3 years ago

Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi

Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi
Emil Alexov, Arghya Chakravorty, Zhe Jia, Lin Li
The standard treatment of ions in the framework of the Poisson–Boltzmann equation relies on molecular surfaces, which are commonly constructed along with the Stern layer. The molecular surface determines where ions can be present. In the Gaussian-based smooth dielectric function in DelPhi, smooth boundaries between the solute and solvent take the place of molecular surface. Therefore, this invokes the question of how to model mobile ions in the water phase without a definite solute-solvent boundary. This article reports a natural extension of the Gaussian-based smooth dielectric function approach that treats mobile ions via Boltzmann distribution with an added desolvation penalty. Thus, ion concentration near macromolecules is governed by the local electrostatic potential and the desolvation penalty (from being partially desolvated). The approach is tested against the experimental salt dependence of binding free energy on 7 protein–protein complexes and 12 DNA–protein complexes, resulting in Pearson correlations of 0.95 and 0.88, respectively. © 2017 Wiley Periodicals, Inc. A new approach of modeling ions in the framework of Gaussian-based smooth dielectric function in Poisson–Boltzmann equation (PBE) is reported. In addition to the Boltzmann term in traditional PBE, ions concentration is altered by a solvation penalty when they translocate from bulk solvent to the space regions with lower dielectric constant. To calculate the solvation penalty, this article adds a Born-based solvation energy term into PBE. Calculated salt dependence of the binding free energy results in Pearson correlation of 0.88–0.95 with experiments.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.24831

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