Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions.
Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions.
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DOI：
10.1103/physrevlett.102.087801
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发表时间：
2009-02-27
影响因子：
8.6
通讯作者：
Delarue M
中科院分区：
文献类型：
--
作者：
Koehl P;Orland H;Delarue M
我们提出了泊松-玻尔兹曼模型的扩展，其中溶剂被建模为可变密度的自定向偶极子的集合。使用 Yukawa 势场隐式包含这些偶极子之间的相互作用。该模型得出一组方程，其解给出了偶极子密度；我们用后者来研究生物分子周围的水的组织。计算出的水密度分布类似于分子动力学模拟得出的水密度分布。我们还获得了多余的自由能，可以区分蛋白质的正确构象和错误构象。
We present an extension to the Poisson-Boltzmann model in which the solvent is modeled as an assembly of self-orienting dipoles of variable densities. Interactions between these dipoles are included implicitly using a Yukawa potential field. This model leads to a set of equations whose solutions give the dipole densities; we use the latter to study the organization of water around biomolecules. The computed water density profiles resemble those derived from molecular dynamics simulations. We also derive an excess free energy that discriminates correct from incorrect conformations of proteins.