带电生物分子结构周围离子分布的计算：右手螺旋和左手螺旋DNA的结果

Klement R, Soumpasis D M, Jovin T M

Max-Planck-Institute für Biophysikalische Chemie, Göttingen, Federal Republic of Germany.

Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):4631-5. doi: 10.1073/pnas.88.11.4631.

We introduce an efficient computational methodology employing the potentials of mean force approach for estimating the detailed three-dimensional ionic distributions around arbitrarily complex charged biomolecular structures for all monovalent salt concentrations of practical interest (e.g., 0.1-5.0 M NaCl). Such distributions are required for specifying thermodynamic and structure-specific features of ion-mediated interactions of charged proteins, DNA and RNA, membranes, and macromolecular assemblies. As a first application, we present results for distributions around the B and ZI conformers of the DNA oligomer d(C-G)18.d(C-G)18. The ionic microenvironment depends strongly on the DNA conformation, sequence, and bulk salt concentrations.

我们介绍了一种高效的计算方法，该方法利用平均力势方法来估计在所有实际感兴趣的单价盐浓度（例如，0.1 - 5.0 M NaCl）下，围绕任意复杂带电生物分子结构的详细三维离子分布。这些分布对于确定带电蛋白质、DNA和RNA、膜以及大分子组装体的离子介导相互作用的热力学和结构特异性特征是必需的。作为第一个应用，我们给出了DNA寡聚物d(C-G)18.d(C-G)18的B型和Z型构象周围分布的结果。离子微环境强烈依赖于DNA构象、序列和本体盐浓度。