超越泊松-玻尔兹曼模型：生物分子-水和水-水相互作用的建模
Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions.
作者信息
Koehl Patrice, Orland Henri, Delarue Marc
机构信息
Department of Computer Science and Genome Center, University of California, Davis, Davis, California 95616, USA.
出版信息
Phys Rev Lett. 2009 Feb 27;102(8):087801. doi: 10.1103/PhysRevLett.102.087801. Epub 2009 Feb 24.
Abstract
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.
摘要
我们提出了泊松-玻尔兹曼模型的一种扩展，其中溶剂被建模为密度可变的自取向偶极子的集合。这些偶极子之间的相互作用通过一个汤川势场隐式包含。该模型导出了一组方程，其解给出了偶极子密度；我们用后者来研究生物分子周围水的组织情况。计算得到的水密度分布类似于从分子动力学模拟得出的分布。我们还推导了一种过量自由能，它能区分蛋白质的正确构象和错误构象。
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