Laboratoire de Physique de la Matière Condensé et Nanostructures, Université Claude Bernard Lyon 1, CNRS, UMR 5586, Domaine scientifique de la Doua, F-69622 Villeurbanne Cedex, France.
Phys Chem Chem Phys. 2011 Sep 7;13(33):15055-61. doi: 10.1039/c1cp20719a. Epub 2011 Jul 25.
In this work we show how the ab initio determination of van der Waals coefficients within time-dependent density functional theory can be used to build efficient and accurate atomistic models that describe the long-range interactions of proteins with other proteins and of proteins with semi-conducting surfaces. The model parameters are fitted so that they reproduce the ab initio van der Waals coefficients of amino acids and dipeptides. We then assess the quality of our results by comparing ab initio van der Waals coefficients for larger peptides with the coefficients yielded by the models. The different sets of parameters can be easily incorporated in current empirical force field methods, thus providing an essential ingredient for molecular dynamics simulations of proteins close to surfaces.
在这项工作中，我们展示了如何在含时密度泛函理论中从头确定范德华系数，从而构建高效、准确的原子模型，描述蛋白质与其他蛋白质以及蛋白质与半导体表面的长程相互作用。模型参数经过拟合，以再现氨基酸和二肽的从头范德华系数。然后，我们通过比较较大肽的从头范德华系数与模型得出的系数来评估结果的质量。不同的参数集可以很容易地纳入当前的经验力场方法，从而为接近表面的蛋白质的分子动力学模拟提供重要成分。
