Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation
Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation
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DOI：
10.1063/1.4864460
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发表时间：
2014-02-21
影响因子：
4.4
通讯作者：
Fenley, Marcia O.
中科院分区：
文献类型：
--
作者：
Harris, Robert C.;Boschitsch, Alexander H.;Fenley, Marcia O.
实验结果表明，核酸周围的反离子数目与非线性泊松-玻尔兹曼方程(NLPBE)预测的数目不同。一些研究已经将这些数据与尺寸修正的泊松-玻尔兹曼方程SMPBE中的离子尺寸进行了匹配，但本研究表明，其他参数，如斯特恩层厚度和分子表面定义，可以改变结合离子的数量，其幅度与改变离子尺寸相当。因此，这些参数必须同时与实验数据进行匹配。此外，本文给出的数据表明，静电结合自由能对盐浓度的对数G(El)的导数SK对这些参数很敏感，SK的实验测量可以用来对模型进行参数化。然而，尽管更好的斯特恩层厚度和离子尺寸以及更好的分子表面定义可以改善模型对生物分子和SK周围离子数量的预测，但Delta G(El)本身对参数更敏感，例如内部介电常数，而这些参数反过来又不会显著影响生物分子周围的离子分布。因此，改进SMPBE中使用的离子大小和斯特恩层厚度的估计不一定会改善该模型对Delta G(El)的预测。(C)2014 AIP出版有限责任公司。
Experimental results have demonstrated that the numbers of counterions surrounding nucleic acids differ from those predicted by the nonlinear Poisson-Boltzmann equation, NLPBE. Some studies have fit these data against the ion size in the size-modified Poisson-Boltzmann equation, SMPBE, but the present study demonstrates that other parameters, such as the Stern layer thickness and the molecular surface definition, can change the number of bound ions by amounts comparable to varying the ion size. These parameters will therefore have to be fit simultaneously against experimental data. In addition, the data presented here demonstrate that the derivative, SK, of the electrostatic binding free energy, Delta G(el), with respect to the logarithm of the salt concentration is sensitive to these parameters, and experimental measurements of SK could be used to parameterize the model. However, although better values for the Stern layer thickness and ion size and better molecular surface definitions could improve the model's predictions of the numbers of ions around biomolecules and SK, Delta G(el) itself is more sensitive to parameters, such as the interior dielectric constant, which in turn do not significantly affect the distributions of ions around biomolecules. Therefore, improved estimates of the ion size and Stern layer thickness to use in the SMPBE will not necessarily improve the model's predictions of Delta G(el). (C) 2014 AIP Publishing LLC.