cam（一种具有400多个残基的蛋白）。结果表明，通过使用SAPHYR模型可以改善模拟系统的结构和动力学特性，并且该模型与具有周期性边界条件的模拟相比，可显着节省计算量。

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