Misra V K, Hecht J L, Sharp K A, Friedman R A, Honig B
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.
J Mol Biol. 1994 Apr 29;238(2):264-80. doi: 10.1006/jmbi.1994.1286.
In this paper, finite-difference solutions to the nonlinear Poisson-Boltzmann (NLPB) equation are used to calculate the salt dependent contribution to the electrostatic DNA binding free energy for both the lambda cI repressor and the EcoRI endonuclease. For the protein-DNA systems studied, the NLPB method describes nonspecific univalent salt dependent effects on the binding free energy which are in excellent agreement with experimental results. In these systems, the contribution of the ion atmosphere to the binding free energy substantially destabilizes the protein-DNA complexes. The magnitude of this effect involves a macromolecular structure dependent redistribution of both cations and anions around the protein and the DNA which is dominated by long range electrostatic interactions. We find that the free energy associated with global ion redistribution upon binding is more important than changes associated with local protein-DNA interactions (ion-pairs) in determining salt effects. The NLPB model reveals how long range salt effects can play a significant role in the relative stability of protein-DNA complexes with different structures.
在本文中，非线性泊松 - 玻尔兹曼（NLPB）方程的有限差分法被用于计算λcI阻遏蛋白和EcoRI核酸内切酶与盐相关的静电DNA结合自由能贡献。对于所研究的蛋白质 - DNA系统，NLPB方法描述了与单价盐相关的非特异性效应，这些效应与结合自由能有关，且与实验结果高度吻合。在这些系统中，离子氛对结合自由能的贡献极大地破坏了蛋白质 - DNA复合物的稳定性。这种效应的大小涉及蛋白质和DNA周围阳离子和阴离子的大分子结构依赖性重新分布，这主要由长程静电相互作用主导。我们发现，在确定盐效应时，与结合时全局离子重新分布相关的自由能比与局部蛋白质 - DNA相互作用（离子对）相关的变化更为重要。NLPB模型揭示了长程盐效应如何在不同结构的蛋白质 - DNA复合物的相对稳定性中发挥重要作用。
